1887

Abstract

is a priority foodborne pathogen of public health concern and phenotypic serotyping provides critical information for surveillance and outbreak detection activities. Public health and food safety laboratories are increasingly adopting whole-genome sequencing (WGS) for characterizing pathogens, but it is imperative to maintain serotype designations in order to minimize disruptions to existing public health workflows. Multiple tools have been developed for predicting serotypes from WGS data, including SRST2, SerotypeFinder and EToKi EBEis, but these tools were not designed with the specific requirements of diagnostic laboratories, which include: speciation, input data flexibility (fasta/fastq), quality control information and easily interpretable results. To address these specific requirements, we developed ECTyper (https://github.com/phac-nml/ecoli_serotyping) for performing both speciation within and , and serotype prediction. We compared the serotype prediction performance of each tool on a newly sequenced panel of 185 isolates with confirmed phenotypic serotype information. We found that all tools were highly concordant, with 92–97 % for O-antigens and 98–100 % for H-antigens, and ECTyper having the highest rate of concordance. We extended the benchmarking to a large panel of 6954 publicly available genomes to assess the performance of the tools on a more diverse dataset. On the public data, there was a considerable drop in concordance, with 75–91 % for O-antigens and 62–90 % for H-antigens, and ECTyper and SerotypeFinder being the most concordant. This study highlights that predictions show high concordance with phenotypic serotyping results, but there are notable differences in tool performance. ECTyper provides highly accurate and sensitive serotype predictions, in addition to speciation, and is designed to be easily incorporated into bioinformatic workflows.

Funding
This study was supported by the:
  • Public Health Agency of Canada
    • Principle Award Recipient: KyryloBessonov
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000728
2021-12-03
2022-01-28
Loading full text...

Full text loading...

/deliver/fulltext/mgen/7/12/mgen000728.html?itemId=/content/journal/mgen/10.1099/mgen.0.000728&mimeType=html&fmt=ahah

References

  1. World Health Organization WHO estimates of the global burden of foodborne diseases: foodborne disease burden epidemiology reference groupestimates of the global burden of foodborne diseases: foodborne disease burden epidemiology reference group 2007-2015 World Health Organization; 2015
    [Google Scholar]
  2. Havelaar AH, Kirk MD, Torgerson PR, Gibb HJ, Hald T et al. World Health Organization Global Estimates and Regional Comparisons of the Burden of Foodborne Disease in 2010. PLoS Med 2015; 12:e1001923 [View Article] [PubMed]
    [Google Scholar]
  3. Thomas MK, Murray R. Canadian Burden of Food-borne Illness Estimates Working Group. Estimating the burden of food-borne illness in Canada. Can Commun Dis Rep 2014; 40:299–302
    [Google Scholar]
  4. Thomas MK, Murray R, Flockhart L, Pintar K, Pollari F et al. Estimates of the Burden of Foodborne Illness in Canada for 30 specified pathogens and unspecified agents, Circa 2006. Foodborne Pathog Dis 2013; 10:639–648 [View Article] [PubMed]
    [Google Scholar]
  5. van der Putten BCL, Matamoros S, Mende DR, Scholl ER, Consortium C et al. Escherichia ruysiae sp. nov., a novel Gram-stain-negative bacterium, isolated from a faecal sample of an international traveller. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
    [Google Scholar]
  6. van der Putten BCL, Matamoros S, Mende DR, Schultsz C. Escherichia ruysiae sp. nov., isolated from an international traveller. Int J Syst Evol Microbiol 2021; 71:004609
    [Google Scholar]
  7. van der Putten BC, Matamoros S, Schultsz C. Genomic evidence for revising the Escherichia genus and description of Escherichia ruysiae sp. nov. BioRxiv 2019781724
    [Google Scholar]
  8. Ooka T, Ogura Y, Katsura K, Seto K, Kobayashi H et al. Defining the genome features of Escherichia albertii, an emerging enteropathogen closely related to Escherichia coli . Genome Biol Evol 2015; 7:3170–3179 [View Article] [PubMed]
    [Google Scholar]
  9. Maheux AF, Boudreau DK, Bergeron MG, Rodriguez MJ. Characterization of Escherichia fergusonii and Escherichia albertii isolated from water. J Appl Microbiol 2014; 117:597–609 [View Article] [PubMed]
    [Google Scholar]
  10. Achtman M, Wain J, Weill F-X, 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]
  11. Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C et al. Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology (Reading) 2012; 158:1005–1015 [View Article] [PubMed]
    [Google Scholar]
  12. de Been M, Pinholt M, Top J, Bletz S, Mellmann A et al. Core genome multilocus sequence typing scheme for high- resolution typing of Enterococcus faecium . J Clin Microbiol 2015; 53:3788–3797 [View Article] [PubMed]
    [Google Scholar]
  13. Clermont O, Gordon DM, Brisse S, Walk ST, Denamur E. Characterization of the cryptic Escherichia lineages: rapid identification and prevalence. Environ Microbiol 2011; 13:2468–2477 [View Article] [PubMed]
    [Google Scholar]
  14. Walk ST, Rasko DA. The “Cryptic” Escherichia. EcoSal Plus 2015; 6: [View Article]
    [Google Scholar]
  15. Pettengill EA, Pettengill JB, Binet R. Phylogenetic analyses of shigella and enteroinvasive escherichia coli for the identification of molecular epidemiological markers: whole-genome comparative analysis does not support distinct genera designation. Front Microbiol 2015; 6:1573. [View Article] [PubMed]
    [Google Scholar]
  16. Liu B, Knirel YA, Feng L, Perepelov AV, Senchenkova SN et al. Structure and genetics of Shigella O antigens. FEMS Microbiol Rev 2008; 32:627–653 [View Article] [PubMed]
    [Google Scholar]
  17. van den Beld MJC, Warmelink E, Friedrich AW, Reubsaet FAG, Schipper M et al. Incidence, clinical implications and impact on public health of infections with Shigella spp. and entero-invasive Escherichia coli (EIEC): results of a multicenter cross-sectional study in the Netherlands during 2016-2017. BMC Infect Dis 2019; 19:1037. [View Article] [PubMed]
    [Google Scholar]
  18. Ewing WH. Edwards and Ewing’s identification of Enterobacteriaceae. Edwards and Ewing’s Identification of Enterobacteriaceae 1986
    [Google Scholar]
  19. Ørskov F. Ørskov I. 2 Serotyping of Escherichia coli. Methods in Microbiology. In Elsevier vol. 14 1984 pp 43–112
    [Google Scholar]
  20. Van Goethem N, Descamps T, Devleesschauwer B, Roosens NHC, Boon NAM et al. Status and potential of bacterial genomics for public health practice: a scoping review. Implement Sci 2019; 14:79 [View Article] [PubMed]
    [Google Scholar]
  21. Lerouge I, Vanderleyden J. O-antigen structural variation: mechanisms and possible roles in animal/plant-microbe interactions. FEMS Microbiol Rev 2002; 26:17–47 [View Article] [PubMed]
    [Google Scholar]
  22. Liu B, Furevi A, Perepelov AV, Guo X, Cao H et al. Structure and genetics of Escherichia coli O antigens. FEMS Microbiol Rev 2019; 44:655–683 [View Article]
    [Google Scholar]
  23. Samuel G, Reeves P. Biosynthesis of O-antigens: genes and pathways involved in nucleotide sugar precursor synthesis and O-antigen assembly. Carbohydr Res 2003; 338:2503–2519 [View Article] [PubMed]
    [Google Scholar]
  24. Ooka T, Seto K, Ogura Y, Nakamura K, Iguchi A et al. O-antigen biosynthesis gene clusters of Escherichia albertii: their diversity and similarity to Escherichia coli gene clusters and the development of an O-genotyping method. Microb Genom 2019; 5:000314 [View Article] [PubMed]
    [Google Scholar]
  25. Ratiner YA. New flagellin-specifying genes in some Escherichia coli strains. J Bacteriol 1998; 180:979–984 [View Article] [PubMed]
    [Google Scholar]
  26. Chui H, Chan M, Hernandez D, Chong P, McCorrister S et al. Rapid, sensitive, and specific Escherichia coli H antigen typing by matrix-assisted laser desorption ionization-time of flight-based peptide mass fingerprinting. J Clin Microbiol 2015; 53:2480–2485 [View Article] [PubMed]
    [Google Scholar]
  27. Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS et al. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli . J Clin Microbiol 2014; 52:1501–1510 [View Article] [PubMed]
    [Google Scholar]
  28. Lane MC, Lockatell V, Monterosso G, Lamphier D, Weinert J et al. Role of motility in the colonization of uropathogenic Escherichia coli in the urinary tract. Infect Immun 2005; 73:7644–7656 [View Article]
    [Google Scholar]
  29. Duan Q, Zhou M, Zhu L, Zhu G. Flagella and bacterial pathogenicity: Flagella and bacterial pathogenicity. J Basic Microbiol 2013; 53:1–8
    [Google Scholar]
  30. Inouye M, Dashnow H, Raven L-A, 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]
  31. Joensen KG, Tetzschner AMM, Iguchi A, Aarestrup FM, Scheutz F. Rapid and easy in silico serotyping of Escherichia coli isolates by use of whole-genome sequencing data. J Clin Microbiol 2015; 53:2410–2426 [View Article] [PubMed]
    [Google Scholar]
  32. Zhou Z, Alikhan N-F, Mohamed K, Fan Y. Agama Study Group et al. The EnteroBase user’s guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity. Genome Res 2020; 30:138–152 [View Article] [PubMed]
    [Google Scholar]
  33. O’Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res 2016; 44:D733–45 [View Article] [PubMed]
    [Google Scholar]
  34. Ondov BD, Treangen TJ, Melsted P, Mallonee AB, Bergman NH et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol 2016; 17:132 [View Article] [PubMed]
    [Google Scholar]
  35. Matthews TC, Bristow FR, Griffiths EJ, Petkau A, Adam J et al. The Integrated Rapid Infectious Disease Analysis (IRIDA. Platform Bioinformatics 2018
    [Google Scholar]
  36. Iguchi A, Iyoda S, Kikuchi T, Ogura Y, Katsura K et al. A complete view of the genetic diversity of the Escherichia coli O-antigen biosynthesis gene cluster. DNA Res 2015; 22:101–107 [View Article] [PubMed]
    [Google Scholar]
  37. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
    [Google Scholar]
  38. Paradis E, Schliep K. ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics 2019; 35:526–528 [View Article] [PubMed]
    [Google Scholar]
  39. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012; 9:357–359 [View Article] [PubMed]
    [Google Scholar]
  40. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 2009; 25:2078–2079 [View Article] [PubMed]
    [Google Scholar]
  41. Shen W, Le S, Li Y, Hu F. SeqKit: A cross-platform and ultrafast toolkit for fasta/q file manipulation. PLoS ONE 2016; 11: [View Article] [PubMed]
    [Google Scholar]
  42. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
    [Google Scholar]
  43. Seemann T. Shovill: Faster SPAdes assembly of Illumina reads. Tilgjengelig fra Tilgjengelig fra 2017 https://github. com/tseemann/shovill
    [Google Scholar]
  44. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article] [PubMed]
    [Google Scholar]
  45. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  46. Uelze L, Borowiak M, Deneke C, Szabó I, Fischer J et al. Performance and accuracy of four open-source tools for in silico serotyping of Salmonella spp. based on whole-genome short-read sequencing data. Appl Environ Microbiol 2020; 86: [View Article]
    [Google Scholar]
  47. Sato MP, Ogura Y, Nakamura K, Nishida R, Gotoh Y et al. Comparison of the sequencing bias of currently available library preparation kits for Illumina sequencing of bacterial genomes and metagenomes. DNA Res 2019; 26:391–398 [View Article] [PubMed]
    [Google Scholar]
  48. Stenutz R, Weintraub A, Widmalm G. The structures of Escherichia coli O-polysaccharide antigens. FEMS Microbiol Rev 2006; 30:382–403 [View Article] [PubMed]
    [Google Scholar]
  49. Yoshida CE, Kruczkiewicz P, Laing CR, Lingohr EJ, Gannon VPJ et al. The Ssalmonella in silico typing resource (SISTRsistr): an open web-accessible tool for rapidly typing and subtyping d Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella genome asseGenome Assemblies. PLoS ONE 2016; 11:0147101 [View Article] [PubMed]
    [Google Scholar]
  50. Afgan E, Baker D, Batut B, van den Beek M, Bouvier D et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update. Nucleic Acids Res 2018; 46:W537–W544 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000728
Loading
/content/journal/mgen/10.1099/mgen.0.000728
Loading

Data & Media loading...

Supplements

Supplementary material 1

EXCEL

Supplementary material 2

EXCEL

Supplementary material 3

EXCEL

Supplementary material 4

EXCEL

Supplementary material 5

EXCEL

Most cited this month Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error