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Volume 7, Issue 2

Whole-genome comparative analysis of Malaysian clinical isolates Open Access

Abstract

, a soil-dwelling Gram-negative bacterium, is the causative agent of the endemic tropical disease melioidosis. Clinical manifestations of infection range from acute or chronic localized infection in a single organ to fulminant septicaemia in multiple organs. The diverse clinical manifestations are attributed to various factors, including the genome plasticity across strains. We previously characterized strains isolated in Malaysia and noted different levels of virulence in model hosts. We hypothesized that the difference in virulence might be a result of variance at the genome level. In this study, we sequenced and assembled four Malaysian clinical isolates, UKMR15, UKMPMC2000, UKMD286 and UKMH10. Phylogenomic analysis showed that Malaysian subclades emerged from the Asian subclade, suggesting that the Malaysian strains originated from the Asian region. Interestingly, the low-virulence strain, UKMH10, was the most distantly related compared to the other Malaysian isolates. Genomic island (GI) prediction analysis identified a new island of 23 kb, GI9c, which is present in and , but not . Genes encoding known virulence factors were present across all four genomes, but comparative analysis of the total gene content across the Malaysian strains identified 104 genes that are absent in UKMH10. We propose that these genes may encode novel virulence factors, which may explain the reduced virulence of this strain. Further investigation on the identity and role of these 104 proteins may aid in understanding pathogenicity to guide the design of new therapeutics for treating melioidosis.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Burkholderia pseudomallei , comparative genomics , genomic island and virulence factors
Funding
This study was supported by the:
  • Universiti Kebangsaan Malaysia (MY) (Award DIP-2015-022)
    • Principle Award Recipient: SheilaNathan
  • Ministry of Education Malaysia (MY) (Award FRGS/1/2016/SKK11/UKM/01/1)
    • Principle Award Recipient: SheilaNathan
  • Kementerian Sains, Teknologi dan Inovasi (Award 02-05-20-SF0006)
    • Principle Award Recipient: SheilaNathan
© 2021 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution NonCommercial License.
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2021-02-10
2024-04-18
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References

  1. Inglis TJ, Garrow SC, Henderson M, Clair A, Sampson J et al. Burkholderia pseudomallei traced to water treatment plant in Australia. Emerg Infect Dis 2000; 6:56–59 [View Article][PubMed]
     [Google Scholar]
  2. Wuthiekanun V, Smith MD, Dance DAB, White NJ. Isolation of Pseudomonas pseudomallei from soil in North-Eastern Thailand. Trans R Soc Trop Med Hyg 1995; 89:41–43 [View Article][PubMed]
     [Google Scholar]
  3. White NJ. Melioidosis. Lancet 2003; 361:1715–1722 [View Article][PubMed]
     [Google Scholar]
  4. Lim C, Peacock SJ, Limmathurotsakul D. Association between activities related to routes of infection and clinical manifestations of melioidosis. Clin Microbiol Infect 2016; 22:79.e1–79.e3 [View Article][PubMed]
     [Google Scholar]
  5. 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][PubMed]
     [Google Scholar]
  6. 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][PubMed]
     [Google Scholar]
  7. Holden MTG, Titball RW, Peacock SJ, Cerdeño-Tárraga AM, Atkins T et al. Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei . Proc Natl Acad Sci USA 2004; 101:14240–14245 [View Article][PubMed]
     [Google Scholar]
  8. Pearson T, Giffard P, Beckstrom-Sternberg S, Auerbach R, Hornstra H. Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer. BMC Biol 2009; 7:78 [View Article]
     [Google Scholar]
  9. Tuanyok A, Leadem BR, Auerbach RK, Beckstrom-Sternberg SM, Beckstrom-Sternberg JS et al. Genomic islands from five strains of Burkholderia pseudomallei . BMC Genomics 2008; 9:566 [View Article][PubMed]
     [Google Scholar]
  10. 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][PubMed]
     [Google Scholar]
  11. Lee S-H, Ooi S-K, Mahadi NM, Tan M-W, Nathan S. Complete killing of Caenorhabditis elegans by Burkholderia pseudomallei is dependent on prolonged direct association with the viable pathogen. PLoS One 2011; 6:e16707 [View Article][PubMed]
     [Google Scholar]
  12. Lee S-H, Chong C-E, Lim B-S, Chai S-J, Sam K-K et al. Burkholderia pseudomallei animal and human isolates from Malaysia exhibit different phenotypic characteristics. Diagn Microbiol Infect Dis 2007; 58:263–270 [View Article][PubMed]
     [Google Scholar]
  13. Chin C-S, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [View Article][PubMed]
     [Google Scholar]
  14. Seppey M, Manni M, Zdobnov EM. BUSCO: assessing genome assembly and annotation completeness. Methods Mol Biol 2019; 1962:227–245 [View Article][PubMed]
     [Google Scholar]
  15. Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res 2018; 3:124 [View Article]
     [Google Scholar]
  16. Kislyuk AO, Katz LS, Agrawal S, Hagen MS, Conley AB et al. A computational genomics pipeline for prokaryotic sequencing projects. Bioinformatics 2010; 26:1819–1826 [View Article][PubMed]
     [Google Scholar]
  17. Otto TD, Dillon GP, Degrave WS, Berriman M. RATT: rapid annotation transfer tool. Nucleic Acids Res 2011; 39:e57 [View Article]
     [Google Scholar]
  18. Lowe TM, Eddy SR. TRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article]
     [Google Scholar]
  19. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article][PubMed]
     [Google Scholar]
  20. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H et al. Gene Ontology: tool for the unification of biology. Nat Genet 2000; 25:25–29 [View Article]
     [Google Scholar]
  21. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H et al. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 1999; 27:29–34 [View Article][PubMed]
     [Google Scholar]
  22. Darling AE, Mau B, Perna NT. progressiveMauve: multiple genome alignment with gene gain, loss and rearrangement. PLoS One 2010; 5:e11147 [View Article][PubMed]
     [Google Scholar]
  23. Li L, Stoeckert CJ, Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res 2003; 13:2178–2189 [View Article][PubMed]
     [Google Scholar]
  24. Laing C, Buchanan C, Taboada EN, Zhang Y, Kropinski A. Pan-Genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions. BMC Bioinformatics 2010; 11:461 [View Article]
     [Google Scholar]
  25. Laing C, Villegas A, Taboada EN, Kropinski A, Thomas JE et al. Identification of Salmonella enterica species- and subgroup-specific genomic regions using Panseq 2.0. Infect Genet Evol 2011; 11:2151–2161 [View Article][PubMed]
     [Google Scholar]
  26. Huelsenbeck JP, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 2001; 17:754–755 [View Article][PubMed]
     [Google Scholar]
  27. Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A et al. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol 2012; 61:539–542 [View Article][PubMed]
     [Google Scholar]
  28. Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 2003; 19:1572–1574 [View Article][PubMed]
     [Google Scholar]
  29. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v4: recent updates and new developments. Nucleic Acids Res 2019; 47:W256–W259 [View Article]
     [Google Scholar]
  30. Langille MGI, Brinkman FSL. IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics 2009; 25:664–665 [View Article][PubMed]
     [Google Scholar]
  31. 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]
  32. Johnson SL, Bishop-Lilly KA, Ladner JT, Daligault HE, Davenport KW et al. Complete genome sequences for 59 Burkholderia isolates, both pathogenic and near neighbor. Genome Announc 2015; 3:18–20 [View Article][PubMed]
     [Google Scholar]
  33. 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 [View Article][PubMed]
     [Google Scholar]
  34. Sarovich DS, Garin B, De Smet B, Kaestli M, Mayo M. Phylogenomic analysis reveals an Asian origin for African Burkholderia pseudomallei and further supports melioidosis endemicity in Africa. mSphere 2016; 1:e00089-15 [View Article][PubMed]
     [Google Scholar]
  35. Sim SH, Yu Y, Lin CH, Karuturi RKM, Wuthiekanun V et al. The core and accessory genomes of Burkholderia pseudomallei: implications for human melioidosis. PLoS Pathog 2008; 4:e1000178 [View Article][PubMed]
     [Google Scholar]
  36. Currie BJ, Fisher DA, Howard DM, Burrow JN. Neurological melioidosis. Acta Trop 2000; 74:145–151 [View Article][PubMed]
     [Google Scholar]
  37. Chen L, Yang J, Yu J, Yao Z, Sun L et al. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 2005; 33:D325–D328 [View Article][PubMed]
     [Google Scholar]
  38. Sarovich DS, Price EP, Webb JR, Ward LM, Voutsinos MY. Variable virulence factors in Burkholderia pseudomallei (melioidosis) associated with human disease. PLoS One 2014; 9:e91682 [View Article][PubMed]
     [Google Scholar]
  39. Gerdes K, Maisonneuve E. Bacterial persistence and toxin-antitoxin loci. Annu Rev Microbiol 2012; 66:103–123 [View Article][PubMed]
     [Google Scholar]
  40. Butt A, Müller C, Harmer N, Titball RW. Identification of type II toxin-antitoxin modules in Burkholderia pseudomallei . FEMS Microbiol Lett 2013; 338:86–94 [View Article][PubMed]
     [Google Scholar]
  41. Keren I, Shah D, Spoering A, Kaldalu N, Lewis K. Specialized persister cells and the mechanism of multidrug tolerance in Escherichia coli . J Bacteriol 2004; 186:8172–8180 [View Article][PubMed]
     [Google Scholar]
  42. Barnes JL, Ketheesan N. Route of infection in melioidosis. Emerg Infect Dis 2005; 11:638–639 [View Article][PubMed]
     [Google Scholar]
  43. Reckseidler-Zenteno SL, DeVinney R, Woods DE. The capsular polysaccharide of Burkholderia pseudomallei contributes to survival in serum by reducing complement factor C3b deposition. Infect Immun 2005; 73:1106–1115 [View Article][PubMed]
     [Google Scholar]
  44. Reckseidler-Zenteno SL. Capsular polysaccharides produced by the bacterial pathogen Burkholderia pseudomallei . In Nedra Karunaratne D. editor The Complex World of Polysaccharides London: IntechOpen; 2012 pp 127–152
     [Google Scholar]
  45. 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][PubMed]
     [Google Scholar]
  46. Price EP, Currie BJ, Sarovich DS. Genomic insights into the melioidosis pathogen, Burkholderia pseudomallei . Curr Trop Med Rep 2017; 4:95–102 [View Article]
     [Google Scholar]
  47. Podin Y, Sarovich DS, Price EP, Kaestli M, Mayo M et al. Burkholderia pseudomallei isolates from Sarawak, Malaysian Borneo, are predominantly susceptible to aminoglycosides and macrolides. Antimicrob Agents Chemother 2014; 58:162–166 [View Article][PubMed]
     [Google Scholar]
  48. Chew SC. The Southeast Asian connection in the first Eurasian world economy 200 BC AD 500. In Hall TD. editor Comparing Globalizations: Historical and World-Systems Approaches Springer International Publishing; 2018 pp 91–117
     [Google Scholar]
  49. Nathan S, Chieng S, Kingsley PV, Mohan A, Podin Y. Melioidosis in Malaysia: incidence, clinical challenges, and advances in understanding pathogenesis. Trop Med Infect Dis 2018; 3:25 [View Article][PubMed]
     [Google Scholar]
  50. Tumapa S, Holden MTG, Vesaratchavest M, Wuthiekanun V, Limmathurotsakul D et al. Burkholderia pseudomallei genome plasticity associated with genomic island variation. BMC Genomics 2008; 9:190 [View Article][PubMed]
     [Google Scholar]
  51. Challacombe JF, Stubben CJ, Klimko CP, Welkos SL, Kern SJ et al. Interrogation of the Burkholderia pseudomallei genome to address differential virulence among isolates. PLoS One 2014; 9:e115951 [View Article][PubMed]
     [Google Scholar]
  52. Ainelo A, Tamman H, Leppik M, Remme J, Hõrak R. The toxin GraT inhibits ribosome biogenesis. Mol Microbiol 2016; 100:719–734 [View Article][PubMed]
     [Google Scholar]
  53. Butt A, Higman VA, Williams C, Crump MP, Hemsley CM et al. The HicA toxin from Burkholderia pseudomallei has a role in persister cell formation. Biochem J 2014; 459:333–344 [View Article][PubMed]
     [Google Scholar]
  54. Wood TL, Wood TK. The HigB/HigA toxin/antitoxin system of Pseudomonas aeruginosa influences the virulence factors pyochelin, pyocyanin, and biofilm formation. Microbiologyopen 2016; 5:499–511 [View Article][PubMed]
     [Google Scholar]
  55. Wen W, Liu B, Xue L, Zhu Z, Niu L. Autoregulation and virulence control by the toxin-antitoxin system SavRS in Staphylococcus aureus . Infect Immun 2018; 86:e00032-18 [View Article][PubMed]
     [Google Scholar]
  56. Soheili S, Ghafourian S, Sekawi Z, Neela VK, Sadeghifard N et al. The mazEF toxin-antitoxin system as an attractive target in clinical isolates of Enterococcus faecium and Enterococcus faecalis . Drug Des Devel Ther 2015; 9:2553–2561 [View Article][PubMed]
     [Google Scholar]
  57. Schuster CF, Mechler L, Nolle N, Krismer B, Zelder M-E et al. The mazEF toxin-antitoxin system alters the β-lactam susceptibility of Staphylococcus aureus . PLoS One 2015; 10:e0126118 [View Article][PubMed]
     [Google Scholar]
  58. Zhang Y, Inouye M. The inhibitory mechanism of protein synthesis by YoeB, an Escherichia coli toxin. J Biol Chem 2009; 284:6627–6638 [View Article][PubMed]
     [Google Scholar]
  59. Yamaguchi Y, Park J-H, Inouye M. Toxin-antitoxin systems in bacteria and archaea. Annu Rev Genet 2011; 45:61–79 [View Article][PubMed]
     [Google Scholar]
  60. Drenkard E. Antimicrobial resistance of Pseudomonas aeruginosa biofilms. Microbes Infect 2003; 5:1213–1219 [View Article][PubMed]
     [Google Scholar]
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Whole-genome comparative analysis of Malaysian Burkholderia pseudomallei clinical isolates
M Gen 7, 000527 (2021); https://doi.org/10.1099/mgen.0.000527
/content/journal/mgen/10.1099/mgen.0.000527
/content/journal/mgen/10.1099/mgen.0.000527
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