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Volume 8, Issue 6

Virulence plasmid pINV as a genetic signature for phylogeny Open Access

Abstract

is a major health burden in low- and middle-income countries, where it is a leading cause of mortality associated with diarrhoea in children, and shows an increasing incidence among travellers and men having sex with men. Like all spp., has evolved from commensal following the acquisition of a large plasmid pINV, which contains genes essential for virulence. Current sequence typing schemes of are based on combinations of chromosomal genetic loci, since pINV-encoded virulence genes are often lost during growth in the laboratory, making these elements inappropriate for sequence typing. By performing comparative analysis of pINVs from strains isolated from different geographical regions and belonging to different serotypes, we found that in contrast to plasmid-encoded virulence genes, plasmid maintenance genes are highly stable pINV-encoded elements. For the first time, to our knowledge, we have developed a plasmid multilocus sequence typing (pMLST) method based on different combinations of alleles of the and toxin–antitoxin (TA) systems, and the partitioning system. This enables typing of pINV plasmids into distinct ‘virulence sequence types’ (vSTs). Furthermore, the phylogenies of vST alleles and bacterial host core genomes suggests an intimate co-evolution of pINV with the chromosome of its bacterial host, consistent with previous findings. This work demonstrates the potential of plasmid maintenance loci as genetic characteristics to study as well as to trace the molecular phylogenesis of pINV and the phylogenetic relationship of this plasmid with its bacterial host.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): MLST , partitioning systems , Shigella , TA systems , virulence plasmid pINV and vST
Funding
This study was supported by the:
  • Wellcome Trust (Award 221924/Z/20/Z)
    • Principle Award Recipient: ChristophM Tang
  • Wellcome Trust (Award 102908/Z/13/Z)
    • Principle Award Recipient: ChristophM Tang
© 2022 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2022-06-27
2024-04-24
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References

  1. Galata V, Fehlmann T, Backes C, Keller A. PLSDB: a resource of complete bacterial plasmids. Nucleic Acids Res 2019; 47:D195–D202 [View Article] [PubMed]
     [Google Scholar]
  2. Tickell KD, Brander RL, Atlas HE, Pernica JM, Walson JL et al. Identification and management of Shigella infection in children with diarrhoea: a systematic review and meta-analysis. Lancet Glob Health 2017; 5:e1235–e1248 [View Article] [PubMed]
     [Google Scholar]
  3. Baker S, The HC. Recent insights into Shigella. Curr Opin Infect Dis 2018; 31:449–454 [View Article] [PubMed]
     [Google Scholar]
  4. Livio S, Strockbine NA, Panchalingam S, Tennant SM, Barry EM et al. Shigella isolates from the global enteric multicenter study inform vaccine development. Clin Infect Dis 2014; 59:933–941 [View Article] [PubMed]
     [Google Scholar]
  5. Kotloff KL, Nataro JP, Blackwelder WC, Nasrin D, Farag TH et al. Burden and aetiology of diarrhoeal disease in infants and young children in developing countries (the Global Enteric Multicenter Study, GEMS): a prospective, case-control study. Lancet 2013; 382:209–222 [View Article] [PubMed]
     [Google Scholar]
  6. Kotloff KL, Riddle MS, Platts-Mills JA, Pavlinac P, Zaidi AKM. Shigellosis. Lancet 2018; 391:801–812 [View Article] [PubMed]
     [Google Scholar]
  7. Lan R, Reeves PR. Escherichia coli in disguise: molecular origins of Shigella. Microbes Infect 2002; 4:1125–1132 [View Article] [PubMed]
     [Google Scholar]
  8. Mattock E, Blocker AJ. How do the virulence factors of Shigella work together to cause disease?. Front Cell Infect Microbiol 2017; 7:64 [View Article] [PubMed]
     [Google Scholar]
  9. Schroeder GN, Hilbi H. Molecular pathogenesis of Shigella spp.: controlling host cell signaling, invasion, and death by type III secretion. Clin Microbiol Rev 2008; 21:134–156 [View Article] [PubMed]
     [Google Scholar]
  10. Venkatesan MM, Goldberg MB, Rose DJ, Grotbeck EJ, Burland V et al. Complete DNA sequence and analysis of the large virulence plasmid of Shigella flexneri. Infect Immun 2001; 69:3271–3285 [View Article] [PubMed]
     [Google Scholar]
  11. Pilla G, Tang CM. Going around in circles: virulence plasmids in enteric pathogens. Nat Rev Microbiol 2018; 16:484–495 [View Article] [PubMed]
     [Google Scholar]
  12. McVicker G, Hollingshead S, Pilla G, Tang CM. Maintenance of the virulence plasmid in Shigella flexneri is influenced by Lon and two functional partitioning systems. Mol Microbiol 2019; 111:1355–1366 [View Article] [PubMed]
     [Google Scholar]
  13. McVicker G, Tang CM. Deletion of toxin-antitoxin systems in the evolution of Shigella sonnei as a host-adapted pathogen. Nat Microbiol 2016; 2:16204 [View Article] [PubMed]
     [Google Scholar]
  14. Hawkey J, Monk JM, Billman-Jacobe H, Palsson B, Holt KE. Impact of insertion sequences on convergent evolution of Shigella species. PLoS Genet 2020; 16:e1008931 [View Article] [PubMed]
     [Google Scholar]
  15. Pilla G, McVicker G, Tang CM. Genetic plasticity of the Shigella virulence plasmid is mediated by intra- and inter-molecular events between insertion sequences. PLoS Genet 2017; 13:e1007014 [View Article] [PubMed]
     [Google Scholar]
  16. Muthuirulandi Sethuvel DP, Devanga Ragupathi NK, Anandan S, Veeraraghavan B. Update on: Shigella new serogroups/serotypes and their antimicrobial resistance. Lett Appl Microbiol 2017; 64:8–18 [View Article] [PubMed]
     [Google Scholar]
  17. Allison GE, Verma NK. Serotype-converting bacteriophages and O-antigen modification in Shigella flexneri. Trends Microbiol 2000; 8:17–23 [View Article] [PubMed]
     [Google Scholar]
  18. The HC, Thanh DP, Holt KE, Thomson NR, Baker S. The genomic signatures of Shigella evolution, adaptation and geographical spread. Nat Rev Microbiol 2016; 14:235–250 [View Article] [PubMed]
     [Google Scholar]
  19. Lacher DW, Steinsland H, Blank TE, Donnenberg MS, Whittam TS. Molecular evolution of typical enteropathogenic Escherichia coli: clonal analysis by multilocus sequence typing and virulence gene allelic profiling. J Bacteriol 2007; 189:342–350 [View Article] [PubMed]
     [Google Scholar]
  20. Ribot EM, Fair MA, Gautom R, Cameron DN, Hunter SB et al. Standardization of pulsed-field gel electrophoresis protocols for the subtyping of Escherichia coli O157:H7, Salmonella, and Shigella for PulseNet. Foodborne Pathog Dis 2006; 3:59–67 [View Article] [PubMed]
     [Google Scholar]
  21. Pupo GM, Lan R, Reeves PR. Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics. Proc Natl Acad Sci USA 2000; 97:10567–10572 [View Article] [PubMed]
     [Google Scholar]
  22. Lan R, Stevenson G, Reeves PR. Comparison of two major forms of the Shigella virulence plasmid pINV: positive selection is a major force driving the divergence. Infect Immun 2003; 71:6298–6306 [View Article] [PubMed]
     [Google Scholar]
  23. Lan R, Lumb B, Ryan D, Reeves PR. Molecular evolution of large virulence plasmid in Shigella clones and enteroinvasive Escherichia coli. Infect Immun 2001; 69:6303–6309 [View Article] [PubMed]
     [Google Scholar]
  24. Carattoli A, Zankari E, García-Fernández A, Voldby Larsen M, Lund O et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother 2014; 58:3895–3903 [View Article] [PubMed]
     [Google Scholar]
  25. Liu J, Pholwat S, Zhang J, Taniuchi M, Haque R et al. Evaluation of molecular serotyping assays for Shigella flexneri directly on stool samples. J Clin Microbiol 2021; 59:e02455-20 [View Article] [PubMed]
     [Google Scholar]
  26. Knirel YA, Sun Q, Senchenkova SN, Perepelov AV, Shashkov AS et al. O-antigen modifications providing antigenic diversity of Shigella flexneri and underlying genetic mechanisms. Biochemistry 2015; 80:901–914 [View Article] [PubMed]
     [Google Scholar]
  27. Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R et al. Circos: an information aesthetic for comparative genomics. Genome Res 2009; 19:1639–1645 [View Article] [PubMed]
     [Google Scholar]
  28. Darling ACE, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004; 14:1394–1403 [View Article] [PubMed]
     [Google Scholar]
  29. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
     [Google Scholar]
  30. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [View Article] [PubMed]
     [Google Scholar]
  31. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article] [PubMed]
     [Google Scholar]
  32. Hadfield J, Croucher NJ, Goater RJ, Abudahab K, Aanensen DM et al. Phandango: an interactive viewer for bacterial population genomics. Bioinformatics 2018; 34:292–293 [View Article] [PubMed]
     [Google Scholar]
  33. Zhou Z, Charlesworth J, Achtman M. HierCC: a multi-level clustering scheme for population assignments based on core genome MLST. Bioinformatics 20213645–3646 [View Article] [PubMed]
     [Google Scholar]
  34. Siguier P, Perochon J, Lestrade L, Mahillon J, Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res 2006; 34:D32–D36 [View Article] [PubMed]
     [Google Scholar]
  35. Buchrieser C, Glaser P, Rusniok C, Nedjari H, D’Hauteville H et al. The virulence plasmid pWR100 and the repertoire of proteins secreted by the type III secretion apparatus of Shigella flexneri. Mol Microbiol 2000; 38:760–771 [View Article] [PubMed]
     [Google Scholar]
  36. Wei J, Goldberg MB, Burland V, Venkatesan MM, Deng W et al. Complete genome sequence and comparative genomics of Shigella flexneri serotype 2a strain 2457T. Infect Immun 2003; 71:2775–2786 [View Article] [PubMed]
     [Google Scholar]
  37. Public Health Agency of Canada Reported Cases from 1991 to 2019 in Canada – Notifiable Diseases On-line. Ottawa: Public Health Agency of Canada; https://diseases.canada.ca/notifiable/charts?c=yl
  38. Public Health England Sexually Transmitted Shigella spp in England 2016 to 2020 (Health Protection Report vol. 15, no. 7) London: Public Health England; 2021
     [Google Scholar]
  39. McCrickard LS, Crim SM, Kim S, Bowen A. Disparities in severe shigellosis among adults – foodborne diseases active surveillance network, 2002–2014. BMC Public Health 2018; 18:221 [View Article] [PubMed]
     [Google Scholar]
  40. Khalil IA, Troeger C, Blacker BF, Rao PC, Brown A et al. Morbidity and mortality due to shigella and enterotoxigenic Escherichia coli diarrhoea: the Global Burden of Disease Study 1990-2016. Lancet Infect Dis 2018; 18:1229–1240 [View Article] [PubMed]
     [Google Scholar]
  41. Baker KS, Dallman TJ, Field N, Childs T, Mitchell H et al. Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species. Nat Commun 2018; 9:1462 [View Article] [PubMed]
     [Google Scholar]
  42. Bowen A, Grass J, Bicknese A, Campbell D, Hurd J et al. Elevated risk for antimicrobial drug-resistant Shigella infection among men who have sex with men, United States, 2011–2015. Emerg Infect Dis 2016; 22:1613–1616 [View Article] [PubMed]
     [Google Scholar]
  43. Gilbart VL, Simms I, Jenkins C, Furegato M, Gobin M et al. Sex, drugs and smart phone applications: findings from semistructured interviews with men who have sex with men diagnosed with Shigella flexneri 3a in England and Wales. Sex Transm Infect 2015; 91:598–602 [View Article] [PubMed]
     [Google Scholar]
  44. Gray MD, Lacher DW, Leonard SR, Abbott J, Zhao S et al. Prevalence of Shiga toxin-producing Shigella species isolated from French travellers returning from the Caribbean: an emerging pathogen with international implications. Clin Microbiol Infect 2015; 21:765.E9–765.E14 [View Article] [PubMed]
     [Google Scholar]
  45. Halimeh FB, Rafei R, Osman M, Kassem II, Diene SM et al. Historical, current, and emerging tools for identification and serotyping of Shigella. Braz J Microbiol 2021; 52:2043–2055 [View Article] [PubMed]
     [Google Scholar]
  46. 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]
     [Google Scholar]
  47. Lobersli I, Wester AL, Kristiansen A, Brandal LT. Molecular differentiation of Shigella spp. from enteroinvasive E. coli. Eur J Microbiol Immunol 2016; 6:197–205
     [Google Scholar]
  48. Pavlovic M, Luze A, Konrad R, Berger A, Sing A et al. Development of a duplex real-time PCR for differentiation between E. coli and Shigella spp. J Appl Microbiol 2011; 110:1245–1251 [View Article] [PubMed]
     [Google Scholar]
  49. Wirth T, Falush D, Lan R, Colles F, Mensa P et al. Sex and virulence in Escherichia coli: an evolutionary perspective. Mol Microbiol 2006; 60:1136–1151 [View Article] [PubMed]
     [Google Scholar]
  50. Holt KE, Baker S, Weill F-X, Holmes EC, Kitchen A et al. Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nat Genet 2012; 44:1056–1059 [View Article] [PubMed]
     [Google Scholar]
  51. Rodríguez-Beltrán J, DelaFuente J, León-Sampedro R, MacLean RC, San Millán Á. Beyond horizontal gene transfer: the role of plasmids in bacterial evolution. Nat Rev Microbiol 2021; 19:347–359 [View Article] [PubMed]
     [Google Scholar]
  52. Werren JH. Selfish genetic elements, genetic conflict, and evolutionary innovation. Proc Natl Acad Sci USA 2011; 108 (Suppl. 2):10863–10870 [View Article] [PubMed]
     [Google Scholar]
  53. Wein T, Hülter NF, Mizrahi I, Dagan T. Emergence of plasmid stability under non-selective conditions maintains antibiotic resistance. Nat Commun 2019; 10:2595 [View Article] [PubMed]
     [Google Scholar]
  54. Harrison E, Guymer D, Spiers AJ, Paterson S, Brockhurst MA. Parallel compensatory evolution stabilizes plasmids across the parasitism-mutualism continuum. Curr Biol 2015; 25:2034–2039 [View Article] [PubMed]
     [Google Scholar]
  55. San Millan A, Peña-Miller R, Toll-Riera M, Halbert ZV, McLean AR et al. Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids. Nat Commun 2014; 5:5208 [View Article] [PubMed]
     [Google Scholar]
  56. Bouma JE, Lenski RE. Evolution of a bacteria/plasmid association. Nature 1988; 335:351–352 [View Article] [PubMed]
     [Google Scholar]
  57. Carattoli A. Resistance plasmid families in Enterobacteriaceae. Antimicrob Agents Chemother 2009; 53:2227–2238 [View Article] [PubMed]
     [Google Scholar]
  58. Rozwandowicz M, Brouwer MSM, Fischer J, Wagenaar JA, Gonzalez-Zorn B et al. Plasmids carrying antimicrobial resistance genes in Enterobacteriaceae. J Antimicrob Chemother 2018; 73:1121–1137 [View Article] [PubMed]
     [Google Scholar]
  59. San Millan A. Evolution of plasmid-mediated antibiotic resistance in the clinical context. Trends Microbiol 2018; 26:978–985 [View Article] [PubMed]
     [Google Scholar]
  60. Muthuramalingam M, Whittier SK, Picking WL, Picking WD. The Shigella type III secretion system: an overview from top to bottom. Microorganisms 2021; 9:451 [View Article] [PubMed]
     [Google Scholar]
  61. Maurelli AT, Baudry B, d’Hauteville H, Hale TL, Sansonetti PJ. Cloning of plasmid DNA sequences involved in invasion of HeLa cells by Shigella flexneri. Infect Immun 1985; 49:164–171 [View Article] [PubMed]
     [Google Scholar]
  62. Kirkup BC, Chang L, Chang S, Gevers D, Polz MF. Vibrio chromosomes share common history. BMC Microbiol 2010; 10:137 [View Article] [PubMed]
     [Google Scholar]
  63. Yamaichi Y, Fogel MA, McLeod SM, Hui MP, Waldor MK. Distinct centromere-like parS sites on the two chromosomes of Vibrio spp. J Bacteriol 2007; 189:5314–5324 [View Article] [PubMed]
     [Google Scholar]
  64. Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML et al. DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae. Nature 2000; 406:477–483 [View Article] [PubMed]
     [Google Scholar]
  65. Reuter S, Connor TR, Barquist L, Walker D, Feltwell T et al. Parallel independent evolution of pathogenicity within the genus Yersinia. Proc Natl Acad Sci USA 2014; 111:6768–6773 [View Article] [PubMed]
     [Google Scholar]
  66. Bernaquez I, Gaudreau C, Pilon PA, Bekal S. Evaluation of whole-genome sequencing-based subtyping methods for the surveillance of Shigella spp. and the confounding effect of mobile genetic elements in long-term outbreaks. Microb Genom 2021; 7:11 [View Article] [PubMed]
     [Google Scholar]
  67. Yassine I, Lefèvre S, Hansen EE, Ruckly C, Carle I et al. Population structure analysis and laboratory monitoring of Shigella by core-genome multilocus sequence typing. Nat Commun 2022; 13:551 [View Article] [PubMed]
     [Google Scholar]
  68. Yang F, Yang J, Zhang X, Chen L, Jiang Y et al. Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery. Nucleic Acids Res 2005; 33:6445–6458 [View Article] [PubMed]
     [Google Scholar]
  69. 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]
  70. Yao Z, Valvano MA. Genetic analysis of the O-specific lipopolysaccharide biosynthesis region (rfb) of Escherichia coli K-12 W3110: identification of genes that confer group 6 specificity to Shigella flexneri serotypes Y and 4a. J Bacteriol 1994; 176:4133–4143 [View Article] [PubMed]
     [Google Scholar]
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Virulence plasmid pINV as a genetic signature for Shigella flexneri phylogeny
M Gen 8, 000846 (2022); https://doi.org/10.1099/mgen.0.000846
/content/journal/mgen/10.1099/mgen.0.000846
/content/journal/mgen/10.1099/mgen.0.000846
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