SEQUENCE LISTING

[0001] A sequence listing in electronic (ASCII text file) format is filed with this application and incorporated herein by reference. The name of the ASCII text file is “2021_2010A_ST25.txt”; the file was created on October 26, 2021; the size of the file is 132 KB.

FIELD OF THE INVENTION

[0002] The technology described herein relates to compositions, systems and methods for monitoring microbes, such a microbial pathogens.

BACKGROUND

[0003] Sepsis is a life-threatening condition that results from microbial infections (e.g., bacterial, viral, parasitic, or fungal) and the body’s associated response causing damage to tissues. Sepsis is a major cause of death in American intensive care units. While microbes can directly damage tissues, resulting inflammatory responses can cause further damage and lead to septic shock and death. Early detection of infection and accurate identification of the infecting microbes are keys to successful treatment as different microbes are most susceptible to different treatments. Patients in septic shock should be treated as soon as possible to derive optimal benefit from antimicrobial therapies. Systems and methods for monitoring microbial pathogens in the selected sample are needed to aid in detection, prevention, early intervention and treatment of infectious disease. The present invention is directed to these and other important goals.

BRIEF SUMMARY

[0004] The present invention is generally directed to compositions, systems and methods for monitoring microbes, such a microbial pathogens, using microbe-targeting molecules (MTMs) and engineered MTMs as defined herein. These compositions, systems and methods can be used to monitor and detect the presence of one or more microbes in a sample, including but not limited to, a patient sample, an animal or animal model sample, an agricultural sample, a food and beverage sample, an environmental sample, a pharmaceutical sample, a biological sample, and a non-biological sample.

[0005] The microbial monitoring systems and methods of the present invention can be used in a variety of types of civilian and military monitoring or surveillance, for example, where the system collects detection device data, including but not limited to, the presence of a microbial pathogen and/or identification of the pathogen in a sample, and uses that data for monitoring of infectious disease, antibiotic resistance, and biothreats, in some cases in real time. Combining pathogen detection devices with communication devices such as a mobile phone provides opportunities to deliver potentially disruptive technologies to drive development of novel health systems by increasing access to testing, diagnosis and treatment of infectious diseases, while improving outbreak detection, disease surveillance and guiding a precision public health response. The disclosed systems and methods also enable public participation, for example, via engagement in outbreak detection through crowd sourced or “citizen science” initiatives or via targeted prevention messaging so that individuals and communities can access digital care pathways for an integrated clinical and public health system of detection, care and disease control.

MTMs

[0006] As summarized above, the invention is directed to compositions, systems and methods that utilize “microbe-targeting molecules” (MTMs) and engineered MTMs to monitor microbes, such a microbial pathogens. MTMs and engineered MTMs have the shared characteristic of binding to one or more microbe-associated molecular patterns (MAMPs). MTMs distinguish and bind microbes and microbial components from a sample based on the identity of the MAMP produced by the microbe, rather than the identity of microbe itself. While some MAMPs are produced by only a single species of microbe, other MAMPs are shared across species. Thus, while some MTMs of the invention bind to only MAMPs of a particular species of microbe, other MTMs of the invention can bind to MAMPs produced by all members of a particular class, order, family, genus or sub-genus of microbe.

[0007] As used herein, “MTM” and “engineered MTM” refers to any of the molecules described herein (or described in patents or patent application incorporated by reference) that can bind to a microbe or microbe component. Unless the context indicates otherwise, the term “MTM” is used to describe all MTMs of the invention, both naturally-occurring and engineered forms of these constructs.

[0008] MTMs can be used to contact, detect, and optionally isolate, microbes and microbial components from a sample based on the identity of the MAMP produced by the microbe, rather than the identity of microbe itself. While some MAMPs are produced by only a single species of microbe, other MAMPs are shared across species.

[0009] Given that the MTMs of the invention are defined based on their binding activity, it will be apparent that both naturally-occurring and engineered MTMs will comprise at least one microbe-binding domain, i.e. a domain that recognizes and binds to one or more MAMPs (including, at least two, at least three, at least four, at least five, or more) as described herein. A microbe-binding domain can be a naturally-occurring or a synthetic molecule. In some aspects, a microbe-binding domain can be a recombinant molecule. In addition to the microbe-binding domain, the MTMs of the invention will typically have one or more additional domains that may include, but are not limited to, an oligomerization domain, a signal domain, an anchor domain, a collagen-like domain, a fibrinogen-like domain, an immunoglobulin domain, and an immunoglobulin-like domain.

[0010] As non-limiting examples of the MTMs of the invention, three broad categories of MTMs are encompassed within the invention, namely: (i) collectin-based MTMs, (ii) ficolin- based MTMs, and (iii) toll-like receptor-based MTMs.

[0011] Thus, and in a first embodiment, the present invention is directed to compositions comprising collectin-based MTMs. The collectin-based MTMs are either naturally-occurring collectin proteins or engineered MTM fusion proteins that comprise at least one collectin microbe-binding domain and at least one additional domain.

[0012] The naturally-occurring collectin protein may be any one of (i) mannose-binding lectin (MBL), (ii) surfactant protein A (SP-A), (iii) surfactant protein D (SP-D), (iv) collectin liver 1 (CL-L1), (v) collectin placenta 1 (CL-P1), (vi) conglutinin collectin of 43 kDa (CL-43), (vii) collectin of 46 kDa (CL-46), (viii) collectin kidney 1 (CL-K1), (ix) conglutinin, and (x) a sequence variant having at least 85% sequence identity to any one of (i)-(ix).

[0013] In one aspect of this embodiment, the collectin is (i) a naturally-occurring MBL, (ii) a truncated form of naturally-occurring MBL, (iii) an engineered form of MBL, or (iv) a sequence variant having at least 85% sequence identity to any one of (i), (ii) or (iii). [0014] In a specific aspect of this embodiment, the collectin is a naturally-occurring MBL as set forth in SEQ ID NO: 1 or a sequence variant having at least 85% sequence identity with SEQ ID NO: 1 that retains the activity of the native protein.

[0015] In another specific aspect of this embodiment, the collectin is a truncated form of naturally-occurring MBL as set forth in any one of SEQ ID NOs:2-5 or a sequence variant having at least 85% sequence identity with any one of SEQ ID NOs:2-5 that retains the activity of the native protein.

[0016] The collectin microbe-binding domain of the collectin-based engineered MTMs comprises a carbohydrate recognition domain (CRD) of a collectin. The collectin may be any one of (i) mannose-binding lectin (MBL), (ii) surfactant protein A (SP-A), (iii) surfactant protein D (SP-D), (iv) collectin liver 1 (CL-L1), (v) collectin placenta 1 (CL-P1), (vi) conglutinin collectin of 43 kDa (CL-43), (vii) collectin of 46 kDa (CL-46), (viii) collectin kidney 1 (CL- Kl), (ix) conglutinin, and (x) a sequence variant having at least 85% sequence identity to any one of (i)-(ix).

[0017] The at least one additional domain of the collectin-based engineered MTMs may be one or more of (xi) a collectin cysteine-rich domain, (xii) a collectin collagen-like domain, (xiii) a collectin coiled-coil neck domain, (xiv) a ficolin short N-terminal domain, (xv) a ficolin collagen-like domain, (xvi) a Toll-like receptor (TLR) transmembrane helix, (xvii) a TLR C- terminal cytoplasmic signaling domain, (xviii) an oligomerization domain, (xix) a signal domain, (xx) an anchor domain, (xxi) a collagen-like domain, (xxii) a fibrinogen-like domain, (xxiii) an immunoglobulin domain, (xxiv) an immunoglobulin-like domain, and (xxv) a sequence variant having at least 85% sequence identity to any one of (xi)-(xxiv).

[0018] In certain aspects of this embodiment, the at least one additional domain is an immunoglobulin domain. For example, the immunoglobulin domain may comprise the amino acid sequence of SEQ ID NO: 12 or a sequence variant thereof having at least 85% sequence identity to SEQ ID NO: 12.

[0019] In certain aspects of this embodiment, the collectin microbe-binding domain comprises the CRD of MBL or a sequence variant thereof having at least 85% sequence identity to the CRD of MBL. For example, the CRD of MBL may comprise the amino acid sequence of any one of SEQ ID NOs:l, 2, 3, 4, and 5 or a sequence variant thereof having at least 85% sequence identity to any one of SEQ ID NOs: 1, 2, 3, 4, and 5. [0020] In certain aspects of this embodiment, the MTM comprises the CRD of MBL or a sequence variant thereof having at least 85% sequence identity to the CRD of MBL and an immunoglobulin domain. For example, the CRD of MBL may comprise the amino acid sequence of any one of SEQ ID NOs: 1, 2, 3, 4, and 5 or a sequence variant thereof having at least 85% sequence identity to any one of SEQ ID NOs: 1, 2, 3, 4, and 5, and an immunoglobulin domain comprising the amino acid sequence of SEQ ID NO12: or a sequence variant thereof having at least 85% sequence identity to SEQ ID NO: 12.

[0021] In certain aspects of this embodiment, the compositions comprise at least one collectin-based engineered MTM, wherein the collectin-based engineered MTM is an FcMBL of SEQ ID NO: 6, 7, 8 or 9, or a sequence variant thereof having at least 85% sequence identity to SEQ ID NO:6, 7, 8 or 9. FcMBL MTMs comprise a mannose-binding ligand (MBL) linked to the Fc domain of human IgG (Fc).

[0022] In certain other aspects of this embodiment, the compositions comprise at least two collectin-based engineered MTMs, wherein the two MTMs are selected from SEQ ID NO:6, 7, 8 or 9, or sequence variants thereof having at least 85% sequence identity to SEQ ID NO:6, 7, 8 or 9.

[0023] In a second embodiment, the invention is directed to compositions comprising ficolin- based MTMs. The fi colin-based MTMs are either naturally-occurring ficolin proteins or engineered MTM fusion proteins that comprise at least one ficolin microbe-binding domain and at least one additional domain.

[0024] The naturally-occurring ficolin protein may be any one of (i) ficolin 1, (ii) ficolin 2, (iii) ficolin 3, and (iv) a sequence variant having at least 85% sequence identity to any one of (i)- (iii).

[0025] The ficolin microbe-binding domain of the ficolin-based engineered MTMs may comprise the fibrinogen-like domain of a ficolin. The ficolin may be any one of (i) ficolin 1, (ii) ficolin 2, (iii) ficolin 3, and (iv) a sequence variant having at least 85% sequence identity to any one of (i)-(iii).

[0026] The at least one additional domain of the ficolin-based engineered MTMs may be one or more of (v) a ficolin short N-terminal domain, (vi) a ficolin collagen-like domain, (vii) a collectin cysteine-rich domain, (viii) a collectin collagen-like domain, (ix) a collectin coiled-coil neck domain, (x) a TLR transmembrane helix, (xi) a TLR C-terminal cytoplasmic signaling domain, (xii) an oligomerization domain, (xiii) a signal domain, (xiv) an anchor domain, (xv) a collagen-like domain, (xvi) a fibrinogen-like domain, (xvii) an immunoglobulin domain, (xviii) an immunoglobulin-like domain, and (xix) a sequence variant having at least 85% sequence identity to any one of (v)-(xviii).

[0027] In certain aspects of this embodiment, the at least one additional domain is an immunoglobulin domain. For example, the immunoglobulin domain may comprise the amino acid sequence of SEQ ID NO: 12 or a sequence variant thereof having at least 85% sequence identity to SEQ ID NO: 12.

[0028] In certain aspects of this embodiment, the ficolin-based engineered MTMs comprise a ficolin microbe-binding domain comprising the fibrinogen-like domain of any one of SEQ ID NOs: 21, 22 and 23 or a sequence variant thereof having at least 85% sequence identity to any one of SEQ ID NOs:21, 22 and 23.

[0029] In certain aspects of this embodiment, the ficolin-based engineered MTMs comprise a ficolin microbe-binding domain comprising the fibrinogen-like domain of any one of SEQ ID NOs: 21, 22 and 23 or a sequence variant thereof having at least 85% sequence identity to any one of SEQ ID NOs: 21, 22 and 23 and an immunoglobulin domain comprising the amino acid sequence of SEQ ID NO: 12 or a sequence variant thereof having at least 85% sequence identity to SEQ ID NO: 12.

[0030] In a third embodiment, the invention is directed to compositions comprising toll-like receptor (TLR)-based MTMs. The TLR-based MTMs are either naturally-occurring TLR proteins or engineered MTM fusion proteins that comprise at least one TLR microbe-binding domain and at least one additional domain.

[0031] The naturally-occurring TLR protein may be any one of (i) TLR1, (ii) TLR2, (iii) TLR3, (iv) TLR4, (v) TLR5, (vi) TLR6, (vii) TLR7, (viii) TLR8, (ix) TLR9, (x) TLR10, and (xi) a sequence variant having at least 85% sequence identity to any one of (i)-(x).

[0032] The TLR microbe-binding domain of the TLR-based engineered MTMs may comprise the N-terminal ligand-binding domain of a TLR. The TLR may be any one of (i) TLR1, (ii) TLR2, (iii) TLR3, (iv) TLR4, (v) TLR5, (vi) TLR6, (vii) TLR7, (viii) TLR8, (ix) TLR9, (x) TLR10, and (xi) a sequence variant having at least 85% sequence identity to any one of (i)-(x).

[0033] The at least one additional domain of the TLR-based engineered MTMs may be one or more of (xii) a TLR transmembrane helix, (xiii) a TLR C-terminal cytoplasmic signaling domain, (xiv) a ficolin short N-terminal domain, (xv) a ficolin collagen-like domain, (xvi) a collectin cysteine-rich domain, (xvii) a collectin collagen-like domain, (xviii) a collectin coiled- coil neck domain, (xix) an oligomerization domain, (xx) a signal domain, (xxi) an anchor domain, (xxii) a collagen-like domain, (xxiii) a fibrinogen-like domain, (xxiv) an immunoglobulin domain, (xxv) an immunoglobulin-like domain, and (xxvi) a sequence variant having at least 85% sequence identity to any one of (xii)-(xxv).

[0034] In certain aspects of this embodiment, the at least one additional domain is an immunoglobulin domain. For example, the immunoglobulin domain may comprise the amino acid sequence of SEQ ID NO: 12 or a sequence variant thereof having at least 85% sequence identity to SEQ ID NO: 12.

[0035] In certain aspects of this embodiment, the TLR-based engineered MTMs comprise a TLR microbe-binding domain comprising the N-terminal ligand-binding domain of any one of SEQ ID NOs:24-33 or a sequence variant thereof having at least 85% sequence identity to any one of SEQ ID NOs:24-33.

[0036] In certain aspects of this embodiment, the TLR-based engineered MTMs comprise a TLR microbe-binding domain comprising the N-terminal ligand-binding domain of any one of SEQ ID NOs:24-33 or a sequence variant thereof having at least 85% sequence identity to any one of SEQ NOs:24-33 and an immunoglobulin domain comprising the amino acid sequence of SEQ ID NO: 12 or a sequence variant thereof having at least 85% sequence identity to SEQ ID NO: 12.

Compositions

[0037] In a fourth embodiment, the invention is directed to compositions comprising one or more of the MTMs of the invention. In certain aspects of this embodiment, the compositions comprise at least one naturally-occurring MTM. In certain other aspects of this embodiment, the compositions comprise one collectin-based engineered MTM, wherein the collectin-based engineered MTM is an FcMBL of SEQ ID NO:6, 7, 8 or 9, or a sequence variant thereof having at least 85% sequence identity to SEQ ID NO:6, 7, 8 or 9. In certain other aspects of this embodiment, the compositions comprise at least two collectin-based engineered MTMs, wherein one of the collectin-based engineered MTMs is an FcMBL of SEQ ID NO:6, 7, 8 or 9, or a sequence variant thereof having at least 85% sequence identity to SEQ ID NO:6, 7, 8 or 9. In certain other aspects of this embodiment, the compositions comprise one naturally-occurring collectin MTM (e.g. MBL) and one collectin-based engineered MTM, wherein the collectinbased engineered MTM is an FcMBL of SEQ ID NO:6, 7, 8 or 9, or a sequence variant thereof having at least 85% sequence identity to SEQ ID NO:6, 7, 8 or 9. In certain other aspects of this embodiment, the compositions comprise one naturally-occurring collectin MTM (e.g. MBL) and at least two collectin-based engineered MTMs, wherein one of the collectin-based engineered MTMs is an FcMBL of SEQ ID NO:6, 7, 8 or 9, or a sequence variant thereof having at least 85% sequence identity to SEQ ID NO:6, 7, 8 or 9.

[0038] In certain aspects of this embodiment, the compositions further comprise a carrier or diluent, such as an aqueous solution comprising sodium acetate having a pH of about 3.2.

[0039] In a fifth embodiment, the invention is directed to compositions according to any of the preceding embodiments, further comprising a therapeutic agent, for example, one or more antimicrobial agents.

Substrates and Devices

[0040] The MTMs and compositions of the invention may be applied to substrates and used in collection devices (and related methods) to detect, capture and/or identify microbes and microbial components in a sample, such as a patient sample or an environmental sample.

[0041] The sample collection devices of the present invention thus generally comprise a substrate onto which a composition comprising MTMs of the invention is applied. Thus, and in a sixth embodiment, the invention is directed to a substrate comprising MTMs as defined herein. In a seventh embodiment, the invention is directed to a sample collection device comprising a substrate as defined herein, i.e. a substrate comprising MTMs, as also defined herein.

[0042] In some aspects, a composition comprising MTMs can be coated directly onto the sample collection device comprising a substrate. In some aspects, a composition comprising MTMs can be coated onto a substrate and then affixed to the sample collection device.

[0043] In some aspects, the substrate may be a magnetic microbead, a paramagnetic microbead, a microporous membrane, a hollow fiber, a filter, any other fluid filtration membrane, flow device, electronic chip, a graphene matrix, a graphene oxide matrix, cellulose paper, nitrocellulose, hydrogel, and any combination thereof. In some aspects, the substrate comprises a chip in an electronic device. In some aspects, the substrate comprises a filter in an air filtration device. In some aspects, the substrate comprises a filter in a breath analysis device. [0044] In some aspects, the sample collection device comprises a breath analysis device comprising a mouthpiece for receiving a breath sample of a subject. In some aspects, a sample collection device comprises an air filtration device comprising an air inlet for receiving a sample. An air filtration system of the present invention can be located in a room, on a plane or a ship, or in an outdoor space, for example. In some aspects, a sample collection device comprises a mouthpiece that can be configured to interface with an electronic device, including but not limited to a mobile phone or a breath analysis device.

[0045] A sample can include but is not limited to, a patient sample, an animal or animal model sample, an agricultural sample, a food and beverage sample, an environmental sample, a pharmaceutical sample, a biological sample, and a non-biological sample. A biological sample can include but is not limited to, cells, tissue, peripheral blood, and a bodily fluid. Exemplary biological samples include, but are not limited to, a biopsy, a tumor sample, biofluid sample; blood; serum; plasma; urine; feces; sperm; mucus; tissue biopsy; organ biopsy; synovial fluid; bile fluid; cerebrospinal fluid; mucosal secretion; effusion; sweat; saliva; and/or tissue sample etc. The sample can be collected from any source, including, e.g., human, animal, plant, environment, and organic or inorganic materials, suspected of being infected or contaminated by a microbe(s). Environmental samples include, but are not limited to, air samples, liquid samples, and dry samples. Suitable air samples include, but are not limited to, an aerosol, an atmospheric sample, and a ventilator discharge. Suitable dry samples include, but are not limited to, soil. Pharmaceutical samples include, but are not limited to, drug material samples and therapeutic fluid samples, for example, for quality control or detection of endotoxins. Suitable therapeutic fluids include, but are not limited to, a dialysis fluid.

Systems

[0046] In an eighth embodiment, the invention is directed to systems comprising the substrates and sample collection devices of the invention for use in monitoring microbes, such a microbial pathogens.

[0047] The system for pathogen monitoring of the invention can comprise, for example, a sample collection device, where the sample collection device comprises or interfaces with a substrate coated with a composition of the present invention for binding to or capturing one or more microbes or microbial components, such as MAMPs. The system can further comprise a detection device for detecting and optionally identifying one or more pathogens. For example, the system can comprise an identification library for identifying the detected pathogen(s). The system can further comprise a communication device for communicating information regarding the detected or identified pathogen(s). In some aspects, the communication device can communicate the information to a database, wirelessly or wired. In some aspects, the database can include one or more of an artificial intelligence system, a clinical decision support system, a contact tracing system, a global disease network, or a pathogen identification library. In a nonlimiting example, a smartphone can serve as a point-of-care (POC) device or used in the field, for example, to detect airborne or water pathogens, or an infected subject by taking a breath sample. In some aspects, the communication device can communicate a message, for example an alarm, indicating the presence of a pathogen or a pathogen level exceeding a threshold. A single device can comprise some or all components of the system.

[0048] As a nonlimiting example, the system can communicate with a database capable of receiving, organizing, and analyzing detailed, real-time data directly from the detection devices such as rapid-testing infectious disease tests, which improves disease surveillance and epidemic preparedness. In some aspects, the system can be integrated into a rapid-testing platform which has data connectivity and reporting. For example, the system can communicate wirelessly via existing cellular networks (e g., without additional requirements for setup) and connect to a cloud, where the cloud enables information exchange with secure protocols. The information exchange can be flexible such that it can be retrofitted into existing systems and adapt to other sources of data input, for example, use of mobile phone camera images to upload detection device test results. The network can cover a wide geographical area and coordinate with local cellular network companies, where information is accessible securely through devices such as mobile devices (e.g., smartphone) or a computer, for example via an application or secure server. [0049] In one aspect of this embodiment, the system for microbe monitoring comprises a sample collection device comprising at least one substrate coated with, or otherwise displaying, one or more MTMs, and a detection device.

[0050] In a first specific example of such a system, the substrate of the sample collection device is coated with a composition comprising one or more collectin-based MTMs, wherein the MTMs comprise at least one collectin microbe-binding domain and at least one additional domain, wherein the collectin microbe-binding domain comprises the carbohydrate recognition domain (CRD) of a collectin selected from the group consisting of

(i) mannose-binding lectin (MBL),

(ii) surfactant protein A (SP-A),

(iii) surfactant protein D (SP-D),

(iv) collectin liver 1 (CL-L1),

(v) collectin placenta 1 (CL-P1),

(vi) conglutinin collectin of 43 kDa (CL-43),

(vii) collectin of 46 kDa (CL-46),

(viii) collectin kidney 1 (CL-K1),

(ix) conglutinin, and

(x) a sequence variant having at least 85% sequence identity to any one of (i)-(ix), and wherein the at least one additional domain is one or more domains selected from the group consisting of

(xi) a collectin cysteine-rich domain,

(xii) a collectin collagen-like domain,

(xiii) a collectin coiled-coil neck domain,

(xiv) a ficolin short N-terminal domain,

(xv) a ficolin collagen-like domain,

(xvi) a TLR transmembrane helix,

(xvii) a TLR C-terminal cytoplasmic signaling domain,

(xviii) an oligomerization domain,

(xix) a signal domain,

(xx) an anchor domain,

(xxi) a collagen-like domain,

(xxii) a fibrinogen-like domain,

(xxiii) an immunoglobulin domain,

(xxiv) an immunoglobulin-like domain, and

(xxv) a sequence variant having at least 85% sequence identity to any one of (xi)-(xxiv). [0051] In this first specific example, the collectin microbe-binding domain may comprise the CRD of MBL or a sequence variant thereof having at least 85% sequence identity to the CRD of MBL. The CRD of MBL may comprise the amino acid sequence of any one of SEQ ID NOs: 1, 2, 3, 4, and 5 or a sequence variant thereof having at least 85% sequence identity to any one of SEQ ID NOs: 1, 2, 3, 4, and 5.

[0052] In this first specific example, the MTM may be one or more of SEQ ID NOs: 6-9, or a sequence variant thereof having at least 85% sequence identity to any one of SEQ ID NOs:6-9.

[0053] In this first specific example, the at least one additional domain may be an immunoglobulin domain. For example, the immunoglobulin domain may comprise the amino acid sequence of SEQ ID NO: 12 or a sequence variant thereof having at least 85% sequence identity to SEQ ID NO: 12.

[0054] In a second specific example of such a system, the substrate of the sample collection device is coated with a composition comprising one or more ficolin-based MTMs, wherein the MTMs comprise at least one ficolin microbe-binding domain and at least one additional domain, wherein the ficolin microbe-binding domain comprises the fibrinogen-like domain of a ficolin selected from the group consisting of

(i) ficolin 1,

(ii) ficolin 2,

(iii) ficolin 3, and

(iv) a sequence variant having at least 85% sequence identity to any one of (i)-(iii), and wherein the at least one additional domain is one or more domains selected from the group consisting of

(v) a ficolin short N-terminal domain,

(vi) a ficolin collagen-like domain,

(vii) a collectin cysteine-rich domain,

(viii) a collectin collagen-like domain,

(ix) a collectin coiled-coil neck domain,

(x) a TLR transmembrane helix,

(xi) a TLR C-terminal cytoplasmic signaling domain,

(xii) an oligomerization domain,

(xiii) a signal domain, (xiv) an anchor domain,

(xv) a collagen-like domain,

(xvi) a fibrinogen-like domain,

(xvii) an immunoglobulin domain,

(xviii) an immunoglobulin-like domain, and

(xix) a sequence variant having at least 85% sequence identity to any one of (v)-(xviii). [0055] In this second specific example, the ficolin microbe-binding domain may comprise the fibrinogen-like domain of any one of SEQ ID NOs:21, 22 and 23, or a sequence variant thereof having at least 85% sequence identity to any one of SEQ ID NOs:21, 22 and 23. [0056] In this second specific example, the at least one additional domain may be an immunoglobulin domain. For example, the immunoglobulin domain may comprise the amino acid sequence of SEQ ID NO: 12 or a sequence variant thereof having at least 85% sequence identity to SEQ ID NO: 12.

[0057] In a third specific example of such a system, the substrate of the sample collection device is coated with a composition comprising one or more toll-like receptor (TLR)-based MTMs, wherein the MTMs comprise at least one TLR microbe-binding domain and at least one additional domain, wherein the TLR microbe-binding domain comprises the N-terminal ligand-binding domain of a TLR selected from the group consisting of

(i) TLR1,

(ii) TLR2,

(iii) TLR3,

(iv) TLR4,

(v) TLR5,

(vi) TLR6,

(vii) TLR7,

(vii) TLR8,

(viii) TLR9,

(ix) TLR10, and

(x) a sequence variant having at least 85% sequence identity to any one of (i)-(ix), and wherein the at least one additional domain is one or more domains selected from the group consisting of

(xi) a TLR transmembrane helix,

(xii) a TLR C-terminal cytoplasmic signaling domain,

(xiii) a ficolin short N-terminal domain,

(xiv) a ficolin collagen-like domain,

(xv) a collectin cysteine-rich domain,

(xvi) a collectin collagen-like domain,

(xvii) a collectin coiled-coil neck domain,

(xviii) an oligomerization domain,

(xix) a signal domain,

(xx) an anchor domain,

(xxi) a collagen-like domain,

(xxii) a fibrinogen-like domain,

(xxiii) an immunoglobulin domain,

(xxiv) an immunoglobulin-like domain, and

(xxv) a sequence variant having at least 85% sequence identity to any one of (xi)-(xxiv). [0058] In this third specific example, the TLR microbe-binding domain may comprise the N- terminal ligand-binding domain of any one of SEQ ID NOs:24-33 or a sequence variant thereof having at least 85% sequence identity to any one of SEQ ID NOs:24-33.

[0059] In this third specific example, the at least one additional domain may be an immunoglobulin domain. For example, the immunoglobulin domain may comprise the amino acid sequence of SEQ ID NO: 12 or a sequence variant thereof having at least 85% sequence identity to SEQ ID NO: 12.

[0060] In each of the aspects and examples of this embodiment, the composition may comprise or further comprise at least one naturally-occurring MTM.

[0061] In each of the aspects and examples of this embodiment, the composition may further comprises one or more antimicrobial agents.

[0062] In each of the aspects and examples of this embodiment, the composition may comprise at least two collectin-based MTMs of claim 2, wherein at least one of the collectin- based MTMs is an FcMBL of SEQ ID NO:6, 7, 8 or 9 or a sequence variant thereof having at least 85% sequence identity to SEQ ID NO:6, 7, 8 or 9.

[0063] In each of the aspects and examples of this embodiment, the substrate may be, but is not limited to, a magnetic microbead, a paramagnetic microbead, a microporous membrane, a hollow fiber, a filter, any other fluid filtration membrane, flow device, electronic chip, a graphene matrix, a graphene oxide matrix, cellulose paper, nitrocellulose, and hydrogel, or a combination thereof.

[0064] In each of the aspects and examples of this embodiment, the device may be a mobile phone comprising an electronic chip or a breath analysis device comprising an electronic chip. [0065] In each of the aspects and examples of this embodiment, the substrate may further comprise a plasmonic and/or piezoelectric component.

[0066] In each of the aspects and examples of this embodiment, the device may be an air filtration device comprising a filter or a breath analysis device comprising a filter.

[0067] In each of the aspects and examples of this embodiment, the sample may be, but is not limited to, a patient sample, an animal sample, an animal model sample, an agricultural sample, a food and beverage sample, an environmental sample, a pharmaceutical sample, a biological sample, and a non-biological sample, or a combination thereof. For example, the sample may comprise a breath sample, an air sample or a blood sample.

[0068] In each of the aspects and examples of this embodiment, the detection device may be, but is not limited to, a spectrometer, an electrochemical detection device, a polynucleotide detection device, a fluorescence anisotropy device, a fluorescence resonance energy transfer device, an electron transfer device, an enzyme assay, a lateral flow assay, a magnetism device, an electrical conductivity device, an isoelectric focusing device, a chromatograph, an immunoprecipitation device, an immunoseparation device, an aptamer binding device, a fdtration device, electrophoresis device, a CCD camera, an immunoassay, an ELISA, a Gram staining device, an immunostaining device, a flow cytometer, a microscope, an immunofluorescence device, a western blot device, a polymerase chain reaction (PCR) device, RT-PCR device, an isothermal amplification device, a fluorescence in situ hybridization device, a sequencing device, a next gen sequencing device, a mass spectrometer, an ion mobility spectrometer, a surface plasmon resonance device, and a localized-surface plasmon resonance device, or a combination thereof. [0069] In each of the aspects and examples of this embodiment, the system may further comprise a pathogen identification library.

[0070] In each of the aspects and examples of this embodiment, the system may further comprise a communication device. As an example, the communication device may be configured to communicate information regarding the detected or identified pathogen(s) to a database. As an example, the database may comprise an artificial intelligence system, a clinical decision support system, a contact tracing system, a global disease network, or a pathogen identification library, or a combination thereof. In a nonlimiting example, a smartphone can serve as a point-of-care (POC) device or used in the field, for example, to detect airborne or water pathogens, or an infected subject by taking a breath sample.

[0071] In each of the aspects and examples of this embodiment, the microbe may be a pathogenic microbe.

Methods

[0072] In a ninth embodiment, the invention is directed to methods of using the devices and systems of the invention. Methods for monitoring microbes, such a microbial pathogens, of the invention can comprise contacting a sample suspected of containing a microbe with a sample collection device under conditions where MTMs contained within (or on) the device bind to one or more microbes or microbial components, such as MAMPs, in the sample, and detecting and optionally identifying one or more microbes. Upon detection and/or identification of the microbe(s), such as a pathogenic microbe(s), the method can further comprise communicating information regarding the detected or identified microbe(s) to one or more databases and/or providing an alarm, for example, in the case of a stationary air filtration device in a room, on a plane or a ship, or in an outdoor space. In some aspects, the database can include one or more of an artificial intelligence system, a clinical decision support system, a contact tracing system, a global disease network, or a pathogen identification library. Identifying the microbe(s) can include comparing data collected from the detection device to an identification library in the detection device or in an external database.

[0073] In each of these methods, the methods may further comprise identifying the microbe bound by the MTMs. [0074] In each of these methods, the device may comprise two or more MTMs having different binding specificities.

[0075] In one specific example of this embodiment, the method is a method for microbial pathogen monitoring comprising (a) collecting a sample using a sample collection device of claim 1 under conditions permitting binding of a MAMP in the sample to MTMs, and (b) detecting a microbial pathogen in the sample.

[0076] In this specific example, the substrate of the sample collection device is coated with a composition comprising one or more MTMs of the invention and one or more antimicrobial agents. The method may further comprise identifying the microbial pathogen. The identifying of the microbial pathogen may comprise comparing data collected from the sample to a pathogen identification library. The method may also further comprise combining data collected from the sample with data selected from geospatial data, physiological monitoring data, data from another source, or a combination thereof. The method may further comprise communicating to a database. The database may comprise an artificial intelligence system, a contact tracing system, a pathogen identification library, or combinations thereof. The method may further comprise performing contact tracing.

BRIEF DESCRIPTION OF THE DRAWINGS

[0077] FIG. 1. Diagram of various components and embodiments of a pathogen monitoring system.

[0078] FIG. 2A. Diagram of a substrate coated with one or more MTMs, such as FcMBL, that capture PAMPs of a pathogen present in a sample, such as an air or fluid sample.

[0079] FIG. 2B. Diagram of a substrate coated with one or more MTMs, such as FcMBL, that capture PAMPs of a pathogen present in a sample, such as an air or fluid sample, where the pathogen is identified using a pathogen-specific antibody.

[0080] FIG. 3. Schematic of an exemplary pathogen monitoring system.

[0081] FIG. 4. Diagram of an exemplary traveler screening and contract tracing system and method.

[0082] FIG. 5. Diagram showing the structure of exemplary collectins and ficolins. DETAILED DESCRIPTION

I. Definitions

[0083] As used herein, “a” or “an” may mean one or more. As used herein when used in conjunction with the word “comprising,” the words “a” or “an” may mean one or more than one. As used herein “another” may mean at least a second or more. Furthermore, unless otherwise required by context, singular terms include pluralities and plural terms include the singular.

[0084] As used herein, “about” refers to a numeric value, including, for example, whole numbers, fractions, and percentages, whether or not explicitly indicated. The term “about” generally refers to a range of numerical values (e.g., +/- 5-10% of the recited value) that one of ordinary skill in the art would consider equivalent to the recited value (e.g., having the same function or result). In some instances, the term “about” may include numerical values that are rounded to the nearest significant figure.

II. The Present Invention

[0085] As summarized above, the present invention is generally directed to compositions, systems and methods for monitoring microbes, such a microbial pathogens, using microbetargeting molecules (MTMs) and engineered MTMs as defined herein. These compositions, systems and methods can be used to monitor and detect the presence of one or more microbes in a sample, including but not limited to, a patient sample, an animal or animal model sample, an agricultural sample, a food and beverage sample, an environmental sample, a pharmaceutical sample, a biological sample, and a non-biological sample.

[0086] The important characteristic of the MTMs used in the compositions, devices and methods of the invention is that these constructs contact and bind microbes and microbial components in a sample based on the identity of the MAMP produced by the microbe, rather than the identity of microbe itself. While some MAMPs are produced by only a single species of microbe, other MAMPs are shared across species. Thus, while some MTMs of the invention bind to only MAMPs of a particular species of microbe, other MTMs of the invention can bind to MAMPs produced by all members of a particular class, order, family, genus or sub-genus of microbe.

[0087] As used herein, “MTM” and “engineered MTM” refers to any of the molecules described herein (or described in patents or patent application incorporated by reference) that can bind to a microbe or microbe component. Unless the context indicates otherwise, the term “MTM” is used to describe all MTMs of the invention, both naturally-occurring and engineered forms of these constructs. The terms “microbe-targeting molecule” and “microbe-binding molecule” are used interchangeably herein.

MAMPs

[0088] Before discussing the compositions, systems and methods of the invention, it will be helpful to understand the molecules to which the MTMs bind. As indicated above, each of the MTMs of the invention binds to at least one microbe-associated molecular pattern (MAMP). Some MTMs bind at least two, at least three, at least four, at least five, or more than five MAMPs.

[0089] As used herein and throughout the specification, the term “microbe-associated molecular patterns” or “MAMPs” refers to molecules, components or motifs associated with or secreted or released by microbes or groups of microbes (whole and/or lysed and/or disrupted) that are generally recognized by corresponding pattern recognition receptors (PRRs) of the MTM microbe-binding domains defined herein. In some aspects, the MAMPs encompass molecules associated with cellular components released during cell damage or lysis. Examples of MAMPs include, but are not limited to, microbial carbohydrates (e.g., lipopolysaccharide or LPS, mannose), endotoxins, microbial nucleic acids (e.g., bacterial, fungal or viral DNA or RNA; e g., nucleic acids comprising a CpG site), microbial peptides (e.g., flagellin), peptidoglycans, lipoteichoic acids, N-formylmethionine, lipoproteins, lipids, phospholipids or their precursors (e.g., phosphochloline), and fungal glucans.

[0090] In some aspects, microbe components comprise cell wall or membrane components known as pathogen-associated molecular patterns (PAMPs) including lipopolysaccharide (LPS) endotoxin, lipoteichoic acid, and attached or released outer membrane vesicles. In some aspects, a microbe comprises a host cell membrane and a pathogen component or a PAMP.

[0091] In some aspects, microbe components comprise damage-associated molecular patterns (DAMPs), also known as danger-associated molecular patterns, danger signals, and alarmin. These biomolecules can initiate and sustain a non-infectious inflammatory response in a subject, in contrast to PAMPs which initiate and sustain an infectious pathogen-induced inflammatory response. Upon release from damaged or dying cells, DAMPs activate the innate immune system through binding to pattern recognition receptors (PRRs). DAMPs are recognized by immune receptors, such as toll-like receptors (TLRs) and NOD-like receptor family, pyrin domain containing 3 (NLRP3), expressed by sentinel cells of the immune system. DAMPs include portions of nuclear and cytosolic proteins, ECM (extracellular matrix), mitochondria, granules, ER (endoplasmic reticulum), and plasma membrane.

[0092] In some aspects, MAMPs include carbohydrate recognition domain (CRD)-binding motifs. As used herein, the term “carbohydrate recognition domain (CRD)-binding motifs” refers to molecules or motifs that are bound by a molecule or composition comprising a CRD (i.e. CRDs recognize and bind to CRD-binding motifs). As used herein, the term “carbohydrate recognition domain” or “CRD” refers to one or more regions, at least a portion of which, can bind to carbohydrates on a surface of microbes or pathogens. In some aspects, the CRD can be derived from a lectin, as described herein. In some aspects, the CRD can be derived from a mannan-binding lectin (MBL). Accordingly, in some aspects, MAMPs are molecules, components or motifs associated with microbes or groups of microbes that are recognized by lectin-based MTMs (collectin-based MTMs) described herein that have a CRD domain. In one embodiment, MAMPs are molecules, components, or motifs associated with microbes or groups of microbes that are recognized by mannan-binding lectin (MBL).

[0093] In some aspects, MAMPs are molecules, components or motifs associated with microbes or groups of microbes that are recognized by a C-reactive protein (CRP)-based MTMs (collectin-based MTMs).

[0094] For clarity, MAMPs as used herein includes microbe components such as MAMPs, PAMPs and DAMPs as defined above.

[0095] When necessary, and unless otherwise detectable without pre-treatment, MAMPs can be exposed, released or generated from microbes in a sample by various sample pretreatment methods. In some aspects, the MAMPs can be exposed, released or generated by lysing or killing at least a portion of the microbes in the sample. Without limitations, any means known or available to the practitioner for lysing or killing microbe cells can be used. Exemplary methods for lysing or killing the cells include, but are not limited to, physical, mechanical, chemical, radiation, biological, and the like. Accordingly, pre-treatment for lysing and/or killing the microbe cells can include application of one or more of ultrasound waves, vortexing, centrifugation, vibration, magnetic field, radiation (e.g., light, UV, Vis, IR, X-ray, and the like), change in temperature, flash-freezing, change in ionic strength, change in pH, incubation with chemicals (e.g. antimicrobial agents), enzymatic degradation, and the like.

Microbes

[0096] As used herein, the term “microbe”, and the plural “microbes”, generally refers to microorganism(s), including bacteria, virus, fungi, parasites, protozoan, archaea, protists, e.g., algae, and a combination thereof. The term “microbe” encompasses both live and dead microbes. The term “microbe” also includes pathogenic microbes or pathogens, e.g., bacteria causing diseases such as sepsis, plague, tuberculosis and anthrax; protozoa causing diseases such as malaria, sleeping sickness and toxoplasmosis; and fungi causing diseases such as ringworm, candidiasis or histoplasmosis.

[0097] In some aspects, the microbe is a human pathogen, in other words a microbe that causes at least one disease in a human.

[0098] In some aspects, the microbe is a Gram-positive bacterial species, a Gram-negative bacterial species, a mycobacterium, a fungus, a parasite, protozoa, or a virus. In some aspects, the Gram-positive bacterial species comprises bacteria from the class Bacilli. In some aspects, the Gram-negative bacterial species comprises bacteria from the class Gammaproteobacteria. In some aspects, the mycobacterium comprises bacteria from the class Actinobacteria. In some aspects, the fungus comprises fungus from the class Saccharomycetes.

[0099] In some aspects, the microbe is Staphylococcus aureus, Streptococcus pyogenes, Klebsiella pneumoniae, Pseudomonas aeruginosa, Mycobacterium tuberculosis, Candida albicans, ox Escherichia coli. In some aspects, the microbe is S. aureus strain 3518, S. pyogenes strain 011014, K. pneumoniae strain 631, E. coli strain 41949, P. aeruginosa strain 41504, C. albicans strain 1311, or M. tuberculosis strain H37Rv.

[00100] In some aspects, the microbe is Bartonella henselae, Borrelia burgdorferi, Campylobacter jejuni, Campylobacterfetus, Chlamydia trachomatis, Chlamydia pneumoniae, Chylamydia psittaci, Simkania negevensis, Escherichia coli (e.g., 0157:H7 and K88), Ehrlichia chafeensis, Clostridium botulinum, Clostridium perfringens, Clostridium tetani, Enterococcus faecalis, Haemophilius influenzae, Haemophilius ducreyi, Coccidioides immitis, Bordetella pertussis, Coxiella burnetii, Ureaplasma urealyticum, Mycoplasma genitalium, Trichomatis vaginalis, Helicobacter pylori, Helicobacter hepaticus, Legionella pneumophila, Mycobacterium tuberculosis, Mycobacterium bovis, Mycobacterium africanum, Mycobacterium leprae, Mycobacterium asiaticum, Mycobacterium avium, Mycobacterium celatum, Mycobacterium celonae, Mycobacterium fortuitum, Mycobacterium genavense, Mycobacterium haemophilum, Mycobacterium intr acellular e, Mycobacterium kansasii, Mycobacterium malmoense, Mycobacterium marinum, Mycobacterium scrofulaceum, Mycobacterium simiae, Mycobacterium szulgai, Mycobacterium ulcerans, Mycobacterium xenopi, Corynebacterium diptheriae, Rhodococcus equi, Rickettsia aeschlimannii, Rickettsia africae, Rickettsia conorii, Arcanobacterium haemolyticum, Bacillus anthracia, Bacillus cereus, Lysteria monocytogenes, Yersinia pestis, Yersinia enterocolitica, Shigella dysenteriae, Neisseria meningitides, Neisseria gonorrhoeae, Streptococcus bovis, Streptococcus hemolyticus, Streptococcus mutans, Streptococcus pyogenes, Streptococcus pneumoniae, Staphylococcus aureus, Staphylococcus epidermidis, Staphylococcus pneumoniae, Staphylococcus saprophyticus, Vibrio cholerae, Vibrio parahaemolyticus, Salmonella typhi, Salmonella paratyphi, Salmonella enteritidis, Treponema pallidum, Human rhinovirus, Human coronavirus such as SARS-CoV-2, Dengue virus, Filoviruses (e.g., Marburg and Ebola viruses), Hantavirus, Rift Valley virus, Hepatitis B, C, and E, Human Immunodeficiency Virus (e.g., HIV-1, HIV-2), HHV-8, Human papillomavirus, Herpes virus (e.g., HV-I and HV-II), Human T-cell lymphotrophic viruses (e.g., HTLV-I and HTLV-II), Bovine leukemia virus, Influenza virus, Guanarito virus, Lassa virus, Measles virus, Rubella virus, Mumps virus, Chickenpox (Varicella virus), Monkey pox, Epstein Bahr virus, Norwalk (and Norwalk-like) viruses, Rotavirus, Parvovirus Bl 9, Hantaan virus, Sin Nombre virus, Venezuelan equine encephalitis, Sabia virus, West Nile virus, Yellow Fever virus, causative agents of transmissible spongiform encephalopathies, Creutzfeldt-Jakob disease agent, variant Creutzfeldt-Jakob disease agent, Candida, Cryptcooccus, Cryptosporidium, Giardia lamblia, Microsporidia, Plasmodium vivax, Pneumocystis carinii, Toxoplasma gondii, Trichophyton mentagrophytes, Enterocytozoon bieneusi, Cyclospora cayetanensis, Encephalitozoon hellem, or Encephalitozoon cuniculi, among other viruses, bacteria, archaea, protozoa, and fungi. In yet other aspects, the microbe is a bioterror agent (e.g., B. anthracis, and smallpox).

[00101] As used herein, “microbe component” and “microbial component” refer to any part of a microbe such as cell wall components, cell membrane components, cell envelope components, cytosolic components, intracellular components, nucleic acid (DNA or RNA), or organelles in the case of eukaryotic microbes. The terms “microbe component” and “microbial component” have the same meaning and they are used interchangeably herein. In some aspects, the microbial component comprises a component from a Gram-positive bacterial species, a Gram-negative bacterial species, a mycobacterium, a fungus, a parasite, a virus, or any microbe described herein or known in the art.

Sample

[00102] The MTMs defined herein can be used to detect, isolate and/or identify a microbe or a microbial component in a sample. A sample can include but is not limited to, a patient sample, an animal or animal model sample, an agricultural sample, a food and beverage sample, an environmental sample, a pharmaceutical sample, a biological sample, and a non-biological sample. A biological sample can include but is not limited to, cells, tissue, peripheral blood, and a bodily fluid. Exemplary biological samples include, but are not limited to, a biopsy, a tumor sample, biofluid sample; blood; serum; plasma; urine; sperm; mucus; tissue biopsy; organ biopsy; synovial fluid; bile fluid; cerebrospinal fluid; mucosal secretion; effusion; sweat; saliva; and/or tissue sample etc. The biological sample can be collected from any source, including, e.g., human or animal suspected of being infected or contaminated by a microbe(s). Biological fluids can include a bodily fluid and may be collected in any clinically acceptable manner. Biological fluids can include, but are not limited to, mucous, phlegm, saliva, sputum, blood, plasma, serum, serum derivatives, bile, sweat, amniotic fluid, menstrual fluid, mammary fluid, peritoneal fluid, interstitial fluid, urine, semen, synovial fluid, interocular fluid, a joint fluid, an articular fluid, and cerebrospinal fluid (CSF). A fluid may also be a fine needle aspirate or biopsied tissue. Blood fluids can be obtained by standard phlebotomy procedures and may be separated into components such as plasma for analysis. Centrifugation can be used to separate out fluid components to obtain plasma, buffy coat, erythrocytes, cells, pathogens and other components. [00103] In some aspects, the sample, such as a fluid, may be purified before introduction to a device or a system of the invention. For example, filtration or centrifugation to remove particulates and chemical interference may be used. Various filtration media for removal of particles includes filter paper, such as cellulose and membrane filters, such as regenerated cellulose, cellulose acetate, nylon, PTFE, polypropylene, polyester, polyethersulfone, polyarylethersulfone, polycarbonate, and polyvinylpyrolidone. [00104] Environmental samples include, but are not limited to, air samples, liquid and fluid samples, and dry samples. Suitable air samples include, but are not limited to, an aerosol, an atmospheric sample, and a ventilator discharge. Suitable dry samples include, but are not limited to, soil. Environmental fluids include, for example, saturated soil water, groundwater, surface water, unsaturated soil water; and fluids from industrialized processes such as waste water. Agricultural fluids can include, for example, crop fluids, such as grain and forage products, such as soybeans, wheat, and corn.

[00105] Pharmaceutical samples include, but are not limited to, drug material samples and therapeutic fluid samples, for example, for quality control or detection of endotoxins. Suitable therapeutic fluids include, but are not limited to, a dialysis fluid.

Subject

[00106] The present invention, including the compositions, systems and methods, may be used in conjunction with a subject. As used herein, a “subject” is a human, a non-human primate, bird, horse, cow, goat, sheep, a companion animal, such as a dog, cat or rodent, or other mammal.

MTMs

[00107] As summarized above, the invention is directed to compositions and sample collection devices, and systems and methods that use the devices, where the devices comprise a substrate that, in turn, comprises MTMs of the invention, i.e. MTMs that bind to one or more MAMPs.

[00108] MTMs distinguish and bind microbes and microbial components from a sample, such as a patient sample or an environmental sample, based on the identity of the MAMP produced by the microbe, rather than the identity of microbe itself. While some MAMPs are produced by only a single species of microbe, other MAMPs are shared across species. Thus, while some MTMs of the invention bind to only MAMPs of a particular species of microbe, other MTMs of the invention can bind to MAMPs produced by all members of a particular class, order, family, genus or sub-genus of microbe.

[00109] As will be apparent, while the “MTMs” of the invention include naturally-occurring molecules and proteins, the “engineered MTMs” of the invention are those have been manipulated in some manner by the hand of man. As used herein and throughout the specification, the term “engineered MTM” includes any non-naturally-occurring MTM. Engineered MTMs of the invention retain the binding specificity to a MAMP of the wild-type (i.e. naturally-occurring) molecule on which the engineered MTM is based.

[00110] The MTMs of the invention are defined based on their binding activity, therefore both naturally-occurring and engineered MTMs will comprise at least one microbe-binding domain, i.e. a domain that recognizes and binds to one or more MAMPs (including, at least two, at least three, at least four, at least five, or more) as described herein. A microbe-binding domain can be a naturally-occurring or a synthetic molecule. In some aspects, a microbe-binding domain can be a recombinant molecule.

[00111] Acceptable microbe-binding domains for use in the MTMs of the invention are limited only in their ability to recognize and bind at least one MAMP. In some aspects, the microbe-binding domain may comprise some or all of a peptide; polypeptide; protein; peptidomimetic; antibody; antibody fragment; antigen-binding fragment of an antibody; carbohydrate-binding protein; lectin; glycoprotein; glycoprotein-binding molecule; amino acid; carbohydrate (including mono-; di-; tri- and poly-saccharides); lipid; steroid; hormone; lipid- binding molecule; cofactor; nucleoside; nucleotide; nucleic acid; DNA; RNA; analogues and derivatives of nucleic acids; peptidoglycan; lipopolysaccharide; small molecule; endotoxin; bacterial lipopolysaccharide; and any combination thereof.

[00112] In particular aspects, the microbe-binding domain can be a microbe-binding domain of a lectin. An exemplary lectin is mannan binding lectin (MBL) or other mannan binding molecules. Non-limiting examples of acceptable microbe-binding domains also include microbebinding domains from toll-like receptors, nucleotide oligomerization domain-containing (NOD) proteins, complement receptors, collectins, ficolins, pentraxins such as serum amyloid and C- reactive protein, lipid transferases, peptidoglycan recognition proteins (PGRs), and any combinations thereof. In some aspects, microbe-binding domains can be microbe-binding molecules described in the International Patent Application No. WO 2013/012924, the contents of which are incorporated by reference in their entirety.

[00113] The MTMs of the invention will typically have one or more domains in addition to a microbe-binding domain. Such domains include, but are not limited to, an oligomerization domain, a signal domain, an anchor domain, a collagen-like domain, a fibrinogen-like domain, an immunoglobulin domain, and an immunoglobulin-like domain.

[00114] Engineered MTMs of the invention include, but are not limited to, MTMs identical to a naturally-occurring MTM but having at least one amino acid change in comparison to the wildtype molecule on which they are based. Such “sequence-variant engineered MTMs” have at least 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99 sequence identity, though in all cases less than 100% sequence identity, to the wild-type molecule on which they are based. The changes may be any combination of additions, insertions, deletions and substitutions, where the altered amino acids may be naturally-occurring or non- naturally-occurring amino acids, and conservative or non-conservative changes.

[00115] Engineered MTMs of the invention also include, but are not limited to, MTMs that comprise domains from two or more different MTMs, i.e. fusion proteins. Such “domain-variant engineered MTMs” have domains from 2, 3, 4, 5 or more different proteins. For example, MTMs can be a fusion protein comprising a microbe-binding domain and an oligomerization domain, or a fusion protein comprising a microbe-binding domain and a signal domain, or a fusion protein comprising a microbe-binding domain, an oligomerization domain, and signal domain, to name a few examples. In each case, the domains within a domain-variant engineered MTM are from at least two different proteins. Other examples of such MTMs include fusion proteins comprising at least the microbe-binding domain of a lectin and at least a part of a second protein or peptide, e.g., but not limited, to an Fc portion of an immunoglobulin.

[00116] Engineered MTMs of the invention further include, but are not limited to, MTMs that comprise domains from two or more different MTMs, wherein at least one of the domains is a sequence variant of the wild-type domain upon which it is based, i.e. having at least one amino acid change in comparison to the wild-type molecule on which it is based. These “sequence- and domain-variant engineered MTMs” have domains from 2, 3, 4, 5 or more different proteins, and at least one of the domains has at least 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99 sequence identity, though in all cases less than 100% sequence identity, to the wild-type domain on which it is based. The changes may be any combination of additions, insertions, deletions and substitutions, where the altered amino acids may be naturally-occurring or non-naturally-occurring amino acids, and conservative or nonconservative changes.

[00117] As non-limiting examples of the MTMs of the invention, three broad categories of suitable MTMs are defined in the following paragraphs, namely: (i) collectin-based MTMs, (ii) ficolin-based MTMs, and (iii) toll-like receptor-based MTMs. It should be understood that these three categories are not the only categories of MTMs encompassed by the invention.

Collectin-based MTMs

[00118] The MTMs of the invention include collectin-based MTMs. These MTMs are either naturally-occurring collectin proteins or engineered MTM fusion proteins that comprise at least one collectin microbe-binding domain, such as the lectin carbohydrate-recognition domain (CRD), and at least one additional domain

[00119] Collectins (collagen-containing C-type lectins) are a family of collagenous calciumdependent lectins that function in defense, thus playing an important role in the innate immune system. They are soluble molecules comprising pattern recognition receptors (PRRs) within the microbe-binding domain that recognize and bind to particular oligosaccharide structures or lipids displayed on the surface of microbes, i.e. MAMPs of oligosaccharide origin. Upon binding of collectins to a microbe, clearance of the microbe is achieved via aggregation, complement activation, opsonization, and activation of phagocytosis.

[00120] Members of the family have a common structure, characterized by four parts or domains arranged in the following N- to C-terminal arrangement: (i) a cysteine-rich domain, (ii) a collagen-like domain, (iii) a coiled-coil neck domain, and (iv) a microbe-binding domain which includes a C-type lectin domain, also termed the carbohydrate recognition domain (CRD). The functional form of the molecule is a trimer made up of three identical chains. MAMP recognition is mediated by the CRD in presence of calcium. See FIG. 5.

[00121] There are currently nine recognized members of the family: (i) mannose-binding lectin (MBL; mannose-binding lectin; e.g. SEQ ID NO:1), (ii) surfactant protein A (SP-A; SEQ ID NO: 13), (iii) surfactant protein D (SP-D; SEQ ID NO: 14), (iv) collectin liver 1 (CL-L1; SEQ ID NO: 15), (v) collectin placenta 1 (CL-P1; SEQ ID NO: 16), (vi) conglutinin collectin of 43 kDa (CL-43; SEQ ID NO: 17), (vii) collectin of 46 kDa (CL-46; SEQ ID N0: 18), (viii) collectin kidney 1 (CL-K1; SEQ ID NO: 19), and (ix) conglutinin (SEQ ID NO:20). Each of these proteins is an MTM of the invention.

[00122] MBL (Homo sapiens; GenBank: AAH69338.1; SEQ ID NO: 1):

[00123] Surfactant protein A (SP-A; Homo sapiens; GenBank: AAA36632.1; SEQ ID NO: 13):

[00124] Surfactant protein D (SP-D; Homo sapiens; GenBank: AAB59450.1; SEQ ID NO: 14)

[00125] Collectin liver 1 (CL-L1; also known as collectin- 10; Homo sapiens; NCBI Reference Sequence: NP_006429.2; SEQ ID NO: 15):

[00126] Collectin placenta 1 (CL-P1; Homo sapiens; GenBank: BAB72147.1;

NO: 16):

[00127] Conglutinin collectin (CL-43; Bos taurus; GenBank: AAI16148; SEQ ID NO: 17): [00128] Collectin of 46 kDa (CL-46; Bos taurus; GenBank: AAM34742; SEQ

[00129] Collectin kidney 1 (CL-K1; also known as collectin-11; Homo sapiens; GenBank:

BAF43301.1; SEQ ID NO: 19):

[00130] Conglutinin (Bos taurus; GenBank: BAA04983; SEQ ID NO:20):

[00131] The MTMs of the invention also include other collectin-based molecules that bind to one or more MAMPs, e.g. those MTMs comprising at least a portion (e.g. domain) of a lectin- based molecule in the case of an engineered MTM. As used herein, the term “collectin-based molecule” refers to a molecule comprising a microbe-binding domain derived from a collectin, such as a lectin. The term “lectin” as used herein refers to any molecule including proteins, natural or genetically modified (e.g., recombinant), that interacts specifically with saccharides (e.g., carbohydrates). The term “lectin” as used herein can also refer to lectins derived from any species, including, but not limited to, plants, animals (e.g. mammals, such as human), insects and microorganisms, having a desired carbohydrate binding specificity. Examples of plant lectins include, but are not limited to, the Leguminosae lectin family, such as ConA, soybean agglutinin, peanut lectin, lentil lectin, and Galanthus nivalis agglutinin (GNA) from the Galanthus (snowdrop) plant. Other examples of plant lectins are the Gramineae and Solanaceae families of lectins. Examples of animal lectins include, but are not limited to, any known lectin of the major groups S-type lectins, C-type lectins, P-type lectins, and Ltype lectins, and galectins. In some aspects, the carbohydrate recognition domain can be derived from a C-type lectin, or a fragment thereof. C-type lectin can include any carbohydrate-binding protein that requires calcium for binding (e.g., MBL). In some aspects, the C-type lectin can include, but are not limited to, collectin, DC-SIGN, and fragments thereof. Without wishing to be bound by theory, DC-SIGN can generally bind various microbes by recognizing high-mannose-containing glycoproteins on their envelopes and/or function as a receptor for several viruses such as HIV and Hepatitis C. [00132] Collectin-based engineered MTMs of the invention are MTMs that comprise at least a microbe-binding domain of a collectin. These MTMs may also include one or more of the other domains of a collectin, e.g. a cysteine-rich domain, a collagen-like domain, and/or a coiled-coil neck domain, as well as one or more domains not typically found in a collectin, such as an oligomerization domain, a signal domain, an anchor domain, a collagen-like domain, a fibrinogen-like domain, an immunoglobulin domain, and/or an immunoglobulin-like domain. When a collectin-based engineered MTM has each of the domains of a wild-type collectin, the MTM will be a sequence-variant engineered MTM as defined above. When a collectin-based engineered MTM has fewer that all of the domains of a wild-type collectin, the MTM will be a domain-variant engineered MTM or a sequence- and domain-variant engineered MTM as defined above.

[00133] Collectin-based engineered MTMs comprise a microbe-binding domain derived from at least one carbohydrate-binding protein selected from the group consisting of: MBL; SP-A; SP- D; CL-L1, CL-P1; CL-34; CL-46; CL-K1, conglutinin; maltose-binding protein; arabinose- binding protein; glucose-binding protein; Galanthus nivalis agglutinin; peanut lectin; lentil lectin; DC-SIGN; and C-reactive protein; and any combinations thereof.

MBL

[00134] In particular aspects and embodiments of the invention, the MTM may be MBL, whether full-length human MBL (SEQ ID NO: 1), mature human MBL without the signal sequence (e.g. SEQ ID NO:2), a truncated human MBL that retains microbe surface-binding (e.g. SEQ ID NO:3), the carbohydrate recognition domain (CRD) of human MBL (e.g. SEQ ID NON), or the neck and carbohydrate recognition domain of human MBL (e.g. SEQ ID NO:5), whether used alone or in combination with a second protein in the form of a fusion protein, such as a FcMBL protein as defined herein.

[00135] The amino acid sequence of full-length human MBL (SEQ ID NO: 1 ; GenBank: AAH69338.1) is: [00136] The amino acid sequence of mature human MBL without the signal sequence (SEQ ID NO:2) is:

[00137] The amino acid sequence of a truncated MBL that retains microbe surface-binding (SEQ ID NO:3) is: [00138] The amino acid sequence of the carbohydrate recognition domain (CRD) of human

MBL (SEQ ID NO:4) is:

[00139] The amino acid sequence of the neck and carbohydrate recognition domain of MBL (SEQ ID NO:5) is:

[00140] The truncated forms of the naturally-occurring protein include portions of any one of SEQ ID NOs: l-5 lacking 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80 or more amino acids from the amino-terminus of the protein, or the carboxy-terminus of the protein, or internally within the protein, or any combination thereof.

[00141] Alternatively, the truncated forms of the naturally-occurring protein of any one of SEQ ID NOs: l-5 have a deletion of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45% or 50% of the amino acids from the amino-terminus of the protein, or the carboxy -terminus of the protein, or internally within the protein, or any combination thereof.

[00142] As to particularly useful truncated forms of the protein, one example is the full-length amino acid sequence of the carbohydrate recognition domain (CRD) of MBL, shown in SEQ ID NO:4. In addition, suitable CRDs include CRDs having an amino acid sequence of about 10 to about 110 amino acid residues, or about 50 to about 100 amino acid residues, of SEQ ID NO:4. In some aspects, the microbe-binding domain can have an amino acid sequence of at least about 5, at least about 10, at least about 15, at least about 20, at least about 30, at least about 40, at least about 50, at least about 60, at least about 70, at least about 80, at least about 90, at least about 100, at least about 110 amino acid residues or more, of SEQ ID NO:4. Accordingly, in some aspects, the carbohydrate recognition domain of an engineered MBL protein can comprise SEQ ID NO:4. In some aspects, the carbohydrate recognition domain of an engineered MBL protein can comprise a fragment of SEQ ID NO:4 as defined above. Also, exemplary amino acid sequences of such fragments include, but are not limited to, ND, EZN (where Z is any amino acid, e.g., P), NEGEPNNAGS (SEQ ID NO: 10) or a fragment thereof comprising EPN, GSDEDCVLL or a fragment thereof comprising E, and LLLKNGQWNDVPCST (SEQ ID NO: 11) or a fragment thereof comprising ND. Modifications to such CRD fragments, e.g., by conservative substitution (i.e., where an amino acid is replace by an amino acid within the same class of amino acids, where the classes are: aliphatic amino acids (G, A, L, V, I); hydroxyl or sulfur/selenium-containing amino acids (S, C, U, T, M); aromatic amino acids (F, Y, W); basic amino acids (H, K, R); and acidic amino acids (D, E, N, Q)), are also within the scope described herein. In some aspects, the MBL or a fragment thereof used in the microbe surface-binding domain of the engineered MBLs described herein can be a wild-type molecule or a recombinant molecule.

[00143] The sequence variants of the naturally-occurring protein and the truncated forms thereof (e.g. SEQ ID NOs:l-5) include proteins having at least 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99% sequence identity to any one of SEQ ID NOs:l-5, or truncated forms thereof, that retain the ability to reduce platelet activation in blood of the protein upon which they are based.

Engineered MTM comprising MBL

[00144] In other particular aspects and embodiments of the invention, the MTM is an engineered MTM comprising MBL, as defined above, and a second protein in the form of a fusion protein. An exemplary fusion protein comprises some or all of naturally-occurring MBL, such as the carbohydrate recognition domain (CRD) of MBL, and a portion of an immunoglobulin, such as the Fc domain. In use, the Fc domain dimerizes and strengthens the avidity and affinity of the binding by MBLs to monomeric sugars. In some aspects, the N- terminus of fusion proteins can further comprise an oligopeptide linker adapted to bind a solid substrate and orient the CRD of the MBL domain away from a substrate to which it is immobilized. As discussed above, engineered forms of MBLs are known in the art and include each of the forms of MBL disclosed in U.S. Patent No. 9,150,631, U.S. Patent Pub.

2016/0311877, U.S. Patent Pub. 2019/0077850, U.S. Patent No. 9,593,160, U.S. Patent No. 10,435,457, U.S. Patent Pub. 2015/0173883 and International Application Publication No. WO 2011/090954, the entire disclosures of which are hereby incorporated by reference in their entirety.

[00145] FcMBL is a specific engineered form of MBL of the invention that comprises the neck and CRD domains of MBL linked to an IgG Fc domain. Proline 81 of mature MBL (SEQ ID

NO:2) is a convenient N-terminal point at which to begin the sequence of this engineered construct. For example, the neck and CRD domains (SEQ ID NO:5) of MBL are fused downstream (C-terminal) to the Fc domain of human IgG (Fey). The Fc domain may include the CH2-CH3 interface of the IgG Fc domain, which contains the binding sites for a number of Fc receptors including Staphylococcal protein A. In use, the Fc domain dimerizes and strengthens the avidity and affinity of the binding by MBLs to monomeric sugars. FcMBL is described in detail in U.S. Patent No. 9,150,631, the entire disclosure of which is hereby incorporated by reference in its entirety.

[00146] Specific examples of FcMBLs that may be used in each of the aspects and embodiments of the invention include, but are not limited to, proteins where the neck and CRD domains of MBL are linked to an Fc component of human IgGl, with examples of the resulting constructs set forth in SEQ ID NOs:6, 7 and 9, and proteins where the CRD domain alone of

MBL is linked to an Fc component of human IgGl, with an example of the resulting construct set forth in SEQ ID NO: 8.

[00147] FcMBL.81 (SEQ ID NO:6):

[00148] AKT -FcMBL (SEQ ID NO:7):

[00149] FcMBL.111 (SEQ ID N0:8):

[00150] FcMBL (SEQ ID NOV):

[00151] In SEQ ID NOV, the residues with a single underscore correspond to the Fc portion, the residues with a double underscore correspond to the MBL neck, and those residues without underscore correspond to the MBL carbohydrate-binding domain.

[00152] Various genetically engineered versions of the MTM (e.g., FcMBL) are described in International Application Pub. Nos. WO 2011/090954 and WO 2013/012924, as well as US Patents 9,150,631 and 9,593,160, the contents of each of which are incorporated herein by reference in their entireties. Lectins and other mannose binding molecules are also described in, for example, US 9,150,631 and US 9,632,085, and PCT application publication nos. W 0/2011/090954, WO2013012924 and WO/2013/130875, the contents of all of which are incorporated herein by reference in their entireties.

[00153] In aspects where the MTM is FcMBL, the Fc region or a fragment thereof can comprise at least one mutation, e.g., to modify the performance of the engineered MBL. For example, in some aspects, the half-life of the engineered MBL described herein can be increased, e.g., by mutating the lysine (K) at the residue 232 to alanine (A) as shown in the Fc domain sequence provided in SEQ ID NO: 12. Other mutations, e.g., located at the interface between the CH2 and CH3 domains shown in Hinton et al (2004) J Biol Chem. 279:6213-6216 and Vaccaro C. et al. (2005) Nat Biotechnol. 23: 1283-1288, can be also used to increase the half-life of the IgGl and thus the engineered MBL.

[00154] SEQ ID NO: 12:

[00155] In some aspects and embodiments, the FcMBL of the invention comprises or consists of an amino acid sequence having at least 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99% sequence identity to any one of SEQ ID NOs:6-9, that retain the active of protein upon which they are based.

[00156] The exemplary MBL sequences provided herein are not construed to be limiting. For example, while the exemplary sequences provided herein are derived from a human species, amino acid sequences of the same carbohydrate recognition domain in plants and other animal species such as mice, rats, porcine, bovine, feline, and canine are known in the art and within the scope described herein.

Other Collectins

[00157] In addition to the aspects and embodiments of the invention defined above that comprise the collectin MBL (whether naturally-occurring or engineered), the present invention encompasses use of any other collectin in an MTM that binds MAMPs, when used in conjunction with the methods and compositions of the invention. Thus, any of the following additional collectins may also be used in the aspects and embodiments of the invention as defined herein: (i) surfactant protein A (SP-A; SEQ ID NO: 13), (ii) surfactant protein D (SP-D; SEQ ID NO: 14), (iii) collectin liver 1 (CL-L1; SEQ ID NO: 15), (iv) collectin placenta 1 (CL-P1; SEQ ID NO: 16), (v) conglutinin collectin of 43 kDa (CL-43; SEQ ID NO: 17), (vi) collectin of 46 kDa (CL-46; SEQ ID NO: 18), (vii) collectin kidney 1 (CL-K1; SEQ ID NO: 19), and (viii) conglutinin (SEQ ID NO: 20).

[00158] As with MBL, both naturally-occurring collectins and engineered forms of the proteins may be used in the invention. Engineered forms of the proteins include, but are not limited to, truncated forms of the naturally-occurring proteins, sequence variants of the naturally- occurring proteins, sequence variants of the truncated forms of the proteins, fusion proteins comprising the naturally-occurring protein, fusion proteins comprising the truncated forms of the proteins, and fusion proteins comprising the sequence variants.

[00159] The truncated forms of the naturally-occurring collectins include portions of any one of SEQ ID NOs: 13-20 lacking 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80 or more amino acids from the amino-terminus of the protein, or the carboxyterminus of the protein, or internally within the protein, or any combination thereof.

[00160] Alternatively, the truncated forms of the naturally-occurring protein of any one of SEQ ID NOs: 13-20 have a deletion of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45% or 50% of the amino acids from the amino-terminus of the protein, or the carboxy -terminus of the protein, or internally within the protein, or any combination thereof.

[00161] The sequence variants of the naturally-occurring protein and the truncated forms thereof (e.g. SEQ ID NOs:13-20) include proteins having at least 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99% sequence identity to any one of SEQ ID NOs: 13-20, or truncated forms thereof, that retain the activity of the protein upon which they are based. Ficolin-based MTMs

[00162] Ficolins are a family of lectins that activate the lectin pathway of complement activation upon binding to a pathogen. Ficolins are soluble molecules comprising pattern recognition receptors (PRRs) within a microbe-binding domain that recognize and selectively bind acetylated compounds, typically N-acetylglucosamine (GlcNAc), produced by pathogens. The lectin pathway is activated by binding of a ficolin to an acetylated compound on the pathogen surface, which activates the serine proteases MASP-1 and MASP-2, which then cleave C4 into C4a and C4b, and cleave C2 into C2a and C2b. C4b and C2b then bind together to form C3-convertase of the classical pathway, leading to the eventual lysis of the target cell via the remainder of the steps in the classical pathway.

[00163] Members of the family have a common structure, characterized by three parts or domains arranged in the following N- to C-terminal arrangement: (i) a short N-terminal domain, (ii) a collagen-like domain, and (iii) a fibrinogen-like domain that makes up the microbe-binding domain. The functional form of the molecule is a trimer made up of three identical chains. See FIG. 5

[00164] There are currently three recognized members of the family: ficolin 1 (M-ficolin), ficolin 2 (L-ficolin), and ficolin 3 (H-fi colin). Each of these proteins is an MTM of the invention. The amino acid sequences of the human forms of the proteins are provided in the following paragraphs, with the fibrinogen-like domain underlined:

[00165] Ficolin 1 precursor - SEQ ID NO:21 - NP 001994.2 - Homo sapiens

[00166] Ficolin 2 isoform a precursor - SEQ ID NO:22 - NP 004099.2 - Homo sapiens

[00167] Ficolin 3 isoform 1 precursor - SEQ ID NO:23 - NP 003656.2 - Homo sapiens MDLLWILPSL WLLLLGGPAC LKTQEHPSCP GPRELEASKV VLLPSCPGAP GSPGEKGAPG

[00168] As with the collectins, both naturally-occurring ficolins and engineered forms of the proteins may be used in the invention. Engineered forms of the proteins include, but are not limited to, truncated forms of the naturally-occurring proteins, sequence variants of the naturally- occurring proteins, sequence variants of the truncated forms of the proteins, fusion proteins comprising the naturally-occurring protein, fusion proteins comprising the truncated forms of the proteins, and fusion proteins comprising the sequence variants.

[00169] The truncated forms of the naturally-occurring ficolins include portions of any one of SEQ ID NOs:21-23 lacking 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80 or more amino acids from the amino-terminus of the protein, or the carboxy -terminus of the protein, or internally within the protein, or any combination thereof.

[00170] Alternatively, the truncated forms of the naturally-occurring protein of any one of SEQ ID NOs:21-23 have a deletion of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45% or 50% of the amino acids from the amino-terminus of the protein, or the carboxy -terminus of the protein, or internally within the protein, or any combination thereof.

[00171] The sequence variants of the naturally-occurring protein and the truncated forms thereof (e.g. SEQ ID NOs:21-23) include proteins having at least 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99% sequence identity to any one of SEQ ID NOs:21-23, or truncated forms thereof that retain the activity of the protein upon which they are based. [00172] The MTMs of the invention also include other ficolin-based molecules that bind to one or more MAMPs (acetylated compounds for the ficolins), e.g. those MTMs comprising at least a portion (e.g. domain) of a ficolin-based molecule in the case of an engineered MTM. As used herein, the term “ficolin-based molecule” refers to a molecule comprising a microbebinding domain derived from a ficolin. The term “ficolin” as used herein refers to any molecule including proteins, natural or genetically modified (e.g., recombinant), that interacts specifically with acetylated compounds (e.g., GlcNAc). The term “ficolin” as used herein can also refer to ficolins derived from any species, including, but not limited to, plants, animals (e.g. mammals, such as human), insects and microorganisms, having the desired binding specificity.

[00173] Ficolin-based engineered MTMs of the invention are MTMs that comprise at least a microbe-binding domain of a ficolin, e.g. the fibrinogen-like domain of a ficolin. These MTMs may also include one or more of the other domains of a ficolin, e.g. a short N-terminal domain and/or a collagen-like domain, as well as one or more domains not typically found in a ficolin, such as a collectin cysteine-rich domain, a collectin collagen-like domain, a collectin coiled-coil neck domain, a TLR transmembrane helix, a TLR C-terminal cytoplasmic signaling domain, an oligomerization domain, a signal domain, an anchor domain, a collagen-like domain, a fibrinogen-like domain, an immunoglobulin domain, and an immunoglobulin-like domain. When a ficolin-based engineered MTM has each of the domains of a wild-type ficolin, the MTM will be a sequence-variant engineered MTM as defined above. When a ficolin-based engineered MTM has fewer that all of the domains of a wild-type ficolin, the MTM will be a domain-variant engineered MTM or a sequence- and domain-variant engineered MTM as defined above.

[00174] Ficolin-based engineered MTMs comprise a microbe-binding domain comprising at least one fibrinogen-like domain of a ficolin selected from the group consisting of ficolin 1, ficolin 2, and ficolin 3.

[00175] In certain aspects, the at least one additional domain is an immunoglobulin domain. For example, the immunoglobulin domain may comprise the amino acid sequence of SEQ ID NO: 12 or a sequence variant thereof having at least 85% sequence identity to SEQ ID NO: 12. [00176] In some aspects, the MTMs and engineered MTMs of the invention comprise a microbe-binding domain comprising the fibrinogen-like domain of ficolin 1 of SEQ ID NO:21, optionally with an immunoglobulin domain of SEQ ID NO: 12. In other aspects, the MTMs and engineered MTMs of the invention comprise a microbe-binding domain comprising the fibrinogen-like domain of ficolin 2 of SEQ ID NO:22, optionally with an immunoglobulin domain of SEQ ID NO: 12. In further aspects, the MTMs and engineered MTMs of a microbebinding domain comprising the fibrinogen-like domain of ficolin 3 of SEQ ID NO:23, optionally with an immunoglobulin domain of SEQ ID NO: 12.

[00177] In some aspects, the engineered MTMs of the invention comprise an microbe-binding domain having an amino acid sequence selected from SEQ ID NO:21 - SEQ ID NO:23, or an amino acid sequence that is at least 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical to any one of SEQ ID NO:21 - SEQ ID NO:23, but less than 100% identical, and that retains the microbe-binding activity of the wild-type protein.

[00178] In some aspects, the ficolin-based engineered MTMs comprise a ficolin microbebinding domain comprising the fibrinogen-like domain of any one of SEQ ID NOs:21, 22 and 23 or a sequence variant thereof having at least 85% sequence identity to any one of SEQ ID NOs:21, 22 and 23 and an immunoglobulin domain comprising the amino acid sequence of SEQ ID NO: 12 or a sequence variant thereof having at least 85% sequence identity to SEQ ID NO: 12. [00179] In some aspects, the microbe-binding domain comprising a fibrinogen-like domain of a ficolin from a primate, mouse, rat, hamster, rabbit, or any other species as described herein.

[00180] The exemplary sequences provided herein for the ficolins are not to be construed as limiting. For example, while the exemplary sequences provided herein are derived from a human, amino acid sequences of ficolins from other species such as mice, rats, porcine, bovine, feline, and canine are known in the art and within the scope described herein.

Toll-like receptor-based MTMs

[00181] Toll-like receptors (TLRs) comprise a family of proteins that are integral to the proper functioning of the innate immune system. The proteins are type I integral membrane proteins (i.e. single-pass, membrane-spanning receptors) that are typically found on the surface of sentinel cells, such as macrophages and dendritic cells, but can also be found on the surface of other leukocytes including natural killer cells, T cells and B cells, and non-immune cells including epithelial cell, endothelial cells, and fibroblasts. After microbes have gained entry to a subject, such as a human, through the skin or mucosa, they are recognized by TLR-expressing cells, which leads to innate immune responses and the development of antigen-specific acquired immunity. TLRs thus recognize MAMPs by microbes. [00182] Members of the family have a common structure, characterized by three parts or domains arranged in the following N- to C-terminal arrangement: (i) an N-terminal ligandbinding domain, i.e. the microbe-binding domain, (ii) a single transmembrane helix (~ 20 amino acids), and (iii) a C-terminal cytoplasmic signaling domain.

[00183] The ligand-binding domain is a glycoprotein comprising 550-800 amino acid residues (depending on the identity of the TLR), constructed of tandem copies of leucine-rich repeats (LRR), which are typically 22-29 residues in length and that contains hydrophobic residues spaced at distinctive intervals. The receptors share a common structural framework in their extracellular, ligand-binding domains. The domains each adopt a horseshoe-shaped structure formed by the leucine-rich repeat motifs.

[00184] The functional form of a TLR is a dimer, with both homodimers and heterodimers being known. In the case of heterodimers, the different TLRs in the dimer may have different ligand specificities. Upon ligand binding, TLRs dimerize their ectodomains via their lateral faces, forming “m”-shaped structures. Dimerization leads to downstream signaling.

[00185] A set of endosomal TLRs comprising TLR3, TLR7, TLR8 and TLR9 recognize nucleic acids derived from viruses as well as endogenous nucleic acids in context of pathogenic events. Activation of these receptor leads to production of inflammatory cytokines as well as type I interferons (interferon type I) to help fight viral infection.

[00186] There are a number of recognized human members of the family, including TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, and TLR10. Each of these proteins may be used as an MTM of the invention. The amino acid sequences of the human forms of the proteins are provided in the following paragraphs, with the extracellular domain that comprises the N-terminal ligand-binding domain underlined:

[00187] TLR1 (toll-like receptor 1 precursor) - NCBI Reference Sequence: NP_003254.2 (SEQ ID NO:24)

[00188] TLR2 (toll-like receptor 2 precursor) - NCBI Reference Sequence: NP_001305722.1

(SEQ ID NO:25)

[00189] TLR3 (toll-like receptor 3 precursor) - NCBI Reference Sequence: NP 003256.1 (SEQ ID NO:26)

[00190] TLR4 (toll-like receptor 4 isoform D) - NCBI Reference Sequence: NP 612567.1 (SEQ ID NO:27)

[00191] TLR5 (toll-like receptor 5 precursor) - NCBI Reference Sequence: NP_003259.2 (SEQ ID NO:28)

[00192] TLR6 (toll-like receptor 6 precursor) - NCBI Reference Sequence: NP 006059.2 (SEQ ID NO:29)

[00193] TLR7 (toll-like receptor 7 precursor) - NCBI Reference Sequence: NP 057646.1 (SEQ ID NO:30)

[00194] TLR8 (toll-like receptor 8 isoform 1) - UniProtKB/Swiss-Prot: Q9NR97.1 (SEQ ID

NO:31) VVLTENDSRY NNMYVDSIKQ Y

[00195] TLR9 (toll-like receptor 9 precursor) - NCBI Reference Sequence: NP 059138.1 (SEQ ID NO:32)

[00196] TLR10 (toll-like receptor 10 isoform a) - NCBI Reference Sequence: NP-001017388.1 (SEQ ID NO:33)

[00197] As with the collectins, both naturally-occurring TLR and engineered forms of the proteins may be used in the invention. Engineered forms of the proteins include, but are not limited to, truncated forms of the naturally-occurring proteins, sequence variants of the naturally- occurring proteins, sequence variants of the truncated forms of the proteins, fusion proteins comprising the naturally-occurring protein, fusion proteins comprising the truncated forms of the proteins, and fusion proteins comprising the sequence variants.

[00198] The truncated forms of the naturally-occurring TLRs include portions of any one of SEQ ID NOs:24-33 lacking 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, 25, 30, 35, 40, 45, 50, 55, 60, 65, 70, 75, 80 or more amino acids from the amino-terminus of the protein, or the carboxy -terminus of the protein, or internally within the protein, or any combination thereof.

[00199] Alternatively, the truncated forms of the naturally-occurring protein of any one of SEQ ID NOs:24-33 have a deletion of at least 1%, 2%, 3%, 4%, 5%, 6%, 7%, 8%, 9%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45% or 50% of the amino acids from the amino-terminus of the protein, or the carboxy -terminus of the protein, or internally within the protein, or any combination thereof.

[00200] The sequence variants of the naturally-occurring protein and the truncated forms thereof (e.g. SEQ ID NOs:24-33) include proteins having at least 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98 or 99% sequence identity to any one of SEQ ID NOs:24-33, or truncated forms thereof that retain the activity of the protein upon which they are based.

[00201] The MTMs of the invention also include other TLR-based molecules that bind to one or more MAMPs, e.g. those MTMs comprising at least a portion (e.g. domain) of a TLR-based molecule in the case of an engineered MTM. As used herein, the term “TLR-based molecule” refers to a molecule comprising a microbe-binding domain (i.e. an N-terminal ligand-binding domain) derived from a TLR. The term “TLR” as used herein refers to any molecule including proteins, natural or genetically modified (e.g., recombinant), that interacts specifically with an MAMP and that has a Toll IL-1 receptor (TIR) domain in their signaling domain. The term “TLR” as used herein can also refer to TLR derived from any species, including, but not limited to, plants, animals (e.g. mammals, such as human), insects and microorganisms, having the desired binding specificity.

[00202] TLR-based engineered MTMs of the invention are MTMs that comprise at least a microbe-binding domain of a TLR, e.g. the N-terminal ligand-binding domain of a TLR. These MTMs may also include one or more of the other domains of a TLR, e.g. a transmembrane helix and/or a C-terminal cytoplasmic signaling domain, as well as one or more domains not typically found in a TLR, such as a ficolin short N-terminal domain, a ficolin collagen-like domain, a collectin cysteine-rich domain, a collectin collagen-like domain, a collectin coiled-coil neck domain, an oligomerization domain, a signal domain, an anchor domain, a collagen-like domain, a fibrinogen-like domain, an immunoglobulin domain, and an immunoglobulin-like domain. When a TLR-based engineered MTM has each of the domains of a wild-type TLR, the MTM will be a sequence-variant engineered MTM as defined above. When a TLR-based engineered MTM has fewer that all of the domains of a wild-type TLR, the MTM will be a domain-variant engineered MTM or a sequence- and domain-variant engineered MTM as defined above.

[00203] TLR-based engineered MTMs comprise a microbe-binding domain comprising at least one N-terminal ligand-binding domain of a TLR selected from the group consisting of TLR1, TLR2, TLR3, TLR4, TLR5, TLR6, TLR7, TLR8, TLR9, and TLR10.

[00204] In certain aspects of this embodiment, the at least one additional domain is an immunoglobulin domain. For example, the immunoglobulin domain may comprise the amino acid sequence of SEQ ID NO: 12 or a sequence variant thereof having at least 85% sequence identity to SEQ ID NO: 12.

[00205] In some aspects, the MTMs and engineered MTMs of the invention comprise a microbe-binding domain comprising the N-terminal ligand-binding domain of TLR1 of SEQ ID NO:24, or the N-terminal ligand-binding domain of TLR2 of SEQ ID NO:25, or the N-terminal ligand-binding domain of TLR3 of SEQ ID NO:26, or the N-terminal ligand-binding domain of TLR4 of SEQ ID NO:27, or the N-terminal ligand-binding domain of TLR5 of SEQ ID NO:28, or the N-terminal ligand-binding domain of TLR6 of SEQ ID NO:29, or the N-terminal ligandbinding domain of TLR7 of SEQ ID NO:30, or the N-terminal ligand-binding domain of TLR8 of SEQ ID NO:31, or the N-terminal ligand-binding domain of TLR9 of SEQ ID NO:32, or the N-terminal ligand-binding domain of TLR10 of SEQ ID NO:33. In each of these examples, MTMs and engineered MTMs may further comprise an immunoglobulin domain of SEQ ID NO: 12.

[00206] In some aspects, the engineered MTMs of the invention comprise an microbe-binding domain having an amino acid sequence selected from SEQ ID NO:24 - SEQ ID NO:33, or an amino acid sequence that is at least 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, or 99% identical to any one of SEQ ID NO:24 - SEQ ID NO:33, but less than 100% identical, and that retains the microbe-binding activity of the wild-type protein.

[00207] In certain aspects of this embodiment, the TLR-based engineered MTMs comprise a TLR microbe-binding domain comprising the N-terminal ligand-binding domain of any one of SEQ ID NOs:24-33 or a sequence variant thereof having at least 85% sequence identity to any one of SEQ ID NOs:24-33 and an immunoglobulin domain comprising the amino acid sequence of SEQ ID NO: 12 or a sequence variant thereof having at least 85% sequence identity to SEQ ID NO: 12.

[00208] In some aspects, the microbe-binding domain comprising a N-terminal ligand-binding domain of a TLR from a primate, mouse, rat, hamster, rabbit, or any other subject as described herein.

[00209] The exemplary sequences provided herein for the TLRs are not to be construed as limiting. For example, while the exemplary sequences provided herein are derived from a human, amino acid sequences of TLRs from other species such as mice, rats, porcine, bovine, feline, and canine are known in the art and within the scope described herein.

[00210] In some further aspects, the MTMs of the invention are those described in at least one of the following: US provisional application numbers 61/296,222, 61/508,957, 61/604,878, 61/605,052, 61/605,081, 61/788,570, 61/846,438, 61/866,843, 61/917,705, 62/201,745, 62/336,940, 62/543, 614; PCT application numbers PCT/US2011/021603, PCT/US2012/047201, PCT/US2013/028409 , PCT/US2014/028683, PCT/US2014/046716, PCT/US2014/071293, PCT/US2016/045509, PCT/US2017/032928; US patent application numbers 13/574,191, 14/233,553, 14/382,043, 14/766,575, 14/831,480, 14/904,583, 15/105,298, 15/415,352, 15/483,216, 15/668,794, 15/750,788, 15/839,352, 16/059,799, 16/302,023, 16/553,635; and US patent numbers 9,150,631, 9,593,160, 9,632,085, 9,791,440, and 10,435,457; the contents of each of which are incorporated by reference herein in their entireties.

Compositions comprising MTMs

[00211] The invention includes compositions comprising one or more of types of MTMs defined herein, i.e. both naturally-occurring MTMs and engineered MTMs. As indicated above, particular MTMs can be defined based on (i) structural terms (e.g. based on the components of the MTM; the amino acid sequence of the MTM; the nucleic acid sequence of the MTM; etc.), (ii) functional terms (e.g. the identity of the MAMP bound by the PRR portion of the microbebinding domain; the affinity or avidity of binding to the MAMP; etc.), or (iii) both structural and functional terms. When a composition is defined as comprising two or more types of MTMs, it should be understood that “types” of MTMs in the composition differ based on structural and/or functional terms from each other. When there is more than one type of MTM in a composition, the composition is said to comprise a mixture of different types of MTMs within the composition.

[00212] An advantage of the present invention is the composition can be customized based on the particular use of the devices or substrate.

[00213] The compositions may comprise different types of MTMs within one category of

MTMs, as defined herein, or the compositions may comprise different types of MTMs within two or more different categories of MTMs, as defined herein. Thus, the compositions of the invention include “cocktails” of different types of MTMs, wherein the composition can include 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more different types of MTMs within a single composition.

[00214] The compositions of the invention may comprise mixtures of naturally-occurring

MTMs (e.g. MBLs), mixture of both naturally-occurring MTMs (e.g. MBLs) and the engineered MTMs defined herein (e.g. FcMBLs), or mixtures of only engineered MTMs (e.g., FcMBLs).

[00215] Depending on the manner in which the MTMs are used, the compositions comprising one or more different type of MTM may include suitable carriers and diluents. Suitable carriers and diluents are commonly known and will vary depending on the MTM being used and the mode of use. Examples of suitable carriers and diluents include water, buffered water, saline, buffered saline, dextrose, glycerol, ethanol, and combinations thereof, propylene glycol, polysorbate 80 (Tween-80™), poly(ethylene)glycol 300 and 400 (PEG 300 and 400), hydrophilic and hydrophobic carriers, and combinations thereof. Hydrophobic carriers include, for example, fat emulsions, lipids, PEGylated phospholipids, polymer matrices, biocompatible polymers, lipospheres, vesicles, particles, and liposomes, other stabilizing agents, solubilizing agents and surfactants, buffers and preservatives, tonicity agents, bulking agents, and lubricating agents. In one embodiment of the invention, the composition comprises as a carrier or diluent, an aqueous solution comprising sodium acetate having a pH of about 3.2.

[00216] The compositions of the invention may also comprise one or more antimicrobial agents. An MTM binds to and isolates one or more microbes or microbe components. An antimicrobial agent can optionally be included to treat (e.g. kill or inactivate) one or more known or suspected pathogens.

[00217] When the compositions comprise one or more antimicrobial agents, suitable agents include, but are not limited to, antibiotics, antivirals and antifungals. Antibiotics can be from classes including but not limited to Cephalosporin, Glycopeptide, Cyclic lipopeptide, Aminoglycoside, Macrolide, Oxazolidinone, Fluoroquinolones, Lincosamides, or Carbapenem. Antifungals can be from classes including but not limited to Polyenes, Azoles, Nucleoside Analog, Echinocandin, or Allylamine. Antivirals can be from classes including but not limited to CCR5 anatonists, Fusion inhibitors, Nucleoside/Nucleotide reverse transcriptase inhibitors (NRTIs), Non-nucleoside reverse transcriptase inhibitors (NNRTIs), Nucleotide reverse transcriptase inhibitors (NtRTIs), Integrase inhibitors, Protease inhibitors, DNA polymerase inhibitors, Guanosine analogs, Interferon-alpha, M2 ion channel blockers, Nucleoside inhibitors, NS5A polymerase inhibitors, NS3/4A protease inhibitors, Neuraminidase inhibitors, Nucleoside analogs, and Direct acting antivirals (DAAs). Examples of antimicrobials include but are not limited to aminoglycosides, ansamycins, beta-lactams, bis-biguanides, carbacephems, carbapenems, cationic polypeptides, cephalosporins, fluoroquinolones, glycopeptides, iron- sequestering glycoproteins, linosamides, lipopeptides, macrolides, monobactams, nitrofurans, oxazolidinones, penicillins, polypeptides, quaternary ammonium compounds, quinolones, silver compounds, sulfonamides, tetracyclines, and any combinations thereof.

[00218] Some exemplary antibiotics that may be included in the compositions of the invention include, but are not limited to, broad penicillins, amoxicillin (e.g., Ampicillin, Bacampicillin, Carbenicillin Indanyl, Mezlocillin, Piperacillin, Ticarcillin), Penicillins and Beta Lactamase Inhibitors (e.g., Amoxicillin-Clavulanic Acid, Ampicillin-Sulbactam, Benzylpenicillin, Cioxacillin, Dicloxacillin, Methicillin, Oxacillin, Penicillin G, Penicillin V, Piperacillin Tazobactam, Ticarcillin Clavulanic Acid, Nafcillin), Cephalosporins (e.g., Cephalosporin I Generation, Cefadroxil, Cefazolin, Cephalexin, Cephalothin, Cephapirin, Cephradine), Cephalosporin II Generation (e.g., Cefaclor, Cefamandole, Cefonicid, Cefotetan, Cefoxitin, Cefprozil, Cefmetazole, Cefuroxime, Loracarbef), Cephalosporin III Generation (e.g., Cefdinir, Ceftibuten, Cefoperazone, Cefixime, Cefotaxime, Cefpodoxime proxetil, Ceftazidime, Ceftizoxime, Ceftriaxone), Cephalosporin IV Generation (e.g., Cefepime), Macrolides and Lincosamides (e.g., Azithromycin, Clarithromycin, Clindamycin, Dirithromycin, Erythromycin, Lincomycin, Troleandomycin), Quinolones and Fluoroquinolones (e.g., Cinoxacin, Ciprofloxacin, Enoxacin, Gatifloxacin, Grepafloxacin, Levofloxacin, Lomefloxacin, Moxifloxacin, Nalidixic acid, Norfloxacin, Ofloxacin, Sparfloxacin, Trovafloxacin, Oxolinic acid, Gemifloxacin, Perfloxacin), Carbapenems (e g., Imipenem-Cilastatin, Meropenem), Monobactams (e.g., Aztreonam), Aminoglycosides (e.g., Amikacin, Gentamicin, Kanamycin, Neomycin, Netilmicin, Streptomycin, Tobramycin, Paromomycin), Glycopeptides (e.g., Teicoplanin, Vancomycin), Tetracyclines (e.g., Demeclocycline, Doxycycline, Methacycline, Minocycline, Oxytetracycline, Tetracycline, Chlortetracycline), Sulfonamides (e.g., Mafenide, Silver Sulfadiazine, Sulfacetamide, Sulfadiazine, Sulfamethoxazole, Sulfasalazine, Sulfisoxazole, Trimethoprim-Sulfamethoxazole, Sulfamethizole), Rifampin (e.g., Rifabutin, Rifampin, Rifapentine), Oxazolidinones (e.g., Linezolid, Streptogramins, Quinupristin Dalfopristin), Bacitracin, Chloramphenicol, Fosfomycin, Isoniazid, Methenamine, Metronidazole, Mupirocin, Nitrofurantoin, Nitrofurazone, Novobiocin, Polymyxin, Spectinomycin, Trimethoprim, Colistin, Cycloserine, Capreomycin, Ethionamide, Pyrazinamide, Para-aminosalicylic acid, Erythromycin ethyl succinate, and the like.

[00219] Some exemplary antifungals that may be included in the compositions of the invention include, but are not limited to, polyene antifungals, Amphotericin B, Candicidin, Filipin, Hamycin, Natamycin, Nystatin, Rimocidin, imidazole antifungals, triazole antifungals, thiazole antifungals, Bifonazole, Butoconazole, Clotrimazole, Econazole, Fenti conazole, Isoconazole, Ketoconazole, Luliconazole, Miconazole, Omoconazole, Oxiconazole, Sertaconazole, Sulconazole, Tioconazole, Triazoles[edit], Albaconazole, Efinaconazole, Epoxiconazole, Fluconazole, Isavuconazole, Itraconazole, Posaconazole, Propi conazole, Ravuconazole, Terconazole, Voriconazole, Abafungin, Allylamines, amorolfm, butenafme, naftifine, terbinafme, Echinocandins, Anidulafungin, Caspofungin, Micafungin, Aurones, Benzoic acid, Ciclopirox, Flucytosine, 5-fluorocytosin, Griseofulvin, Haloprogin, Tolnaftate, Undecylenic acid, Triacetin, Crystal violet, Castellani's paint, Orotomide, Miltefosine, Potassium iodide, Coal tar, Copper(II) sulfate, Selenium disulfide, Sodium thiosulfate, Piroctone olamine, lodoquinol, clioquinol, Acrisorcin, Zinc pyrithione, and Sulfur. Additional antifungals known in the art can also be used.

[00220] Some exemplary antivirals that may be included in the compositions of the invention include, but are not limited to, Abacavir, Acyclovir, Adefovir, Amantadine, Ampligen, Amprenavir, antiretroviral, Arbidol, Atazanavir, Atripla, Boceprevir, Cidofovir, Combivir, Daclatasvir, Darunavir, Delavirdine, Dasabuvir, Didanosine, Docosanol, Dolutegravir, Doravirine, Ecoliever, Edoxudine, Efavirenz, Elbasvir, Emtricitabine, Enfuvirtide, Entecavir, Etravirine, Famciclovir, Fomivirsen, Fosamprenavir, Foscamet, Fosfonet, Fusion inhibitor, Ganciclovir, Gemcitabine, Glecaprevir, Grazoprevir, Ibacitabine, Idoxuridine, Imiquimod, Imunovir, Indinavir, Inosine, Integrase inhibitor, Interferon, Interferon type I, Interferon type II, Interferon type III, Lamivudine, Ledipasvir, Lopinavir, Lopiravir, Loviride, Maraviroc, Methisazone, Moroxydine, Nelfinavir, Nevirapine, Nexavir, Nitazoxanide, Norvir, Nucleoside analogues, Ombitasvir, Oseltamivir (Tamiflu), Paritaprevir, Peglyated Interferon-alpha, Peginterferon alfa-2a, Penciclovir, Peramivir, Pibrentasvir, Pleconaril, Podophyllotoxin, Protease inhibitor, Pyramidine, Raltegravir, Reverse transcriptase inhibitor, Ribavirin, Rilpivirine, Rimantadine, Ritonavir, Saquinavir, Simeprevir, Sofosbuvir, Stavudine, Synergistic enhancer (antiretroviral), Telaprevir, Telbivudine, Tenofovir, Tenofovir disoproxil, Tipranavir, Trifluridine, Trizivir, Tromantadine, Truvada, Valaciclovir (Valtrex), Valganciclovir, Velpatasvir, Vicriviroc, Vidarabine, Viramidine, Voxilaprevir, Zalcitabine, Zanamivir (Relenza), Zidovudine. Additional antivirals known in the art can also be used.

[00221] The compositions of the invention can take many different forms, varying widely based on (i) the identity of the MTMs in the composition, (ii) the identity of other components in the composition, and (iii) the intended use of the composition, to name only a few of the relevant factors.

[00222] In some aspects, MTM compositions (e.g., engineered MTMs as described therein), methods, systems, and assays are further described in at least one of the following: US provisional application numbers 61/296,222, 61/508,957, 61/604,878, 61/605,052, 61/605,081, 61/788,570, 61/846,438, 61/866,843, 61/917,705, 62/201,745, 62/336,940, 62/543, 614; PCT application numbers PCT/US2011/021603, PCT/US2012/047201, PCT/US2013/028409 , PCT/US2014/028683, PCT/US2014/046716, PCT/US2014/071293, PCT/US2016/045509, PCT/US2017/032928; US patent application numbers 13/574,191, 14/233,553, 14/382,043, 14/766,575, 14/831,480, 14/904,583, 15/105,298, 15/415,352, 15/483,216, 15/668,794, 15/750,788, 15/839,352, 16/059,799, 16/302,023, 16/553,635; and US patent numbers 9,150,631, 9,593,160, 9,632,085, 9,791,440, and 10,435,457; the contents of each of which are incorporated by reference herein in their entireties.

Labels

[00223] The MTMs of the present invention may be labeled to allow them to be detected after binding to microbes or microbial components. The identity of the detectable label is limited only in that it can be discerned by the human eye or via a detector in the context of the detection device. Suitable detectable labels include colored or fluorescent particles, such a Europium particles or colloidal gold. Other acceptable labels include latex, which may itself be tagged with colored or fluorescent dyes, and magnetic or paramagnetic components. A further detectable label is a plasmonic fluor, wherein instead of assaying for a color change, one detects fluorescence. Ultrabright fluorescent nanolabels can also be used to improve the limit of detection in the detection devices of the invention, compared with conventional fluorophores. [00224] Other detectable labels include, but are not limited to, an enzyme (e.g., peroxidase, alkaline phosphatase, glucose oxidase), a metal (e.g., gold for electron microscopy applications), a fluorescent marker (e.g., for immunofluorescence and flow cytometry applications, including CYE dyes, fluorescein isothiocyanate, rhodamine, phycoerytherin, phycocyanin, allophycocyanin, o-phthaldehyde and fluorescamine), a fluorescence-emitting metals (e.g., ¹⁵² Eu), a radioactive marker (e.g., radioisotopes for diagnostic purposes, including ³ H, ¹³¹ I, ³⁵ S, ¹⁴ C, and ¹²⁵ I), a chemiluminescent marker (e.g., luminol, luciferin, isoluminol, theromatic acridinium ester, imidazole, acridinium salt and oxalate ester), and a protein tag (e.g., biotin, phycobiliprotein, c-Myc, HA, VSV-G, HSV, FLAG, V5, or HIS). Side Groups

[00225] The MTMs of the invention can be engineered to display side groups that augment, enhance or otherwise alter selected characteristics of the MTMs. For example, the MTMs of the invention may be engineered to display polyfluoro groups on any portion of the molecule. Such groups include fluoropolymers comprising terminal polyfluoro-oligomeric groups. These groups can aid in reducing thrombosis that may result, for example, when blood comes into contact with non-self surfaces. Coating of such surfaces with MTMs displaying polyfluoro-groups can reduce coagulation.

Substrates and Devices

[00226] The present invention includes sample collection devices comprising MTMs (and related methods) to detect, capture and/or identify microbes and microbial components in a sample, such as a patient sample or an environmental sample. The sample collection device comprises or interfaces with a substrate coated with a composition of the present invention for binding to or capturing one or more MAMPs.

[00227] Suitable substrates include, but are not limited to, a magnetic microbead, a paramagnetic microbead, a microporous membrane, a hollow fiber, a filter, any other fluid filtration membrane, flow device, electronic chip, a graphene matrix, a graphene oxide matrix, cellulose paper, nitrocellulose, hydrogel, and any combination thereof. In some aspects, the substrate comprises a chip in an electronic device. In some aspects, the substrate comprises a filter in an air filtration device. In some aspects, the substrate comprises a filter in a breath analysis device.

[00228] In some aspects, a composition comprising MTMs is coated directly onto the sample collection device comprising a substrate. In some aspects, a composition comprising MTMs is coated onto a substrate and then the substrate is affixed to the sample collection device.

[00229] There are various methods for coating a substrate with a composition of the present invention. Immobilization (via coating) of MTMs onto a surface can be either non-specific (e.g., by adsorption to the surface) or specific (e.g. where another molecule, such as a linker, immobilized on the surface is used to capture the MTM). MTMs may be linked to the surface through one or more linkers which may be cleavable to accommodate release or elution of the bound target molecules for subsequent analysis. Coating also includes, but is not limited to, pretreatment of a substrate using plasma treatment, corona treatment, or flame treatment.

[00230] An exemplary plasma treatment includes drying the substrate to eliminate residual moisture with filtered, compressed air; treating the substrate with a carbon dioxide plasma to introduce carboxylate moieties to enable the chemical crosslinking of the one or more MTMs of the composition. As a non-limiting example, the substrate may be a hollow fiber that is contacted with a buffer, for example, 2-(N-morpholino) ethanesulfonic acid (MES) buffer containing the MTM FcMBL (described above) and l-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC), a zero-length carboxyl-to-amino crosslinker. While filling the hollow fibers with the MES/EDC/FcMBL solution (EDC:FcMBL ratio of 1000: 1), the dialysate compartment is filled with MES buffer only. After the devices are filled, they are capped and incubated overnight at 2- 8oC during which time the EDC crosslinks the FcMBL protein to the inner lumen of the hollow fibers. The following day, the FcMBL-coupled devices are washed with excess phosphate buffered saline (PBS) solution containing 10 mM ethylenediaminetetraacetic acid (EDTA) (PBS/EDTA) through both the blood and dialysate compartments to remove the MES buffer, unbound protein, and EDC.

[00231] A corona treatment is a surface modification technique that uses a low temperature corona discharge plasma to impart changes in the properties of a surface. An exemplary method includes generating a corona plasma by the application of high voltage to an electrode that has a sharp tip, where the plasma forms at the tip. A linear array of electrodes can be used to create a curtain of corona plasma. The substrate may be passed through the corona plasma curtain in order to change the surface energy of the material, and then a composition comprising MTMs can be applied to the surface. In some aspects, a non-covalent bonding process can be used. [00232] A flame treatment comprises applying a gas flame to the surface of a material to improve adhesion. By rapidly applying intense heat to a surface, molecular chains are broken, and polar functional groups are added. Flame treatment also burns off dust, fibers, oils, and other surface contaminants. Following such treatment, a composition comprising MTMs can be applied to the surface.

[00233] In some aspects, the composition may be linked to an ELISA plate. Use of an ELISA plate can allow for multiplexing of samples. Enzyme-linked immunosorbent assay, also called ELISA, enzyme immunoassay or EIA, is a biochemical technique used mainly in immunology to detect the presence of an antibody or an antigen in a sample. The ELISA has been used as a diagnostic tool in medicine and plant pathology, as well as a quality control check in various industries. Different forms of ELISA are well known to those skilled in the art. The standard techniques known in the art for ELISA are described in "Methods in Immunodiagnosis", 2nd Edition, Rose and Bigazzi, eds. John Wiley & Sons, 1980; and Oellerich, M. 1984, J. Clin. Chem. Clin. Biochem. 22:895-904. These references are hereby incorporated by reference in their entirety.

[00234] In some aspects, the composition is coated and/or immobilized on the solid phase of multi-well plate, i.e., conjugated to a solid surface (usually a polystyrene micro titer plate, e.g., an “ELISA plate”). Immobilization can be either non-specific (e.g., by adsorption to the surface) or specific (e.g. where another molecule immobilized on the surface is used to capture the microbe-targeting molecule).

[00235] In some aspects, the device can be configured to be applied to a subject at a clinician’s office. In some aspects, the device can be configured to be used in the home, or in a public setting.

Systems

[00236] As suggested above, the sample collection devices of the invention can be used in systems (and methods) for detecting, identifying and/or monitoring microbes, such as pathogenic microbes. Such systems can be used in a variety of applications, from simply detecting infection in a single individual subject to monitoring disease outbreak in a population.

[00237] FIG. 1 includes exemplary components and embodiments of a system for pathogen monitoring. The system can comprise a sample collection device, as defined herein, where the sample collection device comprises or interfaces with a substrate coated with a composition of the present invention for binding to or capturing one or more MAMPs of a microbe. In some aspects, a sample collection device can comprise a breath analysis device comprising a mouthpiece for receiving a breath sample of a subject. In some aspects, a sample collection device comprises an air filtration device comprising an air inlet for receiving a sample. An air filtration system of the present invention can be located in a room, on a plane or a ship, or in an outdoor space. In some aspects, a sample collection device comprises a mouthpiece that can be configured to interface with an electronic device, including but not limited to a mobile phone or a breath analysis device. Any of the sample collection devices can be stationary or portable. [00238] The system can further comprise a detection device for detecting and optionally identifying one or more pathogens. In some aspects, the detection device can comprise an identification library for identifying the detected microbe(s) (e.g. pathogenic microbe(s)), for example where a detected signal can be compared to a library of known signals and used to detect and/or identify a pathogen. Examples of detection devices can include, but are not limited to, labeled or unlabeled polyreactive antibodies; labeled or unlabeled natural antibodies; spectrometer, electrochemical detection device, polynucleotide detection device, fluorescence anisotropy device, fluorescence resonance energy transfer device, electron transfer device, enzyme assay, a lateral flow assay, magnetism device, electrical conductivity device, isoelectric focusing device, chromatograph, immunoprecipitation device, immunoseparation device, aptamer binding device, filtration device, electrophoresis device, CCD camera, immunoassay, ELISA, Gram staining device, immunostaining device, microscope, immunofluorescence device, western blot device, polymerase chain reaction (PCR), RT-PCR, isothermal amplification device, fluorescence in situ hybridization device, sequencing device, next gen sequencing device, mass spectrometer, ion mobility spectrometer, surface plasmon resonance device, localized-surface plasmon resonance device, or substantially any combination thereof.

[00239] In some aspects, the detection device comprises plasmon resonance (PR), such as surface plasmon resonance (SPR) and localized surface plasmon resonance (LSPR), which is highly sensitive to changes that occur at the interface between a metal and a dielectric medium (e.g. water, air, etc.). PR technology utilizes surface plasmons (electromagnetic waves) that can be excited at certain metal interfaces, for example, graphene silver and gold. When incident light is coupled with the metal interface at angles greater than the critical angle, the reflected light exhibits a sharp attenuation. An SPR device comprises an optical biosensor that measures binding events of biomolecules at a metal surface by detecting changes in the local refractive index. Thus, when a particle binds to the surface of the sensor and interacts with the surface motion, the resonance frequency of the transduced signal is altered. For the binding of small nanoscale particles, such as nucleic acids, polypeptides or proteins, the addition of mass approximately corresponds to an increase of the thickness of the surf ace/sub strafe and the resonance frequency decreases. [00240] Because SPR and LSPR sensors are based on simple optical components, including a light source, a detector, optics, microfluidics and surface chemistry, they can be integrated into portable diagnostic devices. In the case of SPR, the plasmonic material can comprise a gold film, which requires a prism or waveguide to excite the plasmon, while colloidal nanostructures or nanostructured films are directly excited in LSPR. MTMs can be attached to these nanostructures. In addition to the use of gold and silver as surfaces for SPR, graphene may be used. Graphene is a single layer, two-dimensional structure nanomaterial that exhibits exceptional physical, electrical and chemical properties. The unique parameters of graphene are electron mobility, thermal conductivity, high surface area and electrical conductivity.

[00241] The system can further comprise a communication device for communicating information regarding the detected or identified pathogen(s) to a database. In some aspects, the database can include one or more of an artificial intelligence system, a clinical decision support system, a contact tracing system, a global disease network, or a pathogen identification library. In a nonlimiting example, a smartphone can serve as a point-of-care (POC) device or used in the field, for example, to detect airborne or water pathogens, or an infected subject by taking a breath sample.

[00242] As a non-limiting example shown in FIG. 1, a system comprises a point of care mobile phone comprising a sample collection device such a mouthpiece to collect a breath sample, where the mouthpiece can be integral or interface with the mobile phone. The mobile phone comprises an electronic chip with a graphene or graphene oxide matrix, where a composition of the present invention can be coated onto the matrix, as shown in FIG. 2A and FIG. 2B. In some aspects, the mobile phone further comprises plasmonic and/or piezoelectric components for the selective detection of long-wavelength infrared radiation with improved electromechanical performance and thermal capabilities. In some aspects, the point of care mobile phone can comprise an SPR or LSPR based detection system, for example as described in Fan Z, Geng Z, Fang W, et al. Smartphone Biosensor System with Multi-Testing Unit Based on Localized Surface Plasmon Resonance Integrated with Microfluidics Chip. Sensors (Basel).

2020; 20(2):446, published 2020 Jan 13, doi:10.3390/s20020446, which is incorporated by reference herein in its entirety.

[00243] As another non-limiting example, a system comprises a point of care platform comprising a rapid detection device such as a lateral flow assay for detecting MAMPs, e.g., PAMPs in a sample, described in international application number PCT/US21/37021, filed June 11, 2021, which is incorporated by reference herein in its entirety. The detection device data can be combined with geospatial data, e.g., data collected directly from a mobile device, allowing for real-time screening, tracing and mapping of infectious disease, thus allowing for interventions to be rapidly focused. In addition, direct reporting of the detection device data can be an integral part of the testing process, allowing clinicians to receive direct feedback about test results for purposes of disease surveillance.

[00244] In these aspects, where the detection device comprises a mobile device, the use of a camera on the device to interpret and transmit images, for example, of a lateral flow test data, can provide improved test sensitivity and reporting. For example, as described in Scherr, T.F. et al, Mobile phone imaging and cloud-based analysis for standardized malaria detection and reporting, Sci Rep., 2016; 6(1):28645, doi: 10.1038/srep28645, which is incorporated by reference in its entirety.

[00245] FIG. 3 is a schematic of an exemplary pathogen monitoring system comprising a sample detection device (“Point of care testing”) for generating detection device data and communicating with one or more databases. The communicating of the detection data can be performed manually or automatically. In some aspects, the data is communicated to one or more databases wired or wirelessly, e.g. via existing cellular networks or ad hoc connectivity using mobile phones. In some aspects, the detection device data can be communicated to a local database, for example, where the device detection data can be used for local clinical decision support. In some aspects, the detection device data can be combined with other data such as geospatial data, physiological or syndromic monitoring data such as temperature, blood pressure, heart rate or other biomarkers, or any combination thereof. In some aspects, the detection device data can be combined or integrated with information from different sources or testing sites, for example, to inform clinical management, antimicrobial policy, disease surveillance as well as areas with potential disease outbreaks. Additionally, the information can be used for health surveillance having the ability to directly capture testing data and fill gaps in current infectious disease and antibiotic resistance surveillance. In some aspects, the device detection data can be used for remote clinical decision support. For example, a cloud-based artificial intelligence system could incorporate patient data, detection device data, and up-to-date epidemiology, including drug-resistance profiles, to guide clinical treatment. This could be beneficial in settings where specialist input is unavailable and would support optimization of antimicrobial use. In some aspects, the detection device data can be communicated to a global disease network, for example, to inform disease surveillance, generate outbreak alerts, inform outbreak preparedness and monitoring control programs, and providing information regarding a traveler’s infectious disease status. In these aspects, an artificial intelligence system can be used to generate the communicated information. The detection device data can also be communicated to the Internet of Things (loT).

[00246] The pathogen monitoring system can be integrated into a network, e.g., of one or more databases, without significant additional infrastructure requirements, taking advantage of the geographical spread of rapid testing. For example, health facilities using the system can be connected to a central laboratory through rapid testing devices and automatically capture data on real-time disease frequency and healthcare use according to location. The pathogen monitoring systems and devices can comprise systems to provide secure data connections.

[00247] Infectious disease detection and diagnostic systems having communication and connectivity enable a robust system of real-time disease modeling and epidemic forecasting. The provision of direct patient-level data in the context of existing global surveillance systems through CDC or WHO could serve as a platform to enhance prediction of major disease outbreaks. The incorporation of a low-cost non-invasive or minimally-invasive MAMP, e.g., PAMP detecting smartphone, capable of recording and communicating detection data, physiological data including biomarkers, could serve as an additional layer of syndromic surveillance to real-time disease forecasting. The system could enhance performance of early detection of disease onset in a susceptible population. Targeted control interventions, including vector control and health resource mobilization, could be deployed before an outbreak. For example, the system of the present invention can be used for screening a traveler for infectious disease status by having the traveler exhale into a sample collection device of the invention, which is diagnostic for at least one pathogen. The system can determine the infectious disease status of a group of travelers prior to the travelers undertaking a journey (e.g. at position 102 of FIG. 4), allowing the results of the diagnostic test to be reported prior to or contemporaneous with the arrival of the travelers at their destination worldwide (e.g. at positions such as 104 of FIG. 4). Alternatively, the system can determine the infectious disease status of each traveler in a group prior to the traveler undertaking a journey (e.g. at positions such as 104 of FIG. 4), allowing the results of the diagnostic test to be reported prior to or contemporaneous with the arrival of the group of travelers at a destination (e.g. at position 102 of FIG. 4).

[00248] The system can also be used in biometric analysis. For example, use of the system allows for the mass analysis of one or more subjects at the sample time, along with biometric analysis via a stand-alone device or smartphone to accompany the digital POC assay. This approach allows 1, 10, 1000, or 1,000,000 people to be tested in 15+ minutes. Thus, the system is useful in screening at mass gatherings.

[00249] In addition, the use of detection device data, e.g., real-time epidemiological data, could further strengthen strategies such as emerging infectious disease vaccinations.

[00250] Further, the use of detection device data can be used to confirm diagnosis using other methods. For example, a subject provides a sample to the system upon entering a clinical site, and detection device data can be used to confirm a clinical diagnosis, or in reverse, the diagnosis can be used to confirm that detection device data.

[00251] The systems and methods of the present invention can also be used for animal health, where monitoring of large-scale farming environments or migratory populations would be useful for zoonotic outbreaks and impact on human health care.

[00252] The systems and methods of the present invention can also be used for monitoring of military and civilian aircrafts, ships and bases for bio-threats. For example, an air filtration system can collect a sample, such as an air sample, continuously or at certain timepoints, a detection device can analyze a sample, and if a pathogen is detected, e.g., is present or exceeds a threshold concentration, it can optionally be identified, and message can be communicated via the system, e.g., an alarm, and optionally device detection data and other information can be communicated to a remote database.

[00253] In one aspect of this embodiment, the system for microbe monitoring comprises a sample collection device comprising at least one substrate coated with, or otherwise displaying, one or more MTMs, and a detection device.

[00254] In a first specific example of such a system, the substrate of the sample collection device is coated with a composition comprising one or more collectin-based MTMs, wherein the MTMs comprise at least one collectin microbe-binding domain and at least one additional domain, wherein the collectin microbe-binding domain comprises the carbohydrate recognition domain (CRD) of a collectin selected from the group consisting of

(i) mannose-binding lectin (MBL),

(ii) surfactant protein A (SP-A),

(iii) surfactant protein D (SP-D),

(iv) collectin liver 1 (CL-L1),

(v) collectin placenta 1 (CL-P1),

(vi) conglutinin collectin of 43 kDa (CL-43),

(vii) collectin of 46 kDa (CL-46),

(viii) collectin kidney 1 (CL-K1),

(ix) conglutinin, and

(x) a sequence variant having at least 85% sequence identity to any one of (i)-(ix), and wherein the at least one additional domain is one or more domains selected from the group consisting of

(xi) a collectin cysteine-rich domain,

(xii) a collectin collagen-like domain,

(xiii) a collectin coiled-coil neck domain,

(xiv) a ficolin short N-terminal domain,

(xv) a ficolin collagen-like domain,

(xvi) a TLR transmembrane helix,

(xvii) a TLR C-terminal cytoplasmic signaling domain,

(xviii) an oligomerization domain,

(xix) a signal domain,

(xx) an anchor domain,

(xxi) a collagen-like domain,

(xxii) a fibrinogen-like domain,

(xxiii) an immunoglobulin domain,

(xxiv) an immunoglobulin-like domain, and

(xxv) a sequence variant having at least 85% sequence identity to any one of (xi)-(xxiv). [00255] In this first specific example, the collectin microbe-binding domain may comprise the CRD of MBL or a sequence variant thereof having at least 85% sequence identity to the CRD of MBL. The CRD of MBL may comprise the amino acid sequence of any one of SEQ ID NOs: 1, 2, 3, 4, and 5 or a sequence variant thereof having at least 85% sequence identity to any one of SEQ ID NOs: 1, 2, 3, 4, and 5.

[00256] In this first specific example, the MTM may be one or more of SEQ ID NOs: 6-9, or a sequence variant thereof having at least 85% sequence identity to any one of SEQ ID NOs:6-9.

[00257] In this first specific example, the at least one additional domain may be an immunoglobulin domain. For example, the immunoglobulin domain may comprise the amino acid sequence of SEQ ID NO: 12 or a sequence variant thereof having at least 85% sequence identity to SEQ ID NO: 12.

[00258] In a second specific example of such a system, the substrate of the sample collection device is coated with a composition comprising one or more ficolin-based MTMs, wherein the MTMs comprise at least one ficolin microbe-binding domain and at least one additional domain, wherein the ficolin microbe-binding domain comprises the fibrinogen-like domain of a ficolin selected from the group consisting of

(i) ficolin 1,

(ii) ficolin 2,

(iii) ficolin 3, and

(iv) a sequence variant having at least 85% sequence identity to any one of (i)-(iii), and wherein the at least one additional domain is one or more domains selected from the group consisting of

(v) a ficolin short N-terminal domain,

(vi) a ficolin collagen-like domain,

(vii) a collectin cysteine-rich domain,

(viii) a collectin collagen-like domain,

(ix) a collectin coiled-coil neck domain,

(x) a TLR transmembrane helix,

(xi) a TLR C-terminal cytoplasmic signaling domain,

(xii) an oligomerization domain,

(xiii) a signal domain,

(xiv) an anchor domain,

(xv) a collagen-like domain, (xvi) a fibrinogen-like domain,

(xvii) an immunoglobulin domain,

(xviii) an immunoglobulin-like domain, and

(xix) a sequence variant having at least 85% sequence identity to any one of (v)-(xviii). [00259] In this second specific example, the ficolin microbe-binding domain may comprise the fibrinogen-like domain of any one of SEQ ID NOs:21, 22 and 23, or a sequence variant thereof having at least 85% sequence identity to any one of SEQ ID NOs:21, 22 and 23. [00260] In this second specific example, the at least one additional domain may be an immunoglobulin domain. For example, the immunoglobulin domain may comprise the amino acid sequence of SEQ ID NO: 12 or a sequence variant thereof having at least 85% sequence identity to SEQ ID NO: 12.

[00261] In a third specific example of such a system, the substrate of the sample collection device is coated with a composition comprising one or more toll-like receptor (TLR)-based MTMs, wherein the MTMs comprise at least one TLR microbe-binding domain and at least one additional domain, wherein the TLR microbe-binding domain comprises the N-terminal ligand-binding domain of a TLR selected from the group consisting of

(i) TLR1,

(ii) TLR2,

(iii) TLR3,

(iv) TLR4,

(v) TLR5,

(vi) TLR6,

(vii) TLR7,

(vii) TLR8,

(viii) TLR9,

(ix) TLR10, and

(x) a sequence variant having at least 85% sequence identity to any one of (i)-(ix), and wherein the at least one additional domain is one or more domains selected from the group consisting of

(xi) a TLR transmembrane helix, (xii) a TLR C-terminal cytoplasmic signaling domain,

(xiii) a ficolin short N-terminal domain,

(xiv) a ficolin collagen-like domain,

(xv) a collectin cysteine-rich domain,

(xvi) a collectin collagen-like domain,

(xvii) a collectin coiled-coil neck domain,

(xviii) an oligomerization domain,

(xix) a signal domain,

(xx) an anchor domain,

(xxi) a collagen-like domain,

(xxii) a fibrinogen-like domain,

(xxiii) an immunoglobulin domain,

(xxiv) an immunoglobulin-like domain, and

(xxv) a sequence variant having at least 85% sequence identity to any one of (xi)-(xxiv). [00262] In this third specific example, the TLR microbe-binding domain may comprise the N- terminal ligand-binding domain of any one of SEQ ID NOs:24-33 or a sequence variant thereof having at least 85% sequence identity to any one of SEQ ID NOs:24-33.

[00263] In this third specific example, the at least one additional domain may be an immunoglobulin domain. For example, the immunoglobulin domain may comprise the amino acid sequence of SEQ ID NO: 12 or a sequence variant thereof having at least 85% sequence identity to SEQ ID NO: 12.

[00264] In each of the aspects and examples of this embodiment, the composition may comprise or further comprise at least one naturally-occurring MTM.

[00265] In each of the aspects and examples of this embodiment, the composition may further comprises one or more antimicrobial agents.

[00266] In each of the aspects and examples of this embodiment, the composition may comprise at least two collectin-based MTMs of claim 2, wherein at least one of the collectinbased MTMs is an FcMBL of SEQ ID NO:6, 7, 8 or 9 or a sequence variant thereof having at least 85% sequence identity to SEQ ID NO:6, 7, 8 or 9. Methods

[00267] The devices and systems of the invention may be used in a wide variety of applications including, but not limited to, methods of detecting the presence of a microbe or microbial component in a sample of bodily fluid or breath of a subject or in an environmental sample, for example. Such methods include contacting the sample with a sample collection device of the invention under conditions that permit binding of microbes or microbial components by MTMs displayed by the device, thus detecting microbes or microbial components in the sample. In one aspect, the microbe is a bacteria. In another aspect, the microbe is a virus. In further aspect, the microbe is a fungus. In further aspect, the microbe is a protozoan. Optionally, such methods can include one or more of the following additional steps: (i) quantifying the amount of microbe or microbial component in the sample; (ii) identifying the microbe in the sample; (iii) sending information regarding the microbe to a receiver, such as a database.

[00268] An exemplary method for pathogen monitoring can comprise collecting a sample, binding to one or more MAMPs, and detecting and optionally identifying one or more pathogen(s). Upon detection and/or identification of the pathogen(s), the method can further comprise communicating information regarding the detected or identified pathogen(s) to one or more databases and/or providing an alarm, for example, in the case of a stationary air filtration device in a room, on a plane or a ship, or in an outdoor space. In some aspects, the database can include one or more of an artificial intelligence system, a clinical decision support system, a contact tracing system, a global disease network, or a pathogen identification library. Identifying the pathogen(s) can include comparing data collected from the detection device to an identification library in the detection device or in an external database.

[00269] Collecting a sample can be done by contacting a MTM-coated substrate with a sample. Examples include but are not limited collecting a breath sample via a mouthpiece or a device that a subject can breathe into, and collecting an air or breath sample via an air inlet of a device such as an air filtration device. As a non-limiting example, the sample can be collected at a point of care, for example, before a passenger boards an airplane or enters a building. In some aspects, a sample can be continuously collected or collected at certain timepoints, for example, using an air filtration device located in a room, on a plane or a ship, or in an outdoor space. [00270] After the sample is collected, forming a complex with the composition, the captured microbe can remain bound on the substrates during detection and/or identification, or be isolated from the substrate prior to detection and/or identification, for example, using a detection device described herein. Such preparation can include but is not limited to eluting the microbe or microbe components, contacting the microbe or microbe components with a protease, contacting the microbe or microbe components with a solution that is more acidic than the microbe or microbe components, and/or contacting the microbe or microbe components with a matrix or matrix solution. In some aspects, the step of isolating comprises applying a magnet to the sample, for example to capture an engineered MTM linked to a magnetic substrate. In some aspects, the use of magnetic microparticles (e.g., superparamagnetic microparticles) can allow for easier washing and recovery of the microparticles, for automating the time of incubation with the sample, and also for working with whole blood with no interference from the erythrocytes. In some aspects, the magnet can be any magnetic material capable, a handheld magnet, a magnet formatted to a plate design such as a multi-well magnetic separator, a neodymium magnet tube rack, an automated magnet, and the like.

[00271] After the sample is collected, the sample is analyzed to detect and/or identify a pathogen. The analysis can be performed on one or several samples simultaneously.

[00272] The microbes and/or microbial matter (e.g., MAMPs) bound to MTM-coated (e.g., lectin-coated) substrates (e.g., magnetic microbead, a paramagnetic microbead, a microporous membrane, a hollow fiber, a filter, any other fluid filtration membrane, flow device, electronic chip, a graphene matrix, a graphene oxide matrix, cellulose paper, nitrocellulose, hydrogel) or a solid surface can be detected by any methods known in the art or as described herein. Examples of detection methods can include, but are not limited to, spectrometry, electrochemical detection, polynucleotide detection, fluorescence anisotropy, fluorescence resonance energy transfer, electron transfer, enzyme assay, magnetism, electrical conductivity, isoelectric focusing, chromatography, immunoprecipitation, immunoseparation, aptamer binding, filtration, electrophoresis, use of a CCD camera, immunoassay, ELISA, Gram staining, immunostaining, microscopy, immunofluorescence, western blot, polymerase chain reaction (PCR), RT-PCR, isothermal amplification, fluorescence in situ hybridization, sequencing, mass spectrometry, raman spectrometry, surface plasmon resonance, or substantially any combination thereof. The captured microbe can remain bound on the PRR-coated solid substrates during detection and/or analysis, or be isolated form the PRR-coated solid substrates prior to detection and/or analysis. [00273] In some embodiments of any of the aspects, the microbes and/or microbial matter (e.g., MAMPs) bound to PRR-coated (e.g., lectin-coated) solid substrates (e.g., polymeric or magnetic particles or beads) can be detected by ELLecSA as defined herein, an example which is described in detail in the section “An exemplary enzyme-linked lectin sorbent assay (ELLecSA)” below. Additional information various embodiments of FcMBL based assays can be found, e.g., in PCT application no. PCT/US2012/047201 and no. PCT/US2013/028409, the contents of all of which are incorporated herein by reference in their entireties.

[00274] In any of these aspects, the method can further comprise preparing a sample for analysis, e.g., isolating the microbe or microbe components which can include eluting the microbe or microbe components from the device. In some aspects, the step of isolating comprises washing the support with a buffer to remove unbound cells or biomolecules. The buffer can be any buffer as described herein, including but not limited to tris-buffered-saline, phosphate buffer saline, water, HPLC grade H2O, comprising octyl-P-D-glucopyranoside and/or calcium (TBSG Ca ²⁺ ) with surfactants. In some aspects, the step of washing can be performed at least 1, at least 2, at least 3, at least 4, or at least 5 times.

[00275] In some aspects, calcium depletion may be used to elute microbes or microbe components from the device. In some aspects, the sample is place in Trazol for nucleic acid enrichment.

[00276] When the MTM used in conjunction with the sample collection device is a speciesspecific MTM, for example, the microbe being detected by the sample collection device can be identified to the taxonomic level of species. However, when the MTM(s) used in conjunction with the sample collection device are not species-specific, i.e. the MTM(s) recognize and bind a family or genus of microbes and cannot identify the microbe to the taxonomic level of species, a further identification means may be used to identify the microbe to the selected taxonomic level. [00277] The invention is also directed to methods of detecting a microbe in a sample, comprising contacting a sample suspected of containing a microbe with a sample collection device or substrate of the invention comprising MTMs under conditions permitting binding of a microbe or a component of a microbe by MTMs coated on, or otherwise displayed by, the sample collection device or substrate, thereby detecting a microbe in a sample. Upon detection and/or identification of the microbe(s), the method can further comprise communicating information regarding the detected or identified microbe(s) to one or more databases and/or providing an alarm.

[00278] The invention is also directed to methods of detecting a microbial infection in a subject, comprising contacting a biological sample of a subject suspected of having a microbial infection with a sample collection device or substrate of the invention comprising MTMs under conditions permitting binding of a microbe or a component of a microbe by MTMs coated on, or otherwise displayed by, the sample collection device or substrate, thereby detecting a microbial infection in the subject. Upon detection and/or identification of the microbe(s), the method can further comprise communicating information regarding the detected or identified microbe(s) to one or more databases and/or providing an alarm.

[00279] The invention is also directed to methods of diagnosing a microbial infection in a subject, comprising contacting a biological sample of a subject suspected of having a microbial infection with a sample collection device or substrate of the invention comprising MTMs under conditions permitting binding of a microbe or a component of a microbe by MTMs coated on, or otherwise displayed by, the sample collection device or substrate, thereby diagnosing a microbial infection in the subject. Upon diagnosing a microbial infection, the method can further comprise communicating information regarding the detected or identified microbe(s) to one or more databases and/or providing an alarm.

[00280] In relevant aspects of these methods, the methods may further comprise identifying the microbe bound by the MTMs.

[00281] In relevant aspects of these methods, the sample may be a biological sample. For example, the biological sample may be exhalation from the subject or the subject’ s blood.

[00282] In relevant aspects of these methods, the device may comprise two or more MTMs having different binding specificities.

[00283] In relevant aspects of these methods, the device may comprise one or more MTMs set forth in SEQ ID NOs: 6, 7, 8 and 9.

[00284] In one specific example of this embodiment, the method is a method for microbial pathogen monitoring comprising (a) collecting a sample using a sample collection device of claim 1 under conditions permitting binding of a MAMP in the sample to MTMs, and (b) detecting a microbial pathogen in the sample. [00285] In this specific example, the substrate of the sample collection device is coated with a composition comprising one or more MTMs of the invention and one or more antimicrobial agents. The method may further comprise identifying the microbial pathogen. The identifying of the microbial pathogen may comprise comparing data collected from the sample to a pathogen identification library. The method may also further comprise combining data collected from the sample with data selected from geospatial data, physiological monitoring data, data from another source, or a combination thereof. The method may further comprise communicating to a database. The database may comprise an artificial intelligence system, a contact tracing system, a pathogen identification library, or combinations thereof. The method may further comprise performing contact tracing.

[00286] In some embodiments of any of the aspects, compositions (e.g., engineered microbe targeting molecules as described further therein), methods, systems, and assays are further described in at least one of the following: US Provisional Applications 61/296,222, 61/508,957, 61/604,878 , 61/605,052 , 61/605,081, 61/788,570, 61/846,438, 61/866,843, 61/917,705, 62/201,745, 62/336,940, 62/543, 614; PCT application numbers PCT/US2011/021603, PCT/US2012/047201, PCT/US2013/028409 , PCT/US2014/028683, PCT/US2014/046716, PCT/US2014/071293, PCT/US2016/045509, PCT/US2017/032928; US Patent Application numbers 13/574, 191, 14/233,553, 14/382,043 , 14/766,575, 14/831,480, 14/904,583, 15/105,298, 15/415,352, 15/483,216 , 15/668,794, 15/750,788, 15/839,352, 16/059,799, 16/302,023, 16/553,635; and US Patent numbers 9,150,631, 9,593,160, 9,632,085, 9,791,440, and 10,435,457; the contents of each of which are incorporated by reference herein in their entireties.

Incorporation by Reference

[00287] References and citations to other documents, such as patents, patent applications, patent publications, journals, books, papers, web contents, have been made throughout this disclosure. All such documents are hereby incorporated herein by reference in their entirety for all purposes. Equivalents

[00288] Various modifications of the invention and many further aspects thereof, in addition to those shown and described herein, will become apparent to those skilled in the art from the full contents of this document, including references to the scientific and patent literature cited herein. The subject matter herein contains important information, exemplification and guidance that can be adapted to the practice of this invention in its various aspects and equivalents thereof.