1887

Abstract

Multi-locus sequence typing (MLST) is a widely used method for categorizing bacteria. Increasingly, MLST is being performed using next-generation sequencing (NGS) data by reference laboratories and for clinical diagnostics. Many software applications have been developed to calculate sequence types from NGS data; however, there has been no comprehensive review to date on these methods. We have compared eight of these applications against real and simulated data, and present results on: (1) the accuracy of each method against traditional typing methods, (2) the performance on real outbreak datasets, (3) the impact of contamination and varying depth of coverage, and (4) the computational resource requirements.

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2017-07-04
2024-11-04
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References

  1. Silk BJ, Mahon BE, Griffin PM, Gould LH, Tauxe R V et al. Vital signs: listeria illnesses, deaths, and outbreaks - United States, 2009–2011. Morb Mortal Wkly Rep 2013; 62:448–452
    [Google Scholar]
  2. Siegman-Igra Y, Levin R, Weinberger M, Golan Y, Schwartz D et al. Listeria monocytogenes infection in Israel and review of cases worldwide. Emerg Infect Dis 2002; 8:305–310 [View Article][PubMed]
    [Google Scholar]
  3. Scharff RL, Besser J, Sharp DJ, Jones TF, Peter GS et al. An economic evaluation of PulseNet: a network for foodborne disease surveillance. Am J Prev Med 2016; 50:S66–73 [View Article][PubMed]
    [Google Scholar]
  4. Ragon M, Wirth T, Hollandt F, Lavenir R, Lecuit M et al. A new perspective on Listeria monocytogenes evolution. PLoS Pathog 2008; 4:e1000146 [View Article][PubMed]
    [Google Scholar]
  5. Achtman M, Wain J, Weill FX, Nair S, Zhou Z et al. Multilocus sequence typing as a replacement for serotyping in Salmonella enterica . PLoS Pathog 2012; 8:e1002776 [View Article][PubMed]
    [Google Scholar]
  6. Swaminathan B, Gerner-Smidt P, Ng LK, Lukinmaa S, Kam KM et al. Building PulseNet International: an interconnected system of laboratory networks to facilitate timely public health recognition and response to foodborne disease outbreaks and emerging foodborne diseases. Foodborne Pathog Dis 2006; 3:36–50 [View Article][PubMed]
    [Google Scholar]
  7. GMI Steering Committee.. Global Microbial Identifier Charter and Structure www.globalmicrobialidentifier.org/about-gmi/charter-and-structure. Global Microbial Identifier Steering Committee:; Lyngby;: 2013
    [Google Scholar]
  8. Maiden MC, Bygraves JA, Feil E, Morelli G, Russell JE et al. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci USA 1998; 95:3140–3145 [View Article][PubMed]
    [Google Scholar]
  9. Timme RE, Rand H, Shumway M, Trees EK, Simmons M. Bacterial pathogen genome datasets for bioinformatics pipelines. PLOS Currents: Tree of Life 2017 (in press)
    [Google Scholar]
  10. Page AJ, de Silva N, Hunt M, Quail MA, Parkhill J et al. Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data. Microb Genom 2016; 2:e000083 [View Article][PubMed]
    [Google Scholar]
  11. Jolley KA, Maiden MC. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 2010; 11:595 [View Article][PubMed]
    [Google Scholar]
  12. Pouseele H, Janssens K. 2016; Method of typing nucleic acid or amino acid sequences based on sequence analysis. WIPO. https://patentscope.wipo.int/search/en/detail.jsf?docId=WO2016124600
  13. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article][PubMed]
    [Google Scholar]
  14. Tewolde R, Dallman T, Schaefer U, Sheppard CL, Ashton P et al. MOST: a modified MLST typing tool based on short read sequencing. PeerJ 2016; 4:e2308 [View Article][PubMed]
    [Google Scholar]
  15. Inouye M, Conway TC, Zobel J, Holt KE. Short read sequence typing (SRST): multi-locus sequence types from short reads. BMC Genomics 2012; 13:338 [View Article][PubMed]
    [Google Scholar]
  16. Larsen MV, Cosentino S, Rasmussen S, Friis C, Hasman H et al. Multilocus sequence typing of total-genome-sequenced bacteria. J Clin Microbiol 2012; 50:1355–1361 [View Article][PubMed]
    [Google Scholar]
  17. Page AJ, Taylor B, Keane JA. Multilocus sequence typing by BLAST from de novo assemblies against PubMLST. JOSS 2016; 1:JPage2016 [View Article]
    [Google Scholar]
  18. Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U et al. Updating benchtop sequencing performance comparison. Nat Biotechnol 2013; 31:294–296 [View Article][PubMed]
    [Google Scholar]
  19. Inouye M, Dashnow H, Raven LA, Schultz MB, Pope BJ et al. SRST2: rapid genomic surveillance for public health and hospital microbiology labs. Genome Med 2014; 6:90 [View Article][PubMed]
    [Google Scholar]
  20. Holt KE, Wertheim H, Zadoks RN, Baker S, Whitehouse CA et al. Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health. Proc Natl Acad Sci USA 2015; 112:E3574E3581 [View Article][PubMed]
    [Google Scholar]
  21. Gupta A, Jordan IK, Rishishwar L. stringMLST: a fast k-mer based tool for multilocus sequence typing. Bioinformatics 2017; 33:119–121 [View Article][PubMed]
    [Google Scholar]
  22. Connor TR, Loman NJ, Thompson S, Smith A, Southgate J et al. CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community. Microb Genom 2016; 2:e000086
    [Google Scholar]
  23. di Tommaso P, Palumbo E, Chatzou M, Prieto P, Heuer ML et al. The impact of Docker containers on the performance of genomic pipelines. PeerJ 2015; 3:e1273 [View Article][PubMed]
    [Google Scholar]
  24. Page AJ, de Silva N, Hunt M, Quail MA, Parkhill J et al. Robust high-throughput prokaryote de novo assembly and improvement pipeline for Illumina data. Microb Genom 2016; 2:e000083 [View Article][PubMed]
    [Google Scholar]
  25. Chen Y, Burall LS, Luo Y, Timme R, Melka D et al. Isolation, enumeration and whole genome sequencing of Listeria monocytogenes in stone fruits linked to a multistate outbreak. Appl Environ Microbiol 2016; 82:7030–7040
    [Google Scholar]
  26. Multistate outbreak of Shiga toxin-producing Escherichia coli O121 infections linked to raw clover sprouts; 2014 www.cdc.gov/ecoli/2014/o121-05-14/index.html
  27. Hoffmann M, Luo Y, Monday SR, Gonzalez-Escalona N, Ottesen AR et al. Tracing origins of the Salmonella Bareilly strain causing a food-borne outbreak in the United States. J Infect Dis 2016; 213:502–508 [View Article][PubMed]
    [Google Scholar]
  28. Liu L, Li Y, Li S, Hu N, He Y et al. Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012; 2012:1–11 [View Article][PubMed]
    [Google Scholar]
  29. Parkhill J, Dougan G, James KD, Thomson NR, Pickard D et al. Complete genome sequence of a multiple drug resistant Salmonella enterica serovar Typhi CT18. Nature 2001; 413:848–852 [View Article][PubMed]
    [Google Scholar]
  30. Salter SJ, Cox MJ, Turek EM, Calus ST, Cookson WO et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol 2014; 12:87 [View Article][PubMed]
    [Google Scholar]
  31. Makendi C, Page AJ, Wren BW, Le Thi Phuong T, Clare S et al. A phylogenetic and phenotypic analysis of Salmonella enterica serovar Weltevreden, an emerging agent of diarrheal disease in tropical regions. PLoS Negl Trop Dis 2016; 10:e0004446 [View Article][PubMed]
    [Google Scholar]
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