1887

Abstract

Burkholderia pseudomallei is a Gram-negative environmental bacterium that causes melioidosis, a disease of high mortality in humans and animals. Multilocus sequence typing (MLST) is a popular and portable genotyping method that has been used extensively to characterise the genetic diversity of B. pseudomallei populations. MLST has been central to our understanding of the underlying phylogeographical signal present in the B. pseudomallei genome, revealing distinct populations on both the intra- and the inter-continental level. However, due to its high recombination rate, it is possible for B. pseudomallei isolates to share the same multilocus sequence type (ST) despite being genetically and geographically distinct, with two cases of ‘ST homoplasy’ recently reported between Cambodian and Australian B. pseudomallei isolates. This phenomenon can dramatically confound conclusions about melioidosis transmission patterns and source attribution, a critical issue for bacteria such as B. pseudomallei that are of concern due to their potential for use as bioweapons. In this study, we used whole-genome sequencing to identify the first reported instances of intracontinental ST homoplasy, which involved ST-722 and ST-804 B. pseudomallei isolates separated by large geographical distances. In contrast, a third suspected homoplasy case was shown to be a true long-range (460 km) dispersal event between a remote Australian island and the Australian mainland. Our results show that, whilst a highly useful and portable method, MLST can occasionally lead to erroneous conclusions about isolate origin and disease attribution. In cases where a shared ST is identified between geographically distant locales, whole-genome sequencing should be used to resolve strain origin.

Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000139
2017-11-14
2019-10-20
Loading full text...

Full text loading...

/deliver/fulltext/mgen/3/11/mgen000139.html?itemId=/content/journal/mgen/10.1099/mgen.0.000139&mimeType=html&fmt=ahah

References

  1. Wiersinga WJ, Currie BJ, Peacock SJ. Melioidosis. N Engl J Med 2012;367:1035–1044 [CrossRef][PubMed]
    [Google Scholar]
  2. Limmathurotsakul D, Peacock SJ. Melioidosis: a clinical overview. Br Med Bull 2011;99:125–139 [CrossRef][PubMed]
    [Google Scholar]
  3. Barnes JL, Ketheesan N. Route of infection in melioidosis. Emerg Infect Dis 2005;11:638–639 [CrossRef][PubMed]
    [Google Scholar]
  4. Gilad J, Harary I, Dushnitsky T, Schwartz D, Amsalem Y. Burkholderia mallei and Burkholderia pseudomallei as bioterrorism agents: national aspects of emergency preparedness. Isr Med Assoc J 2007;9:499–503[PubMed]
    [Google Scholar]
  5. 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 [CrossRef][PubMed]
    [Google Scholar]
  6. Godoy D, Randle G, Simpson AJ, Aanensen DM, Pitt TL et al. Multilocus sequence typing and evolutionary relationships among the causative agents of melioidosis and glanders, Burkholderia pseudomallei and Burkholderia mallei. J Clin Microbiol 2003;41:2068–2079 [CrossRef][PubMed]
    [Google Scholar]
  7. McCombie RL, Finkelstein RA, Woods DE. Multilocus sequence typing of historical Burkholderia pseudomallei isolates collected in Southeast Asia from 1964 to 1967 provides insight into the epidemiology of melioidosis. J Clin Microbiol 2006;44:2951–2962 [CrossRef][PubMed]
    [Google Scholar]
  8. Mayo M, Kaesti M, Harrington G, Cheng AC, Ward L et al. Burkholderia pseudomallei in unchlorinated domestic bore water, Tropical Northern Australia. Emerg Infect Dis 2011;17:1283–1285 [CrossRef][PubMed]
    [Google Scholar]
  9. McRobb E, Sarovich DS, Price EP, Kaestli M, Mayo M et al. Tracing melioidosis back to the source: using whole-genome sequencing to investigate an outbreak originating from a contaminated domestic water supply. J Clin Microbiol 2015;53:1144–1148 [CrossRef][PubMed]
    [Google Scholar]
  10. McRobb E, Kaestli M, Price EP, Sarovich DS, Mayo M et al. Distribution of Burkholderia pseudomallei in northern Australia, a land of diversity. Appl Environ Microbiol 2014;80:3463–3468 [CrossRef][PubMed]
    [Google Scholar]
  11. Chapple SN, Price EP, Sarovich DS, McRobb E, Mayo M et al. Burkholderia pseudomallei genotype distribution in the Northern Territory, Australia. Am J Trop Med Hyg 2016;94:68–72 [CrossRef][PubMed]
    [Google Scholar]
  12. Pearson T, Giffard P, Beckstrom-Sternberg S, Auerbach R, Hornstra H et al. Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer. BMC Biol 2009;7:78 [CrossRef][PubMed]
    [Google Scholar]
  13. De Smet B, Sarovich DS, Price EP, Mayo M, Theobald V et al. Whole-genome sequencing confirms that Burkholderia pseudomallei multilocus sequence types common to both Cambodia and Australia are due to homoplasy. J Clin Microbiol 2015;53:323–326 [CrossRef][PubMed]
    [Google Scholar]
  14. Price EP, Sarovich DS, Smith EJ, Machunter B, Harrington G et al. Unprecedented melioidosis cases in Northern Australia caused by an Asian Burkholderia pseudomallei strain identified by using large-scale comparative genomics. Appl Environ Microbiol 2016;82:954–963 [CrossRef][PubMed]
    [Google Scholar]
  15. Sarovich DS, Garin B, de Smet B, Kaestli M, Mayo M et al. Phylogenomic analysis reveals an Asian origin for African Burkholderia pseudomallei and further supports melioidosis endemicity in Africa. mSphere 2016;1:e00089-15 [CrossRef][PubMed]
    [Google Scholar]
  16. Chewapreecha C, Holden MT, Vehkala M, Välimäki N, Yang Z et al. Global and regional dissemination and evolution of Burkholderia pseudomallei. Nat Microbiol 2017;2:16263 [CrossRef][PubMed]
    [Google Scholar]
  17. Currie BJ, Ward L, Cheng AC. The epidemiology and clinical spectrum of melioidosis: 540 cases from the 20 year Darwin Prospective Study. PLoS Negl Trop Dis 2010;4:e900 [CrossRef][PubMed]
    [Google Scholar]
  18. 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 [CrossRef][PubMed]
    [Google Scholar]
  19. Sarovich DS, Price EP. SPANDx: a genomics pipeline for comparative analysis of large haploid whole genome re-sequencing datasets. BMC Res Notes 2014;7:618 [CrossRef][PubMed]
    [Google Scholar]
  20. Johnson SL, Baker AL, Chain PS, Currie BJ, Daligault HE et al. Whole-genome sequences of 80 environmental and clinical isolates of Burkholderia pseudomallei. Genome Announc 2015;3:e01282-14 [CrossRef][PubMed]
    [Google Scholar]
  21. Sarovich D. Microbial Genome Assembler Pipeline (MGAP): Initial Release. 2017;https://github.com/dsarov/MGAP---Microbial-Genome-Assembler-Pipeline
  22. Swofford DL. PAUP*: Phylogenetic Analysis Using Parsimony (*and other methods) 4.0.b5 Sunderland, MA: Sinauer Associates; 2001
    [Google Scholar]
  23. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014;30:1312–1313 [CrossRef][PubMed]
    [Google Scholar]
  24. Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res 2015;43:e15 [CrossRef][PubMed]
    [Google Scholar]
  25. Jolley KA, Maiden MC. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 2010;11:595 [CrossRef][PubMed]
    [Google Scholar]
  26. Sarovich DS, Chapple SNJ, Price EP, Mayo M, Holden MTG et al. Whole-genome sequencing to investigate a non-clonal melioidosis cluster on a remote Australian island. Microb Genom 2017;3:e0.000117 [CrossRef][PubMed]
    [Google Scholar]
  27. Viberg LT, Sarovich DS, Kidd TJ, Geake JB, Bell SC et al. Within-host evolution of Burkholderia pseudomallei during chronic infection of seven Australasian cystic fibrosis patients. MBio 2017;8:e00356-17 [CrossRef][PubMed]
    [Google Scholar]
  28. Lieberman TD, Michel JB, Aingaran M, Potter-Bynoe G, Roux D et al. Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes. Nat Genet 2011;43:1275–1280 [CrossRef][PubMed]
    [Google Scholar]
  29. Silva IN, Santos PM, Santos MR, Zlosnik JE, Speert DP et al. Long-term evolution of Burkholderia multivorans during a chronic cystic fibrosis infection reveals shifting forces of selection. mSystems 2016;1:e00029-16 [CrossRef][PubMed]
    [Google Scholar]
  30. Tuanyok A, Auerbach RK, Brettin TS, Bruce DC, Munk AC et al. A horizontal gene transfer event defines two distinct groups within Burkholderia pseudomallei that have dissimilar geographic distributions. J Bacteriol 2007;189:9044–9049 [CrossRef][PubMed]
    [Google Scholar]
  31. Sarovich DS, Price EP, Webb JR, Ward LM, Voutsinos MY et al. Variable virulence factors in Burkholderia pseudomallei (melioidosis) associated with human disease. PLoS One 2014;9:e91682 [CrossRef][PubMed]
    [Google Scholar]
  32. Stevens MP, Stevens JM, Jeng RL, Taylor LA, Wood MW et al. Identification of a bacterial factor required for actin-based motility of Burkholderia pseudomallei. Mol Microbiol 2005;56:40–53 [CrossRef][PubMed]
    [Google Scholar]
  33. Sim SH, Yu Y, Lin CH, Karuturi RK, Wuthiekanun V et al. The core and accessory genomes of Burkholderia pseudomallei: implications for human melioidosis. PLoS Pathog 2008;4:e1000178 [CrossRef][PubMed]
    [Google Scholar]
  34. Morris JL, Fane A, Sarovich DS, Price EP, Rush CM et al. Increased neurotropic threat from Burkholderia pseudomallei strains with a B. mallei-like variation in the bimA motility gene, Australia. Emerg Infect Dis 2017;23:eid2305.151417 [CrossRef][PubMed]
    [Google Scholar]
  35. Turner KM, Hanage WP, Fraser C, Connor TR, Spratt BG. Assessing the reliability of eBURST using simulated populations with known ancestry. BMC Microbiol 2007;7:30 [CrossRef][PubMed]
    [Google Scholar]
  36. Inglis TJ, Levy A, Merritt AJ, Hodge M, McDonald R et al. Melioidosis risk in a tropical industrial environment. Am J Trop Med Hyg 2009;80:78–84[PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000139
Loading
/content/journal/mgen/10.1099/mgen.0.000139
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

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