1887

Abstract

A major barrier to using genome sequencing in medical microbiology is the ability to interpret the data. New schemes that provide information about the importance of sequence variation in both clinical and public health settings are required. Meticillin-resistant (MRSA) is an important nosocomial pathogen that is being observed with increasing frequency in community settings. Better tools are needed to improve our understanding of its transmissibility and micro-epidemiology in order to develop effective interventions. Using DNA microarray technology we identified a set of 20 binary targets whose presence or absence could be determined by PCR, producing a PCR binary typing scheme (PCR-BT). This was combined with multi-locus sequence type-based, sequence nucleotide polymorphism typing to form a hierarchical typing scheme. When applied to a set of epidemiologically unrelated isolates, a high degree of concordance was observed with PFGE (98.8 %). The scheme was able to detect the presence or absence of an outbreak strain in eight out of nine outbreak investigations, demonstrating epidemiological concordance. PCR-BT was better than PFGE at distinguishing between outbreak strains, particularly where epidemic MRSA-15 was involved. The method developed here is a rapid, digital typing scheme for for use in both micro- and macro-epidemiological investigations that has the advantage of being suitable for use in routine diagnostic laboratories. The targets are defined and therefore the types can be defined by any platform capable of detecting the sequences used, including whole genome sequencing.

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2013-01-01
2020-10-24
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References

  1. Achtman M. 1996; A surfeit of YATMs?. J Clin Microbiol 34:1870[PubMed]
    [Google Scholar]
  2. Baba T., Takeuchi F., Kuroda M., Yuzawa H., Aoki K., Oguchi A., Nagai Y., Iwama N., Asano K.& other authors ( 2002; Genome and virulence determinants of high virulence community-acquired MRSA. Lancet 359:1819–1827 [CrossRef][PubMed]
    [Google Scholar]
  3. Cooke F. J., Brown N. M. 2010; Community-associated methicillin-resistant Staphylococcus aureus infections. Br Med Bull 94:215–227 [CrossRef][PubMed]
    [Google Scholar]
  4. Cookson B. D., Robinson D. A., Monk A. B., Murchan S., Deplano A., de Ryck R., Struelens M. J., Scheel C., Fussing V.& other authors ( 2007; Evaluation of molecular typing methods in characterizing a European collection of epidemic methicillin-resistant Staphylococcus aureus strains: the HARMONY collection. J Clin Microbiol 45:1830–1837 [CrossRef][PubMed]
    [Google Scholar]
  5. Deplano A., De Mendonça R., De Ryck R., Struelens M. J. 2006; External quality assessment of molecular typing of Staphylococcus aureus isolates by a network of laboratories. J Clin Microbiol 44:3236–3244 [CrossRef][PubMed]
    [Google Scholar]
  6. Dunne W. M., Westblade L. F., Ford B. 2012; Next-generation and whole-genome sequencing in the diagnostic clinical microbiology laboratory. Eur J Clin Microbiol Infect Dis 31:1719–1726 [CrossRef]
    [Google Scholar]
  7. Enright M. C., Day N. P., Davies C. E., Peacock S. J., Spratt B. G. 2000; Multilocus sequence typing for characterization of methicillin-resistant and methicillin-susceptible clones of Staphylococcus aureus. J Clin Microbiol 38:1008–1015[PubMed]
    [Google Scholar]
  8. Enright M. C., Robinson D. A., Randle G., Feil E. J., Grundmann H., Spratt B. G. 2002; The evolutionary history of methicillin-resistant Staphylococcus aureus (MRSA). Proc Natl Acad Sci U S A 99:7687–7692 [CrossRef][PubMed]
    [Google Scholar]
  9. Eyre D. W., Golubchik T., Gordon N. C., Bowden R., Piazza P., Batty E. M., Ip C. L. C., Wilson D. J., Didelot X.& other authors ( 2012; A pilot study of rapid benchtop sequencing of Staphylococcus aureus and Clostridium difficile for outbreak detection and surveillance. BMJ Open 2:e001124 [CrossRef][PubMed]
    [Google Scholar]
  10. Feil E. J., Enright M. C. 2004; Analyses of clonality and the evolution of bacterial pathogens. Curr Opin Microbiol 7:308–313 [CrossRef][PubMed]
    [Google Scholar]
  11. Feil E. J., Smith J. M., Enright M. C., Spratt B. G. 2000; Estimating recombinational parameters in Streptococcus pneumoniae from multilocus sequence typing data. Genetics 154:1439–1450[PubMed]
    [Google Scholar]
  12. Fitzgerald J. R., Sturdevant D. E., Mackie S. M., Gill S. R., Musser J. M. 2001; Evolutionary genomics of Staphylococcus aureus: insights into the origin of methicillin-resistant strains and the toxic shock syndrome epidemic. Proc Natl Acad Sci U S A 98:8821–8826 [CrossRef][PubMed]
    [Google Scholar]
  13. Fluit A. C., Wielders C. L. C., Verhoef J., Schmitz F. J. 2001; Epidemiology and susceptibility of 3,051 Staphylococcus aureus isolates from 25 university hospitals participating in the European SENTRY study. J Clin Microbiol 39:3727–3732 [CrossRef][PubMed]
    [Google Scholar]
  14. Grundmann H., Aanensen D. M., van den Wijngaard C. C., Spratt B. G., Harmsen D., Friedrich A. W.European Staphylococcal Reference Laboratory Working Group 2010; Geographic distribution of Staphylococcus aureus causing invasive infections in Europe: a molecular-epidemiological analysis. PLoS Med 7:e1000215 (epublication) [CrossRef][PubMed]
    [Google Scholar]
  15. Harris S. R., Feil E. J., Holden M. T. G., Quail M. A., Nickerson E. K., Chantratita N., Gardete S., Tavares A., Day N.& other authors ( 2010; Evolution of MRSA during hospital transmission and intercontinental spread. Science 327:469–474 [CrossRef][PubMed]
    [Google Scholar]
  16. Holden M. T. G., Feil E. J., Lindsay J. A., Peacock S. J., Day N. P. J., Enright M. C., Foster T. J., Moore C. E., Hurst L.& other authors ( 2004; Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc Natl Acad Sci U S A 101:9786–9791 [CrossRef][PubMed]
    [Google Scholar]
  17. Khandavilli S., Wilson P., Cookson B., Cepeda J., Bellingan G., Brown J. 2009; Utility of spa typing for investigating the local epidemiology of MRSA on a UK intensive care ward. J Hosp Infect 71:29–35 [CrossRef][PubMed]
    [Google Scholar]
  18. Kuroda M., Ohta T., Uchiyama I., Baba T., Yuzawa H., Kobayashi I., Cui L., Oguchi A., Aoki K.& other authors ( 2001; Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet 357:1225–1240 [CrossRef][PubMed]
    [Google Scholar]
  19. Lindsay J. A., Moore C. E., Day N. P., Peacock S. J., Witney A. A., Stabler R. A., Husain S. E., Butcher P. D., Hinds J. 2006; Microarrays reveal that each of the ten dominant lineages of Staphylococcus aureus has a unique combination of surface-associated and regulatory genes. J Bacteriol 188:669–676 [CrossRef][PubMed]
    [Google Scholar]
  20. Loman N. J., Misra R. V., Dallman T. J., Constantinidou C., Gharbia S. E., Wain J., Pallen M. J. 2012; Performance comparison of benchtop high-throughput sequencing platforms. Nat Biotechnol 30:434–439 [CrossRef][PubMed]
    [Google Scholar]
  21. Luczak-Kadlubowska A., Sabat A., Tambic-Andrasevic A., Payerl-Pal M., Krzyszton-Russjan J., Hryniewicz W. 2008; Usefulness of multiple-locus VNTR fingerprinting in detection of clonality of community- and hospital-acquired Staphylococcus aureus isolates. Antonie van Leeuwenhoek 94:543–553 [CrossRef][PubMed]
    [Google Scholar]
  22. Maiden M. C. J., Bygraves J. A., Feil E., Morelli G., Russell J. E., Urwin R., Zhang Q., Zhou J., Zurth K.& other authors ( 1998; Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A 95:3140–3145 [CrossRef][PubMed]
    [Google Scholar]
  23. Murchan S., Kaufmann M. E., Deplano A., de Ryck R., Struelens M., Zinn C. E., Fussing V., Salmenlinna S., Vuopio-Varkila J.& other authors ( 2003; Harmonization of pulsed-field gel electrophoresis protocols for epidemiological typing of strains of methicillin-resistant Staphylococcus aureus: a single approach developed by consensus in 10 European laboratories and its application for tracing the spread of related strains. J Clin Microbiol 41:1574–1585 [CrossRef][PubMed]
    [Google Scholar]
  24. Murchan S., Aucken H. M., O’neill G. L., Ganner M., Cookson B. D. 2004; Emergence, spread, and characterization of phage variants of epidemic methicillin-resistant Staphylococcus aureus 16 in England and Wales. J Clin Microbiol 42:5154–5160 [CrossRef][PubMed]
    [Google Scholar]
  25. O’Neill G. L., Murchan S., Gil-Setas A., Aucken H. M. 2001; Identification and characterization of phage variants of a strain of epidemic methicillin-resistant Staphylococcus aureus (EMRSA-15). J Clin Microbiol 39:1540–1548 [CrossRef][PubMed]
    [Google Scholar]
  26. Rasschaert G., Vanderhaeghen W., Dewaele I., Janez N., Huijsdens X., Butaye P., Heyndrickx M. 2009; Comparison of fingerprinting methods for typing methicillin-resistant Staphylococcus aureus sequence type 398. J Clin Microbiol 47:3313–3322 [CrossRef][PubMed]
    [Google Scholar]
  27. Robinson D. A., Enright M. C. 2004; Evolution of Staphylococcus aureus by large chromosomal replacements. J Bacteriol 186:1060–1064 [CrossRef][PubMed]
    [Google Scholar]
  28. Robinson D. A., Hollingshead S. K., Musser J. M., Parkinson A. J., Briles D. E., Crain M. J. 1998; The IS1167 insertion sequence is a phylogenetically informative marker among isolates of serotype 6B Streptococcus pneumoniae. J Mol Evol 47:222–229 [CrossRef][PubMed]
    [Google Scholar]
  29. Shopsin B., Gomez M., Montgomery S. O., Smith D. H., Waddington M., Dodge D. E., Bost D. A., Riehman M., Naidich S., Kreiswirth B. N. 1999; Evaluation of protein A gene polymorphic region DNA sequencing for typing of Staphylococcus aureus strains. J Clin Microbiol 37:3556–3563[PubMed]
    [Google Scholar]
  30. Shopsin B., Gomez M., Waddington M., Riehman M., Kreiswirth B. N. 2000; Use of coagulase gene (coa) repeat region nucleotide sequences for typing of methicillin-resistant Staphylococcus aureus strains. J Clin Microbiol 38:3453–3456[PubMed]
    [Google Scholar]
  31. Stephens A. J., Huygens F., Inman-Bamber J., Price E. P., Nimmo G. R., Schooneveldt J., Munckhof W., Giffard P. M. 2006; Methicillin-resistant Staphylococcus aureus genotyping using a small set of polymorphisms. J Med Microbiol 55:43–51 [CrossRef][PubMed]
    [Google Scholar]
  32. Stone M., Bamford K., Wain J. 2009; Detection of single nucleotide polymorphisms based on the multilocus sequence typing database of Staphylococcus aureus using locked nucleic acid oligonucleotides. J Med Microbiol 58:693–695 [CrossRef][PubMed]
    [Google Scholar]
  33. Struelens M. J., Deplano A., Godard C., Maes N., Serruys E. 1992; Epidemiologic typing and delineation of genetic relatedness of methicillin-resistant Staphylococcus aureus by macrorestriction analysis of genomic DNA by using pulsed-field gel electrophoresis. J Clin Microbiol 30:2599–2605[PubMed]
    [Google Scholar]
  34. Tenover F. C., Arbeit R. D., Goering R. V., Mickelsen P. A., Murray B. E., Persing D. H., Swaminathan B. 1995; Interpreting chromosomal DNA restriction patterns produced by pulsed-field gel electrophoresis: criteria for bacterial strain typing. J Clin Microbiol 33:2233–2239[PubMed]
    [Google Scholar]
  35. van Belkum A., Kluytmans J., van Leeuwen W., Bax R., Quint W., Peters E., Fluit A., Vandenbroucke-Grauls C., van den Brule A.& other authors ( 1995; Multicenter evaluation of arbitrarily primed PCR for typing of Staphylococcus aureus strains. J Clin Microbiol 33:1537–1547[PubMed]
    [Google Scholar]
  36. Vos P., Hogers R., Bleeker M., Reijans M., van de Lee T., Hornes M., Frijters A., Pot J., Peleman J.& other authors ( 1995; AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414 [CrossRef][PubMed]
    [Google Scholar]
  37. Zafar A., Stone M., Ibrahim S., Parveen Z., Hasan Z., Khan E., Hasan R., Wain J., Bamford K. 2011; Prevalent genotypes of meticillin-resistant Staphylococcus aureus: report from Pakistan. J Med Microbiol 60:56–62 [CrossRef][PubMed]
    [Google Scholar]
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