1887

Abstract

The characterization and tracking of pathogenic micro-organisms in the clinical laboratory and public health environment demand schemes that are easy to standardize and use, are automated and high-throughput, and provide portable data. A combined genomarkers approach for based on comparative sequence analysis by mass spectrometry has been developed. The scheme targets genes encoding synthesis and assembly of antigens, metabolic pathway enzymes, virulence factors and fluoroquinolone resistance, covering the essential sequences that distinguish between and identify variation within serotypes. This study demonstrated how this single method could replace the combination of methods currently required to determine serotypes, subtypes, antibiotic resistance profiles and the genomic relatedness of isolates. The results revealed genomic variation within seven serotypes previously unreported. This variation can be detected by using nucleotide sequence differences in the flagellin gene as markers that are not detected by traditional serotyping methods.

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2012-11-01
2024-03-29
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References

  1. Bayliss J., Moser R., Bowden S., McLean C. A. 2010; Characterisation of single nucleotide polymorphisms in the genome of JC polyomavirus using MALDI TOF mass spectrometry. J Virol Methods 164:63–67 [View Article][PubMed]
    [Google Scholar]
  2. Blaser M. J., Feldman R. A. 1981; From the centers for disease control. Salmonella bacteremia: reports to the Centers for Disease Control, 1968–1979.. J Infect Dis 143:743–746 [View Article][PubMed]
    [Google Scholar]
  3. Boyd E. F., Li J., Ochman H., Selander R. K. 1997; Comparative genetics of the inv-spa invasion gene complex of Salmonella enterica . J Bacteriol 179:1985–1991[PubMed]
    [Google Scholar]
  4. Breines D. M., Ouabdesselam S., Ng E. Y., Tankovic J., Shah S., Soussy C. J., Hooper D. C. 1997; Quinolone resistance locus nfxD of Escherichia coli is a mutant allele of the parE gene encoding a subunit of topoisomerase IV. Antimicrob Agents Chemother 41:175–179[PubMed]
    [Google Scholar]
  5. Fitzgerald C., Sherwood R., Gheesling L. L., Brenner F. W., Fields P. I. 2003; Molecular analysis of the rfb O antigen gene cluster of Salmonella enterica serogroup O:6,14 and development of a serogroup-specific PCR assay. Appl Environ Microbiol 69:6099–6105 [View Article][PubMed]
    [Google Scholar]
  6. Fitzgerald C., Gheesling L., Collins M., Fields P. I. 2006; Sequence analysis of the rfb loci, encoding proteins involved in the biosynthesis of the Salmonella enterica O17 and O18 antigens: serogroup-specific identification by PCR. Appl Environ Microbiol 72:7949–7953 [View Article][PubMed]
    [Google Scholar]
  7. Fitzgerald C., Collins M., van Duyne S., Mikoleit M., Brown T., Fields P. 2007; Multiplex, bead-based suspension array for molecular determination of common Salmonella serogroups. J Clin Microbiol 45:3323–3334 [View Article][PubMed]
    [Google Scholar]
  8. Honisch C., Chen Y., Mortimer C., Arnold C., Schmidt O., van den Boom D., Cantor C. R., Shah H. N., Gharbia S. E. 2007; Automated comparative sequence analysis by base-specific cleavage and mass spectrometry for nucleic acid-based microbial typing. Proc Natl Acad Sci U S A 104:10649–10654 [View Article][PubMed]
    [Google Scholar]
  9. Khodursky A. B., Zechiedrich E. L., Cozzarelli N. R. 1995; Topoisomerase IV is a target of quinolones in Escherichia coli . Proc Natl Acad Sci U S A 92:11801–11805 [View Article][PubMed]
    [Google Scholar]
  10. Kotetishvili M., Stine O. C., Kreger A., Morris J. G. Jr, Sulakvelidze A. 2002; Multilocus sequence typing for characterization of clinical and environmental Salmonella strains. J Clin Microbiol 40:1626–1635 [View Article][PubMed]
    [Google Scholar]
  11. Lauri A., Castiglioni B., Mariani P. 2011; Comprehensive analysis of Salmonella sequence polymorphisms and development of a LDR-UA assay for the detection and characterization of selected serotypes. Appl Microbiol Biotechnol 91:189–210 [View Article][PubMed]
    [Google Scholar]
  12. Liebana E., Guns D., Garcia-Migura L., Woodward M. J., Clifton-Hadley F. A., Davies R. H. 2001; Molecular typing of Salmonella serotypes prevalent in animals in England: assessment of methodology. J Clin Microbiol 39:3609–3616 [View Article][PubMed]
    [Google Scholar]
  13. Luk J. M., Kongmuang U., Reeves P. R., Lindberg A. A. 1993; Selective amplification of abequose and paratose synthase genes (rfb) by polymerase chain reaction for identification of Salmonella major serogroups (A, B, C2, and D). J Clin Microbiol 31:2118–2123[PubMed]
    [Google Scholar]
  14. McQuiston J. R., Parrenas R., Ortiz-Rivera M., Gheesling L., Brenner F., Fields P. I. 2004a; Sequencing and comparative analysis of flagellin genes fliC, fljB, and flpA from Salmonella . J Clin Microbiol 42:1923–1932 [View Article][PubMed]
    [Google Scholar]
  15. McQuiston J. R., Parrenas R., Ortiz-Rivera M., Gheesling L., Brenner F., Fields P. I. 2004b; Sequencing and comparative analysis of flagellin genes fliC, fljB, and flpA from Salmonella . J Clin Microbiol 42:1923–1932 [View Article][PubMed]
    [Google Scholar]
  16. Morales C. A., Gast R., Guard-Bouldin J. 2006; Linkage of avian and reproductive tract tropism with sequence divergence adjacent to the 5S ribosomal subunit rrfH of Salmonella enterica . FEMS Microbiol Lett 264:48–58 [View Article][PubMed]
    [Google Scholar]
  17. Mortimer C. K., Peters T. M., Gharbia S. E., Logan J. M., Arnold C. 2004; Towards the development of a DNA-sequence based approach to serotyping of Salmonella enterica . BMC Microbiol 4:31 [View Article][PubMed]
    [Google Scholar]
  18. Murase T., Okitsu T., Suzuki R., Morozumi H., Matsushima A., Nakamura A., Yamai S. 1995; Evaluation of DNA fingerprinting by PFGE as an epidemiologic tool for Salmonella infections. Microbiol Immunol 39:673–676[PubMed] [CrossRef]
    [Google Scholar]
  19. Piddock L. J. 2002; Fluoroquinolone resistance in Salmonella serovars isolated from humans and food animals. FEMS Microbiol Rev 26:3–16[PubMed] [CrossRef]
    [Google Scholar]
  20. Powell N. G., Threlfall E. J., Chart H., Rowe B. 1994; Subdivision of Salmonella enteritidis PT 4 by pulsed-field gel electrophoresis: potential for epidemiological surveillance. FEMS Microbiol Lett 119:193–198 [View Article][PubMed]
    [Google Scholar]
  21. Scott F., Threlfall J., Stanley J., Arnold C. 2001; Fluorescent amplified fragment length polymorphism genotyping of Salmonella Enteritidis: a method suitable for rapid outbreak recognition. Clin Microbiol Infect 7:479–485 [View Article][PubMed]
    [Google Scholar]
  22. Sonne-Hansen J., Jenabian S. M. 2005; Molecular serotyping of Salmonella: identification of the phase 1 H antigen based on partial sequencing of the fliC gene. APMIS 113:340–348 [View Article][PubMed]
    [Google Scholar]
  23. Stanssens P., Zabeau M., Meersseman G., Remes G., Gansemans Y., Storm N., Hartmer R., Honisch C., Rodi C. P. other authors 2004; High-throughput MALDI-TOF discovery of genomic sequence polymorphisms. Genome Res 14:126–133 [View Article][PubMed]
    [Google Scholar]
  24. Sukhnanand S., Alcaine S., Warnick L. D., Su W. L., Hof J., Craver M. P., McDonough P., Boor K. J., Wiedmann M. 2005; DNA sequence-based subtyping and evolutionary analysis of selected Salmonella enterica serotypes. J Clin Microbiol 43:3688–3698 [View Article][PubMed]
    [Google Scholar]
  25. Threlfall E. J., Rowe B., Ward L. R. 1989; Subdivision of Salmonella enteritidis phage types by plasmid profile typing. Epidemiol Infect 102:459–465 [View Article][PubMed]
    [Google Scholar]
  26. Ward L. R., de Sa J. D., Rowe B. 1987; A phage-typing scheme for Salmonella enteritidis. Epidemiol Infect 99:291–294 [View Article][PubMed]
    [Google Scholar]
  27. Wattiau P., Boland C., Bertrand S. 2011; Methodologies for Salmonella enterica subsp. enterica subtyping: gold standards and alternatives. Appl Environ Microbiol 77:7877–7885 [View Article][PubMed]
    [Google Scholar]
  28. WHO 2005 Drug-resistant Salmonella. Fact sheet no. 139. Geneva: World Health Organization
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