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Molecular genetic methods in the veterinary clinical bacteriology laboratory: current usage and future applications

Published online by Cambridge University Press:  28 February 2007

Hugh Y. Cai ,
Marie Archambault ,
Carlton L. Gyles  and
John F. Prescott
Hugh Y. Cai
Affiliation:
Laboratory Services Division, Animal Health Laboratory, University of Guelph, Guelph, Ontario N1G 2W1, Canada Department of Pathobiology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
Marie Archambault
Affiliation:
Laboratory Services Division, Animal Health Laboratory, University of Guelph, Guelph, Ontario N1G 2W1, Canada
Carlton L. Gyles
Affiliation:
Department of Pathobiology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
John F. Prescott*
Affiliation:
Department of Pathobiology, University of Guelph, Guelph, Ontario N1G 2W1, Canada
*
*Department of Pathobiology, University of Guelph, Guelph, Ontario N1G 2W1, Canada E-mail: prescott@uoguelph.ca
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Abstract

In the last 5 years, numerous molecular methods have been published for the detection and characterization of bacteria in the field of veterinary medicine. PCR has been the most commonly used technology. Although not currently used for clinical veterinary diagnosis, new technologies such as liquid-phase hybridization, real-time PCR, pathogen load determination and DNA/protein microarray have been described and have many possible applications in the clinical bacteriology laboratory because of their sensitivity and efficiency. This review describes the basic principles and application of recently published DNA-based molecular techniques for the purpose of veterinary clinical bacteriological diagnosis. It covers advances in probe hybridization technology, DNA/RNA amplification techniques and other molecular detection methods, including 16S rRNA analysis for bacterial characterization and DNA microarrays for bacterial detection. The review briefly summarizes the application of molecular methods for the diagnosis of specific important bacterial infections of animals, and for other animal pathogens that are slow or difficult to isolate in the clinical bacteriology laboratory. In addition, the molecular detection of antimicrobial resistance genes and of bovine mastitis pathogens is briefly described and current commercially available tests are listed.

Keywords

molecular geneticsmethodsveterinaryclinical bacteriologymolecular beaconsdisplacement hybridizationpolymerase chain reaction (PCR)real-time PCR
Type
Research Article
Information
Animal Health Research Reviews , Volume 4 , Issue 2 , December 2003 , pp. 73 - 94
Copyright
Copyright © CAB International 2003

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References

Akduman, D, Ehret, JM, Messina, K, Ragsdale, S and Judson, FN (2002). Evaluation of a strand displacement amplification assay (BD ProbeTec-SDA) for detection of Neisseria gonorrhoeae in urine specimens. Journal of Clinical Microbiology 40: 281–283.CrossRefGoogle ScholarPubMed
Barrett, A, Magee, JG and Freeman, R (2002). An evaluation of the BD ProbeTec ET system for the direct detection of Mycobacterium tuberculosis in respiratory samples. Journal of Medical Microbiology 51: 895–898.CrossRefGoogle ScholarPubMed
Bekal, S, Brousseau, R, Masson, L, Prefontaine, G, Fairbrother, J and Harel, J (2003). Rapid identification of Escherichia coli pathotypes by virulence gene detection with DNA microarrays. Journal of Clinical Microbiology 41: 2113–2125.CrossRefGoogle ScholarPubMed
Bekker, CP, de Vos, S, Taoufik, A, Sparagano, OA and Jongejan, F (2002). Simultaneous detection of Anaplasma and Ehrlichia species in ruminants and detection of Ehrlichia ruminantium in Amblyomma variegatum ticks by reverse line blot hybridization. Veterinary Microbiology 89: 223–238.CrossRefGoogle ScholarPubMed
Bergeron, MG (2000). Genetic tools for the simultaneous identification of bacterial species and their antibiotic resistance genes: impact on clinical practice. International Journal of Antimicrobial Agents 16: 1–3.CrossRefGoogle ScholarPubMed
Birtles, RJ, Harrison, TG, Saunders, NA and Molyneux, DH (1995). Proposals to unify the genera Grahamella and Bartonella, with descriptions of Bartonella talpae comb. nov., Bartonella peromysci comb. nov., and three new species, Bartonella grahamii sp. nov., Bartonella taylorii sp. nov., and Bartonella doshiae sp. nov. International Journal of Systematic Bacteriology 45: 1–8.CrossRefGoogle ScholarPubMed
Bockstahler, LE, Li, Z, Nguyen, NY, Van Houten, KA, Brennan, MJ, Langone, JJ and Morris, SL (2002). Peptide nucleic acid probe detection of mutations in Mycobacterium tuberculosis genes associated with drug resistance. Biotechniques 32: 508–510, 512, 514.CrossRefGoogle ScholarPubMed
Bosworth, BT, Dean-Nystrom, EA, Casey, TA and Neibergs, HL (1998). Differentiation of F18ab+ from F18ac+ Escherichia coli by single-strand conformational polymorphism analysis of the major fimbrial subunit gene (fedA). Clinical and Diagnostic Laboratory Immunology 5: 299–302.CrossRefGoogle ScholarPubMed
Bosworth, BT and Casey, TA (1997). Identification of toxin and pilus genes in porcine E. coli using multiple primer pairs via PCR. 97th General Meeting. American Society for Microbiology. B509.Google Scholar
Botteldoorn, N, Heyndrick, M, Rijpens, N and Herman, L (2003). Detection and characterization of verotoxigenic Escherichia coli by a VTEC/EHEC multiplex PCR in porcine faeces and pig carcass swabs. Research in Microbiology 154: 97–104.CrossRefGoogle ScholarPubMed
Brenner, DJ, O'Connor, SP, Winkler, HH and Steigerwalt, AG (1993). Proposals to unify the genera Bartonella and Rochalimaea, with descriptions of Bartonella quintana comb. nov., Bartonella vinsonii comb. nov., Bartonella henselae comb. nov., and Bartonella elizabethae comb. nov., and to remove the family Bartonellaceae from the order Rickettsiales. International Journal of Systematic Bacteriology 43: 777–786.CrossRefGoogle ScholarPubMed
Bricker, BJ, Ewalt, DR, Olsen, SC and Jensen, AE (2003). Evaluation of the Brucella abortus species-specific polymerase chain reaction assay, an improved version of the Brucella AMOS polymerase chain reaction assay for cattle. Journal of Veterinary Diagnostic Investigation 15: 374–378.CrossRefGoogle ScholarPubMed
Burk, C, Braumiller, IG, Becker, H and Martlbauer, E (2002). Nuclease fluorescence assay for the detection of verotoxin genes in raw milk. Letters in Applied Microbiology 35: 153–156.CrossRefGoogle ScholarPubMed
Cai, HY, Archambault, M and Prescott, JF (2003). 16S ribosomal DNA sequence-based identification of veterinary clinical bacteria difficult to identify by conventional phenotypic methods. Journal of Veterinary Diagnostic Investigation 15: 465–469.CrossRefGoogle Scholar
Call, DR, Brockman, FJ and Chandler, DP (2001). Detecting and genotyping Escherichia coli O157: H7 using multiplexed PCR and nucleic acid microarrays. International Journal of Food Microbiology 67: 71–80.CrossRefGoogle ScholarPubMed
Carli, KT and Eyigor, A (2003). Real-time polymerase chain reaction for Mycoplasma gallisepticum in chicken trachea. Avian Diseases 47: 712–717.CrossRefGoogle ScholarPubMed
Chandler, DP, Brown, J, Call, DR, Wunschel, S, Grate, JW, Holman, DA, Olson, L, Stottlemyre, MS and Bruckner-Lea, CJ (2001). Automated immunomagnetic separation and microarray detection of E. coli O157: H7 from poultry carcass rinse. International Journal of Food Microbiology 70: 143–154.CrossRefGoogle ScholarPubMed
Christensen, H, Nordentoft, S and Olsen, JE (1998). Phylogenetic relationships of Salmonella based on rRNA sequences. International Journal of Systematic Bacteriology 48: 605–610.CrossRefGoogle ScholarPubMed
Daly, P, Collier, T and Doyle, S (2002). PCR-ELISA detection of Escherichia coli in milk. Letters in Applied Microbiology 34: 222–226.CrossRefGoogle ScholarPubMed
DeGraves, FJ, Gao, D, Hehnen, HR, Schlapp, T and Kaltenboeck, B (2003). Quantitative detection of Chlamydia psittaci and C. pecorum by high-sensitivity real-time PCR reveals high prevalence of vaginal infection in cattle. Journal of Clinical Microbiology 41: 1726–1729.CrossRefGoogle Scholar
Demidov, VV (2003). PNA and LNA throw light on DNA. Trends in Biotechnology 21: 4–7.CrossRefGoogle ScholarPubMed
Dumler, JS, Barbert, AF, Bekker, CP, Dasch, GA, Palmer, GH, Ray, SC, Rikihisa, Y and Rurangirwa, FR (2001). Reorganization of genera in the families Rickettsiaceae and Anaplasmataceae in the order Rickettsiales: unification of some species of Ehrlichia with Anaplasma, Cowdria with Ehrlichia and Ehrlichia with Neorickettsia, descriptions of six new species combinations and designation of Ehrlichia equi and ‘HGE agent’ as subjective synonyms of Ehrlichia phagocytophila. International Journal of Systematic and Evolutionary Microbiology 51: 2145–65.CrossRefGoogle ScholarPubMed
Englund, S, Bolske, G, Ballagi-Pordany, A and Johansson, KE (2001). Detection of Mycobacterium avium subsp. paratuberculosis in tissue samples by single, fluorescent and nested PCR based on the IS900 gene. Veterinary Microbiology 81: 257–271.CrossRefGoogle ScholarPubMed
Englund, S, Bolske, G and Johansson, KE (2002). An IS900-like sequence found in a Mycobacterium sp. other than Mycobacterium avium subsp. paratuberculosis. FEMS Microbiology Letters 209: 267–271.CrossRefGoogle Scholar
Etoh, Y, Yamamoto, A and Goto, N (1998). Intervening sequences in 16S rRNA genes of Campylobacter sp.: diversity of nucleotide sequences and uniformity of location. Microbiology and Immunology 42: 241–243.CrossRefGoogle ScholarPubMed
Exner, MM and Lewinski, MA (2003). Isolation and detection of Borrelia burgdorferi DNA from cerebral spinal fluid, synovial fluid, blood, urine, and ticks using the Roche MagNA Pure system and real-time PCR. Diagnostic Microbiology and Infectious Disease 46: 235–240.CrossRefGoogle ScholarPubMed
Fang, Y, Wu, WH, Pepper, JL, Larsen, JL, Marras, SA, Nelson, EA, Epperson, WB and Christopher-Hennings, J (2002). Comparison of real-time, quantitative PCR with molecular beacons to nested PCR and culture methods for detection of Mycobacterium avium subsp. paratuberculosis in bovine fecal samples. Journal of Clinical Microbiology 40: 287–291.CrossRefGoogle ScholarPubMed
Fluit, AC, Visser, MR and Schmitz, FJ (2001). Molecular detection of antimicrobial resistance. Clinical Microbiology Reviews 14: 836–871.CrossRefGoogle ScholarPubMed
Forsman, P, Tilsala-Timisjarvi, A and Alatossava, T (1997). Identification of staphylococcal and streptococcal causes of bovine mastitis using 16S-23S rRNA spacer regions. Microbiology 143: 3491–3500.CrossRefGoogle ScholarPubMed
Fortin, NY, Mulchandani, A and Chen, W (2001). Use of real-time polymerase chain reaction and molecular beacons for the detection of Escherichia coli O157: H7. Analytical Biochemistry 289: 281–288.CrossRefGoogle ScholarPubMed
Franck, SM, Bosworth, BT and Moon, HW (1998). Multiplex PCR for enterotoxigenic, attaching and effacing, and Shiga toxin-producing Escherichia coli strains from calves. Journal of Clinical Microbiology 36: 1795–1797.CrossRefGoogle ScholarPubMed
Fukushima, M, Kakinuma, K and Kawaguchi, R (2002). Phylogenetic analysis of Salmonella, Shigella, and Escherichia coli strains on the basis of the gyrB gene sequence. Journal of Clinical Microbiology 40: 2779–2785.CrossRefGoogle ScholarPubMed
Garrido, JM, Cortabarria, N, Oguiza, JA, Aduriz, G and Juste, RA (2000). Use of a PCR method on fecal samples for diagnosis of sheep paratuberculosis. Veterinary Microbiology 77: 379–386.CrossRefGoogle ScholarPubMed
Ge, B, Larkin, C, Ahn, S, Jolley, M, Nasir, M, Meng, J and Hall, RH (2002). Identification of Escherichia coli O157: H7 and other enterohemorrhagic serotypes by EHEC-hlyA targeting, strand displacement amplification, and fluorescence polarization. Molecular and Cellular Probes 16: 85–92.CrossRefGoogle ScholarPubMed
Ghadersohi, AR, Coelen, J and Hirst, RG (1997). Development of a specific DNA probe and PCR for the detection of Mycoplasma bovis. Veterinary Microbiology 56: 87–98.CrossRefGoogle ScholarPubMed
Gravekamp, C, Van de Kemp, H, Franzen, M, Carrington, D, Schoone, GJ, Van Eys, GJ, Everard, CO, Hartskeerl, RA and Terpstra, WJ (1993). Detection of seven species of pathogenic leptospires by PCR using two sets of primers. Journal of General Microbiology 139: 1691–1700.CrossRefGoogle ScholarPubMed
Harkin, KR, Roshto, YM and Sullivan, JT (2003). Clinical application of a polymerase chain reaction assay for diagnosis of leptospirosis in dogs. American Journal of Veterinary Research 222: 1224–1229.Google ScholarPubMed
Heinemann, MB, Garcia, JF, Nunes, CM, Gregori, F, Higa, ZM, Vasconcellos, SA and Richtzenhain, LJ (2000). Detection and differentiation of Leptospira spp. serovars in bovine semen by polymerase chain reaction and restriction fragment length polymorphism. Veterinary Microbiology 73: 261–267.CrossRefGoogle ScholarPubMed
Hirose, K, Kawasaki, Y, Kotani, K, Tanaka, A, Abiko, K and Ogawa, H (2001). Detection of mycoplasma in mastitic milk by PCR analysis and culture method. Journal of Veterinary Medical Science 63: 691–693.CrossRefGoogle ScholarPubMed
Hu, Y, Zhang, Q and Meitzler, JC (1999). Rapid and sensitive detection of Escherichia coli O157: H7 in bovine faeces by a multiplex PCR. Journal of Applied Microbiology 87: 867–876.CrossRefGoogle ScholarPubMed
Hughes, MS, James, G, Ball, N, Scally, M, Malik, R, Wigney, DI, Martin, P, Chen, S, Mitchell, D and Love, DN (2000). Identification by 16S rRNA gene analyses of a potential novel mycobacterial species as an etiological agent of canine leptroi granuloma syndrome. Journal of Clinical Microbiology 38: 953–959.CrossRefGoogle ScholarPubMed
Jayarao, BM, Dore, JJ Jr, Baumbach, GA, Matthews, KR and Oliver, SP (1991). Differentiation of Streptococcus uberis from Streptococcus parauberis by polymerase chain reaction and restriction fragment length polymorphism analysis of 16S ribosomal DNA. Journal of Clinical Microbiology 29: 2774–2778.CrossRefGoogle ScholarPubMed
Khan, MA, Kim, CH, Kakoma, I, Morin, E, Hansen, RD, Hurley, WL, Tripathy, DN and Baek, BK (1998). Detection of Staphylococcus aureus in milk by use of polymerase chain reaction analysis. American Journal of Veterinary Research 59: 807–813.CrossRefGoogle ScholarPubMed
Killgore, GE, Holloway, B and Tenover, FC (2000). A 5' nuclease PCR (TaqMan) high-throughput assay for detection of the mecA gene in staphylococci. Journal of Clinical Microbiology 38: 2516–2519.CrossRefGoogle ScholarPubMed
Kim, CH, Khan, M, Morin, DE, Hurley, WL, Tripathy, DN, Kehrli, M Jr, Oluoch, AO and Kakoma, I (2001). Optimization of the PCR for detection of Staphylococcus aureus nuc gene in bovine milk. Journal of Dairy Science 84: 74–83.CrossRefGoogle ScholarPubMed
Kim, KS, Ko, KS, Chang, MW, Hahn, TW, Hong, SK and Kook, YH (2003). Use of rpoB sequences for phylogenetic study of Mycoplasma species. FEMS Microbiology Letters 226: 299–305.CrossRefGoogle ScholarPubMed
Kim, SG, Shin, SJ, Jacobson, RH, Miller, LJ, Harpending, PR, Stehman, SM, Rossiter, CA and Lein, DA (2002). Development and application of quantitative polymerase chain reaction assay based on the ABI 7700 system (TaqMan) for detection and quantification of Mycobacterium avium subsp. paratuberculosis. Journal of Veterinary Diagnostic Investigation 14: 126–131.CrossRefGoogle ScholarPubMed
Kinyon, JM, Harris, DL and Glock, RD (1977). Enteropathogenicity of various isolates of Treponema hyodysenteriae. Infection and Immunity 15: 638–646.CrossRefGoogle ScholarPubMed
Lanciotti, RS and Kerst, AJ (2001). Nucleic acid sequence-based amplification assays for rapid detection of West Nile and St. Louis encephalitis viruses. Journal of Clinical Microbiology 39: 4506–4513.CrossRefGoogle ScholarPubMed
Lane, DJ, Pace, B, Olsen, GJ, Stahl, DA, Sogin, ML and Pace, NR (1985). Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proceedings of the National Academy of Sciences of the United States of America 82: 6955–6959.CrossRefGoogle ScholarPubMed
La Scola, B, Zeaiter, Z, Khamis, A and Raoult, D (2003). Gene-sequence-based criteria for species definition in bacteriology: the Bartonella paradigm. Trends in Microbiology 11: 318–321.CrossRefGoogle ScholarPubMed
Lascols, C, Lamarque, D, Costa, JM, Copie-Bergman, C, Le Glaunec, JM, Deforges, L, Soussy, CJ, Petit, JC, Delchier, JC and Tankovic, J (2003). Fast and accurate quantitative detection of Helicobacter pylori and identification of clarithromycin resistance mutations in H. pylori isolates from gastric biopsy specimens by real-time PCR. Journal of Clinical Microbiology 41: 4573–4577.CrossRefGoogle Scholar
Lew, AE, Bock, RE, Minchin, CM and Masaka, S (2002). A msp1alpha polymerase chain reaction assay for specific detection and differentiation of Anaplasma marginale isolates. Veterinary Microbiology 86: 325–335.CrossRefGoogle ScholarPubMed
Leyla, G, Kadri, G and Umran, O (2003). Comparison of polymerase chain reaction and bacteriological culture for the diagnosis of sheep brucellosis using aborted fetus samples. Veterinary Microbiology 93: 53–61.CrossRefGoogle ScholarPubMed
Li, Q, Luan, G, Guo, Q and Liang, J (2002). A new class of homogeneous nucleic acid probes based on specific displacement hybridization. Nucleic Acids Research 30: E5.CrossRefGoogle ScholarPubMed
Linton, D, Dewhirst, FE, Clewley, JP, Owen, RJ, Burnens, AP and Stanley, J (1994). Two types of 16S rRNA gene are found in Campylobacter helveticus: analysis, applications and characterization of the intervening sequence found in some strains. Microbiology 140: 847–855.CrossRefGoogle ScholarPubMed
Loens, K, Ursi, D, Ieven, M, van Aarle, P, Sillekens, P, Oudshoorn, P and Goossens, H (2002). Detection of Mycoplasma pneumoniae in spiked clinical samples by nucleic acid sequence-based amplification. Journal of Clinical Microbiology 40: 1339–1345.CrossRefGoogle ScholarPubMed
Loftis, AD, Massung, RF and Levin, ML (2003). Quantitative real-time PCR assay for detection of Ehrlichia chaffeensis. Journal of Clinical Microbiology 41: 3870–3872.CrossRefGoogle ScholarPubMed
Logan, JM, Edwards, KJ, Saunders, NA and Stanley, J (2001). Rapid identification of Campylobacter spp. by melting peak analysis of biprobes in real-time PCR. Journal of Clinical Microbiology 39: 2227–2232.CrossRefGoogle ScholarPubMed
Manterola, L, Tejero-Garces, A, Ficapal, A, Shopayeva, G, Blasco, JM, Marin, CM and Lopez-Goni, I (2003). Evaluation of a PCR test for the diagnosis of Brucella ovis infection in semen samples from rams. Veterinary Microbiology 92: 65–72.CrossRefGoogle ScholarPubMed
McAuliffe, L, Ellis, RJ, Ayling, RD and Nicholas, RA (2003). Differentiation of Mycoplasma species by 16S ribosomal DNA PCR and denaturing gradient gel electrophoresis fingerprinting. Journal of Clinical Microbiology 41: 4844–4847.CrossRefGoogle ScholarPubMed
McKillip, JL and Drake, M (2000). Molecular beacon polymerase chain reaction detection of Escherichia coli O157: H7 in milk. Journal of Food Protection 63: 855–859.CrossRefGoogle ScholarPubMed
Meiri-Bendek, I, Lipkin, E, Friedmann, A, Leitner, G, Saran, A, Friedman, S and Kashi, Y (2002). A PCR-based method for the detection of Streptococcus agalactiae in milk. Journal of Dairy Science 85: 1717–1723.CrossRefGoogle ScholarPubMed
Misawa, N, Kawashima, K, Kondo, F, Kushima, E, Kushima, K and Vandamme, P (2002). Isolation and characterization of Campylobacter, Helicobacter, and Anaerobiospirillum strains from a puppy with bloody diarrhea. Veterinary Microbiology 87: 353–364.CrossRefGoogle ScholarPubMed
Morré, SA, Sillekens, P, Jacobs, MV, van Aarle, P, de Blok, S, van Gemen, B, Walboomers, JMM, Meijer, CJLM and van den Brule, AJC (1996). RNA amplification by nucleic acid sequence-based amplification with an internal standard enables reliable detection of Chlamydia trachomatis in cervical scrapings and urine samples. Journal of Clinical Microbiology 34: 3108–3114.CrossRefGoogle ScholarPubMed
Mott, J, Rikihisa, Y, Zhang, Y, Reed, SM and Yu, CY (1997). Comparison of PCR and culture to the indirect fluorescent-antibody test for diagnosis of Potomac horse fever. Journal of Clinical Microbiology 35: 2215–2219.CrossRefGoogle Scholar
Mullis, KB and Faloona, FA (1987). Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods in Enzymology 155: 335–350.CrossRefGoogle Scholar
Neimark, H, Johansson, KE, Rikihisa, Y and Tully, JG (2001). Proposal to transfer some members of the genera Haemobartonella and Eperythrozoon to the genus Mycoplasma with descriptions of ‘Candidatus Mycoplasma haemofelis’, ‘Candidatus Mycoplasma haemomuris’, ‘Candidatus Mycoplasma haemosuis’ and ‘Candidatus Mycoplasma wenyonii’. International Journal of Systematic and Evolutionary Microbiology 51: 891–899.CrossRefGoogle Scholar
Newby, DT, Hadfield, TL and Roberto, FF (2003). Real-time PCR detection of Brucella abortus: a comparative study of SYBR green I, 5'-exonuclease, and hybridization probe assays. Applied and Environmental Microbiology 69: 4753–4759.CrossRefGoogle ScholarPubMed
Norman, AF, Regnery, R, Jameson, P, Greene, C and Krause, DC (1995). Differentiation of Bartonella-like isolates at the species level by PCR-restriction fragment length polymorphism in the citrate synthase gene. Journal of Clinical Microbiology 33: 1797–803.CrossRefGoogle ScholarPubMed
Nutiu, R and Li, Y (2002) Tripartite molecular beacons. Nucleic Acids Research 30: e94.CrossRefGoogle ScholarPubMed
Oliveira, K, Procop, GW, Wilson, D, Coull, J and Stender, H (2002). Rapid identification of Staphylococcus aureus directly from blood cultures by fluorescence in situ hybridization with peptide nucleic acid probes. Journal of Clinical Microbiology 40: 247–251.CrossRefGoogle ScholarPubMed
O'Mahony, J and Hill, C (2002). A real time PCR assay for the detection and quantitation of Mycobacterium avium subsp. paratuberculosis using SYBR Green and the Light Cycler. Journal of Microbiological Methods 51: 283–293.CrossRefGoogle ScholarPubMed
Patel, JB, Leonard, DG, Pan, X, Musser, JM, Berman, RE and Nachamkin, I (2000). Sequence-based identification of Mycobacterium species using the MicroSeq 500 16S rDNA bacterial identification system. Journal of Clinical Microbiology 38: 246–251.CrossRefGoogle ScholarPubMed
Paton, AW and Paton, JC (1998). Detection and characterization of Shiga toxigenic Escherichia coli by using multiplex PCR assays for stx1, stx2, eaeA, enterohemorrhagic E. coli hlyA, rfbO111, and rfbO157. Journal of Clinical Microbiology 36: 598–602.CrossRefGoogle ScholarPubMed
Phuektes, P, Mansell, PD and Browning, GF (2001). Multiplex polymerase chain reaction assay for simultaneous detection of Staphylococcus aureus and streptococcal causes of bovine mastitis. Journal of Dairy Research 84: 1140–1148.Google ScholarPubMed
Phuektes, P, Browning, GF, Anderson, G and Mansell, PD (2003). Multiplex polymerase chain reaction as a mastitis screening test for Staphylococcus aureus, Streptococcus agalactiae, Streptococcus dysgalactiae and Streptococcus uberis in bulk milk samples. Journal of Dairy Research 70: 149–155.CrossRefGoogle ScholarPubMed
Piatek, AS, Telenti, A, Murray, MR, El-Hajj, H, Jacobs, WR Jr, Kramer, FR and Alland, D (2000). Genotypic analysis of Mycobacterium tuberculosis in two distinct populations using molecular beacons: implications for rapid susceptibility testing. Antimicrobial Agents and Chemotherapy 44: 103–110.CrossRefGoogle ScholarPubMed
Pinnow, CC, Butler, JA, Sachse, K, Hotzel, H, Timms, LL and Rosenbusch, RF (2001). Detection of Mycoplasma bovis in preservative-treated field milk samples. Journal of Dairy Science 84: 1640–1645.CrossRefGoogle ScholarPubMed
Pusterla, N, Leutenegger, CM, Sigrist, B, Chae, JS, Lutz, H and Madigan, JE (2000). Detection and quantitation of Ehrlichia risticii genomic DNA in infected horses and snails by real-time PCR. Veterinary Parasitology 90: 129–135.CrossRefGoogle ScholarPubMed
Quinn, PJ, Markey, BK, Donnelly, WJ and Leonard, FC (2002) Bacterial causes of bovine mastitis. In: Quinn, PJ, Markey, BK, Donnelly, WJ and Leonard, FC (editors). Veterinary Microbiology and Microbial Disease. London: Blackwell Science pp. 465–475.Google Scholar
Redkar, R, Rose, S, Bricker, B and DelVecchio, V (2001). Real-time detection of Brucella abortus, Brucella melitensis and Brucella suis. Molecular and Cellular Probes 15: 43–52.CrossRefGoogle ScholarPubMed
Reischl, U, Youssef, MT, Kilwinski, J, Lehn, N, Zhang, WL, Karch, H and Strockbine, NA (2002). Real-time fluorescence PCR assays for detection and characterization of Shiga toxin, intimin, and enterohemolysin genes from Shiga toxin-producing Escherichia coli. Journal of Clinical Microbiology 40: 2555–2565.CrossRefGoogle ScholarPubMed
Relman, DA, Loutit, JS, Schmidt, TM, Falkow, S and Tompkins, LS (1990). The agent of bacillary angiomatosis. An approach to the identification of uncultured pathogens. New England Journal of Medicine 323: 1573–1580.CrossRefGoogle Scholar
Relman, DA, Schmidt, TM, MacDermott, RP and Falkow, S (1992). Identification of the uncultured bacillus of Whipple's disease. New England Journal of Medicine 327: 293–301.CrossRefGoogle ScholarPubMed
Riffon, R, Sayasith, K, Khalil, H, Dubreuil, P, Drolet, M and Lagace, J (2001). Development of a rapid and sensitive test for identification of major pathogens in bovine mastitis by PCR. Journal of Clinical Microbiology 39: 2584–2589.CrossRefGoogle ScholarPubMed
Sachse, K, Grossmann, E, Jager, C, Diller, R and Hotzel, H (2003). Detection of Chlamydia suis from clinical specimens: comparison of PCR, antigen ELISA, and culture. Journal of Microbiological Methods 54: 233–238.CrossRefGoogle ScholarPubMed
Sails, AD, Fox, AJ, Bolton, FJ, Wareing, DR and Greenway, DL (2003). A real-time PCR assay for the detection of Campylobacter jejuni in foods after enrichment culture. Applied and Environmental Microbiology 69: 1383–1390.CrossRefGoogle ScholarPubMed
Shah, DH, Verma, R, Bakshi, CS and Singh, RK (2002). A multiplex-PCR for the differentiation of Mycobacterium bovis and Mycobacterium tuberculosis. FEMS Microbiology Letters 214: 39–43.CrossRefGoogle ScholarPubMed
Sharma, VK (2002). Detection and quantitation of enterohemorrhagic Escherichia coli O157, O111, and O26 in beef and bovine feces by real-time polymerase chain reaction. Journal of Food Protection 65: 1371–1380.CrossRefGoogle ScholarPubMed
Sreevatsan, S, Bookout, JB, Ringpis, F, Perumaalla, VS, Ficht, TA, Adams, LG, Hagius, SD, Elzer, PH, Bricker, BJ, Kumar, GK, Rajasekhar, M, Isloor, S and Barathur, RR (2000). A multiplex approach to molecular detection of Brucella abortus and/or Mycobacterium bovis infection in cattle. Journal of Clinical Microbiology 38: 2602–2610.CrossRefGoogle ScholarPubMed
Stender, H, Mollerup, TA, Lund, K, Petersen, KH, Hongmanee, P and Godtfredsen, SE (1999). Direct detection and identification of Mycobacterium tuberculosis in smear-positive sputum samples by fluorescence in situ hybridization (FISH) using peptide nucleic acid (PNA) probes. International Journal of Tuberculosis and Lung Disease 3: 830–837.Google ScholarPubMed
Stender, H, Fiandaca, M, Hyldig-Nielsen, JJ and Coull, J (2002). PNA for rapid microbiology. Journal of Microbiological Methods 48: 1–17.CrossRefGoogle ScholarPubMed
Stratmann, J, Strommenger, B, Stevenson, K and Gerlach, GF (2002). Development of a peptide-mediated capture PCR for detection of Mycobacterium avium subsp. paratuberculosis in milk. Journal of Clinical Microbiology 40: 4244–4250.CrossRefGoogle ScholarPubMed
Taillardat-Bisch, AV, Raoult, D and Drancourt, M (2003). RNA polymerase beta-subunit-based phylogeny of Ehrlichia spp., Anaplasma spp., Neorickettsia spp. and Wolbachia pipientis. International Journal of Systematic and Evolutionary Microbiology 53: 455–458.CrossRefGoogle ScholarPubMed
Tang, YW, Von Graevenitz, A, Waddington, MG, Hopkins, MK, Smith, DH, Li, H, Kolbert, CP, Montgomery, SO and Persing, DH (2000). Identification of coryneform bacterial isolates by ribosomal DNA sequence analysis. Journal of Clinical Microbiology 38: 1676–1678.CrossRefGoogle ScholarPubMed
Tasker, S, Helps, CR, Day, MJ, Gruffydd-Jones, TJ and Harbour, DA (2003). Use of real-time PCR to detect and quantify Mycoplasma haemofelis and ‘Candidatus Mycoplasma haemominutum’ DNA. Journal of Clinical Microbiology 41: 439–441.CrossRefGoogle ScholarPubMed
Taylor, MJ, Hughes, MS, Skuce, RA and Neill, SD (2001). Detection of Mycobacterium bovis in bovine clinical specimens using real-time fluorescence and fluorescence resonance energy transfer probe rapid-cycle PCR. Journal of Clinical Microbiology 39: 1272–1278.CrossRefGoogle ScholarPubMed
Torres, MJ, Criado, A, Palomares, JC and Aznar, J (2000). Use of real-time PCR and fluorimetry for rapid detection of rifampin and isoniazid resistance-associated mutations in Mycobacterium tuberculosis. Journal of Clinical Microbiology 38: 3194–3149.CrossRefGoogle ScholarPubMed
Torioni de Echaide, S, Knowles, DP, McGuire, TC, Palmer, GH, Suarez, CE and McElwain, TF (1998). Detection of cattle naturally infected with Anaplasma marginale in a region of endemicity by nested PCR and a competitive enzyme-linked immunosorbent assay using recombinant major surface protein 5. Journal of Clinical Microbiology 36: 777–782.CrossRefGoogle Scholar
Trotha, R, Hanck, T, Konig, W and Konig, B (2001). Rapid ribosequencing—an effective diagnostic tool for detecting microbial infection. Infection 29: 12–16.CrossRefGoogle ScholarPubMed
Tyagi, S and Kramer, FR (1996). Molecular beacons: probes that fluoresce upon hybridization. Nature Biotechnology 14: 303–308.CrossRefGoogle ScholarPubMed
Tyagi, S, Bratu, DP and Kramer, FR (1998). Multicolor molecular beacons for allele discrimination. Nature Biotechnology 16: 49–53.CrossRefGoogle ScholarPubMed
Uyttendaele, M, Schukkink, R, van Gemen, B and Debevere, J (1994) Identification of Camplylobacter jejuni, Campylobacter coli and Camplylobacter lari by the nucleic acid sequence based amplification system NASBATM. Journal of Applied Bacteriology 77: 694–701.CrossRefGoogle Scholar
Van der Vliet, GME, Schukkink, RAF, van Gemen, B, Schepers, P and Klatser, PR (1993). Nucleic acid sequence based amplification (NASBA) for the identification of Mycobacteria. Journal of General Microbiology 139: 2423–2429.Google ScholarPubMed
Wagenaar, J, Zuerner, RL, Alt, D and Bolin, CA (2000). Comparison of polymerase chain reaction assays with bacteriologic culture, immunofluorescence, and nucleic acid hybridization for detection of Leptospira borgpetersenii serovar hardjo in urine of cattle. American Journal of Veterinary Research 61: 316–320.CrossRefGoogle ScholarPubMed
Walker, GT, Little, MC, Nadeau, JG and Shank, DD (1992). Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system. Proceedings of the National Academy of Sciences of the United States of America 89: 392–396.CrossRefGoogle ScholarPubMed
Westin, L, Miller, C, Vollmer, D, Canter, D, Radtkey, R, Nerenberg, M and O'Connell, JP (2001). Antimicrobial resistance and bacterial identification utilizing a microelectronic chip array. Journal of Clinical Microbiology 39: 1097–104.CrossRefGoogle ScholarPubMed
Wilhelm, J, Pingoud, A and Hahn, M (2001). Comparison between Taq DNA polymerase and its Stoffel fragment for quantitative real-time PCR with hybridization probes. Biotechniques 30: 1052–1056.CrossRefGoogle ScholarPubMed
Yang, SJ, Park, KY, Seo, KS, Besser, TE, Yoo, HS, Noh, KM, Kim, SH, Kim, SH, Lee, BK, Kook, YH and Park, YH (2001). Multidrug-resistant Salmonella typhimurium and Salmonella enteritidis identified by multiplex PCR from animals. Journal of Veterinary Science (Suwon-si, Korea) 2: 181–188.CrossRefGoogle ScholarPubMed
Yang, SJ, Park, KY, Kim, SH, No, KM, Besser, TE, Yoo, HS, Kim, SH, Lee, BK and Park, YH (2002). Antimicrobial resistance in Salmonella enterica serovars Enteritidis and Typhimurium isolated from animals in Korea: comparison of phenotypic and genotypic resistance characterization. Veterinary Microbiology 86: 295–301.CrossRefGoogle ScholarPubMed
Zimmermann, K, Eiter, T and Scheiflinger, F (2003). Consecutive analysis of bacterial PCR samples on a single electronic microarray. Journal of Microbiological Methods 55: 471–474.CrossRefGoogle ScholarPubMed