AU2004203283B2 - Nucleic Acid Probe-based Diagnostic Assays for Prokaryotic and Eukaryotic Organisms - Google Patents
Nucleic Acid Probe-based Diagnostic Assays for Prokaryotic and Eukaryotic Organisms Download PDFInfo
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Classifications
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- Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
- Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
- Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
- Y02A50/00—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE in human health protection, e.g. against extreme weather
- Y02A50/30—Against vector-borne diseases, e.g. mosquito-borne, fly-borne, tick-borne or waterborne diseases whose impact is exacerbated by climate change
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- Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
Description
S&F Ref: 577669D1
AUSTRALIA
PATENTS ACT 1990 COMPLETE SPECIFICATION FOR A STANDARD PATENT Name and Address of Applicants: Actual Inventor(s): Address for Service: Invention Title: Enterprise Ireland (trading as BioResearch Ireland), of Glasnevin, Dublin, 9, Republic of Ireland National University of Ireland, Galway, of University Road, Galway, Republic of Ireland Thomas Gerard Barry, Terence James Smith Spruson Ferguson St Martins Tower Level 31 Market Street Sydney NSW 2000 (CCN 3710000177) Nucleic Acid Probe-based Diagnostic Assays for Prokaryotic and Eukaryotic Organisms The following statement is a full description of this invention, including the best method of performing it known to me/us:- 5845c Description Nucleic acid probe-based diagnostic assays for prokarvotic and eukaryotic organisms Technical Field This invention relates to the identification of target sequences for use in nucleic acid assays for the detection and identification ofprokaryotic and/or eukaryotic organisms.
Background Art The ssrA gene, which encodes a small stable high copy number RNA transcript (tmRNA), is found in all bacteria and has recently been identified in chloroplasts and diatoms. It has a dual function both as a tRNA and as an mRNA molecule and is involved in rescuing truncated mRNAs which have lost stop codons, facilitating trans-translation of truncated peptides prior to protease degradation (Keiler, K.C. et al. (1996), Science, 271, 990- 993). The unique function of tmRNAs has directed researchers to analyse the relationship of the secondary structure of these molecules with their function. These studies have focussed on the conservation of the secondary structure of tmRNAs from different microorganisms, and on the evolutionary significance and functional relevance of such structural conservation. Studies were carried out by Matveeva, O et al (1998), Vol.
16, No. 13, 1374-1375 to investigate oligonucleotide binding to RNA molecules using tmRNA as a model of RNA containing secondary structure. The studies did not have as their objective the identification of sites in tmRNA with the goal of designing antisense oligonucleotide for therapeutic purposes.
The number of nucleic acid targets/probes for bacterial diagnostics is currently limited. As such, the need to identify and characterise novel DNA and RNA targets for diagnostic purposes is now seen as a priority. Target nucleic acid sequences for the development of probes can be for example, plasmids, ribosomal RNA genes, intergenic regions, genes encoding virulence factors or random genomic DNA fragments. In addition, a number of RNA molecules have been described which are used as targets for RNA-based detection for example, ribosomal RNA and RNase P.
The basis of any nucleic acid-based probe assay is the requirement for well characterised nucleic acid sequences which are present in all prokaryotes and eukaryotes under study. For reliable detection of a prokaryotic or eukaryotic organism, the nucleic acid probes used should be highly specific not cross-react with nucleic acids from other organisms) and highly sensitive most or all strains of the organism to be detected should react with the probe). Therefore, preferred target sequences would be present in all strains of the organism concerned. Such sequences would have significant sequence variability to allow differentiation of the species concerned from other closely related species but, on the other hand, have sufficient sequence conservation to allow the detection of all strains of the species concerned. In general, the precise identification of a nucleic acid sequence, which could form the basis of a specific nucleic acid probe assay, is tedious, difficult and uncertain. To date there are few general approaches which would facilitate the development of nucleic acid probes for a wide variety of microorganisms. The nucleic acid sequences which have been identified as potentially useful targets for probe development are, for example, rRNA genes and RNA, and the rRNA 16S/23S intergenic region.
The majority of nucleic acid probe/target assays centre on the high copy number ribosomal RNAs (rRNA) and rRNA 16S/23S spacer regions (European Patent No. 0 395 292) of the bacterial cell for the purposes of detection and identification. A number of successful commercial bacterial diagnostic kits have been marketed based on these rRNA probes/targets for the detection of a variety of microrganisms. These include a range of commercial probe kits based on the 16S rRNA gene marketed by Genprobe Inc. San Diego California, and DNA probes based on the 16S/23S spacer region marketed by Innogenetics N.V. Ghent, Belgium. However, many of these diagnostic kits have limitations, including lack of sensitivity due to low copy-number target sequences and lack of specificity due to sequence identity between closely related organisms in many cases.
Nucleic acid-based methods that could be applied directly to samples to give an indication of the viability of any microbes present therein would N be of enormous significance for food, industrial, environmental and medical applications.
tbA disadvantage of DNA-based methods is that they do not distinguish between living and dead organisms. Some studies have focussed on using rRNA and mRNA as indicators of cell viability (Sheridan, G. E. C. et al. (1998) Applied and Environmental Microbiology, 64, 1313-1318). However, these sequences are not satisfactory targets as SrRNA and mRNA can be present in bacterial cells up to 48 hours after cell death.
00 I With the advent of nucleic acid based microarray-like formatting, incorporating simultaneous monitoring of multiple nucleic acid targets, there is now a clear requirement to identify and characterise novel nucleic acid sequences for use as probes and/or target 1o regions to detect and identify viable prokaryotic and eukaryotic cells.
Disclosure of Invention According to a first embodiment of the invention, there is provided use of a ssrA gene or a fragment thereof as a target region in a nucleic acid probe assay to detect or identify a target prokaryotic or eukaryotic organism wherein the ssrA gene or fragment does not comprise any one of the following sequences: SEQ ID Nos:5, 6, 23, 24, 37, 38, 137, 138, 202, 203 and 223.
According to a second embodiment of the invention, there is provided use of tmRNA, an RNA transcript of the ssrA gene, or a fragment thereof as a target region in a nucleic acid probe assay to detect or identify a target prokaryotic or eukaryotic organism, wherein the ssrA gene or fragment does not comprise any one of the following sequences: SEQ ID Nos:5, 6, 23, 24, 37, 38, 137, 138, 202, 203 and 223.
The invention provides use of the ssrA gene or a fragment thereof as a target region in a nucleic acid probe assay for a prokaryotic or eukaryotic organism.
Thus, the invention has application in relation to all organisms other than viruses.
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I
No other nucleic acid probe assay has been reported which uses regions of the ssrA gene as a target region to detect and identify species of prokaryotes and eukaryotes with the attendant advantages.
According to one embodiment of the invention a fragment of the ssrA gene molecule corresponding to a region of high homology from the 5' end of the DNA molecule can be used as a universal target region.
In an alternative embodiment of the invention a fragment of the ssrA gene molecule corresponding to a region of high homology from the 3' end of the DNA molecule can be used as a universal target region.
In a further embodiment of the invention a fragment of the ssrA gene molecule corresponding to a region of low homology can be used as a target region in a nucleic acid probe assay to distinguish between species.
In a still further embodiment of the invention a fragment of the ssrA gene molecule corresponding to a region of low homology can be used as a target region for the generation of a genus specific probe.
As hereinafter described nucleotide sequence alignments of ssrA gene sequences from different organisms show that the 5' and 3' regions of these molecules demonstrate a high degree of homology and are therefore useful as universal target regions. The ssrA genes also demonstrate a more significant degree ofnucleotide sequence variability between closely related organisms than any other bacterial high copy number RNA. These variable regions are ideal targets for nucleic acid assays to distinguish between species.
The invention also provides use of tmRNA, an RNA transcript of the ssrA gene, or a fragment thereof as a target region in a nucleic acid probe assay for a prokaryotic or eukaryotic organism.
According to one embodiment of this aspect of the invention a fragment of a tmRNA molecule corresponding to a region of high homology from the 5' end of the tmRNA molecule can be used as a universal target region.
Alternatively, a fragment of a tmRNA molecule corresponding to a region of high homology from the 3' end of the tmRNA molecule can be used as a universal target region.
According to a further embodiment of this aspect of the invention a fragment of a tmRNA molecule corresponding to a region of low homology can be used as a target region in a nucleic acid probe assay to distinguish between species.
According to a still further embodiment a fragment of a tmRNA molecule corresponding to a region of low homology can be used as a target region for the generation of a genus specific probe.
The nucleic acid probe (DNA or RNA) in accordance with the invention typically consists of at least 10 nucleotides of the ssrA gene and/ or tmRNA transcript or their complementary sequence and is used in a nucleic acid probe hybridisation assay for a prokaryotic or eukaryotic organism. Probe hybridisation to its complementary sequence is typically revealed by labelling the nucleic acid probe with a radioactive or nonradioactive colorimetric or fluorimetric) label.
In preferred embodiments said ssrA gene fragment or said tmRNA fragment can be used as the basis of a primer to be used in an amplification procedure.
Universal oligonucleotide primers directed to the 5' and 3' regions of either the ssrA gene or the tmRNA sequence can be used in accordance with the invention to amplify the ssrA gene or its encoding tmRNA from a wide variety of bacteria, facilitating amplification of a wide range of organisms simultaneously, whilst also enabling specific nucleic acid probe hybridisation and detection.
Preferably, the product of the amplification procedure is used as a target region in a nucleic probe assay.
Further, preferably, a cDNA transcript of a tmRNA molecule is used as a probe in a nucleic acid hybridisation assay.
Such assays can be carried out in vitro or in situ.
The target region as defined herein can be used as the basis of an assay for distinguishing between living and dead prokaryotic or eukaryotic organisms.
In contrast to rRNA and mRNA which can be present in bacterial cells following cell death, tmRNA is rapidly degraded in dead organisms.
Thus, tmRNA can be a useful target for distinguishing between living and dead prokaryotic or eukaryotic organisms either directly by nucleic acid probe hybridisation to isolated bacterial RNA, or by combined RNA amplification and nucleic acid probe hybridisation to the amplified product.
Preferably, the target region is used in a multiple probe format for broad scale detection and/or identification of prokaryotic or eukaryotic organisms.
An ssrA gene probe or a tmRNA transcript probe in accordance with the invention can be linked to a microarray gene chip system for the broad scale high throughput detection and identification of prokaryotic or eukaryotic organisms.
A target region in accordance with the invention can also be used as a probe in an assay to detect prokaryotic or eukaryotic organisms in a sample of matter.
Such a sample of matter can include biological samples such as samples of tissue from the respiratory tract, the uro-genital tract or the gastrointestinal tract, or body fluids such as blood and blood fractions, sputum or cerebrospinal fluid.
An assay in accordance with the invention can also be carried out on food samples, environmental samples including air, water, marine and soil samples, and plant and animal derived samples.
According to the invention a fragment of the ssrA gene or the tmRNA transcript can also be used in an assay to obtain a DNA profile of a prokaryotic or eukaryotic organism and, thereby, distinguish between strains of the same species.
Nucleic acid sequence alignments have shown that sequence variation occurs in the ssrA gene and the tmRNA transcript within individual species. This intra-species sequence variation can be used to distinguish between strains of the same species for epidemiology, tracing of infectious agents for example, in outbreaks, or for population studies.
Other applications of the invention include the use of the ssrA gene, the tmRNA transcript or a DNA sequence complementary thereto, or a fragment thereof, to design an agent directed against infectious prokaryotic or eukaryotic organisms for therapeutic purposes.
Such agents can include antisense mRNA or oligonucleotides, ribozymes, and antagonistic peptides and are suitable for use in any kind of medical condition.
Thus, the invention can be used for the detection of viable organisms only in biological samples using the tmRNA target. Thus, during and following any anti-infectious agent drug treatment, the tmRNA target can be used to monitor the efficacy of the therapy on those specific infectious agents antimicrobial and/or anti-parasitic treatments).
In one embodiment, the target region is used to monitor the efficacy of drug therapies against infectious agents.
In another embodiment, the target region is used to monitor the viability and level of health-promoting organisms in the gastrointestinal tract.
This aspect of the invention relates, for example, to the introduction into the gut flora of health-promoting (probiotic) organisms contained in for example yoghurt or other food to improve health. There is an interest and need to continuously monitor the presence and levels of these organisms to ensure their continued function in promoting health. The tmRNA region can be used as a target to detect viable organisms, for example in faeces, so as to monitor the presence of the health promoting organisms.
In a further embodiment, the assay is used for the quantification of prokaryotic or eukaryotic organisms.
When using probe hybridisation and/or in vitro amplification to detect organisms in a sample it is possible to determine the number of organisms present, based on the signal intensity. Real-time methods of in vitro amplification can also be used to enable the quantification of organisms in a sample. Thus, the ability to quantify the number of organisms in a sample can be important in clinical situations for treatment purposes, for example for antibiotic or other treatments or for monitoring treatment efficacy.
A still further application of the invention is the use of a database of ssrA gene sequences to identify a prokaryotic or eukaryotic organism.
The invention provides a variety of probes for the 5' and 3' homologous regions and the variable regions of the ssrA gene and tmRNA sequences, the probes being derived from these sequences or sequences complementary thereto. Representative sequences are as follows: Actinobacillus actinomycetemcomitans ssrA
GGGGCTGATTCTGGATTCGACGGGATTAGCGAAGCCCGAAGTGC
ACGTCGAGGTGCGGTAGGCCTCGTAAATAAACCGCAAAAAAATA
GTCGCAAACGACGAACAATACGCTTTAGCAGCTTAATAACCTGC
CTTTAGCCTTCGCTCCCCAGCTFJCCGCTCGTAAGACGGGGATAAA
GCGGAGTCAAACCAAAACGAGATCGTGTGGAAGCCACCG7FJTGA
GGATCGAAGCATTAAATTAAATCAAAGTAGCTTAATTGTCGCGT
GTCCGTCAGCAGGATTAAGTGAATTTAAAGACCGGACTAAACGT
GTAGTGCTAACGGCAGAGGAATTTCGGACGGGGGTTCAACTCCC
CCCAGCTCCACCA SEQ ID NO: 1 A ctinobacillus actinomycetemeomitans tmRNA
GGGGCUGAUUCUGGAUUCGACGGGAUUAGCGAAGCCCGAAGU
GCACGUCGAGGUGCGGUAGGCCUCGUAAAUAAACCGCAAj'A
AUAGUCGCAAACGACGAACAAUACGCUUAGCAGCUJAAUAAC
CUGCCUUUAGCCUUCGCUCCCCAGCULJCCGCUCGUAAGACGGG
GAUAAAGCGGAGUCAAACCAAAACGAGAUCGUGUGGAAGCCA
CCGUUUGAGGAUCGAAGCAUUAAUUAAAUCAAAGUAGCUUA
AUUGUCGCGUGUCCGUCAGCAGGAUUAAGUGAAUUUAAAGAC
CGGACUAAACGUGUAGUGCUAACGGCAGAGGAAUUUCGGACG
GGGGUUCAACUCCCCCCAGCUCCACCA SEQ ID NO: 2 Aeromonas salmonicida ssrA, internal partial
AAGATTCACGAAACCCAAGGTGCATGCCGAGGTGCGGTAGGCCT
CGTTAACAAACCGCAAAAAAATAGTCGCAAACGACGAAAACTA
CGCACTAGCAGCtTAATAACCTGCATAGAGCCCTTICTACCCTAGC
TTGCCTGTGTCCTAGGGAATCGGAAGGTCATCCTTCACAGGATC
GTGTGGAAGTCCTGCTCGGGGCGGAAGCATTAAAACCAATCGyAG
CTAGTCAATTCGTGGCGTGTCTCTCCGCAGCGGGTTGGCGAATGT
AAAGAGTGACTAAGCATGTAGTACCGAGGATGTAGTAATY[TGG
ACGGGG SEQ ID NO: 3 Aeromonas salmon icida tmRNA, internal partial
AAGAIJUCACGAAACCCAAGGUGCAUGCCGAGGUGCGGUAGGCC
UCGUUAACAAACCGCAAAUAGUCGCAAACGACGAAAACU
ACGCACUAGCAGCUUAAUAACCUGCAUAGAGCCCUIJCUACCCU
AGCUUGCCUGUGUCCUAGGGAAUCGGAAGGUCAUCCUU1CACAG GAUCGUGUGGAAGUCCUGCUCGGGGCGGAAGCAAAApCA
AUCGAGCUAGUCAAUIJCGUGGCGUGUCUCUCCGCAGCGGGUJIG
GCGAAUGUAAAGAGUGACUAAGCAUGUAGUACCGAGGAUGUA
GUAAUJIUUGGACGGGG SEQ ID NO: 4 Alcaligenes eutroplius ssrA TGGGCCGACCTGGT7FFCGACGTGG7FFACAAAGCAGTGAGGCATA
CCAGCCTACCTAACAGATCAACG
TAACGACGAACGTTACGCACTCGCTAATTIGCGGCCGTCCTCGC
ACTGGCTCGCTGACGGGCTAGGGTCGCAAGACCACGCGAGGTAT
TTACGTCAGATAAGCTCCGGAAGGGTCACGAAGCCGGGGACGA
AAACCTAGTGACTCGCCGTCGTAGAGCGTGTTCGTCCGATGCGC
CGGTTAAATCAAATGACAGAACTAAGTATGTAGAACTCTCTGTG
GAGGGCTTACGGACGCGGGTTCGATTCCCGCCGGCTCCACCA
SEQID NO: Alcaligenes eutrophus tmRNA
UGGGCCGACCUGGUUUCGACGUGGUUACAAAGCAGUGAGGCA
UACCGAGGACCCGUCACCUCG[JUAAUCAAUGGAAUGCAAUAAC
UGCUAACGACGAACGUUACGCACUCGCUUAAUJTGCGGCCGUCC
UCGCACUGGCUCGCUGACGGGCUAGGGUCGCAAGACCACGCGA
GGUAUUACGUCAGAUAAGCUCCGGAAGGGUCACGAAGCCGG
GGACGAAAACCUAGUGACUCGCCGUCGUAGAGCGUGUIJCGUCC
GAUGCGCCGGUUAAAUCAAAUGACAGAACUAAGUAUGUAGAA
CUCUCUGUGGAGGGCIJUACGGACGCGGGUTJCGAUIJCCCGCCGG
CUCCACCA SEQ ID NO: 6 Aquifex aeolicus ssrA
GGGGGCGGAAAGGATTCGACGGGGACAGGCGGTCCCCGAGGAG
CAGGCCGGGTGGCTCCCGTAACAGCCGCTAA&ACAGCTCCCGAAJ
GCTGAACTCGCTCTCGCTGCCTAATTAAACGGCAGCGCGTCCCC
GGTAGGTTTGCGGGTGGCCTACCGGAGGGCGTCAGAGACACCCG
CTCGGGCTACTCGGTCGCACGGGGCTGAGTAGCTGACACCTAC
CCGTGCTACCCTCGGGGAGCTTGCCCGTGGGCGACCCGAGGGGA
AATCCTGAACACGGGCTAAGCCTGTAGAGCCTCGGATGTGGCCG
CCGTCCTCGGACGCGGGTTCGATTFCCCGCCGCCTCCACCA
SEQ ID NO: 7 Aquifex aeolicus tmRNA
GGGGGCGGAAAGGAUUCGACGGGGACAGGCGGUCCCCGAGGA
GCAGGCCGGGUGGCUCCCGUAACAGCCGCUAAAACAGCUCCCG
AAGCUGAACUCGCUCUCGCUGCCUAAUUMAACGGCAGCGCGUC
CCCGGUAGGUUUGCGGGUGGCCUACCGGAGGGCGUCAGAGACA
CCCGCUCGGGCUACUCGGUCGCACGGGGCUGAGUAGCUGACAC
CUAACCCGUGCUACCCUCGGGGAGCUUGCCCGUGGGCGACCCG
AGGGGAAAUCCUGAACACGGGCUAAGCCUGUAGAGCCUCGGAU
GUGGCCGCCGUCCUCGGACGCGGGUUCGAUUCCCGCCGCCUCC
ACCA SEQ ID NO: 8 Bacillus megaterium ssrA, internal partial
AGGGTAGTTCGAGCTTAGG'ITGCGAGTCGAGGAGATGGCCTCGT
TAAAACATCAACGCCAATAATAACTGGCAAATCTAACAATAAJCT
TCGCTTFIAGCTGCATAATAGTAGC'ITAGCGTTCCTCCCTCCATCG
CCCATGTGGTAGGGTAAGGGACTCACTTTAAGTGGGCTACGCCG
GAGTTCGCCGTCTGAGGACGAAGGAAGAGAATAATCAGACTAG
CGACTGGGACGCCTG7FFGGTAGGCAGAACAGCTCGCGAATGATC
AATATGCCAACTACACTCGTAGACGCTTAAGTGGCCATATTTCTG
GACGTGG SEQ ID NO: 9 Bacillus megaterium tmRNA, internal partial
AGGGUAGUUCGAGCUUAGGUUGCGAGUCGAGGAGAUGGCCUC
GUUAAAACAUCAACGCCAAUAAUAACUGGCAAAUCUAACAAU
AACUUCGCUUUAGCUGCAUAAUAGUAGCUTJAGCGUIJCCUCCCU
CCAUCGCCCAUGUGGUAGGGUAAGGGACUCACUUUAAGUGGGC
UACGCCGGAGUTJCGCCGUCUGAGGACGAAGGAAGAGAAUAAU
CAGACUAGCGACUGGGACGCCUGUTUGGUAGGCAGAACAGCUCG
CGAAUGAUCAAUAUGCCAACUACACUCGUAGACGCUUAAGUGG
CCAUAUUUCUGGACGUGG SEQ ID NO: Bacillus subtilis ssrA
GGGGACGTTACGGATTCGACAGGGATGGATCGAGCTTGAGCTGC
GAGCCGAGAGGCGATCTCGTAAACACGCACTTAAATATAACTGG
CAAAACTAACAGTTYJ7AACCAAAACGTAGCATTAGCTGCCTAAT AAGCGCAGCGAGCTCTTICCTGACATTGCCTATGTGTCTG'rGAAG
AGCACATCCAAGTAGGCTACGCTTGCGTTCCCGTCTGAGAACGT
AAGAAGAGATGAACAGACTAGCTCTCGGAAGGCCCGCCCGCAG
GCAAGAAGATGAGTGAAACCATAAATATGCAGGCTACGCTCGTA
GACGCTTAAGTAATCGATGThL'CTGGACGTGGGTTCGACTCCCAC CGTCTCCACCA SEQ ID NO: 11 Bacillus subtilis tniRNA
GGGGACGIJUACGGAUIUCGACAGGGAUGGAUCGAGCUUGAGCU
GCGAGCCGAGAGGCGAUCUCGUAAACACGCACUTJAAAUAUAAC
UGGCAAAACUAACAGUUUUAACCAAAACGUAGCAJJUAGCUGCC
UAAUAAGCGCAGCGAGCUCUUCCUGACAUUGCCUAUGUGUCUG
UGAAGAGCACAUCCAAGUAGGCUACGCUUGCGUUCCCGUCUGA
GAACGUAAGAAGAGAUGAACAGACUAGCUCUCGGAAGGCCCGC
CCGCAGGCAAGAAGAUGAGUGAAACCAUAAAUAUGCAGGCUA
CGCUCGUAGACGCUUAAGUAAUCGAUGUTJUCUGGACGUGGGU
UCGACUCCCACCGUCUCCACCA SEQ ID NO: 12 Bordetelia pertussis ssrA
GGGGCCGATCCGGATTCGACGTGGGTCATGAAACAGCTCAGGGC
ATGCCGAGCACCAGTAAGCTCGJTAATCCACTGGAACACTACAA
ACGCCAACGACGAGCGTCTCGCTCTCGCCGCTfAAGCGGTGAGC CGCTGCACTGATCTGTCCTflGGGTCAGGCGGGGGAAGGCAACTT
CACAGGGGGCAACCCCGAACCGCAGCAGCGACATTCACAAGGA
ATCGGCCACCGCTGGGGTCACACGGCGTTGGTTTAAATTACGTG
AATCGCCCTGGTCCGGCCCGTCGATCGGCTAAGTCCAGGGTTAA
ATCCAAATAGATCGACTAAGCATGTAGAACTGG'ITGCGGAGGGC
TTGCGGACGGGGGTTCAATTCCCCCCGGCTCCACCA
SEQ ID NO: 13 Bordetella pertussis tmRNA
GGGGCCGAUCCGGAUUCGACGUGGGJCAUGAAACAGCTCAGGG
CAUGCCGAGCACCAGUAAGCUCGUUAAUCCACUGGAACACUAC
AAACGCCAACGACGAGCGUCUCGCUCUCGCCGCUUAAGCGGUG
AGCCGCUGCACUGAUCUGUCCUUGGGUCAGGCGGGGGAAGGCA
ACUUCACAGGGGGCAACCCCGAACCGCAGCAGCGACAUUICACA
AGGAAUCGGCCACCGCUGGGGUCACACGGCGUUGGUUUAAAUU
ACGUGAAUCGCCCUGGUCCGGCCCGUCGAUCGGCUAAGUCCAG
GGUUAAAUCCAAAUAGAUCGACUAAGCAUGUAGAACUGGUUG
CGGAGGGCUUGCGGACGGGGGUUCAAUUCCCCCCGGCUCCACC
SEQID NO: 14 Borrelia burgdorferi ssrA
GGGGATGTTTTGGATTTGACTGAAAATGTTA-ATATTGTAAGTTGC
AGGCAGAGGGAATCTCTTAAAACTTCTAAAATAAATGCAAAAAA
TAATAACTFJTACAAGCTCAAATCTTGTAATGGCTGCTTAAGTTAG
CAGAGGGTTTTGTTGAAT7FFGGCTTTGAGGTTCACTTATACTCTF TTCGACATCAAAGCTTGCTTAAAAATGTTTTCAAG7F[GATTTFFA
GGGACTTTTATACTTGAGAGCAATTTGGTGGTTTGCTAGTATTITC
CAA-ACCATATTGCTTAATAAAATACTAGATAAGCYJ7GTAGMAGC
TTATAGTATTA'ITTTTAGGACGCGGGTTCAATTCCCGCCATCTCC
ACCA SEQ ID NO: Borrelia burgdorferi tmRNA
GGGGAUGIJUUUGGAUUUGACUGAAAAUGUUAAUAUUGUAAGU
UGCAGGCAGAGGGAAUCUCUIJAAAACUUCUAAAAUAAAUGCA
AAAAAUAAUAACUUTJACAAGCUCAAAUCUTJGUAAUGGCUGCU
UAAGUUAGCAGAGGGUTJUUGUUGAAUUUGGCUUUIGAGGUUCA
CUUAUACUCUUUUCGACAUCAAAGCUUGCUUAAAAUGUUUU
CAAGULIGAUUUUUAGGGACIJUUUAUACUUGAGAGCAAUUUGG
UGGUUUGCUAGUAUUUCCAAACCAUAUUGCUIJAAUAAAAUAC
UAGAUAAGCUJIGUAGAAGCUUAUAGUAUUAIJIJIUUAGGACGC
GGGUUCAAUUCCCGCCAUCUCCACCA SEQ ID NO: 16 Campylobacterjejuni ssrA GGGAGCGACTTGGCTTCGACAGGAGTAAGTCTGC7F[AGATGGCA
TGTCGCTTTGGGCAAAGCGTAAAAAGCCCAAATAAAATTAAACG
CAAACAACGTTAAATTCGCTCCTGCTTACGCTAAAGCTGCGTAA
GTTCAGTTGAGCCTGAAAT7FIAAGTCATACTATCTAGCTTAATTT TCGGTCATTThFGATAGTGTAGCCTTGCGTTTGACAAGCGTTGAG GTGAAATAAAGTCTTAGCCTFJGCT7frTGAG=nYGGAAGATGAGC GAAGTAGGGTGAAGTAGTCATC7FrTGCTAAGCATGTAGAGGTCT TTGTGGGATTAT7FJTTGGACAGGGGTTCGA7FFCCCCTCGCTTCCA CCA SEQID NO: 17 Campylobacterjejuni tmRNA
GGGAGCGACUUGGCUUCGACAGGAGUAAGUCUGCUJIAGAUGG
CAUGUCGCUUUGGGCAAAGCGUAAAAGCCCAAAUAAAAUIJA
AACGCAAACAACGUUAAAUUCGCUCCUGCUUACGCUAAAGCUG
CGUAAGUUCAGUUGAGCCUGAAAJUUJAAGUCAUACUAUCUAG
CUUAAUIJUUCGGUCAUJUUGAUAGUGUAGCCUUGCGUUIJGA
CAAGCGUUGAGGUGAAAUAAAGUCUUAGCCUIJGCUUIJUGAGU
UIJUGGAAGAUGAGCGAAGUAGGGUGAAGUAGUCAIJCUUIJGCU
AAGCAUGUAGAGGUCUUUGUGGGAUIJAUUUUUGGACAGGGGU
UCGAUTJCCCCUCGCIJUCCACCA SEQ ID NO: 18 Chiamydia trachomatis (D/UJW-3/CX) ssrA GGGGGTGTAAAGGTYI7CGACYL'AGAAATGAAGCGTTAATTGCAT
GCGGAGGGCGTTGGCTGGCCTCCTAAAAAGCCGACAAAACAATA
AATGCCGAACCTAAGGCTGAATGCGAAATTATCAGCTTCGCTGA
TCTCGAAGATCTAAGAGTAGCTGCTTAATTAGCAAAGTTGTTACC
TAAATACGGGTGACCCGGTGYJ'CGCGAGCTCCACCAGAGGTT7F[
CGAAACACCGTCATGTATCTGGTTAGAACTTAGGTCCTTTAATTC
TCGAGGAAATGAGTY[GAAAT7FFAATGAGAGTCGTTAGTCTCTAT
AGGGGTTTCTAGCTGAGGAGACATAACGTATAGTACCTAGGAAC
TAAGCATGTAGAGGTTAGCGGGGAGTTTACTAAGGACGAGAGTT
CGACTCTCTCCACCTCCACCA SEQ ID NO: 19 Chiamydia trachomatis (D/UW-3/CX) tmRNA
GGGGGUGUAAAGGUUUCGACUUAGAAAUGAAGCGUUAAUUGC
AUGCGGAGGGCGUUGGCUGGCCUCCUAAAAAGCCGACAAAACA
AUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUJIAUCAGCUJIC
GCUGAUCUCGAAGAUCUAAGAGUAGCUGCUUAAtUAGCAjG
UUGIJUACCUAAAUACGGGUGACCCGGUGUJICGCGAGCUCCACC
AGAGGUUUUCGAAACACCGUCAUGUAUCUGGUUAGAACUUAG
GUCCUUUAAUUCUCGAGGAAAUGAGUUIJGAAAUUIJAAUGAGA
GUCGUTUAGUCUCUAUAGGGGULJUCUAGCUGAGGAGACAUAAC
GUAUAGUACCUAGGAACUAAGCAUGUAGAGGUUAGCGGGGAG
IJIJIACUAAGGACGAGAGUTUCGACUCUCUCCACCUCCACCA
SEQ ID NO: Chiamydia trachomatis (mouse pneumonitis) ssrA
GGGGGTGTAAAGGTTTCGACTFLAGAAATGAAGCGTTAATTGCAT
GCGGAGGGCGTTGGCTGGCCTCCTAAAAAGCCGACAAAACAATA
AATGCCGAACCTAAGGCTGAATGCGAJ\ATTATCAGCTTCGCTGA
TCTTAATGATCTAAGAGTTGCTGCTTAATTAGCAAAGTTGTTJACC
TAAGTACTGGTAACCCGGTGTTCGCGAGCTCCACCAGAGGTTTTC
GAAACGCCGTCATTTATCTGGTTAGAATTAGGGCCTTTTIAACTCT
CAAGGGAACTAAT'JTGAATFflTAATGAGAGTCGTTGGTCTCTATA
GAGGTTTCTAGCTGAGGAGATATAACGTAAAATATTCTAGAAAC
TAAGCATGTAGAGGTTAGCGGGGAGTTTACTAAGGACGAGAGTT
CGAATCTCTCCACCTCCACCA SEQ ID NO: 21 Chiamydia trachomcais (mouse pneumonitis) tmRNA
GGGGGUGUAAAGGUUUCGACUUAGAAAUGAAGCGUTJAAUUGC
AUGCGGAGGGCGUUGGCUGGCCUCCUAAAAAGCCGACAAAACA
AUAAAUGCCGAACCUAAGGCUGAAUGCGAAAUUAUCAGCUUIC
GCUGAUCUUAAUGAUCUAAGAGUUGCUGCUUAAUUAGCAAAG
UUGLJUACCUAAGUACUGGUAACCCGGUGUUCGCGAGCUCCACC
AGAGGUUUUCGAAACGCCGUCAUUUAUCUGGUUAGAAUUAGG
GCCUJJUUAACUCUCAAGGGAACUAAUTUUGAAUUUUAAUGAGA
GUCGUUGGUCUCUAUAGAGGUUIJCUAGCUGAGGAGAUAUAAC
GUAAAAUAIJUCUAGAAACUAAGCAUGUAGAGGUIJAGCGGGGA
GUUUACUAAGGACGAGAGIJUCGAAUCUCUCCACCUCCACCA
SEQ ID NO: 22 Chiorobium tepidum ssrA
GGGGATGACAGGCTATCGACAGGATAGGTGTGAGATGTCGTTGC
ACTCCGAGTFITCAGCATGGACGGACTCG7FTAAACAAGTCTATGT
ACCAATAGATGCAGACGATTATTCGTATGCAATGGCTGCCTGAT
TAGCACAAGTTAATTCAGAAGCCATCGTCCTGCGGTGAATGCGC
TTACTCTGAAGCCGCCGGATGGCATAACCCGCGCTTGAGCCTAC
GGGTTCGCGCAAGTAAGCTCCGTACATTCATGCCCGAGGGGGTG
TGCGGGTAACCAATCGGGATAAGGGGACGAACGCTGCTGGCGGT
GTAATCGGACCACGAAAAACCAACCACCAGAGATGAGTGTGGT
AACTGCATCGAGCAGTGTCCTGGACGCGGGTTCAAGTCCCGCCA
TCTCCACCA SEQ ID NO: 23 Chiorobium tepidum tmRNA
GGGGAUGACAGGCUAUCGACAGGAUAGGUGUGAGAUGUCGUU
GCACUCCGAGUUUCAGCAUGGACGGACUCGUUAAACAAGUCUA
UGUACCAAUAGAUGCAGACGAUUAUUCGUAUGCAAUGGCUGC
CUGAUUAGCACAAGIJUAAUUCAGAAGCCAUCGUCCUGCGGUGA
AUGCGCUUACUCUGAAGCCGCCGGAUGGCAUAACCCGCGCUTJG
AGCCUACGGGUUCGCGCAAGUAAGCUCCGUACAUIJCAUGCCCG
AGGGGGUGUGCGGGUAACCAAUCGGGAUAAGGGGACGAACGC
UGCUGGCGGUGUAAUCGGACCACGAAAAACCAACCACCAGAGA
UGAGUGUGGUAACUGCAUCGAGCAGUGUCCUGGACGCGGGUU
CAAGJJCCCGCCAUCUCCACCA SEQ ID NO: 24 Cyanophora paradoxa (alga) cyanelle ssrA GGGGCTGTTFIAGGTTFICGACG7FJTTT7ITCTAATTATGTTTGYJ7AAG
CAAGTCGAGGATTTGTTCTATCTCGAAAATCAAGAACTCTCAAA
ATTTAAACGCAACTAATATTGTACGT'ITTAACCGTAA-AGCAGCTT
TCGCTGYJ7TAATAATTACTTTTAATITAAAAACCTAAFTT T TAG GAATTTATTTATTTATFJGYI17ATCCTGCTTAATGAATTAAAAAAA GCTATACTTGTGAATAAACGCATAAT7[TAAAAAAACGGACGTGG GTTCAAATCCCACCAGCTCCACCA SEQ ID NO: Cyanophora paradoxa (alga) cyanelle tmRNA
GGGGCUGUUUAGGUJIUCGACGUUUUUUUCUAAUUAUGUUIJGU
UAAGCAAGUCGAGGAUUUGUUCUAUCUCGAAUCAAGACU
CUCAAAAUUUAAACGCAACUAAUAUUJGUACGUUUTJAACCGUA
AAGCAGCUUUCGCUGUUUAAUAAIJUACUUUUAAUUUAAAAAC
CUAAUUUUJUUAGGAAUUUAUUUAUUUAUUGIJUUAUCCUGCU
UAAUGAAUUAAAAAAAGCUAUACUUGUGAAUAAACGCAUAAU
UUAAAAAAACGGACGUGGGUUCAAAUCCCACCAGCUCcACCA SEQ ID NO: 26 Clostridium acetobutylicum ssrA, 3' partial
AATCTGGCGTCGAGAGCGGGGAAACGAGCCTTACAAAGCTTTGA
GTAAGGAACGGAATTTATGAAGCTACTGAAGTGAAAAGCTTGTT
TGTAGGCGTTTCATGGAGGGAATGTTAJ\AATACAAACTGCACTC
GGAGATGCTTAATGAAACCAT7FfTCGGACAGGGGTTCGATTCCC CTCGCCTCCACCA SEQ ID NO: 27 Clostridium acetobutylicum tmRNA, 3' partial
AAUCUGGCGUCGAGAGCGGGGAAACGAGCCUUACAAAGCUUU
GAGUAAGGAACGGAAUUUAUGAAGCUACUGAAGUGAAAAGCU
UGIJIJ1GUAGGCGUUUCAUGGAGGGAAUGIJUAAAAUACAAACU
GCACUCGGAGAUGCUUAAUGAAACCAUUUUCGGACAGGGGJUU
CGAUUCCCCUCGCCUCCACCA SEQ ID NO: 28 Deinococcus radiodurans ssrA
GGGGGTGACCCGGTTFLCGACAGGGGAACTGAAGGTGATGTTGCG
TGTCGAGGTGCCGTTGGCCTCGTAAACKAACGGCAAAGCCATTT
AACTGGCAACCAGAACTACGCTCTCGCTGC'JTAAGTGAGATGAC
GACCGTGCAGCCCGGCCTTTIGGCGTCGCGGAAGTCACTAAAAAA
GAAGGCTAGCCCAGGCGATTCTCCATAGCCGACGGCGAAACTTT
ATGGAGCTACGGCCTGCGAGAACCTGCCCACTGGTGAGCGCCGG
CCCGACAATCAAACAGTGGGATACACACGTAGACGCACGCTGGA
CGGACCTTTGGACGGCGGTTCGACTCCGCCCACCTCCACCA
SEQ ID NO: 29 Deinococcus radiodurans tmRNA
GGGGGUGACCCGGUUUCGACAGGGGAACUGAAGGUGAUGUTUG
CGUGUCGAGGUGCCGIJUGGCCUCGUAAACAAACGGCAAAGCCA
UUJUAACUGGCAACCAGAACUACGCUCUCGCUGCUUAAGUGAGA
UGACGACCGUGCAGCCCGGCCUUUGGCGUCGCGGAAGUCACUA
AAAAAGAAGGCUAGCCCAGGCGAUUCUCCAUAGCCGACGGCGA
AACUUUAUGGAGCUACGGCCUGCGAGAACCUGCCCACUGGUGA
GCGCCGGCCCGACAAUCAAACAGUGGGAUACACACGUAGACGC
ACGCUGGACGGACCUUUGGACGGCGGUUICGACUCCGCCCACCU
CCACCA SEQID NO: Desulfovibrio desulfuricans ssrA, internal partial
GGGACTGGAACCGTAGCGGCAGGTCGAGGCGCCGCTGGCCTCGT
AAAAAGCGGCACAAAAGTAATTGCCAACAACGATTACGACTAC
GCTTACGCTGCCTAATAACAGCGAGGCAATGACCGTYJAACGGT
CGCGCCGATCAGGGCCATGCCTGATAACCCTGATTGGCGACACT
TATCAGGCTGGCGAAAACCGGCTCTCGCCGGGGTTThL'CGCGAG
GAGTTTACCGGCGGGATTGCTGCGTTGTGCCTGGTCAGGGGCCA
ACAGCGCGGTGAAATACATACTTGACCTAAACCTGTAATGCYJ'C
GTGTGGAATGTFJCTCGGACGGGG SEQ ID NO: 31 Desulfovibric desulfuricans tmRNA, internal partial
GGGACUGGAACCGUAGCGGCAGGUCGAGGCGCCGCUGGCCUCG
UAAAAAGCGGCACAAAAGUAAIJUGCCAACAACGAUUACGACU
ACGCUUACGCUGCCUAAUAACAGCGAGGCAAUGACCGUIJUAAC
GGUCGCGCCGAUCAGGGCCAUGCCUGAUAACCCUGAIJUGGCGA
CACIJIJAUCAGGCUGGCGAAAACCGGCUCUCGCCGGGGUUUUIJC
GCGAGGAGUUIJACCGGCGGGAIJUGCUGCGUUGUGCCUGGUCA
GGGGCCAACAGCGCGGUGAAAUACAUACUUGACCUAAACCUGU
AAUGCUUCGUGUGGAAUGUUCUCGGACGGGG SEQ ID NO: 32 Dichelobacter nodosus ssrA, 3' partial CTCGAGGTGCATGTCGAGAATGAGAGAATCTCGTTJAAATACTFI7
CAAAACTTATAGTTGCAAACGACGACAACTACGCTTTAGCGGCT
TAATTCCCGCTTTCGCTTIACCTAGA7FJTGTCTGTGGGT'PrACCGTA
AGCGACATTAACACAGAATCGCTGGTTAACGCGTCCGCTG'ITAA
TCGG'JTAAATTAAGCGGAATCGCTTGTAAAATGCCTGAGCGTTG
GCTGTTFIATGAGTTAAACCTAATFIAACTGCTCTAAACATGTAGTA
CCAAAAGTTAAGGATTCGCGGACGGGGGTTCAAATCCCCCCGCC
TCCACCA SEQ ID NO: 33 Dichelobacter nodosus tmRNA, 3' partial
CUCGAGGUGCAUGUCGAGAAUGAGAGAAUCUCGUUAAAUACU
UUCAAAACUUAUAGUUGCAAACGACGACAACUACGCUUUAGCG
GCUUAAUIJCCCGCUUUCGCUUACCUAGAUUUGUCUGUGGGUUU
ACCGUAAGCGACALJUAACACAGAAUCGCUGGUUAACGCGUCCG
CUGIJUAAUCGGUUAAAUUAAGCGGAAUCGCUUGUAAAAUGCC
UGAGCGUUGGCUGUUIJAUGAGUUAAACCUAAUTAACUGCUCU
AAACAUGUAGUACCAAAAGUUAAGGAUUCGCGGACGGGGGUU
CAAAUCCCCCCGCCUCCACCA SEQ lID NO: 34 Enterococcusfaecalis ssrA
GGGGGCGTTACGGATTCGACAGGCATAGTTGAGCTTGAATTGCG
TTTCGTAGGTTACGGCTACGTFJAAAACGTTACAGTTAAATATAAC
TGCTAAAAACGAAAACAATTCTTTCGCTTTAGCTGCCTAAAAAC
CAGCTAGCGAAGATCCTCCCGGCATCGCCCATGTGCTCGGGTCA
GGGTCCTAATCGAAGTGGGATACGCTAAATTITTTCCGTCTGTAAA
ATTTAGAGGAGCTTACCAGACTAGCAATACAGAATGCCTGTCAC
TCGGCACGCTGTAAAGCGAACCTYJ'AAATGAGTGTCTATGAACG
TAGAGATTTAAGTGGCAATATGTTTGGACGCGGGTTCGACTCCC
GCCGTCTCCACCA SEQ ID NO: Enterococcusfaecalis tmRNA
GGGGGCGUUACGGAUTJCGACAGGCAUAGUUGAGCUUGAAIJUG
CGUUUCGUAGGUUACGGCUACGUUAAAACGUUACAGUUAAAU
AUAACUGCUAAAAACGAAAACAAUUCUUUCGCUUUAGCUGCCU
AAAAACCAGCUAGCGAAGAUCCUCCCGGCAUCGCCCAUGUGCU
CGGGUCAGGGUCCUAAUCGAAGUGGGAUACGCUAAAIJUUUUC
CGUCUGUAAAAUUUAGAGGAGCUUACCAGACUAGCAAUACAG
AAUGCCUGUCACUCGGCACGCUGUAAAGCGAACCIJUUAAAUGA
GUGUCUAUGAACGUAGAGAUUUAAGUGGCAAUAUGUUUGGAC
GCGGGIJUCGACUCCCGCCGUCUCCACCA SEQ ID NO: 36 Escherichia coli ssrA GGGGCTGATTCTGGATTCGACGGGATYJ7GCGAAACCCAAGGTGC
ATGCCGAGGGGCGGTTGGCCTCGTAAAAAGCCGCAAAAAATAGT
CGCAAACGACGAAAACTACGCTTTAGCAGCTTAATAACCTGCYJ'
AGAGCCCTCTCTCCCTAGCCTCCGCTCYJ'AGGACGGGGATCAAG
AGAGGTCAAACCCAAAAGAGATCGCGTGGAAGCCCTGCCTGGG
GTTGAAGCGTFJAAAACTTAATCAGGCTAGT11TGTTAGTGGCGTGT
CCGTCCGCAGCTGGCAAGCGAATGTAAAGACTGACTAAGCATGT
AGTACCGAGGATGTAGGAATTTCGGACGCGGGTTCAACTCCCGC
CAGCTCCACCA SEQ ID NO: 37 Escherichia coli tmRNA
GGGGCUGAUUCUGGAUUCGACGGGAUIJUGCGAAACCCAAGGU
GCAUGCCGAGGGGCGGUUGGCCUCGUAAAAAGCCGCAAAAAAU
AGUCGCAAACGACGAAAACUACGCIJIJIAGCAGCUUAAUAACCU
GCUUAGAGCCCUCUCUCCCUAGCCUCCGCUCUUAGGACGGGGA
UCAAGAGAGGUCAAACCCAAAAGAGAUCGCGUGGAAGCCCUGC
CUGGGGUUGAAGCGUUAAAACUUAAUCAGGCUAGUUUGUUAG
UGGCGUGUCCGUCCGCAGCUGGCAAGCGAAUGUAAAGACUGAC
UAAGCAU GUAGUACCGAGGAUGUAGGAAUUUCGGACGCGGGU UCAACUCCCGCCAGCUCCACCA SEQ ID NO: 38 Haemophilus influenzae ssrA
GGGGCTGATTCTGGATTCGACGGGATTAGCGAAGCCCAAGGTGC
ACGTCGAGGTGCGGTAGGCCTCGTAAATAAACCGCAAAAAAATA
GTCGCAAACGACGAACAATACGCTTTAGCAGCTTAATAACCTGC
ATTTAGCCTTCGCGCTCCAGCTTCCGCTCGTAAGACGGGGATAAC
GCGGAGTCAAACCAAAACGAGATCGTGTGGAAGCCACCGTFJTGA
GGATCGAAGCACTAAATTGAATCAAACTAGCTTJAAGTY[AGCGT
GTCTGTCCGCATGCTFJAAGTGAAATTAAAGACGAGACTAAACGT
GTAGTACTGAAGGTAGAGTAATTTCGGACGGGGGTTCAACTCCC
CCCAGCTCCACCA SEQ ID NO: 39 Haemophilus influenzae tmRNA
GGGGCUGAIJUCUGGAUUCGACGGGAUUAGCGAAGCCCAAGGU
GCACGUCGAGGUGCGGUAGGCCUCGUAAAUAAACCGCAAAAAA
AUAGUCGCAAACGACGAACAAUACGCIJIJIAGCAGCUUAAUAAC
CUGCAUIUUAGCCUUCGCGCUCCAGCUUCCGCUCGUAAGACGGG
GAUAACGCGGAGUCAAACCAAAACGAGAUCGUGUGGAAGCCAC
CGUUUGAGGAUCGAAGCACUAAAIJUGAAUCAAACUAGCIJUAA
GUWJUAGCGUGUCUGUCCGCAUGCUUAAGUGAAAUUAAAGACG
AGACUAAACGUGUAGUACUGAAGGUAGAGUAAIJUUCGGACGG
GGGUUCAACUCCCCCCAGCUCCACCA SEQ ID NO: Helicobacterpylori (ATCC 43504) ssrA, internal partial
AGATTTC'ITGTCGCGCAGATAGCATGCCAAGCGCTGCTTGTAAA
ACAGCAACAAAAATAACTGTAAACAACACAGATTACGCTCCAGC
TTACGCTAAAGCTGCGTGAG7FTAATCTCCTThIGGAGCTGGACTG ATTAGAATTTCTAGCGTTTrAATCGCTCCATAACCTFJAAGCTAGA CGCTTTTAAAAGGTGGTTCGCC7TITAAACTAAGAAACAAGAAC
TCTTGAAACTATCTTAAGGTTFJTAGAAAGTTGGACCAGAGCTAGT
TTTAAGGCTAAAAACTAACCAATTITTCTAAGCATTGTAGAAGTTT
GTG'TTTAGGGCAAGATTTYJ7GGACTGGG SEQ ID NO: 41 Helicobacterpylori (ATCC 43504) tmRNA, internal partial
AGAIUUCUUGUCGCGCAGAUAGCAUGCCAAGCGCUGCUJIGUAA
AACAGCAACAAAAAUAACUGUAAACAACACAGAUUACGCUCCA
GCUUACGCUAAAGCUGCGUGAGUUAAIJCUCCUUUUGGAGCUG
GACUGAIJUAGAAUUIUCUAGCGUUUTUAAUCGCUCCAUAACCUU
AAGCUAGACGCUUUUAAAAGGUGGUUCGCCUUUUAAACUAAG
AAACAAGAACUCUIJGAAACUAUCUUAAGGIJUUUAGAAAGUUG
GACCAGAGCUAGUUTJUAAGGCUAAAAACUAACCAAUUIJUCUA
AGCAUIJGUAGAAGtUJUGUGUUUAGGGCAAGAUUUUUGGACUG GG SEQ ID NO: 42 Helicobacter pylori (strain 26695) ssrA GGGGCTGACTTGGATTTCGACAGATTTC117GTCGCACAGATAGC
ATGCCAAGCGCTGCTTGTAAAACAGCAACAAAAATAACTGTAAA
CAACACAGATTACGCTCCAGCTTACGCTAAAGCTGCGTGAGTTA
ATCTCCTTTTGGAGCTGGACTGATTAGAATTTCTAGCGTLTTAAT
CGCTCCATAACCTTAAGCTAGACGCTTTAAAAGGTGGTTCGCCT
TTTAAACTAAGAAACAAGAACTCYI7GAAACTATCTCAAGGTTTT
AGAAAGTTGGACCAGAGCTAGTTFITAAGGCTAAAAAACCAACCA
ATTTTCTAAGCATTGTAGAAGTTTGTGTTTAGGGCAAGATThFTG GACTGGGGTTCGATTCCCCACAGCTCCACCA SEQ ID NO: 43 Helicobaciterpylori (strain 26695) tmRNA
GGGGCUGACUUGGAUUUCGACAGAUUUCUUGUCGCACAGAUA
GCAUGCCAAGCGCUGCIJUGUAAAACAGCAACAAAAAUAACUGU
AAACAACACAGAULUACGCUCCAGCUUACGCUAAAGCUGCGUGA
GUUAAUCUCCUUUUGGAGCUGGACUGAUUAGAAUUIJCUAGCG
UIJUUAAUCGCUCCAUAACCUTJAAGCUAGACGCUUUUAAAAGG
UGGUUCGCCUUUUAAACUAAGAAACAAGAACUCUIUGAAACUA
UCUCAAGGUUUUAGAAAGUUGGACCAGAGCUAGUJIUUAAGGC
UAAAAAACCAACCAAUUUUCUAAGCAUUGUAGAAGJUTJGUGU
IIJIAGGGCAAGAUUUUUGGACUGGGGUUCGAUUCCCCACAGCUC
CACCA SEQ ID NO: 44 Kiebsiella aerogenes (NCTC 9528)ssrA, internal partial
GGGATTCGCGAAACCCAAGGTGCATGCCGAGGGGCGGTTGGCCT
CGTAAAAAGCCGCAAAAAAATAGTCGCAAACGACGAAAACTAC
GCT7ITAGCAGC'IFLAATAACCTGCTAAGAGCCCTCTCTCCCTAGCT
TCCGCTCCTAAGACGGGGAATAAAGAGAGGTCAAACCCAAAAG
AGATCGCGTGGAAGCCCTGCCTGGGGTTGAAGCGTTAAAACTAA
TCAGGCTAGThJGTCAGTGGCGTGTCCGTCCGCAGCTGGCCAGC
GAATGTAAAGACTGGACTAAGCATGTAGTGCCGAGGATGTAGGA
ATTTC SEQ ID NO: Kiebsiella aerogenes (NCTC 9528) tmRNA, internal partial
GGGAUIJCGCGAAACCCAAGGUGCAUGCCGAGGGGCGGUUGGCC
UCGUAAAAAGCCGCAAAAAAAUAGUCGCAAACGACGAAAACU
ACGCUUIJAGCAGCUUAAUAACCUGCUAAGAGCCCUCUCUCCCU
AGCUUCCGCUCCUAAGACGGGGAAUAAAGAGAGGUCAAACCCA
AAAGAGAUCGCGUGGAAGCCCUGCCUGGGGUUGAAGCGUUAA
AACUAAUCAGGCUAGUUUGUCAGUGGCGUGUCCGUCCGCAGCU
GGCCAGCGAAUGUAAAGACUGGACUAAGCAUGUAGUGCCGAG
GAUGUAGGAAUUJUC SEQ ID NO: 46 Lactobacillus lactis (NCTC 662)ssrA, internal partial
AAGCACAGTTCGAGCTTGAAFFGCGTTFICGTAGGTTACGTCTACG
TTAAAACGTTACAGTTAAATATAACTGCTAAAAACGAAAACAAC
TCTTACGC'ITTAGCTGCCTAAAAACAGTTAGCGTAGATCCTCTCG
GCATCGCCCATGTGCTCGAGTAAGGGTCTCAAATFITAGTGGGAT
ACGTTAAACTFTTCCGTCTGTAAAGTTFFAAAAGAGATCATCAGAC
TAGCGATACAGAATGCCTGTCACTCGGCAAGCTGTAAAGCGAAA
CCTCAAATGAGTTGACTATGAACGTAGAT7FITIAAGTGTCGATGT GTTT SEQ ID NO: 47 Lactobacillus lactis (NCTC 662) tmRNA, internal partial
AAGCACAGUIJCGAGCUUGAAUUGCGUUJCGUAGGUIUACGUCU
ACGIJUAAAACGUIIJACAGIJUAAAUAUAACUGCUAAAAACGAAA
ACAACUCUUACGCUUUAGCUGCCUAAAA-ACAGUUAGCGUAGAU
CCUCUCGGCAUCGCCCAUGUGCUCGAGUAAGGGUCUCAAAJJIJ
AGUGGGAUACGUUAAACUTJUUCCGUCUGUAAAGUUUAAAAGA
GAUCAUCAGACUAGCGAUACAGAAUGCCUGUCACUCGGCAAGC
UGUAAAGCGAAACCUCAAAUGAGUUGACUAUGAACGUAGAUU
UUUAAGUGUCGAUGUGUUU SEQ ID NO: 48 Legion ella pneumoplzila ssrA, internal partial
GTGGGTTGCAAAACCGGAAGTGCATGCCGAGAAGGAGATCTCTC
GTAAATAAGACTCAATTAAATATAAATGCAAACGATGAAAACTT
TGCTGGTGGGGAAGCTATCGCTGCCTAATAAGCAC'I1TAGTTAA
ACCATCACTGTGTACTGGCCAATAAACCCAGTATCCCGTTCGACC
GAGCCCGCTTATCGGTATCGAATCAACGGTCATAAGAGATAAGC
TAGCGTCCTAATCTATCCCGGGTTATGGCGCGAAACTCAGGGAA
TCGCTGTGTATCATCCTGCCCGTCGGAGGAGCCACAGTTAAATTC
AAAAGACAAGGCTATGCATGTAGAGCTAAAGGCAGAGGACTTG
CGGACGCGG SEQ ID NO: 49 9 Legionella pneumophila tmRNA, internal partial
GUGGGUIJGCAAAACCGGAAGUGCAUGCCGAGAAGGAGAUCUC
UCGUAAAUAAGACUCAAUUAAAUAUAAAUGCAAACGAUGAAA
ACtUUGCUGGUGGGGAAGCUAUCGCUGCCUAAUAAGCACUUU
AGIJUAAACCAUCACUGUGUACUGGCCAAUAAACCCAGUAUCCC
GUUICGACCGAGCCCGCUUAUCGGUAUCGAAUCAACGGUCAUAA
GAGAUAAGCUAGCGUCCUAAUCUAUCCCGGGUUAUGGCGCGAA
ACUCAGGGAAUCGCUGUGUAUCAUCCUGCCCGUCGGAGGAGCC
ACAGUUAAAUUCAAAAGACAAGGCUAUGCAUGUAGAGCUAAA
GGCAGAGGACUUGCGGACGCGG SEQ ID NO: Listeria grayi ssrA, internal partial
ACAGGGATAGGTCGAGCTTGAGTTGCGAGCCGGGGGGATCGGCC
CGTCATCAACGTCAAAGCCAATAATAACTGGCAAACAAAACAAC
AATTTAGCTTTCGCTGCCTAATAGCAGTCTGAATAGCTGATCCTC
CGTGCATCACCCATGTGCTACGGTAAGGGTCTCACTTYJ7AAGTGG
GTTACGCTGGCTFIATCTCCGTCTGGGGCAAACGAGAAGAGCATA
ATCAGACTAGCTAGATAGAGCCCTGACGCCGGGCAGACATCTAT
GCGAAATCCAAATACGGCAACTACGCTCGTAGATGCTCAAGTGC
CGATATTTCTGG SEQ ID NO: 51 Listeria grayi tmRNA, internal partial
ACAGGGAUAGGUCGAGCIJUGAGIJUGCGAGCCGGGGGGAUCGG
CCCGUCAUCAACGUCAAAGCCAAUAAUAACUGGCAAACAAAAC
AACAAU1TUAGCUUUCGCUGCCUAAUAGCAGUCUGAAUAGCUG
AUCCUCCGUGCAUCACCCAUGUGCUACGGUAAGGGUCUCACIUU
UUAAGUGGGUUACGCUGGCIJUAUCUCCGUCUGGGGCAAACGA
GAAGAGCAUAAUCAGACUAGCUAGAUAGAGCCCUGACGCCGGG
CAGACAUCUAUGCGAAAUCCAAAUACGGCAACUACGCUCGUAG
AUGCUCAAGUGCCGAUAUUUCUGG SEQ ID NO: 52 Listeria innocua ssrA, internal partial ACAGGGATAGTTCGAGCTTGAG7FJGCGAGTCGGGGGGATCGTCC
TCGTTATCAACGTCAAAGCCAATAATAACTGGCAAAGAAAAACA
AAACCTAGCTTTCGCTGCCTAATAAGCAGTAGCATAGCTGATCCT
CCGTGCATCGCCCATGTGCTACGGTAAGGGTCTCACTCTAAGTG
GGCTACACTAGTTAATCTCCGTCTGAGGTTAAATAGAAGAGCTT
AATCAGACTAGCTGAATGGAAGCCTG'ITACCGGGCTGATGTTTA
TGCGAAATGCTAATACGGTGACTACGCTCGTAGATATTCAAGTG
CCGATATTTCTGG SEQ ID NO: 53 Listeria innocua tmRNA, internal partial
ACAGGGAUAGUUCGAGCUUGAGUUGCGAGUCGGGGGGAUCGU
CCUCGUUAUCAACGUCAAAGCCAAUAAUAACUGGCAAAGAAAA
ACAAAACCUAGCUUUCGCUGCCUAAUAAGCAGUAGCAUAGCUG
AUCCUCCGUGCAUCGCCCAUGUGCUACGGUAAGGGUCUCACUC
UAAGUGGGCUACACUAGUUAAUCUCCGUCUGAGGUUAAAUAG
AAGAGCUUAAUCAGACUAGCUGAAUGGAAGCCUGUUACCGGG
CUGAUGUUUIAUGCGAAAUGCUAAUACGGUGACUACGCUCGUA
GAUAUIJCAAGUGCCGAUAUU!JCUGG SEQ ID NO: 54 Listeria monocytogenes (NCTC 7973)ssrA, internal partial ACAGGGATAGTTCGAGCTTGAG7FJGCGAGTCGGGGGGATCGTCC
TCGTTATCAACGTCAAAGCCAATAATAACTGGCAAAGAAAAACA
AAACCTAGCTTTCGCTGCCTAATAAGCAGTAGCATAGCTGATCCT
CCGTGCATCGCCCATGTGCTACGGTAAGGGTCTCACTCTAAGTG
GGCTACACTAGTFLAATCTCCGTCTGGGGTTAAATAGAAGAGCTT
AATCAGACTAGCTGAATGGAAGCCTGTFIACCGGGCCGATGTTFIA
TGCGAAATGCTAATACGGTGACTACGCTCGTAGATATTFIAAGTG
CCGATATTTCTGG SEQ ID NO: Listeria monocytogenes (NCTC 7973 )tmRNA, internal partial
ACAGGGAUAGUIUCGAGCUUGAGUUGCGAGUCGGGGGGAUCGU
CCUCGUUAUCAACGUCAAAGCCAAUAAUAACUGGCAAAGAAAA
ACAAAACCUAGCUUUCGCUGCCUAAUAAGCAGUAGCAUAGCUG
AUCCUCCGUGCAUCGCCCAUGUGCUACGGUAAGGGUCUCACUC
UAAGUGGGCUACACUAGUUAAUCUCCGUCUGGGGUTUAAAUAG
AAGAGCUUAAUCAGACUAGCUGAAUGGAAGCCUGUUACCGGG
CCGAUGIJIUAUGCGAAAUGCUAAUACGGUGACUACGCUCGUA
GAUAUUUAAGUGCCGAUAIJUUCUGG SEQ ID NO: 56 Listeria monocytogenes (NCTC 11994) ssrA, internal partial CAAAGCCAATAATAACTGGCAAAGAAAAACAAAACCTAGC7FFJC
GCTGCCTAATAAGCAGTAGCATAGCTGATCCTCCGTGCATCGCC
CATGTGCTACGGTAAGGGTCTCACTCTAAGTGGGCTACACTAG1T
AATCTCCGTCTGGGGTTAAATAGAAGAGCTTAATCAGACTAGCT
GAATGGAAGCCTGTTACCGGGCCGATG7FFTATGCGAAATGCTAA TACGGTGACTACGCTCGTAGATATTT SEQ ID NO: 57 Listeria monocytogenes (NCTC 11994) tmRNA, internal partial
CAAAGCCAAUAAUAACUGGCAAAGAAAAACAAAACCUAGCUUI
UCGCUGCCUAAUAAGCAGUAGCAUAGCUGAUCCUCCGUGCAUC
GCCCAUGUGCUACGGUAAGGGUCUCACUCUAAGUGGGCUACAC
UAGUUAAUCUCCGUCUGGGGUUAAAUAGAAGAGCUUAAUCAG
ACUAGCUGAAUGGAAGCCUGUUACCGGGCCGAUGUUUAUGCG
AAAUGCUAAUACGGUGACUACGCUCGUAGAUAUUTJ
SEQ ID NO: 5 8 Listeria murrayi ssrA, internal partial
ACAGGGATAGTTCGAGCTTGAGTTGCGAGTCGGGGGGATCGTCC
TCGTTIATCAACGTCAAAGCCAATAATAACTGGCAAAGAAAAACA
AAACCTAGCTTTJCGCTGCCTAATAAGCAGTAGCATAGCTGATCCT
CCGTGCATCGCCCATGTGCTACGGTAAGGGTCTCACTCTAAGTG
GGCTACACTAG7F[AATCTCCGTCTGAGGTTAAATAGAAGAGCTT
AATGAGACTAGCTGAATGGAAGCCTGTTACCGGGCTGATGT'ITA
TGCGAAATGCTAATACGGTGACTACGCTCGTAGATATTCAAGTG
CCGATATFJTCTGG SEQ ID NO: 59 Listeria murrayi tmRNA, internal partial
ACAGGGAUAGUUCGAGCUUGAGUTJGCGAGUCGGGGGGAUCGU
CCUCGUUAUCAACGUCAAAGCCAAUAAUAACUGGCAAAGAAAA
ACAAAACCUAGCUUUCGCUGCCUAAUAAGCAGUAGCAUAGCUG
AUCCUCCGUGCAUCGCCCAUGUGCUACGGUAAGGGUCUCACUC
UAAGUGGGCUACACUAGUUAAUCUCCGUCUGAGGUIJAAAUAG
AAGAGCUUAAUGAGACUAGCUGAAUGGAAGCCUGUUACCGGG
CUGAUGUUUAUGCGAAAUGCUAAUACGGUGACUACGCUCGUA
GAUAUTJCAAGUGCCGAUAUUTJUCUGG SEQ ID NO: Listeria weishimeri ssrA, internal partial
ACAGGGATAGTTCGAGCTTGAGTFJGCGAGTCGGGGGGATCGTCC
TCGTTATCAACGTCAAAGCCAATAATAACTGGCAAAGAAAAACA
AAACCTAGCT'JTCGCTGCCTAATAAGCAGTAGCATAGCTGATCCT
CCGTGCATCGCCCATGTGCTACGGTAAGGGTCTCACTCTAAGTG
GGCTACACTGGCTAATCTCCGTCTGAGGTTAGTTGGAAGAGCTT
AATCAGACTAGCTGAATGGAAGCCTGTTACCGGGCCGATGTTTA
TGCGAAATGCTAATACGGTGACTACGCTCGTAGATATTTAAGTG
CCGATA'ITTCTGG SEQ ID NO: 61 Listeria welsh imeri tmRNA, internal partial
ACAGGGAUAGIJUCGAGCUUGAGUUGCGAGUCGGGGGGAUCGU
CCUCGUJ!AUCAACGUCAAAGCCAAUAAUAACUGGCAAAGAAAA
ACAAAACCUAGCUUUCGCUGCCUAAUAAGCAGUAGCAUAGCUG
AUCCUCCGUGCAUCGCCCAUGUGCUACGGUAAGGGUCUCACUC
UAAGUGGGCUACACUGGCUAAUCUCCGUCUGAGGUUAGUUGG
AAGAGCUUAAUCAGACUAGCUGAAUGGAAGCCUGUUACCGGG
CCGAUGUJIUAUGCGAAAUGCUAAUACGGUGACUACGCUCGUA
GAUAUUtJAAGUGCCGAUAUUUCUGG SEQ ID NO: 62 Marinobacter hydrocarbonoclasticus ssrA, internal partial
GCCGGTGACGAACCCTFJGGGTGCATGCCGAGATGGCAGCGAATC
TCGTAAATCCAAAGCTGCAACGTAATAGTCGCAAACGACGAAAA
CTACGCACTGGCGGCGTAAGCCGTTCCAGTCGTCCTGGCTGAGG
CGCCTATAACTCAGTAGCAACATCCCAGGACGTCATCGCTTATA
GGCTGCTCCGTTCACCAGAGCTCACTGGTGYJ7CGGCTAAGATTAA
AGAGCTCGCCTCTTGCACCCTGACCTTCGGGTCGCTTGAGGTTAA
ATCAATAGAAGGACACTAAGCATGTAGACCTCAAGGCCTAGTGC
TGGCGGACGCGG SEQ ID NO: 63 Marinobacter hydrocarbonoclasticus tmRNA, internal partial
GCCGGUGACGAACCCUUGGGUGCAUGCCGAGAUGGCAGCGAAU
CUCGUAAAUCCAAAGCUGCAACGUAAUAGUCGCAAACGACGAA
AACUACGCACUGGCGGCGUAAGCCGUUCCAGUCGUCCUGGCUG
AGGCGCCUAUAACUCAGUAGCAACAUCCCAGGACGUCAUCGCU
UAUAGGCUGCUCCGUUCACCAGAGCUCACUGGUGUUCGGCUAA
GAUJ1AAAGAGCUCGCCUCIJUGCACCCUGACCUUCGGGUCGC-U
GAGGUIJAAAUCAAUAGAAGGACACUAAGCAUGUAGACCUCAA
GGCCUAGUGCUGGCGGACGCGG SEQ ID NO: 64 Mycobacterium avium ssrA, internal partial
TTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAACTGA
CCACCGTAAGCGTCGTTGCAAATAGATAAGCGCCGATTCACATC
AGCGCGACTTACCTCTCGCTGCCTAAGCGACAGCTAGTCCGTCA
GCCCGGGAACGCCCTCGACCCGGAGCCTGGCGTCAGCTAGAGGG
ATCCACCGATGAGTTCGGTCGCGGGACTCATCGGGACACCAACA
GCGACTGGGATCGTCATCCTGGCTTGTTCGCGTGACCAGGAGAT
CCGAGTAGAGGCATAGCGAACTGCGCACGGAGAAGCCYI7GAGG GAATGCCGTAGAACCCGGGTTCGATTCCCAA SEQ ID NO: Mycobacterium avium trnRNA, internal partial
UUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCAACUG
ACCACCGUAAGCGUCGUIJGCAAAUAGAUAAGCGCCGAUUCACA
UCAGCGCGACUJUACCUCUCGCUGCCUAAGCGACAGCUAGUCCG
UCAGCCCGGGAACGCCCUCGACCCGGAGCCUGGCGUCAGCUAG
AGGGAUCCACCGAUGAGUUCGGUCGCGGGACUCAUCGGGACAC
CAACAGCGACUGGGAUCGUCAUCCUGGCUUGUUCGCGUGACCA
GGAGAUCCGAGUAGAGGCAUAGCGAACUGCGCACGGAGAAGCC
UUGAGGGAAUGCCGUAGAACCCGGGUUCGAUUCCCAA
SEQ ID NO: 66 Mycobacterium bovis ssrA, internal partial
TTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAAGAG
ACCACCGTAAGCGTCG7FIGCGACCAAATAAGCGCCGATFICACAT
CAGCGCGACTACGTCTCGCTGCCTAAGCGACGGCTAGTCTGTCA
GACCGGGAACGCCCTCGGCCCGGACCCTGGCATCAGCTAGAGGG
ATCCACCGATGAGTCCGGTCGCGGGACTCCTCGGGACAACCACA
GCGACTGGGATCGTCATCTCGGCTAGTTCGCGTGACCGGGAGAT
CCGAGCAGAGGCATAGCGAACTGCGCACGGAGAAGCCTFJGAGG
GAATGCCGTAGG SEQ ID NO: 67 Mycobacterium bovis tmRNA, internal partial
UUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCAAGAG
ACCACCGUAAGCGUCGUUGCGACCAAAUAAGCGCCGAUUCACA
UCAGCGCGACUACGUCUCGCUGCCUAAGCGACGGCUAGUCUGU
CAGACCGGGAACGCCCUCGGCCCGGACCCUGGCAUCAGCUAGA
GGGAUCCACCGAUGAGUCCGGUCGCGGGACUCCUCGGGACAAC
CACAGCGACUGGGAUCGUCAUCUCGGCUAGUUCGCGUGACCGG
GAGAUCCGAGCAGAGGCAUAGCGAACUGCGCACGGAGAAGCCU
UGAGGGAAUGCCGUAGG SEQ ID NO: 68 Mycobacterium leprae ssrA
GGGGCTGAAAGGTTTCGACTTCGCGCATCGAATCAAGGGAAGCG
TGCCGGTGCAGGCAAGAGACCACCGTAAGCGTCGYI7GCAGCAAT
ATAAGCGCCGATTCATATCAGCGCGACTATGCTCTCGCTGCCTAA
GCGATGGCTAGTCTGTCAGACCGGGAACGCCCTCGTCCCGGAGC
CTGGCATCAGCTAGAGGGATCTACCGATGGGTTCGGTCGCGGGA
CTCGTCGGGACACCAACCGCGACTGGGATCGTCATCCTGGCTAG
TTCGCGTGATCAGGAGATCCGAGTAGAGGCATAGCGAACTACGC
ACGGAGAAGCCTTGAGGGAAATGCCGTAGGACCCGGGTTCGATT
CCCGGCAGCTCCACCA SEQ ID NO: 69 Mycobacterium leprae tmRNA
GGGGCUGAAAGGUUUCGACUUCGCGCAUCGAAUCAAGGGAAG
CGUGCCGGUGCAGGCAAGAGACCACCGUAAGCGUCGUJLGCAGC
AAUAUAAGCGCCGAIJUCAUAUCAGCGCGACUAUGCUCUCGCUG
CCUAAGCGAUGGCUAGUCUGUCAGACCGGGAACGCCCUCGUCC
CGGAGCCUGGCAUCAGCUAGAGGGAUCUACCGAUGGGUUCGGU
CGCGGGACUCGUCGGGACACCAACCGCGACUGGGAUCGUCAUC
CUGGCUAGUUCGCGUGAUCAGGAGAUCCGAGUAGAGGCAUAG
CGAACUACGCACGGAGAAGCCUUGAGGGAAAUGCCGUAGGACC
CGGGUTUCGAUUCCCGGCAGCUCCACCA SEQ ID NO: Mycobacterium paratuberculosis ssrA, internal partial
TTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAACTGA
CCACCGTAAGCGTCGTTGCAAATAGATAAGCGCCGATTCACATC
AGCGCGACTTACCTCTCGCTGCCTAAGCGACAGCTAGTCCGTCA
GCCCGGGAACGCCCTCGACCCGGAGCCTGGCGTCAGCTAGAGGG
ATCCACCGATGAGTTCGGTCGCGGGACTCATCGGGACACCAACA
GCGACTGGGATCGTCATCCTGGCTTGTTCGCGTGACCAGGAGAT
CCGAGTAGAGGCATAGCGAACTGCGCACGGAGAAGCCTTGAGG
GAATGCCGTAGAACCCGGGTTCGATTCCCAA SEQ ID NO: 71 Mycobacterium paratuberculosis tmiRNA, internal partial
UUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCAACUG
ACCACCGUAAGCGUCGUUGCAAAUAGAUAAGCGCCGAUUCACA
UCAGCGCGACIJUACCUCUCGCUGCCUAAGCGACAGCUAGUCCG
UCAGCCCGGGAACGCCCUCGACCCGGAGCCUGGCGUCAGCUAG
AGGGAUCCACCGAUGAGUUCGGUCGCGGGACUCAUCGGGACAC
CAACAGCGACUGGGAUCGUCAUCCUGGCUUGUTUCGCGUGACCA
GGAGAUCCGAGUAGAGGCAUAGCGAACUGCGCACGGAGAAGCC
UUGAGGGAAUGCCGUAGAACCCGGGUIUCGAUUCCCAA
SEQ ID NO: 72 Mycobacterium tuberculosis ssrA GGGGCTGAACGGTTT1CGACTTCGCGCATCGAATCAAGGGAAGCG
TGCCGGTGCAGGCAAGAGACCACCGTAAGCGTCGTTGCGACCAA
ATAAGCGCCGATTCACATCAGCGCGACTACGCTCTCGCTGCCTA
AGCGACGGCTAGTCTGTCAGACCGGGAACGCCCTCGGCCCGGAC
CCTGGCATCAGCTAGAGGGATCCACCGATGAGTCCGGTCGCGGG
ACTCCTCGGGACAACCACAGCGACTGGGATCGTCATCTCGGCTA
GTTCGCGTGACCGGGAGATCCGAGCAGAGGCATAGCGAACTGCG
CACGGAGAAGCCTTGAGGGAATGCCGTAGGACCCGGGTTCGATT
CCCGGCAGCTCCACCA SEQ ID NO: 73 Mycobacterium tuberculosis tmRNA
GGGGCUGAACGGUUUCGACUUCGCGCAUCGAAUCAAGGGAAGC
GUGCCGGUGCAGGCAAGAGACCACCGUAAGCGUCGUUGCGACC
AAAUAAGCGCCGAUUCACAUCAGCGCGACUACGCUCUCGCUGC
CUAAGCGACGGCUAGUCUGUCAGACCGGGAACGCCCUCGGCCC
GGACCCUGGCAUCAGCUAGAGGGAUCCACCGAUGAGUCCGGUC
GCGGGACUCCUCGGGACAACCACAGCGACUGGGAUCGUCAUCU
CGGCUAGUUCGCGUGACCGGGAGAUCCGAGCAGAGGCAUAGCG
AACUGCGCACGGAGAAGCCUUGAGGGAAUGCCGUAGGACCCGG
GUUCGAUJICCCGGCAGCUCCACCA SEQ ID NO: 74 Mycoplasma capricolum ssrA GGGGATGTCATGGAT7ITGACAGGATATCTh[AGTACATATAAGC AGTAGTGTTGTAGACTATAAATACTACTAGGT[AjAAACGC
AAATAAAAACGAAGAAACTTTTJGAAATGCCAGCATTTATGATGA
ATAATGCATCAGCTGGAGCAAACTTTATGTYJ'GCTTAATAACTAC
TAGTTTAGTTATAGTAY[TCACGAATTATAGATATTTAAGCTyf ATTTATAACCGTATTACCCAAGCATAGAATATATGATTGCAjA
TAAATATATTTGAATCTAATTGCAAATGATATTAACCTTTAGT
TAATTTTAGT[AAATATTJTTAATTAGAAAATTAACTAAACTGTAG
AAAGTATGTA7FFAATATATCTTGGACGCGAGTTCGATTCTCGCCA TCTCCACCA SEQ ID NO: Mycoplasma capricolum tmRNA
GGGGAUGUCAUGGAUUUGACAGGAUAUCUUUAGUACAUAUAA
GCAGUAGUGUUGUAGACUAUAAAUACUACUAGGUUUAAAAAA
ACGCAAAUAAAAACGAAGAAACUUUUGAAAUGCCAGCAJUIJA
UGAUGAAUAAUGCAUCAGCUGGAGCAAACUUTUAUGUUUGCUU
AAUAACUACUAGIJIJIAGUUAUAGUAUIJUCACGAAUIJAUAGAU
AUTUUUAAGCUIJUAUUUAUAACCGUAUUTACCCAAGCUIJAAUAG
AAUAUAUGAUIJGCAAUAAAUAUAUUUGAAAUCUAAUUGCAAA
UGAUAUULUAACCUUUAGUUAAUUTUUAGUUAAAUAUtTUUAAUIJ
AGAAAAIJUAACUAAACUGUAGAAAGUAUGUAUIJAAUAUAUCU
UGGACGCGAGUJICGAUUCUCGCCAUCUCCACCA SEQ ID NO: 76 Mycoplasma genitalium (ATTC 33530, ssrA
GGGGATGTTTTGGGTTTGACATAATGCTGATAGACAAACAGTAG
CATTGGGGTATGCCCCTACAGCGCTAGG7FrCATAACCGACAA
AGAAAATAACGAAGTGTTGGTAGAACCAAATTTGATCATTAACC
AACAAGCAAGTGTTAACTFTGCTTF[GCATAAGTAGATACTAAA
GCTACAGCTGGTGAATAGTCATAGTTTGCTAGCTGTCATAGTTTA
TGACTCGAGGTTAAATCGTTCAATI7AACCTFJ1AAJ\AATAGAACT
TGTTGTTTCCATGATTGTTTTGTGATCAATTGGAAACAAGACAA
AATCCACAAAACTAAAATGTAGAAGCTGY[fTGYJ7GTGTCCTTTAT GGAAACGGGTTCGATTCCCGTCATCTCCACCA SEQ ID NO: 77 Mycoplasma genitalium (ATTC 33530, tmRNA
GGGGAUGUUUTJGGGUUUGACAUAAUGCUGAUAGACAAACAGU
AGCAUUGGGGUAUGCCCCUUACAGCGCUAGGIJUCAAUAACCGA
CAAAGAAAAUAACGAAGUGUUGGUAGAACCAAAUUUGAUCAU
UAACCAACAAGCAAGUGUUAACU1IUGCUUUUGCAUAAGUAGA
UACUAAAGCUACAGCUGGUGAAUAGUCAUAGUIJUGCUAGCUG
UCAUAGUUIJAUGACUCGAGGUUAAAUCGUUCAAUUUAACCUIJ
UAAAAAUAGAACUUGUUGUUUCCAUGAUIJGUIJUUGUGAUCAA
IJUGGAAACAAGACAAAAAUCCACAAAACUAAAAUGUAGAAGC
UGUUUGUUGUGUCCUUUAUGGAAACGGGIJUCGAUUCCCGUCA
UCUCCACCA SEQ ID NO: 78 Mycoplasma genitalium (ATTC 33530, tmRNA, internal partial ACATAATGCTGATAGACAA-ACAGTAGCATTGGGGTATGCCCC7F[
ACAGCGCTAGGTTCAATAACCGACAAAGAAAATAACGAAGTGTT
GGTAGATCCAAATYJ'GATCAYI7AACCAACAAGCAAGTGTTAACT
TTGCTTTTGCATAAGTAGATACTAAAGCTACAGCTGGTGAATAGT
CATAGTTTGCTAGCTGTCATAGTTFJATGACTCGAGG7F[AAATCGT TCAATTTAACCTTTAAAAATAGAACTTGTFJGTTTCCATGATTG7Fr
TTGTGATCAATTGGAAACAAGACAAAAATCCACAACTAAAAT
GTAGAAGCTGTTTGTFIGTGTCCYJTATGGAAACGGGTTC
SEQ ID NO: 79
I
Mycoplasma genitalium (ATTC 33530, tmRNA, internal partial
ACAUAAUGCUGAUAGACAAACAGUAGCAUUGGGGUAUGCCCC
UUACAGCGCUAGGUUCAAUAACCGACAAAGAAAAUAACGAAG
UGUUGGUAGAUCCAAAUIJUGAUCAUUAACCAACAAGCAAGUG
UUAACUUUGCUUIJUGCAUAAGUAGAUACUAAAGCUACAGCUG
GUGAAUAGUCAUAGUUUGCUAGCUGUCAUAGUUTJAUGACUCG
AGGUUAAAUCGIJUCAAUUUAACCUUUAAAAAUAGAACUUGIJU
GUTUUCCAUGAUUGUUUUGUGAUCAAUUGGAAACAAGACAAAA
AUCCACAAAACUAAAAUGUAGAAGCUGUUUGUUGUGUCCUUU
AUGGAAACGGGUTUC SEQ ID NO: Mycoplasma pneumophila ssrA
GGGGATGTAGAGGTTTTIGACATAATGTFJGAAAGGAAAACAGTTG
CAGTGGGGTATGCCCCTTACAGCTCTAGGTATAATAACCGACAA
AAATAACGACGAAGT7FFTGGTAGATCCAATGY[GATCGCTAACC
AACAAGCAAGTATCAACTACGCTTTCGCTFJAGAACATACTAAAG
CTACACGAATTGAATCGCCATAGTFJTGGTTCGTGTCACAGT7FIAT
GGCTCGGGGTTAACTGGTTCAACTTAATCCFJAAATTATGAACFF
ATCGThJ7ACTTGTTTGTC7I1ATGATCTAALAGTAAGCGAGACATTA AAACATAAGACTAAACTGTAGAAGCTGThL'TACCAATCCTTTATG GAAACGGGTTCGATTCCCGTCATCTCCACCA SEQ ID NO: 81 Mycoplasma pneumophila tmRNA
GGGGAUGUAGAGGUUIJUGACAUAAUGUUGAAAGGAAAACAGU
UGCAGUGGGGUAUGCCCCUUACAGCUCUAGGUAUAAUAACCGA
CAAAAAUAACGACGAAGUUTJUGGUAGAUCCAAUGIJUGAUCGC
UAACCAACAAGCAAGUAUCAACUACGCUUUCGCUUAGAACAUA
CUAAAGCUACACGAAUIJGAAUCGCCAUAGUUUGGUUCGUGUC
ACAGUUAUGGCUCGGGGUJIAACUGGJUCAACUUAAUCCUUA
AAUUAUGAACUUAUCGUUUACUUGIJUUGUCUUAUGAUCUAAA
GUAAGCGAGACAUUAAAACAUAAGACUAAACUGUAGAAGCUG
UUUUJLACCAAUCCUUUAUGGAAACGGGUUCGAUUCCCGUCAUCU
CCACCA SEQID NO: 82 Neisseria gonorrhoeae (ATCC 19424) ssrA, internal. partial
GGGGGTTGCGAAGCAGATGCGGGCATACCGGGGTCTCAGATTCC
CGTAAAACACTGAATTCAAATAGTCGCAAACGACGAAACTTACG
CTTTAGCCGCTTAAGGCTAGCCGTTGCAGCAGTCGGTCAATGGG
CTGTGTGGCGAAAGCCACCGCAACGTCATCTFIACAT11GACTGGTT
TCCAGCCGGGTFLACTTGGCAGGAAATAAGACTTAAGGTAACTGG
TTFTCCAAAAGGCCTGT11GGTCGGCATGATGGAAATAAGATTTTC
AAATAGACACAACTAAGTATGTAGAACGCT'ITGTAGAGGACTTT
CGGACGGGG SEQ ID NO: 83 Neisseria gonorrhoeae (ATCC 19424) tniRNA, internal partial
GGGGGUUGCGAAGCAGAUGCGGGCAUACCGGGGUCUCAGAUU
CCCGUAAAACACUGAAUUCAAAUAGUCGCAAACGACGAAACUU
ACGCUUUAGCCGCUIJAAGGCUAGCCGUUGCAGCAGUCGGUCAA
UGGGCUGUGUGGCGAAAGCCACCGCAACGUCAUCUUACAUUGA
CUGGU1JUCCAGCCGGGUUACUUGGCAGGAAAUAAGACUUAAG
GUAACUGGUUUCCAAAAGGCCUGUUGGUCGGCAUGAUGGAAA
UAAGAJUTJCAAAUAGACACAACUAAGUAUGUAGAACGCUUU
GUAGAGGACUIJUCGGACGGGG SEQ ID NO: 84 Neisseria gonorrhoeae (FA 1090) ssrA
GGGGGCGACCTTGGTTTCGACGGGGGTTGCGAAGCAGATGCGGG
CATACCGGGGTCTCAGATTCCCGTAAAACACTGAATTCAAATAG
TCGCAAACGACGAAACTTACGCTTTAGCCGCTTAAGGCTAGCCG
TTGCAGCAGTCGGTCAATGGGCTGTGTGGTGAAAGCCACCGCAA
CGTCATCY[ACATFIGACTGG7FFTCCAGCCGGGTTACTTGGCAGGA
AATAAGACTTAAGGTAACTGGTTTCCAAAAGGCCTGTTGGTCGG
CATGATGGAAATAAGATTYI7CAAATAGACACAACTAAGTATGTA
GAACGCTTTGTAGAGGACTTITCGGACGGGGGTTCGATTCCCCCC
GCCTCCACCA SEQ ID NO: Neisseria gonorrhoeae (FA 1090) tmRNA
GGGGGCGACCUUGGUUUCGACGGGGGUUGCGAAGCAGAUGCG
GGCAUACCGGGGUCUCAGAUUCCCGUAAACUGAAUUTCAAA
UAGUCGCAAACGACGAAACUUACGCUUUAGCCGCUUIAAGGCUA
GCCGUUGCAGCAGUCGGUCAAUGGGCUGUGUGGUGAAAGCCAC
CGCAACGUCAUCUUACAUUGACUGGUUUCCAOCCGGGUIJACUU
GGCAGGAAAUAAGACUUAAGGUAACUGGUUUCCAAAAGGCCU
GUUGGUCGGCAUGAUGGAAAUAAGAUTJIJICAAAUAGACACAA
CUAAGUAUGUAGAACGCUTJUGUAGAGGACUUIJCGGACGGGGG
IJUCGAUUCCCCCCGCCUCCACCA SEQ ID NO: 86 Neisseria men ingitidis ssrA GGGGGCGACCTTGGTYI7CGACGGGGGTTGCGAAGCAGATGCGGG
CATACCGGGGTCTCAGAYJ'CCCGTAAAACACTGAATTCAAATAG
TCGCAAACGACGAAACTTACGCTTJTAGCCGCTTAAGGCTAGCCG
TTGCAGCAGTCGGTCAATGGGCTGTGTGGCGAAAGCCACCGCAA
CGTCATCTTACATTJGACTGGTTTJCCTGCCGGGTTAThL'GGCAGGA
AATGAGATTTAAGGTAACTGGTFITCCAAAAGGCCTGTTGGTCGG
CATGATGGAAATAAGATTTTCAAATAGACACAACTAAGTATGTA
GAACGCTTTGTAGAGGACTTTCGGACGGGGGTTCGATTCCCCCC
GCCTCCACCA SEQ ID NO: 87 Neisseria men ingitidis tmiRNA
GGGGGCGACCUIJGGUUUCGACGGGGGUUGCGAAGCAGAUGCG
GGCAUACCGGGGUCUCAGAIJUCCCGUAAAACACUGAAUUCAAA
UAGUCGCAAACGACGAAACUUJACGCUUUAGCCGCIJUAAGGCUA
GCCGUUGCAGCAGUCGGUCAAUGGGCUGUGUGGCGAAAGCCAC
CGCAACGUCAUCUYUACAUIJGACUGGUUYUCCUGCCGGGUUAUUU
GGCAGGAAAUGAGAUUUAAGGUAACUGGUUUCCAAAAGGCCU
GIJUGGUCGGCAUGAUGGAAAUAAGAUUUUCAAAUAGACACAA
CUAAGUAUGUAGAACGCUUUGUAGAGGACUUUCGGACGGGGG
UUCGAUUCCCCCCGCCUCCACCA SEQ ID NO: 88 Nostoc muscorum PCC7 120 ssrA
GGGTCCGTCGGTTTCGACAGGTTGGCGAACGCTACTCTGTGATTC
AGGTCGAGAGTGAGTCTCCTCTGCAAATCAAGGCTCAAAACAAA
AGTAAATGCGAATAACATCGTTAAAT7FJGCTCGTAAGGACGCTC TAGTAGCTGCCTAAATAGCCTC7FPTCAGGTTCGAGCGTCTTCGGT
TTGACTCCGTTAAGGACTGAAGACCAACCCCCAACGGATGCTCT
AGCAATGTTCTCTGGTTGGCTFIGCTAGCTAAGAT7FJAATCAGAGC
ATCCTACG'ITCGGGATAATGAACGATTCCCGCCTTGAGGGTCAG
AAAGGCTAAACCTGTGAATGAGCGGGGGGTCAATACCCAATTFJG
GACAGCAGTTCGACTCTGCTCGATCCACCA SEQ ID NO: 89 Nostoc muscorum PCC7 120 tmRNA
GGGUCCGUCGGUUUCGACAGGUUGGCGAACGCUACUCUGUGAU
UCAGGUCGAGAGUGAGUCUCCUCUGCAAAUCAAGGCUCAAAAC
AAAAGUAAAUGCGAAUAACAUCGUUAAAUUULGCUCGUAAGGA
CGCUCUAGUAGCUGCCUAAAUAGCCUCU[JUCAGGUUCGAGCGU
CUUCGGUUUGACUCCGUUAAGGACUGAAGACCAACCCCCAACG
GAUGCUCUAGCAAUGIJUCUCUGGUUGGCUUGCUAGCUAAGAU
IJUAAUCAGAGCAUCCUACGUUCGGGAUAAUGAACGAUYUCCCGC
CUUGAGGGUCAGAAAGGCUAAACCUGUGAAUGAGCGGGGGGU
CAAUACCCAAUUULGGACAGCAGU1JCGACUCUGCUCGAUCCACC A SEQ ID NO: Odontella sin ensis (diatom) chioroplast ssrA
GGGGCTGACTTGGTTTCGACATTTAAAAATTGTTACAGTATGATG
CAGGTCGAAGTTTCTAATCTTCGTAAAAAAAGAGAAATTTATAA
TAAATGCTAATAATTFJAATTJTCTTCTGTGTTTAAAAGTFITATCAA
CTAAGCAAAATAGTTTAAATTITAAGTThI7GCTG7FfTAAGTTTTAT GCACAT7FJAATGATCTAGTAAATAACTI7GTTJCGCTATAATFJTAT ATTFIATAACTAGACTThI7GTCY[TTTTATAGTTTAGAATAAC1T17A
TCA'ITTCAAACCTCGTTCCATCTAGTFIGAACTAAACCTGTGAACG
AATACTATAATAAAATTTTTAGATGGACGTGGGTTCGACTCCCAT
CAGCTCCACCA SEQ ID NO: 91 Odon tel/a sinensis (diatom) chioroplast tmRNA GGGGCUGACUJ1GGUUUCGACAUUJTAAAAAUIJGUUACAGUAUG
AUGCAGGUCGAAGUUUICUAAUCUTJCGUAAAAAAAGAGAAAIUU
UAUAAUAAAUGCUAAUAAIJIJIAAUUUCUUCUGUGIJUUAAAAG
UUUAUCAACUAAGCAAAAUAGUTJUAAAUUUAAGIJUUUGCUGU
UUAAGUtUUAUGCACAUUIJAAUGAUCUAGUAAAUAACUUUGU
UCGCUAUAAUUAUAUUUAUAACUAGACUUIJUGUCUIUUUUUA
UAGUIJUAGAAUAACUUUAUCAUUUCAAACCUCGIJUCCAUCUA
GUUGAACUAAACCUGUGAACGAAUACUAUAAUAAAAUUUIJUA
GAUGGACGUGGGUUCGACUCCCAUCAGCUCCACCA
SEQ ID NO: 92 Porphyra purpureum (red alga) chioroplast ssrA GGGGCTGCAAGGT'ITCTACA7FFGTGAAAAAACAAATATATGAAA
GTAAAACGAGCTCATTAY[AGAGCTTTFIAGTTAAATAAATGCAG
AAAATAATATTATTGCTTTTFICTCGAAAATTAGCTGTFIGCATAAA
TAGTCTCAA'ITTTTGTAATTCGAAGTGATAGACTCYI7ATACACTA CGAATATTCTGTTAGAGTTGCTCYJ7AATAAAAGAAAAGTAAAAA AATACAAATTCTTATGTTTThJ7ACCTGAATTGATTCAATT[AAGG TTAGTATTTTTTGATThJ7TACAATGGACGTGGGTTCAAGTCCCAC CAGCTCCACCA SEQ ID NO: 93 Porphyra purpureum (red alga) chioroplast tmRNA
GGGGCUGCAAGGUJCUACAUUGUGAAAAAACAAAUAUAUGA
AAGUAAAACGAGCUCAUUAUUAGAGCUUUUAGUUAAAUAAAU
GCAGAAAAUAAUAIJUAIJUGCUIJUUUCUCGAAAAUUJAGCUGUU
GCAUAAAUAGUCUCAAUJLUUUGUAAUUCGAAGUGAUAGACUC
UUAUACACUACGAAUAUUCUGUUAGAGUUGCUCUIJAAUAAAA
GAAAAGUAAAAAAAUACAAAUUCUUAUGUUIUIJIJACCUGAAU
UGAU1JCAAUTJ1AAGGUUAGUAUUUtUUUGAUUUUUACAAUGGA CGUGGGUUCAAGUCCCACCAGCUCCACCA SEQ ID NO: 94 Porphyromonas gin givalis ssrA GGGGCTGACCGGC7ITTGACAGCGTGATGAAGCGGTATGTAAGCA
TGTAGTGCGTGGGTGGCTTIGCACTATAATCTCAGACATCAAAAG
TTTAATTGGCGAAAATAACTACGCTCTCGCTGCGTAATCGAAGA
ATAGTAGATTAGACGCTTCATCGCCGCCAAAGTGGCAGCGACGA
GACATCGCCCGAGCAGCTTTTTCCCGAAGTAGCTCGATGGTGCG
GTGCTGACAAATCGGGAACCGCTACAGGATGCTTCCTGCCTGTG
GTCAGATCGAACGGAAGATAAGGATCGTGCATTGGGTCGTTTCA
GCCTCCGCTCGCTCACGAAAATTCCAACTGAAACTAAACATGTA
GAAAGCATATTGATTCCATGTTTGGACGAGGGTTCAATTCCCTCC
AGCTCCACCA SEQ ID NO: Porphyromonas gin givalis tmRNA
GGGGCUGACCGGCUUUGACAGCGUGAUGAAGCGGUAUGUAAG
CAUGUAGUGCGUGGGUGGCUUGCACUAUAAUCUCAGACAUCA
AAAGUUUAAUUGGCGAAAAUAACUACGCUCUCGCUGCGUAAU
CGAAGAAUAGUAGAUUAGACGCIJUCAUCGCCGCCAAAGUGGCA
GCGACGAGACAUCGCCCGAGCAGCIJUUUUCCCGAAGUAGCUCG
AUGGUGCGGUGCUGACAAAUCGGGAACCGCUACAGGAUGCUUC
CUGCCUGUGGUCAGAUCGAACGGAAGAUAAGGAUCGUGCAUU
GGGUCGUUUCAGCCUCCGCUCGCUCACGAAAAUUCCAACUGAA
ACUAAACAUGUAGAAAGCAUAUUGAUUC CAUGUUJIGGAC GAG GGUUCAAUTUCCCUCCAGCUCCACCA SEQ ID NO: 96 Proteus rettgeri ssrA (NCTC 10975), internal partial
GGGATTTGCGAAACCCAAGGTGCATGCCGAGGGGCGGTTGGCCT
CGTAAAAAGCCGCAAAAAAATAGTCGCAAACGACGAAAACTAC
GCTTTAGCAGC7FFAATAACCTGCTTAGAGCCCTCTCTCCCTAGCC
TCCGCTCTTGGACGGGGATCAAGAGAGGTCAAACCCAAAAGAG
ATCGCGTGGATGCCTFIGCCTGGGGTTGAAGCGTTAAACTTIAATC
AGGATAGTTTGTTGGTGGCGTGTCTGTCCGCAGCTGGCAAATGA
ATTCAAAGACTAGACTAAGCATGTAGTACCGAGGATGTAGAAAT
TIC SEQ ID NO: 97 Proteus rettgeri tmRNA (NCTC 10975), internal partial
GGGAUUUGCGAAACCCAAGGUGCAUGCCGAGGGGCGGUUGGCC
UCGUAAAAAGCCGCAAAAAAAUAGUCGCAAACGACGKAAAACU
ACGCUUUAGCAGCUUAAUAACCUGCUUAGAGCCCUCUCUCCCU
AGCCUCCGCUCUUGGACGGGGAUCAAGAGAGGUCAAACCCAAA
AGAGAUCGCGUGGAUGCCUUGCCUGGGGUUGAAGCGUUAAAC
UUAAUCAGGAUAGU-UUGUUGGUGGCGUGUCUGUCCGCAGCUG
GCAAAUGAAUUCAAAGACUAGACUAAGCAUGUAGUACCGAGG
AUGUAGAAAUUUC SEQ ID NO: 98 Pseudoalteromonas haloplanktoni ssrA, internal partial GGAATTCAAGAAGCCCGAGGTGCATGTCGAGGTGCGGT7ITGCCT
CGTAAAAAAGCCGCAATTTAAAGTAATCGCAAACGACGATAACT
ACTCTCTAGCAGCTTAGGCTGGCTAGCGCTCCTFICCATGTATTCT
TGTGGACTGGA'TTTGGAGTGTCACCCTAACACCTGATCGCGAC
GGAAACCCTGGCCGGGGTTGAAGCGTTAAAACTAAGCGGCCTCG
CCTTTATCTACCGTGTTTIGTCCGGGATTTAAAGGTTAATTIAAATG
ACAATACTAAACATGTAGTACCGACGGTCGAGGCTTTTCGGACG
GGG SEQ ID NO: 99 Pseudoalteromonas haloplanktoni tmiRNA, internal partial
GGAAUUCAAGAAGCCCGAGGUGCAUGUCGAGGUGCGGJIJTGC
CUCGUAAAAAAGCCGCAAIJUUAAAGUAAUCGCAAACGACGAU
AACUACUCUCUAGCAGCUUAGGCUGGCUAGCGCUCCUUCCAUG
UAUUCUUGUGGACUGGAIJUUUGGAGUGUCACCCUAACACCUG
AUCGCGACGGAAACCCUGGCCGGGGUUGAAGCGUUAAAACUAA
GCGGCCUCGCCIJUUAUCUACCGUGUUUGUCCGGGAUULUAAAGG
UIJAAUUAAAUGACAAUACUA-AACAUGUAGUACCGACGGUCGA
GGCUUUUCGGACGGGG SEQ ID NO: 100 Pseudomonas aeruginosa ssrA
GGGGCCGATTAGGATTCGACGCCGGTAACAAAAGTTGAGGGGC
ATGCCGAGTTGGTAGCAGAACTCGTAAATTCGCTGCTGCAAACT
TATAGTTGCCAACGACGACAACTACGCTCTAGCTGCTTAATGCG
GCTAGCAGTCGCTAGGGGATGCCTGTAAACCCGAAACGACTGTC
AGATAGAACAGGATCGCCGCCAAGTTCGCTGTAGACGTAACGGC
TAAAACTCATACAGCTCGCTCCAAGCACCCTGCCACTCGGGCGG
CGCGGAGTTAACTCAGTAGAGCTGGCTAAGCATGTAAAACCGAT
AGCGGAAAGCTGGCGGACGGGGGTTCAAATCCCCCCGGTTCCAC
CA SEQ ID NO: 10 1 Pseudomonas aeruginosa tmRNA
GGGGCCGAUUAGGAUUCGACGCCGGUAACAAAAGUUGAGGGG
CAUGCCGAGIJUGGUAGCAGAACUCGUAAAUUCGCUGCUGCAAA
CUUAUAGUUGCCAACGACGACAACUACGCUCUAGCUGCUUAAU
GCGGCUAGCAGUCGCUAGGGGAUGCCUGUAAACCCGAAACGAC
UGUCAGAUAGAACAGGAUCGCCGCCAAGUUCGCUGUAGACGUA
ACGGCUAAAACUCAUACAGCUCGCUCCAAGCACCCUGCCACUC
GGGCGGCGCGGAGUUAACUCAGUAGAGCUGGCUAAGCAUGUA
AAACCGAUAGCGGAAAGCUGGCGGACGGGGGUUCAAAUCCCCC
CGGUUCCACCA SEQ ID NO: 102 Salmonella typhimurium ssrA
GGGGCTGATTCTGGATTCGACGGGATTFJGCGAAACCCAAGGTGC
ATGCCGAGGGGCGGTTGGCCTCGTAAAAAGCCGCAAAAAAATA
GTCGCAAACGACGAAACCTACGCTTITAGCAGCTTAATAACCTGC
TTAGAGCCCTCTCTCCCTAGCCTCCGCTCTTIAGGACGGGGATCAA
GAGAGGTCAAACCCAAAAGAGATCGCGCGGATGCCCTGCCTGG
GGTTGAAGCGTTAAAACGAATCAGGCTAGTCTGGTAGTGGCGTG
TCCGTCCGCAGGTGCCAGGCGAATGTAAAGACTGACTAAGCATG
TAGTACCGAGGATGTAGGAAT7FICGGACGCGGGTTCAACTCCCG CCAGCTCCACCA SEQ ID NO: 103 Salmonella typhimurium tmRNA
GGGGCUGAUUCUGGAUUCGACGGGAUUUGCGAAACCCAAGGU
GCAUGCCGAGGGGCGGUUGGCCUCGUAAAAAGCCGCAAAAAAA
UAGUCGCAAACGACGAAACCUACGCUUUAGCAGCUIUAAUAACC
UGCUUAGAGCCCUCUCUCCCUAGCCUCCGCUCUUAGGACGGGG
AUCAAGAGAGGUCAAACCCAAAAGAGAUCGCGCGGAUGCCCUG
CCUGGGGUUGAAGCGUUAAAACGAAUCAGGCUAGUCUGGUAG
UGGCGUGUCCGUCCGCAGGUGCCAGGCGAAUGUAAAGACUGAC
UAAGCAUGUAGUACCGAGGAUGUAGGAAUUUCGGACGCGGGU
UCAACUCCCGCCAGCUCCACCA SEQ ID NO: 104 Shewanella putrefaciens ssrA
GGGGGCGATTCTGGATTCGACAGGATTCACGAAACCCTGGGAGC
ATGCCGAGGGGCGGTTGGCCTCGTAAAAAGCCGCAAAGTTATAG
TTGCAAACGACGATAACTACGCTCTAGCCGCTTAATGCCGCTAG
CCATCTACCACACGCTTTGCACATGGGCAGTGGATTTGATGGTCA
TCTCACATCGTGCTAGCGAGGGAACCCTGTCTGGGGGTGAACCG
CGAAACAGTACCGGACTCACCGTGTGGGATCCTGTCYI7TCGGAG
TTCAAACGGTTAAACAATAGAAAGACTAAGCATGTAGCGCCTTG
GATGTAGGTThL'CTGGACGCGGGTTCAAGTCCCGCCGCCTCCACC A SEQ ID NO: 105 Shewanella putrefaciens tmRNA
GGGGGCGAUUCUGGAUUCGACAGGAUUCACGAAACCCUGGGA
GCAUGCCGAGGGGCGGUUGGCCUCGUAAAAAGCCGCAAAGUUA
UAGUUGCAAACGACGAUAACUACGCUCUAGCCGCUUAAUGCCG
CUAGCCAUCUACCACACGCUUUGCACAUGGGCAGUGGAUUUGA
UGGUCAUCUCACAUCGUGCUAGCGAGGGAACCCUGUCUGGGGG
UGAACCGCGAAACAGUACCGGACUCACCGUGUGGGAUCCUGUC
UTUUCGGAGUIUCAAACGGUTUAAACAAUAGAAAGACUAAGCAUG
UAGCGCCUUGGAUGUAGGUUUIJCUGGACGCGGGUUCAAGUCCC
GCCGCCUCCACCA SEQ ID NO: 106 Staphylococcus aureus ssrA GGGGACG7FICATGGATTCGACAGGGGTCCCCCGAGCTCATTJAAG CGTGTCGGAGGGTTGTCTFJCGTCATCAACACACACAGT7FFATAAT
AACTGGCAAATCAAACAATAAT'JTCGCAGTAGCTGCCTAATCGC
ACTCTGCATCGCCTAACAGCAT7FFCCTATGTGCTGTTAACGCGAT
TCAACCTTAATAGGATATGCTAAACACTGCCGTTTGAAGTCTGTT
TAGAAGAAACTTAATCAAACTAGCATCATGTTGGTTGTTTATCAC
TTTTCATGATGCGAAACCTATCGATAAACTACACACGTAGAAAG
ATGTGTATCAGGACCTTTGGACGCGGGTTCAAATCCCGCCGTCTC
CACCA SEQ ID NO: 107 Staphylococcus aureus tmRNA
GGGGACGUUCAUGGAIJUCGACAGGGGUCCCCCGAGCUCAUIJAA
GCGUGUCGGAGGGUUGUCUIJCGUCAUCAACACACACAGJU[JAU
AAUAACUGGCAAAUCAAACAAUAAUIJUCGCAGUAGCUGCCUA
AUCGCACUCUGCAUCGCCUAACAGCAUUUCCUAUGUGCUGUIJA
ACGCGAUUCAACCUUAAUAGGAUAUGCUAAACACUGCCGUUJTG
AAGUCUGUIJUAGAAGAAACIJUAAUCAAACUAGCAUCAUGUUG
GUUGUTUUAUCACIJUUUCAUGAUGCGAAACCUAUCGAUAAACU
ACACACGUAGAAAGAUGUGUAUCAGGACCIJUUGGACGCGGGU
UCAAAUCCCGCCGUCUCCACCA SEQ ID NO: 108 Streptococcus gordonii ssrA
GGGGTCGTTACGGATTCGACAGGCATTATGAGGCATATTYFGCG
ACTCATCTAGCGGATGTAAACGCCAGTTAAATATAACTGCAA
AAATAATACY[CTTACGCTh[AGCTGCCTAAAJ\ACCAGCGGGCG TGACCCGA7FFCGGATTGCTTGTGTCTGATGACAGGTCTTATAU AGCAAGCTACGGTAGAATCTTGTCTAGTGATTh[ACAAGAGATT
GATAGACTCGCTTGATTTGGGCTTGAGTTATGTGTCAAAATCAAG
TTAAAACAATACATAGCCTATGGTTGTAGACAAATGTGTTGGCA
GATGTTTGGACGTGGGTTCGACTCCCACCGGCTCCACCA SEQ ID NO: 109 Streptococcus gordonii tmRNA
GGGGUCGUUACGGAUUCGACAGGCAUUAUGAGGCAUALUUUG
CGACUCAUCUAGCGGAUGUAAAACGCCAGUUAAAUAUAACUGC
AAAAAAUAAUACUUCUUACGCUIJUAGCUGCCUAAAAACCAGCG
GGCGUGACCCGAUIJCGGAUJIGCUUGUGUCUGAUGACAGGUCU
UAUUAUUAGCAAGCUACGGUAGAAUCUUGUCUAGUGAIUUUUA
CAAGAGAUIJGAUAGACUCGCUTJGAUIJUGGGCUUGAGUIJAUGU
GUCAAAAUCAAGUUAAAACAAUACAUAGCCUAUGGUUGUAGA
CAAAUGUGUUGGCAGAUGUUUGGACGUGGGUUCGACUCCCACC
GGCUCCACCA SEQ ID NO: Streptococcus mutans ssrA
GGGGTCGTTACGGATTCGACAGGCATTATGAGACCTATTTTGCG
ACTCATCTAGCGGATGTAAACGCCAGTTAAATATAACTGCAA
AAATACAAATTCTTACGCAGTAGCTGCCTAAAL\ACCAGCCTGTG
TGATCAATAACAAATTGCTTGTGTTTGTGATTJGGTCIIATFJGTTA
ACAAGCTACGTTAGAACTGAGTCAGGCTGTTCTAAAAGAGTTCT
ACTGACTCGCATCGTTAGAGFJTGAGTTATGTATFJGTAACGGTGT
TAAATAAACACATAACCTATAGTTGTAGACAAATGGGTTAGCAG
ATGTTTGGACGTGGGTTCGACTCCCACCGGCTCCACCA
SEQ ID NO: 11I Streptococcus mutans tmRNA GGGGUCGUUACGGAUUCGACAGGCAUUAUGAGACCUAUJ1UIUG
CGACUCAUCUAGCGGAUGUAAAACGCCAGUUAAAUAUAACUGC
AAAAAAUACAAAUUCUUACGCAGUAGCUGCCUAAAAACCAGCC
UGUGUGAUCAAUAACAAAUUGCUUGUGIJUUGUUGAUUGGUCU
UAUUGUUAACAAGCUACGIJUAGAACUGAGUCAGGCUGUUCUA
AAAGAGUUCUACUGACUCGCAUCGUUAGAGIJUUGAGUUAUGU
AUUGUAACGGUGUUA-AAUAAACACAUAACCUAUAGUUGUAGA
CAAAUGGGUUAGCAGAUGUUIJGGACGUGGGUTJCGACUCCCACC
GGCUCCACCA SEQ ID NO: 112 Streptococcus pneumoniae ssrA GGGGTCGTTACGGATTCGACAGGCATTATGAGGCATATThJ7GCG
ACTCGTGTGGCGACGTAAACGCTCAGTTIAAATATAACTGCAAAA
AATAACACTTCTTACGCTCTAGCTGCCTAAAAACCAGCAGGCGT
GACCCGAT7FFGGATTGCTCGTGTTCAATGACAGGTC7FFATTATTA GCGAGATACGATTAAGCCTTGTCIAGCGGT7F[GATAAGAGATTG ATAGACTCGCAGTYI7CTAGACTFJGAGTTATGTGTCGAGGGGCTGT
TAAAATAATACATAACCTATGGTTGTAGACAAATATGTTGGCAG
GTGTTTGGACGTGGGTTCGACTCCCACCGGCTCCACCA
SEQ ID NO: 113 Streptococcus pneumoniae tmRNA
GGGGUCGUUACGGAUUCGACAGGCAUIJAUGAGGCAUAUUUIJG
CGACUCGUGUGGCGACGUAAACGCUCAGUUAAAUAUAACUGCA
AAAAAUAACACUIUCUUACGCUCUAGCUGCCUAAAAACCAGCAG
GCGUGACCCGAUUUGGAUUGCUCGUGULUCAAUGACAGGUCULJ
AIJUAUUAGCGAGAUACGAUUAAGCCUUGUCUAGCGGUUUGAU
AAGAGAUTUGAUAGACUCGCAGUIJUCUAGACUUGAGUUAUGUG
UCGAGGGGCUGUUAAAAUAAUACAUAACCUAUGGUUGUAGAC
AAAUAUGUUGGCAGGUGUJ[UGGACGUGGGUUCGACUCCCACC
GGCUCCACCA SEQ ID NO: 114 Streptococcus pyo genes ssrA GGGGTTGTTACGGATTCGACAGGCATTATGAGGCATGTThI7GCGT
CCCATCGGCAGATGTAAATTGCCAGTTAAATATAACTGCAAAAA
ATACAAACTC7ITACGCTTTJAGCTGCCTAAAAACCAGCTAGCGTG
ACTTCTACAAGATFLGCTTGTGTCCTGTTAGAAGTCTCAAAATAGC
AAGCTACGGTTACGAA-ATTGTCTAGTTFICGTGACAAGAGATTGA
TAGACTCGCAAACTAATGGCTTGAGTTATGTGTCTTTAGTTTGTT
AAATGAAGACATAACCTATGGACGTAGACAAATATGTTGGCAGG
TGTTTGGACGTGGGTTCGACTCCCACCAGCTCCACCA
SEQ ID NO: 115 Streptococcus pyogenes tmRNA
GGGGUUGUUACGGAUUCGACAGGCAUUAUGAGGCAUGUIJUUG
CGUCCCAUCGGCAGAUGUAAAUUGCCAGUYUAAAUAUAACUGCA
AAAAAUACAAACUCUUACGCUUUAGCUGCCUAAAAACCAGCUA
GCGUGACUUCUACAAGAUIJGCUUGUGUCCUGUUAGAAGUCUC
AAAAUAGCAAGCUACGGUUACGAAAUUGUCUAGUUUCGUGAC
AAGAGAUUGAUAGACUCGCAAACUAAUGGCUUGAGUUAUGUG
UCIJUUAGUUUGUUIAAAUGAAGACAUAACCUAUGGACGUAGAC
AAAUAUGUUGGCAGGUGUUUGGACGUGGGU1JCGACUCCCACC AGCUCCACCA SEQ ID NO: 116 Synechococcus sp. PCC63O01 ssrA
GGGGCTGTAATGGTTTCGACGTGTTGGTGAATCCTTCACCGTGAT
TCAGGCCGAGAGGGAGTCCACTCTCGTAAATCCAGGCTCAACCA
AAAGTAACTGCGAACAACATCGTTCCTFJTCGCTCGTAAGGCTGCTCC
TGTAGCTGCTTAAACGCCACAAACTTFJCTGGCTCGAGCGTCTAGTCG
TAGACTCCGTTAATACGCCTAGACTTAAACCCCCAACGGATGCT
CGAGTGGCGGCCTCAGGTCCGTCCTCTCGCTAAGCAAAAACCTG
AGCATCCCGCCAACGGGGATAATCGTTGGCTCCCGCACAGTGGG
TCAACCGTGCTAAGCCTGTGAACGAGCGGAAAGTTACTAGTCAA
TGCGGACAGCGGTTCGAYJ'CCGCTCAGCTCCACCA
SEQ ID NO: 117 Synechococcus sp. PCC6301 tmRNA
GGGGCUGUAAUGGUUUCGACGUGUUGGUGAAUCCUUCACCGU
GA1IJICAGGCCGAGAGGGAGUCCACUCUCGUAAAUCCAGGCUCA
ACCAAAAGUAACUGCGAACAACAUCGUUCCUUUCGCUCGUAAG
GCUGCUCCUGUAGCUGCUUAAACGCCACAAACUUUCUGGCUCG
AGCGUCUAGUCGUAGACUCCGUUAAUACGCCUAGACUUAAACC
CCCAACGGAUGCUCGAGUGGCGGCCUCAGGUCCGUCCUCUCGC
UAAGCAAAAACCUGAGCAUCCCGCCAACGGGGAUAAUCGUJGG
CUCCCGCACAGUGGGUCAACCGUGCUAAGCCUGUGAACGAGCG
GAAAGUUACUAGUCAAUGCGGACAGCGGUUCGAUUCCGCUCAG
CUCCACCA SEQ ID NO: 118 Synechocystis sp. PCC6803 ssrA
GGGGCCGCAATGGTTFJCGACAGGTTGGCGAAAGCTTGCCCGTGA
TACAGGTCGAGAGTGAGTCTCCTCTCGCAAATCAAAGGjCTCAAA
AAAAAGTAACTGCGAATAACATCGTCAGC'ITCAAACGGGTAGCC
ATAGCAGCCTAGTCTGTAAAAGCTACATTFFICTFIGTCAAAGACCG
TTTACTTCYI= CTGACTCCGTTAAGGATTAGAGGTTAACCCCAA CGGATGCTTTGTTTGGCTCTTJCTCTAG7FIAGCTAAACAATCAAGA
CTCAGACTAGAGCATCCCACCATCAGGGATAATCGATGGTCCCC
GTCCTAGGGCTAGAAGGACTAAACCTGTGAATGAGCGGAAAGTT
AATACCCAGTTTGGACAGCAGTTCAATTCTGCTCGGCTCCACCA
SEQ ID NO: 119 Synechocystis sp. PCC6803 tmRNA
GGGGCCGCAAUGGIJUUCGACAGGUUGGCGAAAGCUUGCCCGUG
AUACAGGUCGAGAGUGAGUCUCCUCUCGCAAAUCAAAGGCUCA
AAAAAAAGUAACUGCGAAUAACAUCGUCAGCUUCAAACGGGU
AGCCAUAGCAGCCUAGUCUGUAAAAGCUACAUUUUCUUGUCA
AGACCGUUUACUUCUUUUCUGACUCCGUUTAAGGAtUJAGAGGU UAACCCCAACGGAUGCUUUGUtJUGGCUCUUCUCUAGIJUAGCUA
AACAAUCAAGACUCAGACUAGAGCAUCCCACCAUCAGGGAUAA
UCGAUGGUCCCCGUCCUAGGGCUAGAAGGACUAAACCUGUGAA
UGAGCGGAAAGUUAAUACCCAGUUUGGACAGCAGUUCAAUUC
UGCUCGGCUCCACCA SEQ ID NO: 120 Thermotoga maritima ssrA
GGGGGCGAACGGGTTCGACGGGGATGGAGTCCCCTGGGAAGCG
AGCCGAGGTCCCCACCTCCTCGTAAAAAAGGTGGGACAAAGAAT
AAGTGCCAACGAACCTGTTGCTGTTGCCGCTTAATAGATAAGCG
GCCGTCCTCTCCGAAGTTGGCTGGGCTTCGGAAGAGGGCGTGAG
AGATCCAGCCTACCGATTCAGCTTCGCCTTCCGGCCTGAATCGGG
AAAACTCAGGAAGGCTGTGGGAGAGGACACCCTGCCCGTGGGA
GGTCCCTCCCGAGAGCGAAAACACGGGCTGCGCTCGGAGAAGCC
CAGGGGCCTCCATCTTCGGACGGGGGTTCGAATCCCCCCGCCTC
CACCA SEQ ID NO: 121 Thermotoga maritima tmRNA
GGGGGCGAACGGGUUCGACGGGGAUGGAGUCCCCUGGGAAGC
GAGCCGAGGUCCCCACCUCCUCGUAAAAAAGGUGGGACAAAGA
AUAAGUGCCAACGAACCUGUUGCUGUUGCCGCUIJAAUAGAUA
AGCGGCCGUCCUCUCCGAAGUUGGCUGGGCUUCGGAAGAGGGC
GUGAGAGAUCCAGCCUACCGAUUCAGCUUCGCCUUCCGGCCUG
AAUCGGGAAAACUCAGGAAGGCUGUGGGAGAGGACACCCUGCC
CGUGGGAGGUCCCUCCCGAGAGCGAAAACACGGGCUGCGCUCG
GAGAAGCCCAGGGGCCUCCAUCIJUCGGACGGGGGUUCGAAUCC
CCCCGCCUCCACCA SEQ ID NO: 122 Thermus thermophilus ssrA
GGGGGTGAAACGGTCTCGACGGGGGTCGCCGAGGGCGTGGCTG
CGCGCCGAGGTGCGGGTGGCCTCGTAAAAACCCGCAACGGCATA
ACTGCCAACACCAACTACGCTCTCGCGGCTTAATGACCGCGACC
TCGCCCGGTAGCCCTGCCGGGGGCTCACCGGAAGCGGGGACACA
AACCCGGCTAGCCCGGGGCCACGCCCTCTAACCCCGGGCGAAGC
TTGAAGGGGGCTCGCTCCTGGCCGCCCGTCCGCGGGCCAAGCCA
GGAGGACACGCGAA-ACGCGGACTACGCGCGTAGAGGCCCGCCG
TAGAGACCTTCGGACGGGGGTTCGACTCCCCCCACCTCCACCA
SEQ ID NO: 123 Thermus thermophilus tmRNA
GGGGGUGAAACGGUCUCGACGGGGGUCGCCGAGGGCGUGGCU
GCGCGCCGAGGUGCGGGUGGCCUCGUAAAAACCCGCAACGGCA
UAACUGCCAACACCAACUACGCUCUCGCGGCUUAAUGACCGCG
ACCUCGCCCGGUAGCCCUGCCGGGGGCUCACCGGAAGCGGGGA
CACAAACCCGGCUAGCCCGGGGCCACGCCCUCUAACCCCGGGC
GAAGCUUGAAGGGGGCUCGCUCCUGGCCGCCCGUCCGCGGGCC
AAGCCAGGAGGACACGCGAAACGCGGACUACGCGCGUAGAGGC
CCGCCGUAGAGACCUUCGGACGGGGGUUCGACUCCCCCCACCU
CCACCA SEQ ID NO: 124 Treponema pallidum ssrA
GGGGATGACTAGGTTTCGACTAGGGATGTGGGGTGTTGCGCTGC
AGGTGGAGTGTCGATCTCCTGAFFCGGCGCCT7ITATAACTGCCAA TTCTGACAGT7FFCGACTACGCGCTCGCCGCGTAATCGCGGGCCTG
TGTTTGCGCTGCTCTGAGCGAACATATCGGCCCGACGCCAAACG
GAGCTTGCTCTTJACGTTGTGCACGGCGGACGTAGGGGGACT7FIT
GTCTGTGCTAAGACTCTGGCGCGTGCGGTGCAGGCCTAGCAGAG
TCCGACAAACGCAGTACGCACCGCTAAACCTGTAGGCGCGCAGC
ACTCGCTCTTFLAGGACGGGGGTTCGATTCCCCCCATCTCCACCA
SEQ ID NO: 125 Treponema pallidum tmRNA
GGGGAUGACUAGGUUUCGACUAGGGAUGUGGGGUGUUGCGCU
GCAGGUGGAGUGUCGAUCUCCUGAUUCGGCGCCUUUAUAACUG
CCAAUIUCUGACAGUUUCGACUACGCGCUCGCCGCGUAAUCGCG
GGCCUGUGUUUGCGCUGCUCUGAGCGAACAUAUCGGCCCGACG
CCAAACGGAGCUIJGCUCUUACGUIJGUGCACGGCGGACGUAGGG
GGACIJUUUGUCUGUGCUAAGACUCUGGCGCGUGCGGUGCAGGC
CUAGCAGAGUCCGACAAACGCAGUACGCACCGCUAAACCUGUA
GGCGCGCAGCACUCGCUCUUUAGGACGGGGGUIJCGAUUCCCCC
CAUCUCCACCA SEQ ID NO: 126 Vibric cholerae ssrA
GGGGCTGATTCAGGATTCGACGGGAATTFJTGCAGTCTGAGGTGC
ATGCCGAGGTGCGGTAGGCCTCGTTAACAAACCGCAAAAAAATA
GTCGCAAACGACGAAAACTACGCACTAGCAGCTTAATACCCTGC
TCAGAGCCCTTCCTCCCTAGCTTCCGCTTGTAAGACGGGGAAATC
AGGAAGGTCAAACCAAATCAAGCTGGCGTGGATTCCCCCACCTG
AGGGATGAAGCGCGAGATCTAATTCAGGTTAGCCAITCGTFLAGC
GTGTCGGTFICGCAGGCGGTGGTGAAATTAAAGATCGACTAAGCA
TGTAGTACCAAAGATGAATGGTTTTCGGACGGGGGTTCAACTCC
CCCCAGCTCCACCA SEQ ID NO: 127 Vibrio cholerae tmRNA
GGGGCUGAIJUCAGGAUUCGACGGGAAUUUUGCAGUCUGAGGU
GCAtJGCCGAGGUGCGGUAGGCCUCGUTJA-ACAAACCGCAAAAAA
AUAGUCGCAAACGACGAAAACUACGCACUAGCAGCUUAAUACC
CUGCUCAGAGCCCUUCCUCCCUAGCUUCCGCUUGUAAGACGGG
GAAAUCAGGAAGGUCAAACCAAAUCAAGCUGGCGUGGAUUCCC
CCACCUGAGGGAUGAAGCGCGAGAUCUAAUUCAGGUUAGCCAU
UCGUUAGCGUGUCGGUUCGCAGGCGGUGGUGAAAU-UAAAGAU
CGACUAAGCAUGUAGUACCAAAGAUGAAUGGULJUUCGGACGG
GGGUUCAACUCCCCCCAGCUCCACCA SEQ ID NO: 128 Yersinia pestis ssrA
GGGGCTGATTCTGGATTCGACGGGATTCGCGAAACCCAAGGTGC
ATGCCGAGGTGCGGTGGCCTCGTAAAAAACCGCAALAAAAAATA
GTTGCAAACGACGAAAACTACGCACTAGCAGCTTAATAACCTGC
TTAGAGCCCTCTCTGCCTAGCCTCCGCTCTFLAGGACGGGGATCAA
GAGAGGTCAAACCTAAAAGAGCTCGTGTGGAAACCTFJGCCTGGG
GTGGAAGCATTAAAACTAATCAGGATAGTTTGTCAGTAGCGTGT
CCATCCGCAGCTGGCCGGCGAATGTAATGA7FrGGACTAAGCATG
TAGTGCCGACGGTGTAGTAATTFJCGGACGGGGGTTCAAATCCCC
CCAGCTCCACCA SEQ ID NO: 129 Yersinia pestis tmRNA
GGGGCUGAUUCUGGAUUCGACGGGAUUCGCGAAACCCAAGGU
GCAUGCCGAGGUGCGGUGGCCUCGUAAAAAACCGCAAAAAAAA
UAGIJIGCAAACGACGAAAACUACGCACUAGCAGCUUAAUAACC
UGCUIJAGAGCCCUCUCUGCCUAGCCUCCGCUCUUAGGACGGGG
AUCAAGAGAGGUCAAACCUAAAAGAGCUCGUGUGGAAACCUIJ
GCCUGGGGUGGAAGCAUUAAAACUAAUCAGGAUAGUTUUuCA
GUAGCGUGUCCAUCCGCAGCUGGCCGGCGAAUGUAAUGAUJIGG
ACUAAGCAUGUAGUGCCGACGGUGUAGUAAUUUCGGACGGGG
GUUCAAAUCCCCCCAGCUCCACCA SEQ ID NO: 130 Campylobacter fetus ssrA, internal partial
AGGAGTAAGTCTGCTTAGATGGCATGTCGC[TGGGCAAGCGT
A AAAAGCCCA-AATAAAATTAAACGCAAACAACGTTAAATTCGCT
CCTGCTTACGCTAAAGCTGCGTAAGTTCAGTTGAGCCTGAAATTT
AAGTCATACTATCTAGCTTAA7FITTCGGTCATCTTTGATAGTGTA
GCCTTGCGTTTGACAAGCGTTGAGGTGAAATAAAGTCTTAGCCTT
GCT'ITTGAGThFJ'GGAAGATGAGCGAAGTAGGGTGAAGTAGTCA TCTTTGCTAAGCATGTAGAGGTCTTTGTGGGATTAJThFTGG SEQ ID NO: 131 Campylobacter fetus tmRNA, internal partial
AGGAGUAAGUCUGCUUAGAUGGCAUGUCGCUUUGGGCAAAGC
GUAAAAAGCCCAAAUAAAAUIJAAACGCAAACAACGUUAAAUU
CGCUCCUGCUUACGCUAAAGCUGCGUAAGUUCAGUUGAGCCUG
AAAUUUAAGUCAUACUAUCUAGCUUAAUUUIJCGGUCAUCUUIJ
GAUAGUGUAGCCUUGCGUUUGACAAGCGUUGAGGUGAAAUAA
AGUCUUAGCCIJUGCUUTJUGAGUUUUGGAAGAUGAGCGAAGUA
GGGUGAAGUAGUCAUCUUUGCUAAGCAUGUAGAGGUCUUUGU
GGGAUUAUUIUUGG SEQ ID NO: 132 Campylobacter coli (BM2509) ssrA, internal partial
AGGAGTAAGTCTGCTTAGATGGCATGTCGCTTTGGACAAAGCGT
AAAAAGTCCAAATTAAAATTAAACGCAAATAACGTTAAATTTGC
TCCTGCTTACGCTAAAGCTGCGTAAGTTCAGTTGAGCCCGAAACT
CAAGTGATGCTATCTAGCTTGAAT7FFTGGTCATCTTTGATAGTGT
AGATTGAAAATTGACAACTTTTAATCGAAGTTAAAGTCYJ'AGTCT
AGCTTGAAATT7FFGGAAGGTGAGTTTAGCCAGATGAAGTTTTlCA CC7FFTGCTAAACATGTAGAAGTCTTTGTGGGGTTATTTTTGG SEQ ID NO: 133 Campylobacter coli (BM2509) tmRNA, internal partial
AGGAGUAAGUCUGCUUAGAUGGCAUGUCGCUUUGGACAAGC
GUAAAAAGUCCAAAUUAAAAIUUAAACGCAAAUAACGUUAAAU
UUGCUCCUGCUUACGCUAAAGCUGCGUAAGUUCAGUIJGAGCCC
GAAACUCAAGUGAUGCUAUCUAGCUIJGAAUUUIJGGUCAUCUJI
UGAUAGUGUAGAUUGAAAAUUGACAACUTJUUAAUCGAAGUUA
AAGUCUUAGUCUAGCUUGAAAUTJUUGGAAGGUGAGIJIUAGCC
AGAUGAAGUUIJUCACCUUUIGCUAAACAUGUAGAAGUCUJIUGU
GGGGUUAULJUUUGG SEQ ID NO: 134 Camplyobacter chicken isolate ssrA, internal partial
ACAGGAGTAAGTCTGCTTAGATGGCATGTCGCFFTGGGCAAAGC
GTAAAAAGCCCAAATAAAATTAAACGCAAACAACGTTAAATTCG
CTCCTGCTTACGCTAAAGCTGCGTAAGTTCAGTTGAGCCTGAAAT
TTA-AGTCATACTATCTAGCTTAATI1TTCGGTCATTFLTTGATAGTGT AGCCTTGCGTTTGACAAGCGTTGAGGTGAAATAAGGTCYJ7AGCC TTGCTTTTGAGThL'TGGAAGATGAGCGAAGTAGGGTGAAGTAGT CATCTTTGCTAAGCATGTAGAGGTCTTTGTGGGATTA7FITY[GG SEQ ID NO: 135 Camplyobacter chicken isolate tmRNA, internal partial
ACAGGAGUAAGUCUGCUUAGAUGGCAUGUCGCUUIJGGGCAAA
GCGUAAAAAGCCCAAAUAAAAIJUAAACGCAAACAACGUUAAA
tUCGCUCCUGCUUACGCUAAAGCUGCGUAAGUUCAGUUGAGCC UGAAAIJIJ1AAGUCAUACUAUCUAGCUUAAUUUIJCGGUCAUUU
UUGAUAGUGUAGCCUUGCGUUUGACAAGCGUUGAGGUGAAAU
AAGGUCUUAGCCUUGCUUUUGAGUUUUGGAAGAUGAGCGAAG
UAGGGUGAAGUAGUCAUCUUUGCUAAGCAUGUAGAGGUCUUU
GUGGGAUUAUUUUUGG SEQ ID NO: 136 Clostridium perfringens ssrA, internal partial
ACGGGGGTAGGATGGGTTTGATAAGCGAGTCGAGGGAAGCATG
GTGCCTCGATAATAAAGTATGCAYIAAAGATAAACGCACGAGAT
AAT'ITTGCATTAGCAGCTTAAGTTAGCGCTGCTCATCCTTCCTCA
ATTGCCCACGGTTGAGAGTAAGGGTGTCA7TrAAAAGTGGGGAA CCGAGCCTAGCAAAGCT7FJGAGCTAGGAACGGAATTTATGAAGC
TTACCAAAGAGGAAGTTTGTCTGTGGACGTTCTCTGAGGGAATTT
TAAAACACAAGACTACACTCGTAGAAAGTCTTACTGGTCTGCTTT
CGG SEQ ID NO: 137 Clostridium perfringens tmRNA, internal partial
ACGGGGGUAGGAUGGGUUUGAUAAGCGAGUCGAGGGAAGCAU
GGUGCCUCGAUAAUAAAGUAUGCAUIUAAAGAUAAACGCACGA
GAUAAUUUUGCAIJUAGCAGCUUAAGUUAGCGCUGCUCAUCCU
UCCUCAAUUGCCCACGGIJUGAGAGUAAGGGUGUCAUUUAAAA
GUGGGGAACCGAGCCUAGCAAAGCUUUGAGCUAGGAACGGAA
UTUUAUGAAGCUUACCAAAGAGGAAGUUUGUCUGUGGACGUIJC
UCUGAGGGAAUUIJUAAAACACAAGACUACACUCGUAGAAAGU
CUUACUGGUCUGCUUUCGG SEQ ID NO: 13 8 Ha em oph i/us ducreyi (NCTC 10945) ssrA, internal partial
ACGGGATTAGCGAAGTCCAAGGTGCACGTCGAGGTGCGGTAGGC
CTCGTAACAAACCGCAAAAAAATAGTCGCAAACGACGAACAAT
ACGCTYI7AGCAGCTTLAATAACCTGCATTTAGCCYJ7CGCGCCCTAG
CTTTCGCTCGTAAGACGGGGAGCACGCGGAGTCAAACCAAAACG
AGATCGTGTGGACGCTTCCGCTTGTAGATGAAACACTAAATTGA
ATCAAGCTAGTTTATTTJCTTGCGTGTCTGTCCGCTGGAGATAAGC
GAAATTAA-AGACCAGACTAAACGTGTAGTACTGAAGATAGAGTA
ATTTCGGACCCGGGTTCGACTC SEQ ID NO: 139 Haernophilus ducreyi (NCTC 10945) tmRNA, internal partial
ACGGGAUUAGCGAAGUCCAAGGUGCACGUCGAGGUGCGGUAG
GCCUCGUAACAAACCGCAAAAAAAUAGUCGCAAACGACGAACA
AUACGCUUUAGCAGCUUAAUAACCUGCAUUUAGCCUUCGCGCC
CUAGCUUIUCGCUCGUAAGACGGGGAGCACGCGGAGUCAAACCA
AAACGAGAUCGUGUGGACGCUUCCGCIJUGUAGAUGAAACACU
AAAUUGAAUCAAGCUAGUUUAUUUCUUGCGUGUCUGUCCGCU
GGAGAUAAGCGAAAIJUAAAGACCAGACUAAACGUGUAGUACU
GAAGAUAGAGUAAUUUCGGACCCGGGUUCGACUC
SEQ ID NO: 140 Listeria innocua (food isolate ssrA, internal partial
GGCAAAGAAAAACAAAACCTAGCTFLTCGCTGCCTAATAACCAGT
AGCATAGCTGATCCTCCGTGCATCGCCCATGTGCTACGGTAAGG
GTCTCACTCTAAGTGGGCTACACTAGTTAATCTCCGTCTGAGGTT
AAATAGAAGAGCTTAATCAGACTAGCTGAATGGAAGCCTGTTAC
CGGGCTGATGTTTATGCGAAATGCTAATACGGTGACTACGCTCG
TAGATATTCAA SEQ ID NO: 141 Listeria innocua (food isolate trnRNA, internal partial
GGCAAAGAAAAACAAAACCUAGCUUJICGCUGCCUAAUAACCAG
UAGCAUAGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACGGUAA
GGGUCUCACUCUAAGUGGGCUACACUAGUUAAUCUCCGUCUGA
GGUIJAAAUAGAAGAGCUUAAUCAGACUAGCUGAAUGGAAGCC
UGIJUACCGGGCUGAUGUUUAUGCGAAAUGCUAAUACGGUGAC
UACGCUCGUAGAUAIJUCAA SEQ ID NO: 142 Listeria innocua (food isolate ssrA, internal partial
GGCAAAGAAAAACAAAACCTAGCTTTCGCTGCCTAATAAGCAGT
AGCATAGCTGATCCTCCGTGCATCGCCCATGTGCTACGGTAAGG
GTCTCACTCTAAGTGGGCTACACTAGTTAATCTCCGTCTGAGGTT
AAATAGAAGAGCTTAATCAGACTAGCTGAATGGAAGCCTGTTAC
CGGGCCGATGTTTATGCGAAATGCTAATACGGTGACTACGCTCG
TAGATATTTAA SEQ ID NO: 143 Listeria innocua (food isolate tmRNA, internal partial
GGCAAAGAAAAACAAAACCUAGCUUUCGCUGCCUAAUAAGCAG
UAGCAUAGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACGGUAA
GGGUCUCACUCUAAGUGGGCUACACUAGUUAAUCUCCGUCUGA
GGUJUAAAUAGAAGAGCIJUAAUCAGACUAGCUGAAUGGAAGCC
UGUTUACCGGGCCGAUGUUUAUGCGAAAUGCUAAUACGGUGAC
UACGCUCGUAGAUAUUUAA SEQ ID) NO: 144 Listeria innocua (food isolate ssrA, internal partial
GGCAAAGAAAAACAAAACCTAGCTTTCGCTGCCTAATAAGCAGT
AGAATAGCTGATCCTCCGTGCATCGCCCATGTGCTACGGTAAGG
GTCTCACTCTAAGTGGGCTACACTAGTTAATCTCCGTCTGAGGTT
AAATAGAAGAGCTTAATCGGACTAGCTGAATGGAAGCCTGTTAC
CGGGCCGATGTTTATGCGAAATGCTAATACGGTGACTACGCTCG
TAGATATTTAA SEQ ID NO: 145 Listeria innocua (food isolate tmRNA, internal partial
GGCAAAGAAAAACAAAACCUAGCUUUCGCUGCCUAAUAAGCAG
UAGAAUAGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACGGUAA
GGGUCUCACUCUAAGUGGGCUACACUAGUUAAUCUCCGUCUGA
GGUUAAAUAGAAGAGCUUAAUCGGACUAGCUGAAUGGAAGCC
UGUUACCGGGCCGAUGUUUAUGCGAAAUGCUAAUACGGUGAC
UACGCUCGUAGAUAUJIUAA SEQ ID NO: 146 Listeria innocua (ATCC 122 10) ssrA, internal partial GGCAAAGAAAAACAAAACCTAGCYI7TCGCTGCCTAATAAGCAGT
AGCATAGCTGATCCTCCGTGCATCGCCCATGTGCTACGGTAAGG
GTCTCACTCTAAGTGGGCTACACTAGTTAATCTCCGTCTGGGGTT
AAATAGAAGAGCTTAATCAGACTAGCTGAATGGAAGCCTGTTAC
TGGGCCGATGTTTATGCGAAATGCTAATACGGTGACTACGCTCG
TAGATATTTAA SEQ ID NO: 147 Listeria innocua (ATCC 122 10) tmRNA, internal partial
GGCAAAGAAAAACAAAACCUAGCULIUCGCUGCCUAAUAAGCAG
UAGCAUAGCUGAUCCUCCGUGCAUCGCCCAUGUGCUACGGUAA
GGGUCUCACUCUAAGUGGGCUACACUAGUUAAUCUCCGUCUGG
GGLTAAAUAGAAGAGCUUAAUCAGACUAGCUGAAUGGAAGCC
UGUUACUGGGCCGAUGUUIUAUGCGAAAUGCUAAUACGGUGAC
UACGCUCGUAGAUAIJIJJAA SEQ lID NO: 148 Listeria ivanovii (NCTC 11846) ssrA, internal partial
ACAGGGATAGTTCGAGCTTGAG'ITGCGAGTCGGGGGGATCGTCC
TCGTTATTAACGTCAAAGCCAATAATAACTGGCAAAGAAAAACA
AAACCTAGCTTFICGCTGCCTAATAAGCAGTAGCATAGCTGATCCT
CCGTGCATCGCCCATGTGCTACGGTAAGGGTCTCACTTTAAGTGG
GCTACACTAAATAATCTCCGTCTGGGGTTAGTFJAGAAGAGCTTA
ATCAGACTAGCTGAATGGAAGCCTGTTACCGGGCTGATG7FJTAT GCGAAATGCTAATACGGTGACTACGCTCGTAGATATTT1AAGTGC CGATA7LTTCTGG SEQ ID NO: 149 Listeria ivanovii (NCTC 11846) tmRNA, internal partial
ACAGGGAUAGUUCGAGCUUGAGIJUGCGAGUCGGGGGGAUCGU
CCUCGUJJAUTJAACGUCAAAGCCAAUAAUAACUGGCAAAGAAA
AACAAAACCUAGCUUUCGCUGCCUAAUAAGCAGUAGCAUAGCU
GAUCCUCCGUGCAUCGCCCAUGUGCUACGGUAAGGGUCUCACU
UUAAGUGGGCUACACUAAAUAAUCUCCGUCUGGGGUUAGUUA
GAAGAGCUUAAUCAGACUAGCUGAAUGGAAGCCUGUUACCGG
GCUGAUGUUUAUGCGAAAUGCUAAUACGGUGACUCGCUCGUA
GAUAUUUAAGUGCCGAUAUUUCUGG SEQ ID NO: 150 Listeria seeligeri (NCTC 11856) ssrA, internal partial ACAGGGATAGTTCGAGCTTGAG7FFGCGAGTCGGGGGGATCGTCC
TCGTTATCAACGTCAAAGCCAATAATAACTGGCAAAGAAAAACA
AAACCTAGCTTTCGCTGCCTAATAAGCAGTAGCATAGCTGATCCT
CCGTGCATCGCCCATGTGCTACGGAAAGGGTCTCACTTTAAGTG
GGCTACACTAAATAATCTCCGTCTGGGGTTAG7FJAGAAGAGCTT
AATCAGACTAGCTGAATGGAAGCCTGITACCGGGCTGATGTTFIA
TGCGAAATACTAATACGGTGACTACGCTCGTAGATATTTAAGTG
CCCATATTTCTGG SEQ ID NO: 151 Lisiteria seeligeri (NCTC 11856) tmRNA, internal partial
ACAGGGAUAGUUCGAGCUUGAGUUGCGAGUCGGGGGGAUCGU
CCUCGUUAUCAACGUCAAAGCCAAUAAUAACUGGCAAAGAAAA
ACAAAACCUAGCUUUCGCUGCCUAAUAAGCAGUAGCAUAGCUG
AUCCUCCGUGCAUCGCCCAUGUGCUACGGAAAGGGUCUCACJUU
UAAGUGGGCUACACUAAAUAAUCUCCGUCUGGGGIJUAGUUAG
AAGAGCUUAAUCAGACUAGCUGAAUGGAAGCCUGUUACCGGG
CUGAUGUUUAUGCGAAAUACUAAUACGGUGACUACGCUCGUA
GAUAUUUAAGUGCCCAUAUUUCUGG SEQ ID NO: 152 Salmonella enteritidis ssrA, internal partial
ACGGGATTTGCGAAACCCAAGGTGCATGCCGAGGGGCGGTTGGC
CTCGTAAAAAGCCGCAAAAAAATAGTCGCAAACGACGAAACCT
ACGCTTTAGCAGCTLTAATAACCTGCTTAGAGCCCTCTCTCCCTAG
CCTCCGCTCTTAGGACGGGGATCAAGAGAGGTCAAACCCAAAAG
AGATCGCGTGGATGCCCTGCCTGGGGTTGAAGCGTTAAAACGAA
TCAGGCTAGTCTGGTAGTGGCGTGTCCGTCCGCAGGTGCCAGGC
GAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAA
TTTCGG SEQ ID NO: 15 3 Salmonella enteritidis tmRNA, internal partial
ACGGGALUUGCGAAACCCAAGGUGCAUGCCGAGGGGCGGIJUG
GCCUCGUAAAAAGCCGCAAAAAAAUAGUCGCAAACGACGAAAC
CUACGCUUUAGCAGCUUAAUAACCUGCIJUAGAGCCCUCUCUCC
CUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCC
AAAAGAGAUCGCGUGGAUGCCCUGCCUGGGGUUGAAGCGUIJA
AAACGAAUCAGGCUAGUCUGGUAGUGGCGUGUCCGUCCGCAGG
UGCCAGGCGAAUGUAAAGACUGACUAAGCAUGUAGUACCGAG
GAUGUAGGAAUUUCGG SEQ ID NO: 154 Staphylococcus epidermidis (NCTC 11047) ssrA, internal partial
ACAGGGGTCCCCCGAGCTTATTAAGCGTGTCGGAGGGTTGGCTC
CGTCATCAACACATTTLCGGTTAAATATAACTGACAAATCAAACA
ATAATTTCGCAGTAGCTGCGTAATAGCCACTGCATCGCCTAACA
GCATCTCCTACGTGCTGTTAACGCGATTCAACCCTAGTAGGATAT
GCTAAACACTGCCGCTTGAAGTCTGTTTAGATGAAATATAATCA
AGCTAGTATCATGTTGGYJ7GTTTATTGCTTAGCATGATGCGAAAA
TTATCAATAAACTACACACGTAGAAAGATTTGTATCAGGACCTC
TGG SEQ ID NO: 155 Staphylococcus epidermidis (NCTC 11047) tmRNA, internal partial
ACAGGGGUCCCCCGAGCUUAUIJAAGCGUGUCGGAGGGUUGGCU
CCGUCAUCAACACAUIJUCGGUUAAAUAUAACUGACAAAUCAAA
CAAUAAUUIJCGCAGUAGCUGCGUAAUAGCCACUGCAUCGCCUA
ACAGCAUCUCCUACGUGCUGUUAACGCGAUTUCAACCCUAGUAG
GAUAUGCUAAACACUGCCGCUUGAAGUCUGUUUAGAUGAAAU
AUAAUCAAGCUAGUAUCAUGUUGGUUGUUUAUIJGCUTUAGCAU
GAUGCGAAAAUJJAUCAAUAAACUACACACGUAGAAAGAIJUUG
UAUCAGGACCUCUGG SEQ ID NO: 156 Streptococcus agalactiae (NCTC 818 1) ssrA, internal partial ACAGGCATTATGAGGTATATT7FFGCGACTCATCGGCAGATGTAA
AATGCCAGTTAAATATAACTGCAAAAAATACAAATTCTTACGCA
TTAGCTGCCTAAAAAACAGCCTGCGTGATCTTCACAAGATTGThJ7 GCGTTTTGCTAGAAGGTCTTATTTATCAGCAAACTACG7FITGGCT
ACTGTCTAGTTAGTTAAAAAGAGATTTATAGACTCGCTATGTGA
GGGCTTGAGTTATGTGTCATCACCTAG7ITAAATCAATACATAACC TATAGTTGTAGACAAATATATTAGCAGATGTYI7GG SEQ ID NO: 157 Streptococcus agalactiae (NCTC 818 1) tmRNA, internal partial
ACAGGCAUUAUGAGGUAUAUUUUGCGACUCAUCGGCAGAUGU
AAAAUGCCAGUIJAAAUAUAACUGCAAAAAAUACAAAUIJCU1JA
CGCAUUAGCUGCCUAAAAAACAGCCUGCGUGAUCU]JCACAAGA
UUGUUTUGCGUUUUGCUAGAAGGUCUUAJUUJAUCAGCAAACUA
CGUUYUGGCUACUGUCUAGUUAGUUAAAAAGAGAJLUAUAGAC
UCGCUAUGUGAGGGCUUGAGIJUAUGUGUCAUCACCUAGUIJAA
AUCAAUACAUAACCUAUAGIJUGUAGACAAAUAUAUUAGCAGA
UGUUIJGG SEQ ID NO: 15 8 Bordetella bronchiseptica ssrA
GGGGCCGATCCGGATTCGACGTGGGTCATGAAACAGCTCAAGGC
ATGCCGAGCACCAGTAAGCTCGTFJAATCCACTGGAACACTACAA
ACGCCAACGACGAGCGTTTCGCTCTCGCCGCYI7AAGCGGTGAGC
CGCTGCACTGATCTGTCCTFIGGGTCACGCGGGGGAA
SEQ ID NO: 159 Bordetella bronclziseptica tmRNA
GGGGCCGAUCCGGAUUCGACGUGGGUCAUGAAACAGCUCAAGGC
AUGCCGAGCACCAGUAAGCUCGUIJAAUCCACUGGAACACUACAA
ACGCCAACGACGAGCGUUUCGCUCUCGCCGCUUAAGCGGUGAGC
CGCUGCACUGAUCUGUCCUUGGGUCACGCGGGGGAA
SEQ ID NO: 160 Chiamydia pneumoniae (CWLO2 ssrA
GGGGGTGTATAGGTTFICGACTTGAAAATGAAGTGTTAATTGCAT
GCGGAGGGCGTTGGCTGGCCTCCTAAAAAGCCAACAAAACAATA
AATGCCGAACCTAAGGCTGAATGCGAAATTATFIAGCTTGTTTGA
CTCAGTAGAGGAAAGACTAGCTGCTTAATTAGCAAAAGTTGTTA
GCTAGATAATCTCTAGGTAACCCGGTATCTGCGAGCTCCACCAG
AGGCTTGCAAAATACCGTCATTTATCTGGJ7GGAACTTACTTFICT CTAATTCTCAAGGAAGTTCGY[CGAGATTTI7GAGAGTCATTGGC
TGCTATAGAGGCTTCTAGCTAAGGGAGTCCAATGTAAACAATTC
TAGAAGATAAGCATGTAGAGGTTAGCAGGGAGTTTGTCAAGGAC
GAGAGTTCGAGTCTCTCCACCTCCACCA SEQ ID NO: 161 Chiamydia pneumoniae (CWLO29) tmRNA
GGGGGUGUAUAGGUUUCGACIJUGAAAAUGAAGUGUUAAUUGC
AUGCGGAGGGCGUIUGGCUGGCCUCCUAAAAAGCCAACAAAACA
AUAAAUGCCGAACCUAAGGCUGAAUGCGAAAIJUAUUAGCUUG
UUUGACUCAGUAGAGGAAAGACUAGCUGCUUAAIJUAGCAAAA
GUUGUUAGCUAGAUAAUCUCUAGGUAACCCGGUAUCUGCGAG
CUCCACCAGAGGCUUGCAAAAUACCGUCAUJIUAUCUGGUUGGA
ACUUACUUTJCUCUAAUU-CUCAAGGAAGUUCGIJUCGAGAUUUU
UGAGAGUCAU]JGGCUGCUAUAGAGGCUUCUAGCUAAGGGAGU
CCAAUGUAAACAAUUCUAGAAGAUAAGCAUGUAGAGGUUAGC
AGGGAGUUUGUCAAGGACGAGAGUUCGAGUCUCUCCACCUCCA
CCA SEQ ID NO: 162 Francisella tularensis ssrA
GGGGGCGAATATGGT'ITCGACATGAATGTCAAAATCTAAGGTGC
ATGCCGAGGAAGTACCGTAACCTCGTTAATAACAGTACAAATGC
CAATAATAACTGGCAACAAAAAAGCAAACCGCGTAGCGGCTAA
CGACAGCAACTTTGCTGCTGTFJGCTAAAGCTGCCTAGTCTAGCTT
AATAATCTAGATGCGCACGGATATGATAGTCTTFICTTATGACACT
ATCTATACATCCGTTCATATTCCGCATAAGACGGTCTTTGCTTT=
GTCTGGGAGTTAAGGCTGTATTh7AACAGACTCGCTAACTATTACC
CTGGCTAATTGGGGAATAGTCAAGCTAAACTCAAATAGATTAGC
CTAAGCATGTAGATCCAAAGATCTAGAGTTTGTGGACGCGGGTT
CAAATCCCGCCGCCTCCACCA SEQ ID NO: 163 Francisella tularensis tmRNA
GGGGGCGAAUAUGGUUUCGACAUGAAUGUCAAAAUCUAAGGU
GCAUGCCGAGGAAGUACCGUAACCUCGUUAAUAACAGUACAAA
UGCCAAUAAUAACUGGCAACAAAAAAGCAAACCGCGUAGCGGC
UAACGACAGCAACUUUGCUGCUGIJUGCUAAAGCUGCCUAGUCU
AGCUJIAAUAAUCUAGAUGCGCACGGAUAUGAUAGUCIJUUCUU
AUGACACUAUCUAUACAUCCGUUCAUAIJUCCGCAUAAGACGGU
CUUIUGCUUUUUGUCUGGGAGUUAAGGCUGUAUUUAACAGACU
CGCUAACUAUUACCCUGGCUAAUIUGGGGAAUAGUCAAGCUAA
ACUCAAAUAGAUUAGCCUAAGCAUGUAGAUCCAAAGAUCUAG
AGUU1JGUGGACGCGGGUUCAAAUCCCGCCGCCUCCACCA SEQ ID NO: 164 Guillardia theta (plastid) ssrA GGGGCTGATTFIGGATTCGACATATAAATTTGCGTGThJCATFJATG
AAGCAAGTCAAGTTTAATGATCTTGTAAAAAACATTAAAGTACA
AATAAATGCAAGCAATATAGTTTCATTAGT1CAAAACGTTF1AGT
CTCTTTFJGCATAAGCAAAATGTGTTAATAACT'ITCTTAGTAGAAA
TTGGAGAAGTTTACTAAGATTTATAT7FfACTCCATAATTATTTTA
AAGATGGTAAAAAGGTGATTCATCATTFIGTATGTTFJCTAAACTTT
GTGAAAGAATAGTGGGCTCCAT7FFATAATGAACGTGGGTTCAAA TCCCACCAGCTCCACCA SEQ ID NO: 165 Guillardia theta (plastid) tmRNA
GGGGCUGAUUIJGGAUUJCGACAUAUAAAUUUGCGUGUUUCAUU
AUGAAGCAAGUCAAGUUUAAUGAUCUUGUAAAAAACAUUAAA
GUACAAAUAAAUGCAAGCAAUAUAGUUUCAUUUAGUIJCAAAA
CGUUUAGUCUCUUUUGCAUAAGCAAAAUGUGUUAAUAACUU
CUUAGUAGAAAUUGGAGAAGUUUACUAAGAUTUUAUAUUUACU
CCAUAAUUAUUUUAAAGAUGGUAAAAAGGUGAUUCAUCAUUU
GUAUGUUUCUAAACUUUGUGAAAGAAUAGUGGGCUCCAUUUA
UAAUGAACGUGGGIJUCAAAUCCCACCAGCUCCACCA
SEQ ID NO: 166 Thalassiosira Weissflogii (plastid) ssrA GGGGCTGAT7ITGGTTTCGACATTTAAA-ACTTCTYFCTATGTGTCA GGTCAAAGT7FJGTATTCYFTGTAAAAAAATACTAAAATACTAATA AATGCTAATAATATAATACCG7FFTATTTTTAAAGCAGTAAAAAC
AAAAAAAGAAGCAATGGCTTFIAAATTFITGCTGTATAGTTCATTA
ACTTAGGYI7ATTAAATATTITCA'ITATAACTGGACTFFTCTCTA
GTTTATAGTTTAGAATAAATTTAAATTTTGCAAAACTCGTTCGAA
AATTTTCGGGCTAAACCTGTAAACGCAAATACTAAGAAATTTTA
GATGGACATGGGTTCAATTCCCATCAGTTCCACCA
SEQ ID NO: 167 Thalassiosira Weissflogii (plastid) tmRNA
GGGGCUGAUU(UGGUUUCGACAUUUAAAACIJUCUIJUCUAUGUG
UCAGGUCAAAGUUIJGUAUUCUUUGUAAAAAAAUACUAAAAUA
CUAAUAAAUGCUAAUAAUAUAAUACCGUUUAUUUUUAAAGCA
GUAAAAACAAAAAAAGAAGCAAUGGCUJIUAAAUUULUGCUGUA
UAGUJJCAUUAACIJUAGGUTUAUUAAAUAUUUUUUCAUUAUAAC
UGGACUUUIJCUCUAGUUUAUAGUTJUAGAAUAAAUUUAAAJUUU
UGCAAAACUCGUUCGAAAAUUUUCGGGCUAAACCUGUAAACGC
AAAUACUAAGAAAUIJUUAGAUGGACAUGGGUUCAAUUCCCAU
CAGUUCCACCA SEQ ID NO: 168 Helicobacter pylori ssrA, (clinical isolate internal partial
TGGGGATGTTACGGTTITCGACAGGGGTAGTTCGAGCTTAGGTGG
CGAGTCGAGGGGATCGGCCTCG'ITAAAACGTCAAAGCCTATAAC
TGGCAAACAACAAAACAACTTCGCTTFJAGCAGCTTIAATAAGCTC
TTAGCGGTTCCTCCCTCCATCGCCCATGTGGTAGGGTAAGGGACT
CAAATTAAGTGGGCTACGCTGGATTCCACCGTCTGAGGATGAAA
GAAGAGAACAACCAGACTAGCTACCCGGACGCCCGTCGATAGG
CAGATGGAGTAGCGAATCGCGAATATATCGACTACACTCGTAGA
AGCTTAAGTGCCGATATTCTFIGGACGTGGGTTCGACTCCC
SEQ ID NO: 176 Helicobacter pylori tmRNA, (clinical isolate internal partial
UGGGGAUGUUACGGUUUCGACAGGGGUAGUIJCGAGCUUAGGU
GGCGAGUCGAGGGGAUCGGCCUCGUUAAAACGUCAAAGCCUAU
AACUGGCAAACAACAAAACAACUUCGCUUIJAGCAGCUUAAUAA
GCUCUUAGCGGUIJCCUCCCUCCAUCGCCCAUGUGGUAGGGUAA
GGGACUCAAAIJUAAGUGGGCUACGCUGGAIJUCCACCGUCUGAG
GAUGAAAGAAGAGAACAACCAGACUAGCUACCCGGACGCCCGU
CGAUAGGCAGAUGGAGUAGCGAAUCGCGAAUAUAUCGACUAC
ACUCGUAGAAGCUIJAAGUGCCGAUAUJICUUGGACGUGGGUUC
GACUCCC SEQ ID NO: 177 Helicobacterpylori ssrA, (clinical isolate internal partial
TGGGGACGTTACGGTTTCGACAGGGATAGTTCGAGCTTAGGTFJG
CGAGTCGAGGGGATCGGCCTCGTFJAAAACGTCAAAGCCTATAAT
TGGCAAACAAAACAATC7FFTCTTTAGCTGCTTAATTGCACTAAAG
GTTCCTCCCTCCATCGTCCATGTGGTAGGGTAAGGGACTCAAACT
AAGTGGACTACGCCGGAGTTCGCCGTCTGAGGACAAAGGAAGA
GAACAACCAGACTAGCAACTFJGGAAGCCTGTCGATAGGCCGAAG
AGTTCGCGAAATGCTAATATATCGACTACACTCGTAGAAGCTTA
AGTGCCGATATTTTTGGACGTGGG7ITCGATTCCCT SEQ ID NO: 178 Helicobacterpylori tmRNA, (clinical isolate internal partial
UGGGGACGUUACGGUUUCGACAGGGAUAGUUCGAGCUUAGGU
UGCGAGUCGAGGGGAUCGGCCUCGUUAAAACGUCAAAGCCUAU
AAULIGGCAAACAAAACAAUCUUUCUIJUAGCUGCUUAAUUGCA
CUAAAGGUUCCUCCCUCCAUCGUCCAUGUGGUAGGGUAAGGGA
CUCAAACUAAGUGGACUACGCCGGAGUUCGCCGUCUGAGGACA
AAGGAAGAGAACAACCAGACUAGCAACUUGGAAGCCUGUCGA
UAGGCCGAAGAGUUCGCGAAAUGCUAAUAUAUCGACUACACUC
GUAGAAGCUYUAAGUGCCGAUAUUUUUGGACGUGGGUUCGAUU
CCCU SEQ ID NO: 179 Listeria seeligeri (NCTC 11856) ssrA, internal partial
ACAGGGATAGTTCGAGCTTGAGTTGCGAGTCGGGGGGATCGTCC
TCGTTATCAACGTCAAAGCCAATAATAACTGGCAAAGAAAAACA
AAACCTAGCTTTCGCTGCCTAATAAGCAGTAGCATAGCTGATCCT
CCGTGCATCGCCCATGTGCTACGGAAAGGGTCTCACTTTAAGTG
GGCTACACTAAATAATCTCCGTCTGGGGTTAGTTAGAAGAGCTT
AATCAGACTAGCTGAATGGAAGCCTGTTACCGGGCTGATGTTTIA
TGCGAAATACTAATACGGTGACTACGCTCGTAGATAT7FIAAGTG CCCATATFLTCTGG SEQ ID NO: 180 Listeria seeligeri (NCTC 11856) tmRNA, internal partial
ACAGGGAUAGUUCGAGCUUGAGUTUGCGAGUCGGGGGGAUCGU
CCUCGUTUAUCAACGUCAAAGCCAAUAAUAACUGGCAAAGAAAA
ACAAAACCUAGCUIJUCGCUGCCUAAUAAGCAGUAGCAUAGCUG
AUCCUCCGUGCAUCGCCCAUGUGCUACGGAAAGGGUCUCACIU
UAAGUGGGCUACACUAAAUAAUCUCCGUCUGGGGUUAGUUAG
AAGAGCUUAAUCAGACUAGCUGAAUGGAAGCCUGIJUACCGGG
CUGAUGUUJUAUGCGAAAUACUAAUACGGUGACUACGCUCGUA
GAUAUUUAAGUGCCCAUAUUUCUGG SEQ ID NO: 181 Listeria ivanovii (NCTC 11846) ssrA, internal partial
ACAGGGATAGTTCGAGCTTGAGTTGCGAGTCGGGGGGATCGTCC
TCGTFLATTAACGTCAAAGCCAATAATAACTGGCAAAGAAAAACA
AAACCTAGCTTTCGCTGCCTAATAAGCAGTAGCATAGCTGATCCT
CCGTGCATCGCCCATGTGCTACGGTAAGGGTCTCACTTTAAGTGG
GCTACACTAAATAATCTCCGTCTGGGGTTAGTTJAGAAGAGCTTA
ATCAGACTAGCTGAATGGAAGCCTGTTACCGGGCTGATGTFLTAT
GCGAAATGCTAATACGGTGACTACGCTCGTAGATAT'ITAAGTGC
CGATATTTCTGG SEQ ID NO: 182 Listeria ivan cvii (NCTC 11846) tmRNA, internal partial
ACAGGGAUAGUIJCGAGCUUGAGUUGCGAGUCGGGGGGAUCGU
CCUCGUUAUUAACGUCAAAGCCAAUAAUAACUGGCAAAGAAA
AACAAAACCUAGCUJIUCGCUGCCUAAUAAGCAGUAGCAUAGCU
GAUCCUCCGUGCAUCGCCCAUGUGCUACGGUAAGGGUCUCACU
UYUAAGUGGGCUACACUAAAUAAUCUCCGUCUGGGGUIUAGUUA
GAAGAGCUUAAUCAGACUAGCUGAAUGGAAGCCUGUUACCGG
GCUGAUGUUIJAUGCGAAAUGCUAAUACGGUGACUCGCUCGUA
GAUAUJAAGUGCCGAUAUUUCUGG SEQ ID NO: 183 Mycobacterium africanum (clinical isolate) ssrA, internal partial
ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAAGA
GACCACCGTAAGCGTCGTTGCGACCAAATAAGCGCCGATTCACA
TCAGCGCGACTACGCTCTCGCTGCCTAAGCGACGGCTAGTCTGTC
AGACCGGGAACGCCCTCGGCCCGGACCCTGGCATCAGCTAGAGG
GATCCACCGATGAGTCCGGTCGCGGGACTCCTCGGGACAACCAC
AGCGACTGGGATCGTCATCTCGGCTAGTTCGCGTGACCGGGAGA
TCCGAGCAGAGGCATAGCGAACTGCGCACGGAGAAGCCTTJGAG
GGAATGCCGTA SEQ ID NO: 184 Mycobacterium africanum (clinical isolate) tmRNA, internal partial
ACIJUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCAAG
AGACCACCGUAAGCGUCGUUGCGACCAAAUAAGCGCCGAUUCA
CAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACGGCUAGUC
UGUCAGACCGGGAACGCCCUCGGCCCGGACCCUGGCAUCAGCU
AGAGGGAUCCACCGAUGAGUCCGGUCGCGGGACUCCUCGGGAC
AACCACAGCGACUGGGAUCGUCAUCUCGGCUAGUUCGCGUGAC
CGGGAGAUCCGAGCAGAGGCAUAGCGAACUGCGCACGGAGAAG
CCUUGAGGGAAUGCCGUA SEQ ID NO: 185 Mycobacterium gordonae( clinical isolate)ssrA, internal partial
ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAAGA
GACCACCGTAAGCGTCGTTGCAACCATATAAGCGCCGATTCACA
TCAGCGCGACTACGCTCTCGCTGCCTAAGCGACGGCTAGTCTGTC
GGACCGGGAACGCCCTCGCCCCGGACCCCGGCATCAGCTAGAGG
GATCAACCGATGAGTTCGGTCGCGGGACTCATCGGGACACCAAC
AGCGACTGGGATCGTCATCCTGGCTAGTCCGTGTGACCAGGAGA
TCCGAGCAGAGACATAGCGGACTGCGCACGGAGAAGCCTTGAG
GGAATGCCGTA SEQ ID NO: 186 Mycobacterium gordonae(clinical isolate) tmRNA, internal partial
ACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCAAG
AGACCACCGUAAGCGUCGUUGCAACCAUAUAAGCGCCGAUUCA
CAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACGGCUAGUC
UGUCGGACCGGGAACGCCCUCGCCCCGGACCCCGGCAUCAGCU
AGAGGGAUCAACCGAUGAGUUCGGUCGCGGGACUCAUCGGGAC
ACCAACAGCGACUGGGAUCGUCAUCCUGGCUAGUCCGUGUGAC
CAGGAGAUCCGAGCAGAGACAUAGCGGACUGCGCACGGAGAAG
CCUIJGAGGGAAUGCCGUA SEQ ID NO: 187 Mycobacterium kansasii (clinical isolate) ssrA, internal partial
ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAAGA
GACCACCGTAAGCGTCG'ITGCAACCAAATAAGCGCCGATTCACA
TCAGCGCGACTACGCTCTCGCTGCCTAAGCGACGGCTAGTCTGTC
AGACCGGGACCGCCCTCGACCCGGACTCTGGCATCAGCTAGAGG
GATCAACCGATGAGTTCGGTCGCGGGACTCGTCGGGACACCAAC
AGCGACTGGGATCGTCATCCTGGCTAGTTCGCGTGACCAGGAGA
TCCGAGCAGAGGCATAGCGAACTGCGCACGGAGAAGCC7FJGAG GGAATGCCGTA SEQ ID NO: 188 Mycobacteriumn kansasli (clinical isolate) tmRNA, internal. partial
ACUTUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCAAG
AGACCACCGUAAGCGUCGIJUGCAACCAAAUAAGCGCCGAUUCA
CAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACGGCUAGUC
UGUCAGACCGGGACCGCCCUCGACCCGGACUCUGGCAUCAGCU
AGAGGGAUCAACCGAUGAGUUCGGUCGCGGGACUCGUCGGGAC
ACCAACAGCGACUGGGAUCGUCAUCCUGGCUAGUUCGCGUGAC
CAGGAGAUCCGAGCAGAGGCAUAGCGAACUGCGCACGGAGAAG
CCUUGAGGGAAUGCCGUA SEQ ID NO: 189 Mycobacteriumn chelonae ssrA, internal partial
ACAGCGAGTCTCGACTTAAGGGAAGCGTGCCGGTGCAGGCAAG
AGACCACCGTAAGCGTCATTGCAACCAATTAAGCGCCGATTCTC
ATCAGCGCGACTACGCACTCGCTGCCTAAGCGACTGCGTGTCTG
TCAGACCGGGAGCGCCCTCAGCCCGGACCCTGGCATCAGCTAGA
GGGACAAACTACGGGTTCGGTCGCGGGACCCGTAGGGACATCAA
ACAGCGACTGGGATCGTCATCTCGGCTTGTTICGCGGGACCGAGA
GATCCAAGTAGAGGCATAGCGAACTGCGCACGGAGAAGCCTTA
ATGAACGGCCGTTG SEQ ID NO: 190 Mycobacterium chelonae tmRNA, internal partial
ACAGCGAGUCUCGACUTJAAGGGAAGCGUGCCGGUGCAGGCAAG
AGACCACCGUAAGCGUCAUUGCAACCAAUUAAGCGCCGAUTUCU
CAUCAGCGCGACUACGCACUCGCUGCCUAAGCGACUGCGUGUC
UGUCAGACCGGGAGCGCCCUCAGCCCGGACCCUGGCAUCAGCU
AGAGGGACAAACUACGGGUUCGGUCGCGGGACCCGUAGGGACA
UCAAACAGCGACUGGGAUCGUCAUCUCGGCUUGIJUCGCGGGAC
CGAGAGAUCCAAGUAGAGGCAUAGCGAACUGCGCACGGAGAA
GCCUTJAAUGAACGGCCGUIUG SEQ ID NO: 191 Mycobacterium szulgai (A TCC 35 799) ssrA, internal partial
ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAAGA
GACCACCGTAAGCGTCGYI7GCAACCAATTAAGCGCCGAGAACAC
TCAGCGCGACTTCGCTCTCGCTGCCTAAGCGACAGCAAGTCCGT
CAGACCGGGAAAGCCCTCGACCCGGACCCTGGCGTCATCTAGAG
GGATCCACCGGTGAGTTCGGTCGCGGGACTCATCGGGACACCAA
CAGCGACTGGGATCGTCATCCTGGCTAGTFICGCGTGACCAGGAG
ATCCGAGTAGAGACATAGCGAACTGCGCACGGAGAAGCCTFJGA
GGGAATGCCGTAG SEQ ID NO: 192 Mycobacterium szulgai (A TCC 35 799) tmiRNA, internal partial
ACUIJCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCAAG
AGACCACCGUAAGCGUCGUUGCAACCAAUIJAAGCGCCGAGAAC
ACUCAGCGCGACUIUCGCUCUCGCUGCCUAAGCGACAGCAAGUC
CGUCAGACCGGGAAAGCCCUCGACCCGGACCCUGGCGUCAUCU
AGAGGGAUCCACCGGUGAGUUCGGUCGCGGGACUCAUCGGGAC
ACCAACAGCGACUGGGAUCGUCAUCCUGGCUAGUUCGCGUGAC
CAGGAGAUCCGAGUAGAGACAUAGCGAACUGCGCACGGAGAA
GCCUTUGAGGGAAUGCCGUAG SEQ ID NO: 193 Mycobacterium malmoense (clinical isolate) ssrA, internal partial
ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAAGA
GACCACCGTAAGCGTCGTTLGCAACCATATAAGCGCCGTTTCAAC
ACAGCGCGACTACGCTCTCGCIGCCTAAGCGACAGCTAGTCCGT
CAGACCGGGAACGCCCTCGACCCGGAGCCTGGCGTCAGCTGGAG
GGATCCACCGGTGAGTCCGGTCGCGGGACTCATCGGGACATACA
CAGCGACTGGGATCGTCATCCTGGCTGGTFICGCGTGACCGGGAG
ATCCGAGCAGAGGCATAGCGAACTGCGCACGGAGAAGCCTFJGA
GGGAATGCCGTAG SEQ ID NO: 194 Mycobacterium ma/incense (clinical isolate) tmRNA, internal partial
ACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCAAG
AGACCACCGUAAGCGUCGUUGCAACCAUAUAAGCGCCGUTUCA
ACACAGCGCGACUACGCUCUCGCUGCCUAAGCGACAGCUAGUC
CGUCAGACCGGGAACGCCCUCGACCCGGAGCCUGGCGUCAGCU
GGAGGGAUCCACCGGUGAGUCCGGUCGCGGGACUCAUCGGGAC
AUACACAGCGACUGGGAUCGUCAUCCUGGCUGGUIJCGCGUGAC
CGGGAGAUCCGAGCAGAGGCAUAGCGAACUGCGCACGGAGAAG
CCUUGAGGGAAUGCCGUAG SEQ ID NO: 195 Mycobacterium flavescens ssrA, internal partial
ACTTCGAGCGTCGAATCAAGGGAAGCGTGCCGGTGCAGGCAAG
AGACCACCGTAAGCGTCGTTGCAACCAATTAAGCGCCGATTCCA
ATCAGCGCGACTACGCACTCGCTGCCTAAGCGACTGCGTGTCTG
TCAGCCCGGGAGAGCCCTCGACCCGGTGTCTGGCATCAGCTAGA
GGGATAAACCGGTGGGTCCGGTCGCGGGACTCATCGGGACATCA
AACAGCGACTGGGATCGTCATCCTGACTTG'ITCGCGTGATCAGG
AGATCCGAGTAGAGACATAGCGAACTGCGCACGGAGAAGCCTT
GAGGGAACGCCGTAG SEQ ID NO: 196 Mycobacterium flavescens trnRNA, internal partial
ACUUCGAGCGUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCAAG
AGACCACCGUAAGCGUCGUUGCAACCAAUIJAAGCGCCGAUUCC
AAUCAGCGCGACUACGCACUCGCUGCCUAAGCGACUGCGUGUC
UGUCAGCCCGGGAGAGCCCUCGACCCGGUGUCUGGCAUCAGCU
AGAGGGAUAAACCGGUGGGUCCGGUCGCGGGACUCAUCGGGAC
AUCAAACAGCGACUGGGAUCGUCAUCCUGACUUGIJUCGCGUGA
UCAGGAGAUCCGAGUAGAGACAUAGCGAACUGCGCACGGAGA
AGCCUIJGAGGGAACGCCGUAG SEQ ID NO: 197 Mycobacterium marinum ssrA, internal partial
ACTFJCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAAGA
GACCACCGTAAGCGTCGATGCAACTAGATAAGCGCCGATTCACA
TCAGCGCGACTACGCTCTCGCTGCCTAAGCGACGGCTAGTCTGTC
GGACCGGGAACGCCCTCGCCCCGGACCCCGGCATCAGCTAGAGG
GATCAACCGATGAGTTCGGTCGCGGGGCTCATCGGGACATCAAC
AGCGACTGGGATCGTCATCCTGGCTAGTTCGCGTGACCAGGAGA
TCCGAGCAGAGACCTAGCGGACTGCGCACGGAGAAGCCTTGAG
GGAATGCCGTAG SEQ ID NO: 198 Mycobacterium marinum tmRNA, internal partial
ACULICGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCAAG
AGACCACCGUAAGCGUCGAUGCAACUAGAUAAGCGCCGAUUCA
CAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACGGCUAGUC
UGUCGGACCGGGAACGCCCUCGCCCCGGACCCCGGCAUCAGCU
AGAGGGAUCAACCGAUGAGUUCGGUCGCGGGGCUCAUCGGGAC
AUCAACAGCGACUGGGAUCGUCAUCCUGGCUAGUUCGCGUGAC
CAGGAGAUCCGAGCAGAGACCUAGCGGACUGCGCACGGAGAAG
CCIJUGAGGGAAUGCCGUAG SEQ ID NO: 199 Mycobacterium microti (environmental isolate) ssrA, internal partial
ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAAGA
GACCACCGTAAGCGTCG7FFGCGACCAAATAAGCGCCGATTCACA
TCAGCGCGACTACGCTCTCGCTGCCTAAGCGACGGCTAGTCTGTC
AGACCGGGAACGCCCTCGGCCCGGACCCTGGCATCAGCTAGAGG
GATCCACCGATGAGTCCGGTCGCGGGACTCCTCGGGACAGCCAC
AGCGACTGGGATCGTCATCTCGGCTAGTTCGCGTGACCGGGAGA
TCCGAGCAGAGGCATAGCGAACTGCGCACGGAGAAGCCFFGAG
GGAATGCCGTA SEQ ID NO: 200 Mycobacterium microti (environmental isolate) tmRNA, internal partial
ACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCAAG
AGACCACCGUAAGCGUCGUUGCGACCAAAUAAGCGCCGAUUCA
CAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACGGCUAGUC
UGUCAGACCGGGAACGCCCUCGGCCCGGACCCUGGCAUCAGCU
AGAGGGAUCCACCGAUGAGUCCGGUCGCGGGACUCCUCGGGAC
AGCCACAGCGACUGGGAUCGUCAUCUCGGCUAGJICGCGUGAC
CGGGAGAUCCGAGCAGAGGCAUAGCGAACUGCGCACGGAGAAG
CCUTUGAGGGAAUGCCGUA SEQ ID NO: 201 Mycobacterium smegmatis (ATCC 10143) ssrA, internal partial
ACTTCGAGCATCGAATCCAGGGAAGCGTGCCGGTGCAGGCAAGA
GACCACCGTAAGCGTCGTTGCAACCAATTAAGCGCCGATTCCAA
TCAGCGCGACTACGCCCTCGCTGCCTAAGCGACGGCTGGTCTGT
CAGACCGGGAGTGCCCTCGGCCCGGATCCTGGCATCAGCTAGAG
GGACCCACCCACGGGTTCGGTCGCGGGACCTGTGGGGACATCAA
ACAGCGACTGGGATCGTCATCTCGGCTTGYJ7CGTGTGACCGGGA
GATCCGAGTAGAGACATAGCGAACTGCGCACGGAGAAGCCTCG
AGGACATGCCGTAG SEQ ID NO: 202 Mycobacterium smegmatis (ATCC 10143) ssrA, internal partial
ACUTUCGAGCAUCGAAUCCAGGGAAGCGUGCCGGUGCAGGCAAG
AGACCACCGUAAGCGUCGUUGCAACCAAUJAAGCGCCGAUTJCC
AAUCAGCGCGACUACGCCCUCGCUGCCUAAGCGACGGCUGGUC
UGUCAGACCGGGAGUGCCCUCGGCCCGGAUCCUGGCAUCAGCU
AGAGGGACCCACCCACGGGUUCGGUCGCGGGACCUGUGGGGAC
AUCAAACAGCGACUGGGAUCGUCAUCUCGGCUUGUUCGUGUGA
CCGGGAGAUCCGAGUAGAGACAUAGCGAACUGCGCACGGAGAA
GCCUCGAGGACAUGCCGUAG SEQ ID NO: 203 Mycobacterium xenopi (clinical isolate) ssrA, internal partial
ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAAGA
GACCACCGTAAGCGTCGYJ7GCAACTAAATAAGCGCCGATTCACA
TCAGCGCGACTACGCTCTCGCTGCCTAAGCGACAGCTAGTCCGT
CAGGCCGGGAGTTCCCTCGACCCGGATCCTGGCGTCAGCTAGAG
GGATCCACCGATGGGTTCGGTCGCGGGACCCATCGGGACACCAC
ACAGCGACTGGGATCGCCGTCCCGGCTAGTTCGCGAGACCGGGA
GATCCGAGTAAGGGCAAAGCGAACTGCGCACGGAGAAGCCTTG
AGGGTATGCCGTA SEQ ID NO: 204 Mycobacterium xenopi (clinical isolate) tm-RNA, internal partial
ACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCAAG
AGACCACCGUAAGCGUCGUIJGCAACUAAAUAAGCGCCGAUUCA
CAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACAGCUAGUC
CGUCAGGCCGGGAGUUCCCUCGACCCGGAUCCUGGCGUCAGCU
AGAGGGAUCCACCGAUGGGUUCGGUCGCGGGACCCAUCGGGAC
ACCACACAGCGACUGGGAUCGCCGUCCCGGCUAGUUCGCGAGA
CCGGGAGAUCCGAGUAAGGGCAAAGCGAACUGCGCACGGAGAA
GCCUIUGAGGGUAUGCCGUA SEQ ID NO: 205 Mycobacterium intracellulare (NCTC 10425) ssrA, internal partial
ACTTCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAACC
GACCACCGTAAGCGTCGTT1GCAAACAGATAAGCGCCGATTCACA
TCAGCGCGACTACGCTCTCGCTGCCTAAGCGACAGCTAGTCCGT
CAGACCGGGAACGCCCTCGACCCGGAGCCTGGCGTCAGCTAGAG
GGATCCACCGATGAGTCCGGTCGCGGGACTTATCGGGACACCAA
CAGCGACTGGGATCGTCATCTCGGCTTGTFLCGCGTGACCGGGAG
ATCCGAGTAGAGGCATAGCGAACTGCGCACGGAGAAGTC7F[GAG GGAATGCCGTAG SEQ ID NO: 206 Mycobact~erium intracellulare (NCTC 10425) tmRNA, internal partial
ACUUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCAAC
CGACCACCGUAAGCGUCGUUGCAAACAGAUAAGCGCCGAUUCA
CAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACAGCUAGUC
CGUCAGACCGGGAACGCCCUCGACCCGGAGCCUGGCGUCAGCU
AGAGGGAUCCACCGAUGAGUCCGGUCGCGGGACIJUAUCGGGAC
ACCAACAGCGACUGGGAUCGUCAUCUCGGCUUGIJUCGCGUGAC
CGGGAGAUCCGAGUAGAGGCAUAGCGAACUGCGCACGGAGAA
GUCUUGAGGGAAUGCCGUAG SEQ ID NO: 207 Mycobacterium scrofulaceum (NCTC 10803) ssrA, internal partial
ACATCGCGCATCGAATCAAGGGAAGCGTGCCGGTGCAGGCAAG
AGACCACCGTAAGCGTCGTTGCAACCAATTAAGCGCCGATTCAC
ATCAGCGCGACTACGCTCTCGCTGCCTAAGCGACAGCTAGTCCG
TCAGACCGGGAAAGCCCTCGACCCGGAGCCTGGCGTCAGCTAGA
GGGATCAACCGATGAGTTCGGTCGCGGGACTCATCGGGACACCA
ACAGCGACTGGGATCGTCATCCTGGCTAGTCCGCGTGACCAGGA
GATCCGAGCAGAGGCATAGCGGACTGCGCACGGAGAAGTC7FfG AGGGAATGCCGTTG SEQ ID NO: 208 Mycobacterium scrofulaceum (NCTC 10803) tmiRNA, internal partial
ACAUCGCGCAUCGAAUCAAGGGAAGCGUGCCGGUGCAGGCAAG
AGACCACCGUAAGCGUCGUUGCAACCAAUTJAAGCGCCGAUUCA
CAUCAGCGCGACUACGCUCUCGCUGCCUAAGCGACAGCUAGUC
CGUCAGACCGGGAAAGCCCUCGACCCGGAGCCUGGCGUCAGCU
AGAGGGAUCAACCGAUGAGUUCGGUCGCGGGACUCAUCGGGAC
ACCAACAGCGACUGGGAUCGUCAUCCUGGCUAGUCCGCGUGAC
CAGGAGAUCCGAGCAGAGGCAUAGCGGACUGCGCACGGAGAAG
UCUUGAGGGAAUGCCGUUG SEQ ID NO: 209 Nocardia asteroides ssrA, internal partial
ACTGTGTGCGCCGAGGTAGGGGAAGCGTGTCGGTGCAGGCTGGA
GACCACCGTTAAGCGTCGCGGCAACCAATTAAGCGCCGATTCCA
ATCAGCGCGACTACGCCCTCGCTGCCTGATCAGCGACGGCTAGC
TGTCGGCCCGGGTTGTGTTCCCGAACCCGGATGCCGGCATCATCT
CAGGGAACTCACCGTGTTCGCCGGTCGCGGACGGACACGGGACA
GCAAACAGCGACTGGGATCGTCATCTCGGC7F[GTTCGCGTGACC
GGGAGATCCAAGTAGAGACATAGCGGACTGCACACGGAGAAGC
CCTACTGACTCGACACAG SEQ ID NO: 2 Nocardia asteroides tmiRNA, internal partial
ACUGUGUGCGCCGAGGUAGGGGAAGCGUGUCGGUGCAGGCUG
GAGACCACCGUUAAGCGUCGCGGCAACCAAUUAAGCGCCGAUU
CCAAUCAGCGCGACUACGCCCUCGCUGCCUGAUCAGCGACGGC
UAGCUGUCGGCCCGGGUUGUGUUCCCGAACCCGGAUGCCGGCA
UCAUCUCAGGGAACUCACCGUGUIJCGCCGGUCGCGGACGGACA
CGGGACAGCAAACAGCGACUGGGAUCGUCAUCUCGGCUUGUUC
GCGUGACCGGGAGAUCCAAGUAGAGACAUAGCGGCUGCACACG
GAGAAGCCCUACUGACUCGACACAG SEQ ID NO: 211 Salmonella enteritidis ssrA, internal partial
ACGGGATTTGCGAAACCCAAGGTGCATGCCGAGGGGCGGTTGGC
CTCGTAAAAAGCCGCAAAAAAATAGTCGCAAACGACGAAACCT
ACGCTTTAGCAGCTTAATAACCTGCTTAGAGCCCTCTCTCCCTAG
CCTCCGCTCTTAGGACGGGGATCAAGAGAGGTCAAACCCAAAAG
AGATCGCGTGGATGCCCTGCCTGGGGTTGAAGCGTTAAAACGAA
TCAGGCTAGTCTGGTAGTGGCGTGTCCGTCCGCAGGTGCCAGGC
GAATGTAAAGACTGACTAAGCATGTAGTACCGAGGATGTAGGAA
TTTCGG SEQ ID NO: 212 Salmonella enteritidis tmRNA, internal partial
ACGGGAUIJIGCGAAACCCAAGGUGCAUGCCGAGGGGCGGUUG
GCCUCGUAAAAAGCCGCAAAAAAAUAGUCGCAAACGACGAAAC
CUACGCUUUAGCAGCIJUAAUAACCUGCIJUAGAGCCCUCUCUCC
CUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCC
AAAAGAGAUCGCGUGGAUGCCCUGCCUGGGGUUGAAGCGtUUA
AAACGAAUCAGGCUAGUCUGGUAGUGGCGUGUCCGUCCGCAGG
UGCCAGGCGAAUGUAAAGACUGACUAAGCAUGUAGUACCGAG
GAUGUAGGAAUUUCGG SEQ ID No: 213 Staphylococcus epidermidis (NCTC 11047) ssrA, internal partial
ACAGGGGTCCCCCGAGCTTATTAAGCGTGTCGGAGGGTTGGCTC
CGTCATCAACACATTTCGGYJAAATATAACTGACAAATCAAACA
ATAAT'ITCGCAGTAGCTGCGTAATAGCCACTGCATCGCCTAACA
GCATCTCCTACGTGCTG'ITAACGCGATTCAACCCTAGTAGGATAT
GCTAAACACTGCCGCTTGAAGTCTGTYI7AGATGAAATATAATCA
AGCTAGTATCATGTTGGTTGTTTATFIGC'ITAGCATGATGCGAAAA
TTATCAATAAACTACACACGTAGAAAGATTTGTATCAGGACCTC
TGG SEQ ID NO: 214 Staphylococcus epidermidis (NCTC 11047) tmRNA, internal partial
ACAGGGGUCCCCCGAGCUUAUUAAGCGUGUCGGAGGGUUGGCU
CCGUCAUCAACACAUUUCGGUUAAAUAUAACUGACAAAUCAAA
CAAUAAUUUCGCAGUAGCUGCGUAAUAGCCACUGCAUCGCCUA
ACAGCAUCUCCUACGUGCUGUUAACGCGAUUCAACCCUAGUAG
GAUAUGCUAAACACUGCCGCUUGAAGUCUGUUUAGAUGAAAU
AUAAUCAAGCUAGUAUCAUGUUGGUUGUUUAUUGCIJUAGCAU
GAUGCGAAAAtJUAUCAAUAAACUACACACGUAGAAAGAJUUUG UAUCAGGACCUCUGG SEQ ID NO: 215 100 Streptococcus agalactiae (NCTC 818 1) ssrA, internal partial ACAGGCATTATGAGGTATAT7L17GCGACTCATCGGCAGATGTAA
AATGCCAGTTAAATATAACTGCAAAAAATACAAATTCTTACGCA
TTAGCTGCCTAAAAAACAGCCTGCGTGATCTTCACAAGATTGFLT
GCGTTTTGCTAGAAGGTCTTA'ITTATCAGCAAACTACGTTTGGCT
ACTGTCTAGTTAGTTAAAAAGAGATTTATAGACTCGCTATGTGAG
GGCTTGAGTFJATGTGTCATCACCTAGTTAAATCAATACATAACCT
ATAGTTGTAGACAAATATATFJAGCAGATGTTFIGG SEQ ID NO: 216 Streptococcus agalactiae (NCTC 818 1) tmRNA, internal partial
ACAGGCAUIJAUGAGGUAUAUUULJGCGACUCAUCGGCAGAUGU
AAAAUGCCAGUUAAAUAUAACUGCAAAAAAUACAAAUUCUUA
CGCAUUAGCUGCCUAAAAAACAGCCUGCGUGAUCIJUCACAAGA
UUGUTUUGCGUUUUGCUAGAAGGUCUUAUIJfUAUCAGCAAACUA
CGUUUGGCUACUGUCUAGUUAGIJUAAAAAGAGAUUUAUAGAC
UCGCUAUGUGAGGGCUUGAGUUAUGUGUCAUCACCUAGUIJAA
AUCAAUACAUAACCUAUAGUUGUAGACAAAUAUAUUAGCAGA
UGUUTUGG SEQ ID NO: 217 Of the above sequences SEQ ID NOs 47 to 62, 65 to 68, 71 and 72, 98 and 99, 159 to 168 and 176-2 17 are novel sequences.
The above mentioned sequences can be used to form a database of ssrA gene sequences which can be used to identify a bacterial species, or for the generation of nucleic acid diagnostic assays.
Representative probes identified in accordance with the invention are as follows: Salmonella: 1) Genius specific probe: 5'-CGAATCAGGCTAGTCTGGTAG-3' SEQ ID NO: 218 Mycobacteria: 2) Oligonucleotide probe for detection of tuberculosis complex TB01 5'-ACTCCTCGGACA CCACAGCGA-3' SEQ ID NO: 219 3) Oligonucleotide probes for detection ofM. avium and M paratuberculosis sequences Probe 1: PAV1 5' GTTGCAAATAGATAAGCGCC-3' SEQ ID NO: 220 Probe 2: PAV2 5' TCCGTCAGCCCGGGAACGCC-3' SEQ ID NO: 221 Listeria: 4) Oligonucleotide probe used in the determination of tmRNA integrity after heat killing treatment of cells: LVtm: 5' TTTTGTTTTTCTTTGCCA 3' SEQ ID NO: 222 Escherichia coli: 5) Oligonucleotide probe used in the determination of tmRNA integrity after heat killing treatment of cells: Evtm: 5' AGTTTTCGTCGTTTGCGA 3' SEQ ID NO: 223 Further representative primers identified in accordance with the invention are as follows: Mycobacteria: 1) Degenerative oligonucleotide primers for the amplification of all mycobacterial sequences Primer 10SAAM3 5' CAGGCAA GACCACCGTAA-3' SEQ ID NO: 224 103 3' Primer 10SAAM4 5' GGATCTCC(C/T)G(A/G)TC(A/T)C(A/G)CG(A/G)AC SEQ ID NO: 225 2) Oligonucleotide primers for the amplification ofM. avium and M paratuberculosis Primer: APlfor- 5'-TGCCGGTGCAGGCAACTG-3' SEQ ID NO: 226 lo 3' Primer: AP2rev 5' CACGCGAACAAGCCAGGA-3' SEQ ID NO: 227 Brief Description of the Drawings In the accompanying drawings: Fig. 1 is a clustal alignment of E. coli and V. cholerae ssrA gene sequences; Fig. 2 is a photograph of an agarose gel of total cellular RNA prepared from E. coli and V cholerae cells; Fig. 3 is a photograph of an autoradiogram of hybridisation of a V cholerae oligonucleotide probe to tmRNA transcripts of E. coli and V cholerae; Fig. 4 is a photograph of an agarose gel of the amplified products of universal ssrA gene amplification primers from a panel of organisms; Fig. 5 is a clustal alignment of the ssrA gene sequences from the Listeria species; Fig. 6 is a clustal alignment of the L. monocytogenes and B. subtilus ssrA/tmRNA gene sequences; Fig. 7 is a photograph of an agarose gel of the amplified products of Listeria genus specific PCR amplification primers from a panel of organisms; Fig. 8 is a photograph of an autoradiogram of hybridised Listeria genus specific oligonucleotide probe to a panel of organisms as prepared in Example 4; Fig. 9 is a photograph of an autoradiogram of hybridised L.
monocytogenes species specific probe to a panel of organisms as prepared in Example 7; Fig. 10 is a computer scanned image of a nylon membrane strip used in the multiple colorimetric probe detection of Listeria ssrA gene sequences as described in Example 6.
105 Fig. 11 is a clustal alignment of ssrA gene sequences from C.
trachomatis strains; Fig. 12 is a clustal alignment of ssrA gene sequences from H. pylori strains; Fig. 13 is a clustal alignment of ssrA gene sequences from M genitalium strains; Fig. 14 is a clustal alignment of ssrA gene sequences from N.
gonorrhoeae strains; Fig. 15 is a clustal alignment of ssrA gene sequences from L.
monocytogenes strains; Fig. 16 is a clustal alignment of ssrA gene sequences from L.
monocytogenes strains and the L. innocua strain; Fig. 17 is a photograph of an autoradiogram hybridised Listeria oligonucleotide probe (Evtm) to total RNA samples isolated after medium heat treatment of E. coli cells; Fig. 18 is a photograph of an autoradiogram hybridised Listeria oligonucleotide probe (Evtm) to total RNA samples isolated after extreme heat treatment ofE. coli cells; 106 Fig. 19 is a photograph of an autoradiogram hybridised Listeria oligonucleotide probe (Lvtm) to total RNA samples isolated after medium heat treatment of L. monocytogenes cells; Fig. 20 is a photograph of an autoradiogram hybridised Listeria oligonucleotide probe (Lvtm) to total RNA samples isolated after extreme heat treatment of L. monocytogenes cells; and Fig. 21 is a photograph of an agarose gel of RT-PCR generated tmRNA products at various time points post heat treatment.
The invention will be further illustrated by the following Examples.
Modes for carrying out the Invention Example 1 Examination of the primary nucleotide sequences of available tmRNA sequences.
A comparative primary nucleotide sequence alignment of available tmRNA sequences using the Clustal W nucleic acid alignment programme demonstrated that tmRNA sequences from prokaryotes show a more significant degree of nucleotide sequence variability and non-homology than other bacterial high copy number RNA, as demonstrated in Table 1.
107 Table 1 Percentage nucleotide sequence homology between RNA molecules from different bacteria.
Escherichia coli vs. Bacillus subtilus vs.
Vibrio cholerae Mycobacterium tuberculosis rRNA homology 88 66 tmRNA homology 68 These regions of non-homology between tmRNA sequences from different bacteria are located in the middle of the molecule, and the extent of nucleotide sequence non-homology within the tmRNA molecule indicated that genus as well as species specific probes could be generated to distinguish between and/or detect bacteria.
Nucleotide sequence alignments had previously shown that the 5' and 3' flanking regions of the tmRNA molecules share a high degree of homology both within species and within genus. This observation indicated that universal oligonucleotide primers could be generated to amplify the ssrA gene or its encoding tmRNA from a wide variety of bacteria.
We have now demonstrated that these regions of homology and nonhomology within the nucleotide sequence of tmRNA molecules from 108 different organisms can be used as the basis of identifying and detecting organisms at the molecular level.
Example 2 Development of a V cholerae tmRNA specific probe.
A nucleotide sequence alignment of the E. coli (SEQ ID NO. 37) and V cholerae (SEQ ID NO. 127) ssrA sequences as depicted in Fig. 1, shows that these two bacterial species are phylogenetically closely related. There are however, regions of non-homology between the sequences as evidenced by the absence of asterix marks. An oligonucleotide probe, complementary to the variable region of the V. cholerae ssrA nucleotide sequence underlined in Fig. 1, was synthesised.
The sequence of the V cholerae tmRNA specific probe is AACGAATGGCTAACCTGAA-3' SEQ ID NO. 169 Total RNA was isolated from liquid cultures ofE. coli and V cholerae at the mid-exponential phase and the stationary phase of growth.
Equivalent amounts of the isolated total RNA were electrophoresed on a denaturing formaldehyde agarose gel and blotted onto HYBOND-N nylon membrane as shown in Fig. 2 in which the Lanes 1-4 represent the following: 109 Lane 1: Total E. coli RNA mid-log phase Lane 2: Total V cholerae RNA mid-log phase Lane 3: Total E. coli RNA stationary phase Lane 4: Total V cholerae RNA stationary phase The resulting Northern blot was then hybridised with the V cholerae tmRNA specific probe end-labelled with yP 32 The results of the hybridisation experiment shown in Fig. 3 demonstrate the specificity of the probe as only V cholerae tmRNAs were detected. Moreover, a greater degree of hybridisation signal intensity was observed with the V cholerae tmRNA isolated from cultures during the stationary phase of growth, indicating that a higher copy number of the tmRNA molecule is present in V cholerae cells during this phase.
Example 3 Generation of universal ssrA/tmRNA oligonucleotide amplification primers for the characterisation of unknown ssrA gene and tmRNA sequences.
Clustal W alignment of all available ssrA gene and tmRNA sequences indicated that degenerate oligonucleotide primers could be designed to amplify ssrA gene and tmRNA nucleotide sequences for a wide variety of organisms.
110 Degenerate oligonucleotide primers were synthesised to PCR amplify ssrA gene sequences from total genomic DNA preparations from a broad range of bacteria.
The sequences of the synthesised degenerate oligonucleotides are as follows: tmU5': 5' in vitro PCR amplification primer GGG(A/C)(C/T)TACGG(A/T)TTCGAC- 3' SEQ ID NO: 170 tmU3': 3' in vitro PCR amplification primer GGGA(A/G)TCGAACC(A/G)(C/G)GTCC- 3' SEQ ID NO: 171 Degenerate base positions are in parentheses.
The products of PCR reactions were electrophoresed on an agarose gel and a 350 base pair (approx.) PCR product was amplified in all cases, as shown in Fig. 4, demonstrating the "universality" of the degenerate tmRNA primers.
In Fig. 4 the lanes represent the following: Lane A: Lane 1: Lane 2: Lane 3: Lane 4: Lane 5: Lane 6: o1 Lane 7: Lane 8: Lane 9: Lane 10: Lane 11: Lane 12: Lane 13: Lane 14: Lane 15: Lane 16: Lane B: Molecular weight marker V Escherichia coli Salmonella poona Klebsiella aerogenes Proteus mirabilis Proteus rettgeri Aeromonas hydrophilia Staphyloccus aureus Enterococcusfaecalis Lactobacillus lactis Bacillus subtilus Listeria monocytogenes Listeria innocua Listeria murrayi Listeria welshimeri Listeria grayi Mycobacterium bovis Molecular weight marker V The universal primers amplified the ssrA gene from both Gram positive and Gram negative bacteria, as shown in Table 2.
112 Table 2 Bacterial species tested with universal amplification primers.
PCR Product Escherichia coli Salmonella poona Klebsiella aerogenes Gram negative bacteria Proteus mirabilis Proteus rettgeri Aeromonas hydrophilia Staphyloccus aureus Enterococcusfaecalis Lactobacillus lactis Bacillus subtilus Listeria monocytogenes Gram positive bacteria Listeria innocua Listeria murrayi Listeria welshimeri Listeria grayi Mycobacterium bovis 113 Example 4 Isolation and characterisation of previously unknown bacterial ssrA/tmRNA nucleotide sequences.
The PCR products amplified from genomic DNA from the Listeria species of bacteria and that from the M. bovis bacterium, from Example 2, were subcloned into a T-tailed plasmid vector for the purposes of DNA sequencing. Three recombinant clones were selected for each species and sequenced by the di-deoxy sequencing method. The sequence of both DNA strands for each subclone was determined.
The nucleotide sequence determined for the M. bovis ssrA gene shared 100% homology with the Mycobacterium tuberculosis ssrA gene sequence.
A clustal W alignment of the novel ssrA gene sequences obtained for the Listeria species (SEQ ID NOS 51, 53, 55, 59 and 61) is shown in Fig. This analysis indicated that genus-specific probes and oligonucleotide amplification primers can be generated for Listeria bacteria. Furthermore, the alignment also indicated that a-species specific oligonucleotide probe can be generated which will distinguish L. monocytogenes from the other Listeria species.
In Fig. 5 the proposed genus specific oligonucleotide primers, Ltm 1 and Ltm 2, are boxed, as is the genus specific Listeria oligonucleotide probe, LGtm. The proposed L. monocytogenes species specific oligonucleotide probe sequence, LStm, is underlined and italicised.
To further illustrate that the ssrA gene/tmRNA nucleic acid target is a suitable target for bacterial diagnostics, a comparative alignment of the L.
monocytogenes ssrA gene nucleotide sequence (SEQ ID NO. 55) with the available B. subtilis ssrA gene nucleotide sequence (SEQ ID NO. 11) (a phylogenetically closely related bacteria to Listeria) was carried out as shown in Fig. 6. Analysis of the sequence alignment showed a percentage nucleotide sequence homology of 41%, whereas the corresponding 16S rRNA alignment exhibits a nucleotide sequence percentage homology of 87%, (data not shown).
Example Generation and application of ssrA gene/tmRNA genus-specific amplification primers, genus-specific and species-specific probes for the Listeria bacterial species.
Using the Listeria genus ssrA gene/tmRNA nucleotide sequence alignment of Example 4, regions of the ssrA gene/tmRNA nucleotide sequence were analysed to determine their suitability for the generation of genus-specific amplification primers, and genus-specific and species- 115 specific oligonucleotide probes. In this analysis regions which demonstrated the greatest sequence differences to B. subtilis, were selected in the design of these amplification primers and probes.
The sequences of the synthesised oligonucleotides are as follows: Ltml: Ltm2: 5' Listeria genus specific amplification primer -AAAGCCAATAATAACTGG- 3' SEQ ID NO: 172 3' Listeria genus specific amplification primer -CCAGAAATATCGGCACTT- 3' SEQ ID NO: 173 Listeria genus specific hybridisation probe -GTGAGACCCTTACCGTAG- 3' SEQ ID NO: 174 L. monocytogenes species specific hybridisation probe -TCTATTTAACCCCAGACG- 3' SEQ ID NO: 175 LGtm: LStm: The genus specific amplification primers Ltml and Ltm2 were used in a series of PCR reactions with total genomic DNA from twenty different 116 strains as the template in each case. Only ssrA gene sequences from the Listeria species were amplified (260 base pair product) with these primers (Fig. 7 and Table 3) demonstrating that the ssrA gene/tmRNA is a suitable target for specific in vitro amplification of a bacterial genus. No amplification products were observed for any other bacterial species tested, although PCR products were obtained from the DNA from these bacterial species using the universal primers (tmU5' and tmU3') described in Example 2.
In Fig. 7 the lanes represent the following: Lane A: Lane 1: Lane 2: Lane 3: Lane 4: Lane 5: Lane 6: Lane 7: Lane 8: Lane 9: Lane 10: Lane 11: Lane 12: Lane 13: Molecular weight marker V E. coli S. poona K. aerogenes P. mirabilis P. rettgeri A. hydrophilia S. aureus E. faecalis L. lactis B. subtilus L. monocytogenes strain 1 L. monocytogenes strain 2 L. monocytogenes strain 3 117 Lane Lane Lane Lane Lane Lane Lane Lane L. monocytogenes strain 4 L. monocytogenes clinical isolate L. innocua L. murrayi L. welshimeri L. grayi M. bovis Molecular weight marker V 118 Table 3 Bacterial species tested with Listeria specific amlification primers.
PCR Product Escherichia coli Salmonella poona Kiebsiella aerogenes Gram negative Proteus mirabilis bacteria Proteus rettgeri Aeromonas hydrophilia Staphyloccus aureus Entrococcusfaecalis Lactobacillus lactis Bacillus subtilus Listeria monocytogenes strain 1 Listeria monocytogenes strain 2 Listeria monocytogenes strain 3 Gram positive Listeria monocytogenes strain 4 bacteria Listeria monocytogenes clinical isolate Listeria innocua Listeria murrayi Listeria welshimeri Listeria grayi Mycobacterium bovis 119 The Listeria genus specific oligonucleotide probe, LGtm, was hybridised to the Southern blot depicted in Fig. 4. Positive hybridisation signals were observed only with Listeria species as shown in Fig. 8 and Table 4, demonstrating the utility of the tmRNA sequence as a target in detecting a specific genus.
In Fig. 8 the lanes represent the following: Lane A: Lane 1: Lane 2: Lane 3: Lane 4: Lane 5: Lane 6: Lane 7: Lane 8: Lane 9: Lane 10: Lane 11: Lane 12: Lane 13: Lane 14: Lane 15: Lane 16: Molecular weight marker V Escherichia coli Salmonella poona Klebsiella aerogenes Proteus mirabilis Proteus rettgeri Aeromonas hydrophilia Staphyloccus aureus Enterococcusfaecalis Lactobacillus lactis Bacillus subtilus Listeria monocytogenes Listeria innocua Listeria murrayi Listeria welshimeri Listeria grayi Mycobacterium bovis 120 Lane B: Molecular weight marker V The PCR products generated using the genus-specific amplification described in this Example, and shown in Fig. 7, were Southern blotted and hybridised to the L. monocytogenes species-specific oligonucleotide probe.
A positive hybridisation signal was observed with three of the four typed strains and the clinical isolate ofL. monocytogenes as shown in Fig. 9 and Table 4.
In Fig. 9 the lanes represent the following: Lane A: Lane 1: Lane 2: Lane 3: Lane 4: Lane 5: Lane 6: Lane 7: Lane 8: Lane 9: Lane 10: Lane 11: Lane 12: Lane 13: Molecular weight marker V E. coli S. poona K, aerogenes P. mirabilis P. rettgeri A. hydrophilia S. aureus E. faecalis L. lactis B. subtilus L. monocytogenes strain 1 L. monocytogenes strain 2 L. monocytogenes strain 3 Lane 14: Lane 15: Lane 16: Lane 17: Lane 18: Lane 19: Lane 20: Lane B: L. monocytogenes strain 4 L. monocytogenes clinical isolate L. innocua L. murrayi L. welshimeri L. grayi M. bovis Molecular weight marker V 122 Table 4 Specificity of the Listeria genus-specific probe and the L. monocytogenes species-specific probe.
LGtmn Genusspecific probe LStmi Speciesspecific probe Escherichia ccli Salmonella poona Kiebsiella aerogenes Gram negative Proteus mirabilis bacteria Proteus rettgeri Aeromonas hydrophilia Staphyloccus aureus Entrococcusfaecalis Lactobacillus lactis Bacillus subtilus Listeria monocytogenes strain 1 Listeria monocytogenes strain 2 Listeria monocytogenes strain 3 Gram positive Listeria monocytogenes strain 4 bacteria Listeria monocytogenes clinical isolate Listeria innocua Listeria murrayi Listeria welshimeri Listeria grayi Mycobacterium bovis-- 123 One of the typed L. monocytogenes strains, strain 4, failed to generate a positive signal with this probe. DNA sequencing of the PCR amplified ssrA gene from this strain demonstrated that it contained a probe target region identical to L. innocua. It should be noted however that the ssrA gene from this strain contains other regions where the sequence is identical to the previously characterised L. monocytogenes strain and that these sequences are different to the L. innocua sequence, as shown in Fig. Therefore a species specific oligonucleotide directed to one of these variable regions can be synthesised which would recognise each strain type (isolate) within the species, for example L. monocytogenes.
Example 6 Multiple colorimetric probe detection of Listeria ssrA gene sequences.
LGTm LStm and a Campylobacter upsaliensis 16S 23S rRNA spacer (C 5' CATTAAACTTTAGCAAGGAAGTG SEQ ID NO: 228 oligonucleotide probe were irreversibly bound to nylon membrane strips and hybridised to with amplified ssrA PCR product, using the genus specific primers Ltml and Ltm2 Ltml was labelled with biotin at the end), from L. monocytogenes L. innocua L. ivanovii L.
murrayi L. seeligeri L. welshmeri (14) and L. grayii The ssrA amplified PCR products, using tmU5' and tmU3' (tmU5' was labelled with biotin at the 5' end), were also hybridised to the nylon membrane strips from the Gram-positive bacteria, B. subtilus, L. lactis, S. aureus, S.
epidermis, E. faecalis, C. perfringins (16-21) and the Gram-negative bacteria E. coli, S. enteritidis, P. Rettgeri, K. aerogenes (22-25). As shown in Fig. 10 after hybridisation, development of the colorimetric assay to biotin revealed the following: Strips 1-6 demonstrates that the ssrA amplified PCR product originated from L. monocytogenes combined with the confirmation that the PCR product amplified is from the genus Listeria A and B give colour detection; Strips 7 15 demonstrate that these PCR products originated from the genus Listeria only A gives colour detection; and Strips 16 25 demonstrate that the PCR products are not from the genus Listeria no colour detection. C is a negative oligonucleotide control probe and D is a positive control colorimetric detection assay for all samples.
Example 7 Use of ssrA tmRNA sequences to distinguish between species of organisms.
Clustal W alignments as shown in Figs. 11 (SEQ ID NOS. 19 and 21), 12 (SEQ ID NOS. 41 and 43), 13 (SEQ ID NOS. 77 and 79), 14 (SEQ ID NOS. 83 and 85), 15 and 16 (SEQ ID NO. 53, 55 and 57), indicate that there are nucleotide differences within the ssrA/tmRNA sequences of different strains of the same bacteria. This suggests that the ssrA/tmRNA sequences could potentially be used to discriminate between individual 125 and/or groups of strains within a bacterial species. This may have useful applications in epidemiology and bacterial population analysis.
Example 8 tmRNA integrity analysis after medium and extreme heat treatment of bacterial cells.
E. coli and L. monocytogenes cultures were heat treated at 80°C for min. in the case of E. coli and 40 min. in the case ofL. monocytogenes and at 120°C for 15 min. (autoclaving) after overnight growth and tested for viability at Oh, lh, 2h, 6h, 12h, 24h and 48h after heat treatment. No viability was observed at each time period tested. Total RNA was also isolated at these time periods and electrophoresed on denaturing 1.2% agarose gels and Northern blotted. Each blot was hybridised to, in the case ofE. coli (Figs. 17 and 18) with a radioactively labelled oligonucleotide probe Evtm and in the case ofL. monocytogenes (Figs. 19 and 20) with a radiolabelled LVtm. No tmRNA transcript was detected with each sample tested, demonstrating that tmRNA transcript is degraded after heat treatment. The lanes represented with the notation +ve is a positive control total RNA sample.
126 Example 9 Use of the tmRNA transcript in distinguishing between viable and nonviable bacteria.
A 100 ml culture ofL. monocytogenes was grown overnight in liquid culture. After growth, serial dilutions of the cells were carried out and viability was determined by spread plating on nutrient agar plates.
Simultaneously, total RNA was isolated from a 1 ml aliquot of these cells.
The remainder of the cells were heated at 65 0 C for 20 min. Cells were then removed for both viability analysis and total RNA isolation. Samples were taken for viability and RNA isolation at time periods of 0 h, 2 h, 6 h and 24 h after treatment.
Spread plating on nutrient agar plates indicated that heat treatment killed L. monocytogenes cells, with no viable colony forming units observed. Each RNA sample isolated was then treated with DNase to remove any contaminating DNA and total RNA samples (100 ng) were subjected to Reverse Transcriptase-PCR amplification using the Listeria genus specific ssrA/tmRNA oligonucleotide primers Ltml and Ltm2.
Negative control amplification reactions included primers, target, and Taq polymerase, but no Reverse Transcriptase. The results of the amplification reactions are shown in Fig. 12.
127 Amplified tmRNA RT-PCR products were only observed with the RNA sample which was not heat treated. All other samples gave no RT- PCR product indicating that the tmRNA molecules in these samples may have been degraded in the non-viable heat treated cells.
In Fig. 21 the lanes represent the following: Lane A: Molecular weight marker V; Lane 1: PCR amplification of RNA (no heat treatment of cells) Reverse Transcriptase Taq polymerase (TP); Lane 2: RT-PCR of RNA (no heat treatment of cells), RT, +TP; Lane 3: PCR amplification of RNA (at 0 time after heat treatment), -RT, +TP; Lane 4: RT-PCR of RNA (at 0 time after heat treatment), +RT, +TP; Lane 5: PCR amplification of RNA (at 1 h time after heat treatment), -RT, +TP; Lane 6: RT-PCR of RNA (at 1 h time after heat treatment), +RT, +TP; Lane 7: PCR amplification of RNA (at 2 h time after heat treatment), -RT, +TP; Lane 8: RT-PCR of RNA (at 2 h time after heat treatment), +RT, +TP; Lane 9: PCR amplification of RNA (at 6 h time after heat treatment), -RT, +TP; Lane 10: RT-PCR of RNA (at 6 h time after heat treatment), 128 +RT, +TP; Lane 11: PCR amplification of RNA (at 24 h time after heat treatment), -RT, +TP; Lane 12: RT-PCR of RNA (at 24 h time after heat treatment), +RT, +TP; Lane B: Molecular weight marker V.
Claims (9)
- 002. Use according to claim 1, wherein the ssrA gene or fragment comprises a sequence which is selected from the group comprising SEQ ID Nos: 1-4, 7-22, 25-36, 39- 136, 139-201, 204-222 and 224 to 228.
- 3. Use according to claim 1 or claim 2, wherein a fragment of the ssrA gene molecule corresponding to a region of high homology from the 5' end of the DNA molecule is used as a universal target region.
- 4. Use according to claim 1 or claim 2, wherein a fragment of the ssrA gene molecule corresponding to a region of high homology from the 3' end of the DNA molecule is used as a universal target region.
- 5. Use according to claim 1 or claim 2, wherein a fragment of the ssrA gene molecule corresponding to a region of low homology is used as a target region in a nucleic acid probe assay to distinguish between species.
- 6. Use according to claim 1 or claim 2, wherein a fragment of the ssrA gene molecule corresponding to a region of low homology is used as a target region for the generation of a genus specific probe.
- 7. Use of tmRNA, an RNA transcript of a ssrA gene, or a fragment thereof as a target region in a nucleic acid probe assay to detect or identify a target prokaryotic or eukaryotic organism, wherein the ssrA gene or fragment does not comprise any one of the following sequences: SEQ ID Nos: 5, 6, 23, 24, 37, 38, 137, 138, 202, 203 and 223.
- 8. Use according to claim 7, wherein the ssrA gene or fragment comprises a sequence which is selected from the group comprising SEQ ID Nos: 1-4, 7-22, 25-36, 39- 136, 139-201, 204-222, 224 to 228.
- 9. Use according to claim 7 or claim 8, wherein a fragment of a tmRNA molecule corresponding to a region of high homology from the 5' end of the tmRNA molecule is used as a universal target region. Use according to claim 7 or claim 8, wherein a fragment of a tmRNA molecule corresponding to a region of high homology from the 3' end of the tmRNA molecule is used as a universal target region.
- 874424-: gcc N11. Use according to claim 7 or claim 8, wherein a fragment of a tmRNA tbmolecule corresponding to a region of low homology is used as a target region in a nucleic acid probe assay to distinguish between species. 12. Use according to any of the preceding claims, wherein a fragment of a tmRNA molecule corresponding to a region of low homology is used as a target region for the generation of a genus specific probe. 00 S13. Use according to any one of the preceding claims, wherein said ssrA gene fragment or said tmRNA fragment is used as the basis of a primer to be used in an amplification procedure. io 14. Use according to claim 13, wherein the product of the amplification procedure is used as a target region in a nucleic acid probe assay. Use according to any one of claims 7-14, wherein a cDNA transcript of a tmRNA molecule is used as a probe in a nucleic acid hybridisation assay. 16. Use according to any one of the preceding claims, where the assay is carried Is out in vitro. 17. Use according to any one of claims 1-15, where the assay is carried out in situ. 18. Use according to any one of the preceding claims, wherein the target region is used as the basis of an assay for distinguishing between living and dead prokaryotic or eukaryotic organisms. 19. Use according to any one of the preceding claims, wherein the target region is used in a multiple probe format for broad scale detection and/or identification of prokaryotic or eukaryotic organisms. Use according to claim 19, wherein an ssrA gene probe or a tmRNA transcript probe is linked to a microarray gene chip system for the broad scale high throughput detection and identification of prokaryotic or eukaryotic organisms. 21. Use according to any one of the preceding claims, wherein the target region is used as a probe in an assay to detect prokaryotic or eukaryotic organisms in a sample of matter. 22. Use according to any one of claims 1-15, wherein a fragment of the ssrA gene or the tmRNA transcript is used in an assay to obtain a DNA profile of a prokaryotic or eukaryotic organism and, thereby, distinguish between strains of the same species. 23. Use according to any one of claims 1-15, wherein the ssrA gene, the tmRNA transcript or a DNA sequence complementary thereto, or a fragment thereof, is used to 874424-1 gcc t8 131 design an agent directed against infectious prokaryotic or eukaryotic organisms for Stherapeutic purposes. 24. Use according to any one of claims 1-17, wherein the target region is used to monitor the efficacy of drug therapies against infectious agents. 25. Use according to any one of claims 1-17, wherein the target region is used to ¢C monitor the viability and level of health-promoting organisms in the gastrointestinal tract. 00 C 26. Use according to any one of claims 1-17, wherein the assay is used for the Squantification of prokaryotic or eukaryotic organisms. 27. Use according to any one of claims 1-6 and 11-17, wherein a database of ssrA gene sequences is used to identify a prokaryotic or eukaryotic organism. 28. Use of the ssrA gene or a fragment thereof as a target region in a nucleic acid probe assay for a prokaryotic or eukaryotic organism, substantially as hereinbefore described with reference to any one of the examples. 29. Use of tmRNA, an RNA transcript of the ssrA gene, or a fragment thereof as a target region in a nucleic acid probe assay for a prokaryotic or eukaryotic organism, substantially as hereinbefore described with reference to any one of the examples. Dated 30 July, 2007 Enterprise Ireland (trading as BioResearch Ireland) National University of Ireland, Galway Patent Attorneys for the Applicant/Nominated Person SPRUSON FERGUSON 874424-1 gcc
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