1887

Microbial Genomics logo

Volume 5, Issue 8

A cluster of melioidosis infections in hatchling saltwater crocodiles () resolved using genome-wide comparison of a common north Australian strain of Open Access

Abstract

is a Gram-negative saprophytic bacillus and the aetiological agent of melioidosis, a disease of public-health importance throughout Southeast Asia and northern Australia. Infection can occur in humans and a wide array of animal species, though zoonotic transmission and case clusters are rare. Despite its highly plastic genome and extensive strain diversity, fine-scale investigations into the population structure of indicate there is limited geographical dispersal amongst sequence types (STs). In the ‘Top End’ of northern Australia, five STs comprise 90 % of the overall abundance, the most prevalent and widespread of which is ST-109. In May 2016, ST-109 was implicated in two fatal cases of melioidosis in juvenile saltwater crocodiles at a wildlife park near Darwin, Australia. To determine the probable source of infection, we sampled the crocodile enclosures and analysed the phylogenetic relatedness of crocodile and culture-positive ST-109 environmental park isolates against an additional 135 ST-109 isolates from the Top End. Collectively, our whole-genome sequencing (WGS) and pathology findings confirmed detected in the hatchling incubator as the likely source of infection, with zero SNPs identified between clinical and environmental isolates. Our results also demonstrate little variation across the ST-109 genome, with SNPs in recombinogenic regions and one suspected case of ST homoplasy accounting for nearly all observed diversity. Collectively, this study supports the use of WGS for outbreak source attribution in highly recombinogenic pathogens, and confirms the epidemiological and phylogenetic insights that can be gained from high-resolution sequencing platforms.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Burkholderia pseudomallei , melioidosis , saltwater crocodile , source tracing and whole-genome sequencing
© 2019 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Loading

Article metrics loading...

/content/journal/mgen/10.1099/mgen.0.000288
2019-08-01
2024-04-25
Loading full text...

Full text loading...

/deliver/fulltext/mgen/5/8/mgen000288.html?itemId=/content/journal/mgen/10.1099/mgen.0.000288&mimeType=html&fmt=ahah

References

  1. Wiersinga WJ, Currie BJ, Peacock SJ. Melioidosis. N Engl J Med Overseas Ed 2012; 367:1035–1044 [View Article]
     [Google Scholar]
  2. Cheng AC, Currie BJ. Melioidosis: epidemiology, pathophysiology, and management. Clin Microbiol Rev 2005; 18:383–416 [View Article]
     [Google Scholar]
  3. 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 [View Article]
     [Google Scholar]
  4. Limmathurotsakul D, Golding N, Dance DAB, Messina JP, Pigott DM et al. Predicted global distribution of Burkholderia pseudomallei and burden of melioidosis. Nat Microbiol 2016; 1:15008 [View Article]
     [Google Scholar]
  5. Stewart JD, Smith S, Binotto E, McBride WJ, Currie BJ et al. The epidemiology and clinical features of melioidosis in far North Queensland: implications for patient management. PLoS Negl Trop Dis 2017; 11:e0005411 [View Article]
     [Google Scholar]
  6. Sprague LD, Neubauer H. Melioidosis in animals: a review on epizootiology, diagnosis and clinical presentation. J Vet Med B Infect Dis Vet Public Health 2004; 51:305–320 [View Article]
     [Google Scholar]
  7. Dance DA, King C, Aucken H, Knott CD, West PG et al. An outbreak of melioidosis in imported primates in Britain. Vet Rec 1992; 130:525–529 [View Article]
     [Google Scholar]
  8. Limmathurotsakul D, Thammasart S, Warrasuth N, Thapanagulsak P, Jatapai A et al. Melioidosis in animals, Thailand, 2006-2010. Emerg Infect Dis 2012; 18:325–327 [View Article]
     [Google Scholar]
  9. Thomas AD, Spinks GA, D'Arcy TL, Norton JH, Trueman KF. Evaluation of four serological tests for the diagnosis of caprine melioidosis. Aust Vet J 1988; 65:261–264 [View Article]
     [Google Scholar]
  10. Cottew GS. Melioidosis in sheep in queens land; a description of the causal organism. Aust J Exp Biol Med Sci 1950; 28:677–683
     [Google Scholar]
  11. Forbes-Faulkner JC, Townsend WL, Thomas AD. Pseudomonas pseudomallei infection in camels. Aust Vet J 1992; 69:148 [View Article]
     [Google Scholar]
  12. Choy JL, Mayo M, Janmaat A, Currie BJ. Animal melioidosis in Australia. Acta Trop 2000; 74:153–158 [View Article]
     [Google Scholar]
  13. Sim S, Ong C, Gan Y, Wang D, Koh V et al. Melioidosis in Singapore: clinical, veterinary, and environmental perspectives. Trop Med Infect Dis 2018; 3:31 [View Article]
     [Google Scholar]
  14. Ketterer PJ, Webster WR, Shield J, Arthur RJ, Blackall PJ et al. Melioidosis in intensive piggeries in South eastern Queensland. Aust Vet J 1986; 63:146–149 [View Article]
     [Google Scholar]
  15. Dodin A, Galimand M. [Origin, course and recession of an infectious disease, melioidosis, in temperate countries]. Arch Inst Pasteur Tunis 1986; 63:69–73 (in French)
     [Google Scholar]
  16. Höger ACR, Mayo M, Price EP, Theobald V, Harrington G et al. The melioidosis agent Burkholderia pseudomallei and related opportunistic pathogens detected in faecal matter of wildlife and livestock in northern Australia. Epidemiol Infect 2016; 144:1924–1932 [View Article]
     [Google Scholar]
  17. Hampton V, Kaestli M, Mayo M, Choy JL, Harrington G et al. Melioidosis in birds and Burkholderia pseudomallei dispersal, Australia. Emerg Infect Dis 2011; 17:1310–1312 [View Article]
     [Google Scholar]
  18. 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 [View Article]
     [Google Scholar]
  19. 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 [View Article]
     [Google Scholar]
  20. 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 [View Article]
     [Google Scholar]
  21. Currie BJ, Gal D, Mayo M, Ward L, Godoy D et al. Using BOX-PCR to exclude a clonal outbreak of melioidosis. BMC Infect Dis 2007; 7:68 [View Article]
     [Google Scholar]
  22. Chewapreecha C, Holden MTG, Vehkala M, Välimäki N, Yang Z et al. Global and regional dissemination and evolution of Burkholderia pseudomallei . Nat Microbiol 2017; 2:16263 [View Article]
     [Google Scholar]
  23. Chapple SNJ, Price EP, Mayo M, Currie BJ, Kaestli M et al. Burkholderia pseudomallei genotype distribution in the Northern Territory, Australia. Am J Trop Med Hyg 2016; 94:68–72 [View Article]
     [Google Scholar]
  24. Cheng AC, Ward L, Godoy D, Norton R, Mayo M et al. Genetic diversity of Burkholderia pseudomallei isolates in Australia. J Clin Microbiol 2008; 46:249–254 [View Article]
     [Google Scholar]
  25. 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 [View Article]
     [Google Scholar]
  26. 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 [View Article]
     [Google Scholar]
  27. Kommanee J, Preecharram S, Daduang S, Temsiripong Y, Dhiravisit A et al. Antibacterial activity of plasma from crocodile (Crocodylus siamensis) against pathogenic bacteria. Ann Clin Microbiol Antimicrob 2012; 11:22 [View Article]
     [Google Scholar]
  28. Benedict S, Shilton CM. Providencia rettgeri septicaemia in farmed crocodiles. Microbiol Aust 2016; 37:114–117 [View Article]
     [Google Scholar]
  29. 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 [View Article]
     [Google Scholar]
  30. Currie BJ, Price EP, Mayo M, Kaestli M, Theobald V et al. Use of whole-genome sequencing to link Burkholderia pseudomallei from air sampling to mediastinal melioidosis, Australia. Emerg Infect Dis 2015; 21:2052–2054 [View Article]
     [Google Scholar]
  31. Limmathurotsakul D, Dance DAB, Wuthiekanun V, Kaestli M, Mayo M et al. Systematic review and consensus guidelines for environmental sampling of Burkholderia pseudomallei . PLoS Negl Trop Dis 2013; 7:e2105 [View Article]
     [Google Scholar]
  32. de Lamballerie X, Zandotti C, Vignoli C, Bollet C, de Micco P. A one-step microbial DNA extraction method using "Chelex 100" suitable for gene amplification. Res Microbiol 1992; 143:785–790 [View Article]
     [Google Scholar]
  33. Novak RT, Glass MB, Gee JE, Gal D, Mayo MJ et al. Development and evaluation of a real-time PCR assay targeting the type III secretion system of Burkholderia pseudomallei . J Clin Microbiol 2006; 44:85–90 [View Article]
     [Google Scholar]
  34. 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 [View Article]
     [Google Scholar]
  35. Jolley KA, Maiden MCJ. BIGSdb: scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 2010; 11:595 [View Article]
     [Google Scholar]
  36. 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 [View Article]
     [Google Scholar]
  37. Swofford DL. PAUP*: phylogenetic analysis using parsimony (*and other methods) 4.0.b5. Sunderland, MA: Sinauer Associates; 2001
  38. Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res 2016; 44:W242–W245 [View Article]
     [Google Scholar]
  39. 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 [View Article]
     [Google Scholar]
  40. 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]
     [Google Scholar]
  41. 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 [View Article]
     [Google Scholar]
  42. 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 [View Article]
     [Google Scholar]
  43. Webb JR, Sarovich DS, Price EP, Ward LM, Mayo M et al. Burkholderia pseudomallei lipopolysaccharide genotype does not correlate with severity or outcome in melioidosis: host risk factors remain the critical determinant. Open Forum Infect Dis 2019; 6:ofz091 [View Article]
     [Google Scholar]
  44. Spring-Pearson SM, Stone JK, Doyle A, Allender CJ, Okinaka RT et al. Pangenome analysis of Burkholderia pseudomallei: genome evolution preserves gene order despite high recombination rates. PLoS One 2015; 10:e0140274 [View Article]
     [Google Scholar]
  45. Dale J, Price EP, Hornstra H, Busch JD, Mayo M et al. Epidemiological tracking and population assignment of the non-clonal bacterium, Burkholderia pseudomallei . PLoS Negl Trop Dis 2011; 5:e1381 [View Article]
     [Google Scholar]
  46. Huchzermeyer F. Crocodiles: Biology, Husbandry and Diseases Wallingford: CABI Publishing; 2003
     [Google Scholar]
  47. Kaestli M, Mayo M, Harrington G, Watt F, Hill J et al. Sensitive and specific molecular detection of Burkholderia pseudomallei, the causative agent of melioidosis, in the soil of tropical northern Australia. Appl Environ Microbiol 2007; 73:6891–6897 [View Article]
     [Google Scholar]
  48. Knappik M, Dance DAB, Rattanavong S, Pierret A, Ribolzi O et al. Evaluation of molecular methods to improve the detection of Burkholderia pseudomallei in soil and water samples from Laos. Appl Environ Microbiol 2015; 81:3722–3727 [View Article]
     [Google Scholar]
  49. Price EP, Sarovich DS, Viberg L, Mayo M, Kaestli M et al. Whole-genome sequencing of Burkholderia pseudomallei isolates from an unusual melioidosis case identifies a polyclonal infection with the same multilocus sequence type. J Clin Microbiol 2015; 53:282–286 [View Article]
     [Google Scholar]
  50. Aziz A, Sarovich DS, Harris TM, Kaestli M, McRobb E et al. Suspected cases of intracontinental Burkholderia pseudomallei sequence type homoplasy resolved using whole-genome sequencing. Microb Genom 2017; 3:e000139 [View Article]
     [Google Scholar]
  51. Inglis TJJ, 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 [View Article]
     [Google Scholar]
  52. 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 [View Article]
     [Google Scholar]
  53. Asche V. Melioidosis - a disease for all organs. Today's Life Sci 1991; 3:34–40
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/mgen/10.1099/mgen.0.000288
Loading
A cluster of melioidosis infections in hatchling saltwater crocodiles (Crocodylus porosus) resolved using genome-wide comparison of a common north Australian strain of Burkholderia pseudomallei
M Gen 5, e000288 (2019); https://doi.org/10.1099/mgen.0.000288
/content/journal/mgen/10.1099/mgen.0.000288
/content/journal/mgen/10.1099/mgen.0.000288
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited 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