CLOSTRIDIUM DIFFICILE STRAIN

The present invention relates to the field of nucleic acid amplification based diagnostic assays. More specifically, the present invention provides a PCR based method for detecting a hypervirulent Clostridium difficile strain, preferably toxin producing Clostridium difficile strain 027, in a biological sample, such as a stool sample. The present invention is based on the use of oligonucleotide primers and probes specific to negative and positive markers for hypervirulent Clostridium difficile strains.

BACKGROUND OF THE INVENTION

C. difficile infection (CDI) is a toxin-mediated intestinal disease. The clinical outcomes of CDI can range from asymptomatic colonization to more severe disease syndromes, including severe diarrhoea, abdominal pain, fever and leukocytosis. C. difficile is recognized as the main cause of infectious diarrhoea that develops in patients after hospitalization and antibiotic treatment. Therefore, CDI is now considered to be one of the most important of health care-associated infections. Further, non -hospital-associated reservoirs of C. difficile are also emerging, and C. difficile is capable of spreading in animal hosts (Deneve et al., 2009; Rupnik et al, 2009).

C. difficile testing methods currently include cytotoxigenic culture methods, cyto toxin assays (CYT) detecting the toxins A and B produced by C. difficile, PCR based assays for detection of the tcdB gene of C. difficile, and assays for detection of C. difficile-specific glutamate dehydrogenase (GDH) (Eastwood et al., 2009).

In the prior art, the PCR based test have been found to be reliable, sensitive, and specific diagnostic tools for rapid screening and identification of samples containing C. difficile (Eastwood et al., 2009; Hirvonen et al., 2013; Houser et al., 2010 and WO2012087135). In commercial use is a method disclosed by WO2010116290 (Philips) relating to a multiplex PCR assay for the detection of a toxigenic C. difficile strain by analysing the presence or absence of the cytotoxin tcdB gene and deletions in the tcdC gene.

Although a number of PCR based assays for detecting toxin producing Clostridium difficile strain are already disclosed, there is still a need in the field for a PCR assay which is able to provide high specificity and reliability for the detection of those C. difficile strains which are hypervirulent. The present inventors have now located DNA sequence regions in Clostridium difficile genome that are surprisingly well-suited for specific and sensitive amplification of negative and positive markers relating to hypervirulent Clostridium difficile strains.

The sample matrix, which in diarrhoea diagnostics is commonly a stool or food sample, is likely to contain a host of PCR inhibitors. This reduces amplification efficiency of the PCR reaction and thus even more careful optimization is expected from the amplicon design step to verify that all templates and copy numbers are amplified equally but also efficiently enough. Hence, oligonucleotide design enabling high PCR efficiency (optimally as close to 100% as possible) is required. The detection method used may also affect amplification efficiency and/or bias.

The present inventors have now located DNA sequence regions that are well suited for specific and sensitive amplification and quantification of diarrhoea causing hypervirulent Clostridium difficile strains. The amplicons have been designed to be so specific that they can be combined into any multiplex sets with each other. Naturally a prerequisite to this is that all the disclosed amplicons have also been designed to amplify in the same reaction and cycling conditions. The aim of the invention is to replace antigen testing and culturing as a screening test for hypervirulent Clostridium difficile, and thus provide process improvements for the laboratory and clinical benefits in improved patient management by providing rapidly a rich set of information. Further, infection control could benefit if clinical microbiology laboratories could readily differentiate between non-toxigenic C. difficile and hypervirulent C. difficile.

SUMMARY OF THE INVENTION

One object of the present invention is to provide a method of detecting the presence of a hypervirulent Clostridium difficile strain in a biological sample, the method comprising: performing a nucleic acid amplification reaction comprising DNA extracted from the biological sample as a template, a first oligonucleotide primer set specific for amplifying a target sequence in the C. difficile hydR gene in the reaction, wherein said hydR gene comprises a sequence corresponding to SEQ ID NO: l, and a second oligonucleotide primer set specific for amplifying at least part of the target sequence corresponding to C. difficile sequence set forth in SEQ ID NO:2 in the reaction.

Another object of the present invention is to provide an oligonucleotide primer set comprising an oligonucleotide comprising or consisting of at least 10 contiguous nucleotides present in a nucleotide sequence as set forth in SEQ ID NO:3 and an oligonucleotide comprising or consisting of at least 10 contiguous nucleotides present in a nucleotide sequence as set forth in SEQ ID NO: 4, wherein the oligonucleotide primer set amplifies a target sequence in the C. difficile hydR gene.

Another object of the present invention is to provide an oligonucleotide primer set comprising an oligonucleotide comprising or consisting of at least 10 contiguous nucleotides present in a nucleotide sequence as set forth in SEQ ID NO: 5 and an oligonucleotide comprising or consisting of at least 10 contiguous nucleotides present in a nucleotide sequence as set forth in SEQ ID NO: 6, wherein the oligonucleotide primer set amplifies a specific target sequence in C. difficile genome.

Another object of the present invention is to provide an oligonucleotide primer set comprising an oligonucleotide comprising or consisting of at least 10 contiguous nucleotides present in a nucleotide sequence as set forth in SEQ ID NO: 11 and an oligonucleotide comprising or consisting of at least 10 contiguous nucleotides present in a nucleotide sequence as set forth in SEQ ID NO: 12, wherein the oligonucleotide primer set amplifies a target sequence in the C. difficile tcdB gene.

Another object of the present invention is to provide a kit for detecting a hypervirulent Clostridium difficile strain in a biological sample, the kit comprising: an oligonucleotide primer set as defined above; and a reagent for performing amplification of a nucleic acid in a nucleic acid amplification reaction.

DETAILED DESCRIPTION OF THE INVENTION

The purpose of the method of the present invention is to serve as a primary microbiological screening test for the qualitative identification of hypervirulent C. difficile, and a recurrent disease associated ribotype 027. The method is preferably performed from DNA extracted directly from a biological sample, such as a stool sample, without the use of an enrichment culture. Preferably, the method of the invention is a PCR-based C. difficile assay: such as a qPCR assay, or a qualitative multiplexed nucleic acid-based in vitro diagnostic test intended for detecting of nucleic acid markers corresponding to the detection and identification of hypervirulent Clostridium difficile and toxin producing 027 ribotype selective markers.

As used herein, a "target sequence" present in a nucleic acid sample is a strand of C.

difficile DNA to be primed and extended by a "primer". A target sequence may be either single- stranded or in a duplex with its complementary sequence. Target sequence as defined in the present invention is preferably purified to some degree prior to the amplification reactions described herein.

As used herein, the term "oligonucleotide" refers to any polymer of two or more of nucleotides, nucleosides, nucleobases or related compounds used as a reagent in the DNA amplification methods, such as primers and probes. The oligonucleotide may be DNA and/or RNA and/or analogs thereof. The term oligonucleotide does not denote any particular function to the reagent; rather, it is used generically to cover all such reagents described herein. Specific oligonucleotides of the present invention are described in more detail below. As used herein, an oligonucleotide can be virtually any length, limited only by its specific function in the DNA amplification reaction. Oligonucleotides of a defined sequence and chemical structure may be produced by techniques known to those of ordinary skill in the art, such as by chemical or biochemical synthesis, and by in vitro or in vivo expression from recombinant nucleic acid molecules, e.g., bacterial or viral vectors. Oligonucleotides may be modified in any way, as long as a given modification is compatible with the desired function of a given oligonucleotide. One of ordinary skill in the art can easily determine whether a given modification is suitable or desired for any given oligonucleotide of the present invention. Modifications include, but are not limited to base modifications, sugar modifications or backbone modifications. While design and sequence of oligonucleotides for the present invention depend on their function as described below, several variables must generally be taken into account. Among the most critical are: length, G/C content, melting temperature (Tm), Gibb free energy (G), specificity, self-complementarity and complementarity with other oligonucleotides in the system, polypyrimidine (T, C) or polypurine (A, G) stretches, and the 3'-end sequence. Controlling for these and other variables is a standard and well-known aspect of oligonucleotide design, and various computer programs are readily available to screen large numbers of potential oligonucleotides for optimal ones.

As used herein, the term "PCR reaction", "PCR amplifying" or "PCR amplification" refers generally to cycling polymerase-mediated exponential amplification of nucleic acids employing primers that hybridize to complementary strands, as described for example in Innis et al, PCR Protocols: A Guide to Methods and Applications, Academic Press (1990). Devices have been developed that can perform thermal cycling reactions with

compositions containing fluorescent indicators which are able to emit a light beam of a specified wavelength, read the intensity of the fluorescent dye, and display the intensity of fluorescence after each cycle. The amplification product contains a sequence having sequence identity with a target nucleic acid sequence or its complement and can be detected with, for example, an intercalating dye or a detection probe having specificity for a region of the target nucleic acid sequence or its complement. The PCR reaction as defined in the present invention is preferably performed as a real-time PCR assay.

As used herein, the term "probe" refers to any of a variety of signalling molecules indicative of amplification. For example, SYBR ^® Green and other DNA-binding dyes are detector probes. Some detector probes can be sequence-based, for example 5' nuclease probes. Various detector probes are known in the art, for example TaqMan ^® probes (See U.S. Patent No. 5,538,848). The melting temperature, Tm, of the probes can be increased by addition of modified nucleotides. The amount of modified nucleotides in one probe is preferably 1, 2, 3, 4 or more. The modified nucleotide can be a LNA nucleotide (Exiqon A/S), minor groove binder (MGB™), SuperBase, or Peptide Nucleic Acid (PNA) or any other modification increasing the Tm of the probe.

A person skilled in the art knows that amplified target sequences, i.e. amplicons, naturally vary in related strains. This minor variation can be taken into account while designing primers suitable to amplify said amplicons in the method of the present invention.

Preferably, at least 50, 60, 70, 80, 90 or 100 nucleotides long sequence of each of the target amplicons selected from the group consisting of SEQ ID NOS:l, 2 and 10 is amplified in the method. Preferably, the primers and probes comprise the sequences as defined in the claims and are less than 30, 35, 40, 45, 50 or 55 nucleotides long, and more preferably, less than 50 nucleotides long. Each of the present primers and probes can also be defined as consisting of at least 10, 15, 16, 17, 18, 19 or 20 contiguous nucleotides present in any one of primer or probe sequences selected from the group consisting of SEQ ID NOS:3-9 and 11-13 or comprising a sequence selected from the group consisting of SEQ ID NOS:3-9 and 11-13.

The present invention is directed to a method of detecting the presence of a hypervirulent Clostridium difficile strain in a biological sample. Preferably, the method is a real-time PCR assay. The method can be performed using a DNA chip, gel electrophoresis, a radiation measurement, a fluorescence measurement, or a phosphorescence measurement. A person skilled in the art may use the primers and probes of the invention also in other methods and platforms utilizing PCR or nucleic acid amplification. Said biological sample can be, e.g., a stool sample, an environmental sample or a food sample.

The method comprises the step of: performing a nucleic acid amplification reaction comprising DNA extracted from the biological sample as a template, a first oligonucleotide primer set specific for amplifying a target sequence in the C. difficile hydR gene in the reaction, wherein said hydR gene comprises a sequence corresponding to SEQ ID NO: l, and a second oligonucleotide primer set specific for amplifying at least part of the target sequence corresponding to C. difficile sequence set forth in SEQ ID NO:2 in the reaction. Preferably, the method comprises a step of detecting the presence of a hypervirulent Clostridium difficile strain in said biological sample by any method capable of detecting amplified target sequences in the reaction.

The hypervirulent Clostridium difficile strain is detected in the sample, when the first oligonucleotide primer set does not amplify a specific product, i.e. the target sequence in hydR gene is a negative marker for hypervirulent Clostridium difficile strain, and the second oligonucleotide primer set amplifies a specific product, i.e. the sequence targeted by the second primer set in C. difficile genome is a positive marker for hypervirulent Clostridium difficile strains. The most important hypervirulent Clostridium difficile strain detected by the present method is toxin producing Clostridium difficile strain 027. Thus, the present method is particularly directed to the detection of this Clostridium difficile strain. The presence of C. difficile hydR gene DNA in said sample, however, indicates that Clostridium difficile strain 027 is not present in the examined sample or that in addition to the presence of a toxin producing Clostridium difficile strain 027 there is also presence of another Clostridium difficile strain in the sample. A skilled person of the art is, however, aware that some of hypervirulent C. difficile strains are not classified as 027-ribotype strains, therefore, the present invention is also directed to the detection of hypervirulent 027-ribotype-resembling Clostridium difficile strains.

Preferably, the first oligonucleotide primer set targets the C. difficile hydR gene and amplifies the hydR sequence set forth in SEQ ID NO: 1 so that at least part of the sequence is specifically amplified in the amplification reaction. More preferably, the first oligonucleotide primer set comprises an oligonucleotide comprising or consisting of at least 10 contiguous nucleotides present in the nucleotide sequence as set forth in SEQ ID NO: 3 and an oligonucleotide comprising or consisting of at least 10 contiguous nucleotides present in the nucleotide sequence as set forth in SEQ ID NO: 4, said primers amplifying at least part of the hydR sequence set forth in SEQ ID NO: l . Most preferably, the first oligonucleotide primer set comprises an oligonucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO: 3 and an oligonucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO: 4.

The presence of the target sequence amplified with the first oligonucleotide primer set can be detected by the use of a probe comprising or consisting of at least 10 contiguous nucleotides present in the nucleotide sequence as set forth in SEQ ID NO:7, or preferably, by the use of a probe comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO:7.

The target sequence of the second oligonucleotide primer set in C. difficile genome corresponds to a gene encoding a putative conjugative transposon DNA recombination protein. Preferably, said second oligonucleotide primer set comprises an oligonucleotide comprising or consisting of at least 10 contiguous nucleotides present in a nucleotide sequence as set forth in SEQ ID NO: 5 and an oligonucleotide comprising or consisting of at least 10 contiguous nucleotides present in a nucleotide sequence as set forth in SEQ ID NO: 6. More preferably, the second oligonucleotide primer set comprises an

oligonucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO: 5 and an oligonucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO: 6.

The probes for the second oligonucleotide primer set as defined in SEQ ID NO: 8 and 9 can be used as competitive probes in a same reaction to detect a G/A polymorphism in C. difficile genome in a position corresponding to position 12 in SEQ ID NO:8 or 9. The presence of the target sequence amplified with the second oligonucleotide primer set can be detected by the use of a probe comprising or consisting of at least 10 contiguous nucleotides present in the nucleotide sequence as set forth in SEQ ID NO:7 so that said G/A polymorphism is detected. Preferably, the target sequence amplified with the second oligonucleotide primer set is detected by the use of a probe comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO: 8 or 9.

The amplification reaction as defined in the method may further comprise a third oligonucleotide primer set specific for amplifying C. difficile toxin B gene (tcdB). The third oligonucleotide primer set amplifies at least part of nucleotide region as set forth in SEQ ID NO: 10.

Preferably, the third oligonucleotide primer set comprises an oligonucleotide comprising or consisting of at least 10 contiguous nucleotides present in the nucleotide sequence as set forth in SEQ ID NO: 11 and an oligonucleotide comprising or consisting of at least 10 contiguous nucleotides present in the nucleotide sequence as set forth in SEQ ID NO: 12.

More preferably, the third oligonucleotide primer set comprises an oligonucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO: 11 and an oligonucleotide comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO: 12.

The presence of the target sequence amplified with the third oligonucleotide primer set is detected by the use of a probe comprising or consisting of at least 10 contiguous nucleotides present in the nucleotide sequence as set forth in SEQ ID NO: 13, preferably, by the use of a primer comprising or consisting of the nucleotide sequence as set forth in SEQ ID NO: 13. The present invention is also directed to oligonucleotide primer sets, i.e. oligonucleotides, comprising primers as defined above for the first, second or third oligonucleotide primer set or a mix thereof. The primer sets may also comprise probes as defined above for use with each of the primer sets. The present invention is also directed to the use of these oligonucleotide primer sets for the detection of the presence of a hypervirulent Clostridium difficile strain in a biological sample, such as a stool sample or a food sample.

The present invention also provides kits for detecting a hypervirulent Clostridium difficile strain in a biological sample, a kit may comprise the oligonucleotide primer set as defined above; and a reagent for performing amplification of a nucleic acid. Preferably, the reagent is selected from the group consisting of: DNA polymerase, dNTPs, and a buffer.

Another embodiment of the invention is a method of detecting the presence of a hypervirulent Clostridium difficile strain in a biological sample using oligonucleotide primers and probes with modified nucleotides. Generally, the use of modified nucleotides renders possible shortening of an oligonucleotide primer or probe without compromising its specificity. The amount of modified nucleotides in one primer or probe is preferably 1, 2, 3, 4 or more. The modified nucleotide can be a LNA nucleotide (Exiqon A/S), minor groove binder (MGB™), SuperBase, or Peptide Nucleic Acid (PNA) or any other nucleotide modification having the same effect on the oligonucleotide. The method comprises essentially same steps as the method described above and in the claims but is performed with at least one modified primer or probe. One example of the primers and probes for such method is:

Primer pair 1 (for the detection of hydR gene): SEQ ID NO: 3 and SEQ ID NO: 4 with a probe having the sequence SEQ ID NO: 7.

Primer pair 2 (for the detection of putative conjugative transposon, pet): SEQ ID NO: 5 and SEQ ID NO: 6 with a probe having the sequence CTG TAG ATT TCG GTA CGA (SEQ ID NO: 14), wherein underlined nucleotides are modified nucleotides such as LNA.

Primer pair 3 (for the detection of tcdB gene): SEQ ID NO: 11 and SEQ ID NO: 12 with a probe having the sequence SEQ ID NO: 13. Accordingly, a person skilled in the art would understand that the length of any of the above primers or probes may be shortened in a similar way by using at least one modified nucleotide.

The publications and other materials used herein to illuminate the background of the invention, and in particular, to provide additional details with respect to its practice, are incorporated herein by reference. The present invention is further described in the following example, which is not intended to limit the scope of the invention.

EXPERIMENTAL SECTION

EXAMPLE 1

In this example, the assay of the disclosed invention was used to detect both toxin- producing and non-toxin-producing C. difficile strains. A total of 48 characterized samples representing 37 different ribotypes were tested. This test excluded 027 or genetically very closely related ribotypes.

The assay contains one multiplex PCR reaction which amplifies the target panel (Table 1). Identification of toxin producing C. difficile and differentiation of hypervirulent C. difficile is based on combined detection of these markers. Toxin marker: tcdB gene encodes Toxin B, 027-negative marker: hydR encodes TetR family transcriptional regulator protein and 027-positive marker: pet encodes putative conjugative transposon DNA recombination protein. Primers and probes were as defined in Table 9.

The C. difficile assay should give positive results from different toxin-producing C. difficile strains, and negative results for non-toxin-producing C. difficile strains. Inclusivity (analytical reactivity) is tested to account for potential genetic variation among the targets included in the panel. This example describes the results of the inclusivity of the C. difficile qPCR assay using well characterized strains.

Table 1. C.difficile assay target panel

Marker Target gene Description

region

Toxin B tcdB Detects cytotoxi n (Toxin B)

produci ng C. difficile

Positive hypervirulent marker is

Positive hypervirulent detected only from hypervirulent marker strains (ribotype 027)

Negative hypervirulent Negative marker is not detected marker from ribotype 027 strai ns, but is

positive for other C.difficile strains

Materials and methods

1.1 The list of the bacterial targets

The C.difficile assay covers pathogens causing gastrointestinal infections. A total of 48 characterized samples representing 37 different ribotypes were tested in this inclusivity study covering non-toxinogenic C.difficile and Toxin B producing C.difficile. The list of strains is described in Table 2. This test excluded 027 or genetically very closely related ribotypes.

Strains were collected from commercial available biobanks (ATCC, DSMZ, and Microbiologics). DNA samples were tested in concentrations less than 100 ng/μΐ.

Table 2. Amplidiag C.difficile GE assays inclusivity test panel

# Original code # Original code # i Original code

1 iATCC 51695 17 iATCC BAA-1808 33 ; 106090

2 43599 18 i l06216 34 43603

3 iATCC 17857 19 iATCC BAA-1812 35 ! ATCC 43255

4 iATCC BAA-1871 20 ; ATCC 43601 36 Ϊ AHS 56035

5 Ϊ0329 Ρ (ATCC 9689) 21 :ATCC 43602 37 : ATCC BAA-2156

6 BAA-1813 22 I0527P (ATCC 700057) 38 7727

7 ATCC BAA-1874 23 i l06210 39 AHS 55868

8 :ATCC BAA-1809 24 iATCC BAA-1873 40 ; 106194

9 ;ATCC BAA-1810 25 iATCC BAA-1804 41 ; RHC 7758

10 iATCC BAA-1801 26 ATCC BAA-1811 42 i ATCC BAA-1807

11 iATCC BAA-1382 27 ^AHS 55375 43 i ATCC BAA-1872

12 iATCC 43596 28 Ό833Ρ (ATCC 43593) 44 i ATCC BAA-1806

13 ATCC 43600 29 i RHC 7722 45 ATCC BAA-2155

14 iAHS 56050 30 :AHS 26782 46 i ATCC BAA-1814

15 iATCC 43598 31 :AHS 55985 47 Ϊ 106073

16 Ϊ 106222 32 :ATCC BAA-1875 48 i AHS 56010

1.2 Reagents and instruments qPCR reagents:

qPCR Mastermix, Mobidiag

Assay mixture consisting of C. difficile qPCR primers and probes Devices:

Stratagene MxPro 3000

PCR setup

In reaction:

10 μΐ 2 x Mastermix

5 μΐ 4 x Primer mix

5 μΐ sample / pos. control DNA mix / DNA extraction control / H20

20 μΐ TOTAL

PCR program:

95 °C 10 min

95 °C 15 s 45x

60 °C 60 s RESULTS

Table 3. Identification of markers toxB, pet and hydR in C. difficile strains.

Functionality of controls

Positive controls were detected as positive

Negative control was detected as negative

Internal Amplification Control was detected in all samples

CONCLUSIONS

All 39 toxin-producing strains were identified correctly as ToxB+. All 9 non-toxin- producing strains were correctly identified as negative. No strain gave false positive identification of the 027 ribotype (toxB+, pct+, hydR-).

Controls were detected as expected, which confirmed the reliability of the results.

EXAMPLE 2

In this example, the functionality of the disclosed invention to differentiate 027 ribotype detection was tested. Two very closely related ribotypes, namely 016 and 176, were included in the samples.

Materials and Methods

DNA extraction

The DNA from C. difficile isolates were extracted as described below:

A colony from bacterial cultures was suspended to the lxPBS buffer in the final concentration ca. 1.5 x 10 ^Λ 8 CFU/ml (ref. McFarlan standard 0.5). 100 μΐ of bacterial suspension was transferred to the off-board lysis step following the automated extraction with NucliSENS EasyMAG (bioMerieux) device according to the manufacturer's protocol for Generic 2.0.1 program. DNAs were eluted to the 100 μΐ of elution buffer. Extraction series contained Extraction Control i.e. C. difficile (non-toxin producing strain). Real-time PCR and analysis

The PCR reactions were conducted as defined in Example 1. Internal amplification control, Positive PCR control and Negative PCR control is included to the test series.

A total of 18 different 027 ribotype strains, one 016 ribotype strain and one 176 ribotype strain were tested.

Table 4. Identification of markers toxB, pet and hydR in C. difficile 027 strains.

# Original code Ribotype Characterization toxB et hydR Result

1 ATCC BAA-1805 027 A+B+, Binary toxin cdtB+ + + - 027+

2 ATCC BAA-1803 027 A+B+, Binary toxin cdtB+ + + - 027+

01048P (ATCC BAA-

3 027 A+B+, Binary toxin cdtB+ + + - 027+ 1870)

4 CD14-038 027 n/a + + - 027+

5 CD13-177 027 n/a + + - 027+

6 CD13-032 027 n/a + + - 027+

7 CD13-221 027 n/a + + - 027+

8 CD14-078 027 n/a + + - 027+

9 CD14-072 027 n/a + + - 027+

10 CD14-161 027 n/a + + - 027+

11 CD13-097 027 n/a + + - 027+

12 CD12-100 027 n/a + + - 027+

13 CD13-305 027 n/a + + - 027+

14 CD13-056 027 n/a + + - 027+

15 CD13-004 027 n/a + + - 027+

16 CD13-247 027 n/a + + - 027+

17 CD13-245 027 n/a + + - 027+

18 CD13-108 027 n/a + + - 027+

A+B+, Binary toxin+, tcdC 18bp

19 + + - 027+

AHS 55742 016 del

A+B+, Binary toxin+, tcdC 18bp

20 + + - 027+

AHS 26967 176 del The assay gave a correct positive identification identification of all the 18 different 027 strains, and gave a positive identification of 016 and 176 ribotypes. Thus, the assay detects genetically closely related 016 and 176 ribotypes in addition to 027 ribotype as 027+.

EXAMPLE 3

In this example, the disclosed invention was compared to a prior art method for detecting a 027 presumptive positive C. difficile. The assay of the invention was compared to Xpert C. difficile/Epi (Cepheid) test.

The Xpert C. difficile/Epi test uses the detection of a deletion in tcdC gene to report a positive 027 presumptive finding.

A total of 11 different strains, representing 11 different ribotypes, were tested with both methods and the results were compared.

5. Comparison to Xpert C. difficile Epi (Cepheid) test.

The Xpert C. difficile/Epi test reported 5 strains to be toxigenic C. difficile positive, 027 presumptive positive, while none of the tested strains were actually ribotype 027. Of these 5 strains, the method of the present invention identified only 2 strains as 027 positive, so demonstrating an improved effect in differentiating between a 027 and non-027 ribotype compared to prior art. It is notable that these two C. difficile strains (016 and 176) have been shown to be highly related to hypervirulent C. difficile strains (Knetsch et al., 2011).

The identification of the disclosed markers reported 9 strains correctly as ToxB+, but not 027+, as expected. In summary, the assay of the invention identified 9/11 strains correctly as 027-, while the Xpert C. difficile/Epi test reported 6/11 strains correctly with regard to the presumptive negativity of 027.

EXAMPLE 4

The workflow of the present invention consists of extraction of nucleic acids from stool samples (NucliSens easyMAG), real-time PCR amplification and detection of target gene regions and analysis of results.

In this example, different toxin-producing C. difficile strains were tested as spiked samples in stool background. A total of 35 different strains were used. Each strain was spiked into a stool sample negative for C. difficile. DNA was extracted from stool samples, and qPCR reactions were prepared so that the strain was present in concentrations of either 7,5 CFU/reaction or 75 CFU/reactions as illustrated in Table 6. All samples were tested in duplicate reactions.

The results demonstrate that that the strains were correctly identified as positive in all cases. Table 6. Detection of different toxin-producing C. difficile strains in spiked stool samples.

Cq values of detection of markers

Original Code CFU/rxn tOXB 027+ 027- IC Result

ATCC BAA-1870 7,5 37,14 36,13 n/a 28,32 027+

ATCC 9689 7,5 34,44 n/a 36,47 27,94 ToxB+

ATCC BAA- 1382 7,5 36,37 n/a 37,44 27,77 ToxB+

ATCC 17858 7,5 35,32 n/a n/a 28,55 ToxB+

ATCC 43600 7,5 37,74 n/a 37,21 28,68 ToxB+

ATCC 43596 7,5 37 n/a n/a 28,29 ToxB+

ATCC 43594 7,5 37,89 n/a n/a 28,31 ToxB+

ATCC 43598 7,5 36,23 n/a n/a 28,7 ToxB+

ATCC BAA-1803 7,5 37,14 34,99 n/a 28,46 027+

ATCC BAA-1808 7,5 35,7 n/a 34,32 28,37 ToxB+

ATCC BAA-1811 7,5 35,66 n/a 35,92 28,5 ToxB+

ATCC BAA-1812 7,5 37,13 n/a 37,67 28,43 ToxB+

ATCC BAA-1813 7,5 38,07 n/a 37,5 28,43 ToxB+

ATCC BAA-1815 7,5 37,6 n/a 36,11 28,28 ToxB+

ATCC BAA-1872 7,5 35,38 n/a 36,6 28,36 ToxB+

ATCC BAA-1875 7,5 36,84 n/a 37,56 28,36 ToxB+

ATCC BAA-2155 7,5 35,85 n/a 35,74 28,59 ToxB+

ATCC BAA-2156 7,5 35,73 n/a 35,67 28,3 ToxB+

ATCC BAA-1804 7,5 37,37 n/a 35,5 28,46 ToxB+

ATCC BAA-1806 75 35,7 n/a 35,33 28,97 ToxB+

CD14-038 75 36,09 35,08 n/a 29,12 027+ CD13-177 75 34,53 34,21 n/a 29,05 027+

CD13-032 75 34,72 34,6 n/a 29,13 027+

CD13-221 75 36,09 37,14 n/a 29,42 027+

CD14-078 75 32,07 33,3 n/a 29,12 027+

CD14-072 75 32,9 27,53 43,92 27,52 027+

CD14-161 75 33,53 35,89 n/a 29,24 027+

CD13-097 75 32,72 33,83 n/a 29,14 027+

CD12-100 75 38,56 36,27 n/a 29,34 027+

CD13-305 75 35,97 39,19 n/a 29,43 027+

CD13-056 75 35,46 35,02 n/a 29,14 027+

CD13-004 75 33,22 34,07 n/a 28,93 027+

CD13-247 75 33,75 34,59 n/a 29,08 027+

CD13-245 75 33,08 34,24 n/a 29,02 027+

CD13-108 75 34,55 36,18 n/a 29,04 027+

IC= internal control, controls PC inhibition

CFU/rxn= colony forming units/reaction

Two replicates per sample

EXAMPLE 5

This example describes results from a study of potential false positive results in the C. difficile qPCR assay due to a cross-reaction. Sample material for this designed assay is stool sample. Therefore, pathogens (bacteria, viruses and parasites) associated with gastrointestinal infections, and which are not covered by assay panel, can cause potential cross-reaction. Also bacteria included to commensal flora may cross-react. Furthermore, pathogens including to the assay target panel are added to the cross-reaction study since only the target pathogen should be detected and no cross -reaction among other should happen.

Materials and methods

Reagents, devices and samples qPCR reagents:

Mobidiag's qPCR Mastermix (MM)

Assay mixture consisting of C. difficile qPCR primers and probes (see Table 9) Devices:

Stratagene Mxp3000

PCR setup

In reaction:

10 μ1 2 χ ΜΜ

5 μΐ 4 x Primer

mix

5 μΐ sample / pos. Control DNA mix / H20

20 μΐ

Pos. Control = template mix

95 °C 10 min

95 °C 15 s 40x

60 °C 1 m in

Samples:

DNA (or RNA) extracted from 127 pathogens. Strains have been mainly collected from commercial available biobanks (ATCC, DSMZ, Microbiologics Qnostics and Vircell). Some strains are added from Mobidiag biobank and those strains have been originally purified from patient samples and characterized by HUSLAB (Helsinki University central hospital laboratory).

The amount of DNA was determined by 16S rRNA assay or by NanoDrop. Table 7. Cross-reaction results.

# Species Result n Species, cont. Result

1 Acinetobacter baumannii Negative 65 Haemophilus parainfluenzae Negative

Actinomyces

Negative Negative

2 actinomycetemcomitans 66 Helicobacter mustelae

3 Actinomyces israelii Negative 67 Helicobacter pylori Negative

4 Actinomyces naeslundii Negative 68 Helicobacter pylori Negative

5 Aspergillus fumigatus Negative 69 Human adenovirus 40 Negative

6 Astrovirus Negative 70 Human adenovirus 41 Negative

7 Bacillus cereus Negative 71 Human herpesvirus 2 Negative

8 Bacillus subtilis Negative 72 Kingella kingae Negative

9 Bacteroides fragilis Negative 73 Klebsiella oxytoca Negative

Bacteroides Klebsiella pneumoniae subsp.

Negative Negative

10 thetaiotaomicron 74 pneumoniae

11 Bacteroides vulgatus Negative 75 Kluyvera intermedia Negative

12 Campylobacter coli Negative 76 Lactobacillus acidophilus Negative

13 Campylobacter fetus Negative 77 Lactobacillus casei Negative

Campylobacter jejuni subsp.

Negative Negative

14 jejuni 78 Lactococcus sp.

15 Campylobacter lari Negative 79 Listeria monocytogenes Negative

16 Candida albicans Negative 80 Micrococcus luteus Negative

17 Candida glabrata Negative 81 Moraxella catarrhalis Negative

18 Candida krusei Negative 82 Morganella morganii subsp. morganii Negative

19 Chromobacterium violaceum Negative 83 Neisseria lactamica Negative

20 Citrobacter amalonaticus Negative 84 Neisseria sicca Negative

21 Citrobacter braakii Negative 85 Norovirus genogroup 1 Negative

22 Citrobacter freundii Negative 86 Norovirus genogroup 2 Negative

23 Citrobacter koserii Negative 87 Pasteurella multocida Negative

24 Clostridium histolyticum Negative 88 Peptostreptococcus micros Negative

25 Clostridium perfringens Negative 89 Plesiomonas shigelloides Negative

26 Clostridium septicum Negative 90 Porphyromonas gingivalis Negative

27 Clostridium sordellii Negative 91 Prevotella intermedia Negative

28 Clostridium sporogenes Negative 92 Prevotella loescheii Negative

29 Clostridium tetani Negative 93 Propionibacterium acnes Negative

Carynebacterium

Negative Negative

30 amycolatum 94 Proteus mirabilis

Corynebacterium

Negative Negative

31 diphtheriae 95 Proteus vulgaris

32 Cronobacter sakazakii Negative 96 Providencia rettqeri Negative

33 Cryptosporidiumn parvum Negative 97 Providencia stuartii Negative

34 Cytomegalovirus Negative 98 Pseudomonas aeruginosa Negative

35 Desulfovibrio sp. Negative 99 Raoutella ornithinolytica Negative

36 Dientamoeba fragilis Negative 100 Rhodococcus equi Negative

37 Edward siella tarda Negative 101 Rotavirus A Negative

38 Eggerthella lenta Negative 102 Saccharomyces kudriaczevii Negative Elizabethkingia Negative Negative

39 meningoseptica 103 Salmonella bongoh

Salmonella enterica subsp. enterica ,

Negative Negative

40 Entamoeba histolytica 104 Typhimurium

41 Enterobacter aerogenes Negative 105 Sapovirus Negative

42 Enterobacter cloacae Negative 106 Serratia liquefaciens Negative

43 Enterobacter hormaechei Negative 107 Serratia marcescens subsp. marcescens Negative subsp. hormaechei

44 Enterococcus casseliflavus Negative 108 Shigella boydii Negative

45 Enterococcus faecalis Negative 109 Staphylococcus aureus Negative

46 Enterococcus faecium Negative 110 Staphylococcus epidermidis Negative

47 Enterococcus gallinarum Negative 111 Staphylococcus lugdunensis Negative

Escherichia coli , non

Negative Negative

48 toxigenic 112 Stenotrophomonas maltophilia

49 Escherichia coli, EAEC Negative 113 Streptococcus agalactiae Negative

50 Escherichia coli, EH EC Negative 114 Streptococcus anginosus Negative

51 Escherichia coli, El EC Negative 115 Streptococcus bovis Negative

Streptococcus dysgalactiae subsp.

Negative Negative

52 Escherichia coli, EPEC 116 equisimilis

53 Escherichia coli, ETEC Negative 117 Streptococcus oralis Negative

54 Escherichia fergusonii Negative 118 Streptococcus pneumoniae Negative

55 Escherichia hermanii Negative 119 Streptococcus pyogenes Negative

56 Escherichia vulneris Negative 120 Streptococcus salivarius Negative

57 Fusarium solani Negative 121 Streptococcus viridans Negative

Fusobacterium necrophorum

Negative Negative

58 subsp. necrophorum 122 Streptococcus viridans

Fusobacterium nucleatum

Negative Negative

59 subsp. nucleatum 123 Streptomyces spp.

60 Gardnerella vaginalis Negative 124 Vibrio parhaemolyticus Negative

61 Ciardia lamblia Negative 125 Vibrio vulnificus Negative

Yersinia enterocolitica subsp.

Negative Negative

62 Gordonia ssp. 126 enterocolitica

63 Haemophilus ducreyi Negative 127 Yersinia pseudotuberculosis Negative

64 Haemophilus influenzae Negative

Functionality of controls

Positive controls were detected as positive

Negative controls were detected as negative

Results

The cross -reactivity test showed no false positives.

Table 9. Oligonucleotide primers and probes.

Table 10. Amplicons amplified by the oligonucleotide sets.

ACGGAAACATCAAATAACGAATTGACAATTTCTGTAGATTTCGGTAC

C.dif_pct_hypV GAAAACTTCATGGGAAAGCAGCTTGGTAACCCAATTAAATGAAATA 119 SEQ ID NO:2

CCATATAATAACATTGGTAAAGGTAC

CGAACTTCCTCTATTAAAGCGAATGGGA I I I I I I CTAACCAGCTACA ATGTACCATTTTTCTACGTGTGTAATCATTCGCACTATGAACAACCAA

C.dif_hydR_01 TTCTATTA I I I I I I CATTTGCTGTAAGGGTGTCATCAGCAACAAGATA 232 SEQ ID NO:l

CTCTAAAAAATTATTCATTTGTGAGTAAAGTTCTTTTGTGACACTTCT CAGTATATCTTCTTTAGTTTTAAAGTGATGATACATTGCAC GGAAGTGAATGTATATGAAAACCTAAGTAGATATTAGTATATTTTAT AAATAGAAAGGAGGATATATAAAAGAGTTTTAGCATTTAGATGTAA

Cdif tcdB short 171 SEQ ID NO:10

AAATATTCAATAAAAATATTATAGTAAAGGAGAAAATTTTATGAGTT TAGTTAATAGAAAACAGTTAGAAAAAATGGC

REFERENCES

Deneve, C, Janoira, C, Poilaneb, I., Fantinatob, C, and Collignon, A., New trends in Clostridium difficile virulence and pathogenesis, International Journal of Antimicrobial Agents, 2009 33:24-28.

Eastwood, ., Else P., Charlett, A., and Wilcox, MH., Comparison of Nine Commercially Available Clostridium difficile Toxin Detection Assays, a Real-Time PCR Assay for C. difficile tcdB, and a Glutamate Dehydrogenase Detection Assay to Cytotoxin Testing and Cytotoxigenic Culture Methods, J. Clin. Microbiol., Oct. 2009, p. 3211-3217.

Hirvonen, JJ., Mentula, S., Kaukoranta, S-S., Evaluation of a New Automated

Homogeneous PCR Assay, GenomEra C. difficile, for Rapid Detection of Toxigenic Clostridium difficile in Fecal Specimens, J. Clin. Microbiol. 2013, 51(9):2908. DOI: 10.1128/JCM.01083-13.

Houser, BA., Hattel, AL., and Jayarao, BM., Real-Time Multiplex Polymerase Chain Reaction Assay for Rapid Detection of Clostridium difficile Toxin-Encoding Strains, Foodborne Pathogens And Disease, 2010, 7 (6) :719-726.

Knetsch, CW., Hensgens, MPM., Harmanus, C, van der Bijl, MW., Savelkoul, PHM., Kuijper, EJ., Corver J., and van Leeuwen, HC, Genetic markers for Clostridium difficile lineages linked to hypervirulence, Microbiology (2011), 157, 3113-3123.

Rupnik, M., Wilcox, MH. and Gerding, DN, Clostridium difficile infection:

new developments in epidemiology and pathogenesis, Nature Reviews Microbiology 7,

526-536 (July 2009) p526, doi: 10.1038/nrmicro2164