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Abstract

Orientia tsutsugamushi, formerly Rickettsia tsutsugamushi, is an obligate intracellular pathogen that causes scrub typhus, an underdiagnosed acute febrile disease with high morbidity. Scrub typhus is transmitted by the larval stage (chigger) of Leptotrombidium mites and is irregularly distributed across endemic regions of Asia, Australia and islands of the western Pacific Ocean. Previous work to understand population genetics in O. tsutsugamushi has been based on sub-genomic sampling methods and whole-genome characterization of two genomes. In this study, we compared 40 genomes from geographically dispersed areas and confirmed patterns of extensive homologous recombination likely driven by transposons, conjugative elements and repetitive sequences. High rates of lateral gene transfer (LGT) among O. tsutsugamushi genomes appear to have effectively eliminated a detectable clonal frame, but not our ability to infer evolutionary relationships and phylogeographical clustering. Pan-genomic comparisons using 31 082 high-quality bacterial genomes from 253 species suggests that genomic duplication in O. tsutsugamushi is almost unparalleled. Unlike other highly recombinant species where the uptake of exogenous DNA largely drives genomic diversity, the pan-genome of O. tsutsugamushi is driven by duplication and divergence. Extensive gene innovation by duplication is most commonly attributed to plants and animals and, in contrast with LGT, is thought to be only a minor evolutionary mechanism for bacteria. The near unprecedented evolutionary characteristics of O. tsutsugamushi, coupled with extensive intra-specific LGT, expand our present understanding of rapid bacterial evolutionary adaptive mechanisms.

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2018-07-23
2019-10-18
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References

  1. Watt G, Parola P. Scrub typhus and tropical rickettsioses. Curr Opin Infect Dis 2003;16:429–436 [CrossRef]
    [Google Scholar]
  2. Kelly DJ, Fuerst PA, Ching WM, Richards AL. Scrub typhus: the geographic distribution of phenotypic and genotypic variants of Orientia tsutsugamushi. Clin Infect Dis 2009;48:S203–S230 [CrossRef][PubMed]
    [Google Scholar]
  3. Balcells ME, Rabagliati R, García P, Poggi H, Oddó D et al. Endemic scrub typhus-like illness, Chile. Emerg Infect Dis 2011;17:1659–1663 [CrossRef][PubMed]
    [Google Scholar]
  4. Cosson JF, Galan M, Bard E, Razzauti M, Bernard M et al. Detection of Orientia sp. DNA in rodents from Asia, West Africa and Europe. Parasit Vectors 2015;8:172 [CrossRef][PubMed]
    [Google Scholar]
  5. Izzard L, Fuller A, Blacksell SD, Paris DH, Richards AL et al. Isolation of a novel Orientia species (O. chuto sp. nov.) from a patient infected in Dubai. J Clin Microbiol 2010;48:4404–4409 [CrossRef][PubMed]
    [Google Scholar]
  6. Fletcher W. Tropical typhus. BMJ 1932;2:1140–1141 [CrossRef][PubMed]
    [Google Scholar]
  7. Hotta K, Pham HT, Hoang HT, Trang TC, Vu TN et al. Prevalence and phylogenetic analysis of Orientia tsutsugamushi in small mammals in Hanoi, Vietnam. Vector Borne Zoonotic Dis 2016;16:96–102 [CrossRef][PubMed]
    [Google Scholar]
  8. Maxcy KF. In Soule MH. (editor) Scrub Typhus (Tsutsugamushi Disease) in the US Army During World War II Washington, DC: American Association for the Advancement of Science; 1948; pp.36–50
    [Google Scholar]
  9. Takhampunya R, Tippayachai B, Korkusol A, Promsathaporn S, Leepitakrat S et al. Transovarial transmission of co-existing Orientia tsutsugamushi genotypes in laboratory-reared Leptotrombidium imphalum. Vector Borne Zoonotic Dis 2016;16:33–41 [CrossRef][PubMed]
    [Google Scholar]
  10. Nakayama K, Yamashita A, Kurokawa K, Morimoto T, Ogawa M et al. The whole-genome sequencing of the obligate intracellular bacterium Orientia tsutsugamushi revealed massive gene amplification during reductive genome evolution. DNA Res 2008;15:185–199 [CrossRef][PubMed]
    [Google Scholar]
  11. Cho NH, Kim HR, Lee JH, Kim SY, Kim J et al. The Orientia tsutsugamushi genome reveals massive proliferation of conjugative type IV secretion system and host-cell interaction genes. Proc Natl Acad Sci USA 2007;104:7981–7986 [CrossRef][PubMed]
    [Google Scholar]
  12. Taylor JS, Raes J. Duplication and divergence: the evolution of new genes and old ideas. Annu Rev Genet 2004;38:615–643 [CrossRef][PubMed]
    [Google Scholar]
  13. Puigbò P, Lobkovsky AE, Kristensen DM, Wolf YI, Koonin EV. Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes. BMC Biol 2014;12:66 [CrossRef][PubMed]
    [Google Scholar]
  14. Treangen TJ, Rocha EP. Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet 2011;7:e1001284 [CrossRef][PubMed]
    [Google Scholar]
  15. Bratlie MS, Johansen J, Sherman BT, Huang DW, Lempicki RA et al. Gene duplications in prokaryotes can be associated with environmental adaptation. BMC Genomics 2010;11:588 [CrossRef][PubMed]
    [Google Scholar]
  16. Gevers D, Vandepoele K, Simillion C, van de Peer Y. Gene duplication and biased functional retention of paralogs in bacterial genomes. Trends Microbiol 2004;12:148–154 [CrossRef][PubMed]
    [Google Scholar]
  17. Williamson CHD, Sanchez A, Vazquez A, Gutman J, Sahl JW. Bacterial genome reduction as a result of short read sequence assembly. bioRxiv 2016
    [Google Scholar]
  18. Bzymek M, Lovett ST. Instability of repetitive DNA sequences: the role of replication in multiple mechanisms. Proc Natl Acad Sci USA 2001;98:8319–8325 [CrossRef][PubMed]
    [Google Scholar]
  19. Darmon E, Leach DR. Bacterial genome instability. Microbiol Mol Biol Rev 2014;78:1–39 [CrossRef][PubMed]
    [Google Scholar]
  20. Didelot X, Maiden MCJ. Impact of recombination on bacterial evolution. Trends Microbiol 2010;18:315–322 [CrossRef]
    [Google Scholar]
  21. Achaz G, Rocha EPC, Netter P, Coissac E. Origin and fate of repeats in bacteria. Nucleic Acids Res 2002;30:2987–2994 [CrossRef]
    [Google Scholar]
  22. Enatsu T, Urakami H, Tamura A. Phylogenetic analysis of Orientia tsutsugamushi strains based on the sequence homologies of 56-kDa type-specific antigen genes. FEMS Microbiol Lett 1999;180:163–169 [CrossRef]
    [Google Scholar]
  23. Nakayama K, Kurokawa K, Fukuhara M, Urakami H, Yamamoto S et al. Genome comparison and phylogenetic analysis of Orientia tsutsugamushi strains. DNA Res 2010;17:281–291 [CrossRef][PubMed]
    [Google Scholar]
  24. Duong V, Blassdell K, May TT, Sreyrath L, Gavotte L et al. Diversity of Orientia tsutsugamushi clinical isolates in Cambodia reveals active selection and recombination process. Infect Genet Evol 2013;15:25–34 [CrossRef][PubMed]
    [Google Scholar]
  25. Sonthayanon P, Peacock SJ, Chierakul W, Wuthiekanun V, Blacksell SD et al. High rates of homologous recombination in the mite endosymbiont and opportunistic human pathogen Orientia tsutsugamushi. PLoS Negl Trop Dis 2010;4:e752 [CrossRef][PubMed]
    [Google Scholar]
  26. Wongprompitak P, Duong V, Anukool W, Sreyrath L, Mai TTX et al. Orientia tsutsugamushi, agent of scrub typhus, displays a single metapopulation with maintenance of ancestral haplotypes throughout continental South East Asia. Infect Genet Evol 2015;31:1–8 [CrossRef][PubMed]
    [Google Scholar]
  27. Sahl JW, Matalka MN, Rasko DA. Phylomark, a tool to identify conserved phylogenetic markers from whole-genome alignments. Appl Environ Microbiol 2012;78:4884–4892 [CrossRef][PubMed]
    [Google Scholar]
  28. Milkman R, Bridges MM. Molecular evolution of the Escherichia coli chromosome. III. Clonal frames. Genetics 1990;126:505–517[PubMed]
    [Google Scholar]
  29. Phetsouvanh R, Sonthayanon P, Pukrittayakamee S, Paris DH, Newton PN et al. The diversity and geographical structure of Orientia tsutsugamushi strains from scrub typhus patients in Laos. PLoS Negl Trop Dis 2015;9:e0004024 [CrossRef][PubMed]
    [Google Scholar]
  30. 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]
    [Google Scholar]
  31. Duong V, Mai TTX, Blasdell K, Lo LV, Morvan C et al. Molecular epidemiology of Orientia tsutsugamushi in Cambodia and Central Vietnam reveals a broad region-wide genetic diversity. Infect Genet Evol 2013;15:35–42 [CrossRef][PubMed]
    [Google Scholar]
  32. Keim P, Grunow R, Vipond R, Grass G, Hoffmaster A et al. Whole genome analysis of injectional anthrax identifies two disease clusters spanning more than 13 years. EBioMedicine 2015;2:1613–1618 [CrossRef][PubMed]
    [Google Scholar]
  33. Stone NE, Sidak-Loftis LC, Sahl JW, Vazquez AJ, Wiggins KB et al. More than 50% of Clostridium difficile Isolates from Pet Dogs in Flagstaff, USA, Carry Toxigenic Genotypes. PLoS One 2016;11: [CrossRef][PubMed]
    [Google Scholar]
  34. Kozarewa I, Turner DJ. Amplification-free library preparation for paired-end Illumina sequencing. Methods Mol Biol 2011;733:257–266 [CrossRef][PubMed]
    [Google Scholar]
  35. Nurk S, Bankevich A, Antipov D. Assembling genomes and mini-metagenomes from highly chimeric reads. In Deng M, Jiang R, Sun F, Zhang X. (editors) Research in Computational Molecular Biology. RECOMB 2013 Lecture Notes in Computer Sciencevol. 7821 Berlin, Heidelberg: Springer; 2013
    [Google Scholar]
  36. Quinlan AR. BEDTools: the Swiss-Army tool for genome feature analysis. Curr Protoc Bioinformatics 2014;47:11.12.1–11.12.34 [CrossRef][PubMed]
    [Google Scholar]
  37. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010;26:841–842 [CrossRef]
    [Google Scholar]
  38. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215:403–410 [CrossRef]
    [Google Scholar]
  39. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J et al. BLAST+: architecture and applications. BMC Bioinformatics 2009;10:421 [CrossRef]
    [Google Scholar]
  40. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank. Nucleic Acids Res 2004;33:D34–D38 [CrossRef]
    [Google Scholar]
  41. Sahl JW, Lemmer D, Travis J, Schupp JM, Gillece JD et al. NASP: an accurate, rapid method for the identification of SNPs in WGS datasets that supports flexible input and output formats. Microb Genom 2016;2: [CrossRef][PubMed]
    [Google Scholar]
  42. Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv 2013;1303.3997.
    [Google Scholar]
  43. Delcher AL, Phillippy A, Carlton J, Salzberg SL. Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res 2002;30:2478–2483 [CrossRef]
    [Google Scholar]
  44. McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 2010;20:1297–1303 [CrossRef][PubMed]
    [Google Scholar]
  45. Renvoisé A, Merhej V, Georgiades K, Raoult D. Intracellular Rickettsiales: insights into manipulators of eukaryotic cells. Trends Mol Med 2011;17:573–583 [CrossRef]
    [Google Scholar]
  46. Swofford DL. PAUP* Phylogenetic Analysis Using Parsimony (*and Other Methods). 2002
  47. Nguyen LT, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015;32:268–274 [CrossRef][PubMed]
    [Google Scholar]
  48. Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol 2012;29:1969–1973 [CrossRef][PubMed]
    [Google Scholar]
  49. Bouckaert RR. DensiTree: making sense of sets of phylogenetic trees. Bioinformatics 2010;26:1372–1373 [CrossRef]
    [Google Scholar]
  50. Sahl JW, Allender CJ, Colman RE, Califf KJ, Schupp JM et al. Genomic characterization of Burkholderia pseudomallei isolates selected for medical countermeasures testing: comparative genomics associated with differential virulence. PLoS One 2015;10:e0121052 [CrossRef][PubMed]
    [Google Scholar]
  51. Hendriksen RS, Price LB, Schupp JM, Gillece JD, Kaas RS et al. Population genetics of Vibrio cholerae from Nepal in 2010: evidence on the origin of the Haitian outbreak. MBio 2011;2:e00157-11 [CrossRef][PubMed]
    [Google Scholar]
  52. Hornstra HM, Priestley RA, Georgia SM, Kachur S, Birdsell DN et al. Rapid typing of Coxiella burnetii. PLoS One 2011;6:e26201 [CrossRef][PubMed]
    [Google Scholar]
  53. Morelli G, Song Y, Mazzoni CJ, Eppinger M, Roumagnac P et al. Yersinia pestis genome sequencing identifies patterns of global phylogenetic diversity. Nat Genet 2010;42:1140–1143 [CrossRef]
    [Google Scholar]
  54. Pearson T, Busch JD, Ravel J, Read TD, Rhoton SD et al. Phylogenetic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing. Proc Natl Acad Sci USA 2004;101:13536–13541 [CrossRef][PubMed]
    [Google Scholar]
  55. Pearson T, Hornstra HM, Sahl JW, Schaack S, Schupp JM et al. When outgroups fail; phylogenomics of rooting the emerging pathogen, Coxiella burnetii. Syst Biol 2013;62:752–762 [CrossRef][PubMed]
    [Google Scholar]
  56. Pearson T, Okinaka RT, Foster JT, Keim P. Phylogenetic understanding of clonal populations in an era of whole genome sequencing. Infect Genet Evol 2009;9:1010–1019 [CrossRef]
    [Google Scholar]
  57. Price LB, Johnson JR, Aziz M, Clabots C, Johnston B et al. The epidemic of extended-spectrum-β-lactamase-producing Escherichia coli ST131 is driven by a single highly pathogenic subclone, H30-Rx. MBio 2013;4:e00377-13 [CrossRef][PubMed]
    [Google Scholar]
  58. Price LB, Stegger M, Hasman H, Aziz M, Larsen J et al. Staphylococcus aureus CC398: host adaptation and emergence of methicillin resistance in livestock. MBio 2012;3:e00305-11 [CrossRef][PubMed]
    [Google Scholar]
  59. Hudson RE, Bergthorsson U, Roth JR, Ochman H. Effect of chromosome location on bacterial mutation rates. Mol Biol Evol 2002;19:85–92 [CrossRef][PubMed]
    [Google Scholar]
  60. Driebe EM, Sahl JW, Roe C, Bowers JR, Schupp JM et al. Using whole genome analysis to examine recombination across diverse sequence types of Staphylococcus aureus. PLoS One 2015;10:e0130955 [CrossRef][PubMed]
    [Google Scholar]
  61. 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]
  62. Didelot X, Falush D. Inference of bacterial microevolution using multilocus sequence data. Genetics 2007;175:1251–1266 [CrossRef][PubMed]
    [Google Scholar]
  63. Didelot X, Wilson DJ. ClonalFrameML: efficient inference of recombination in whole bacterial genomes. PLoS Comput Biol 2015;11:e1004041 [CrossRef][PubMed]
    [Google Scholar]
  64. 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 [CrossRef][PubMed]
    [Google Scholar]
  65. Bruen T. PhiPack: PHI Test and Other Tests of Recombination. 2005
  66. Bruen TC, Philippe H, Bryant D. A simple and robust statistical test for detecting the presence of recombination. Genetics 2006;172:2665–2681 [CrossRef][PubMed]
    [Google Scholar]
  67. McWilliam H, Li W, Uludag M, Squizzato S, Park YM et al. Analysis tool web services from the EMBL-EBI. Nucleic Acids Res 2013;41:W597–W600 [CrossRef][PubMed]
    [Google Scholar]
  68. Schliep KP. phangorn: phylogenetic analysis in R. Bioinformatics 2011;27:592–593 [CrossRef][PubMed]
    [Google Scholar]
  69. Sahl JW, Caporaso JG, Rasko DA, Keim P. The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes. PeerJ 2014;2:e332 [CrossRef][PubMed]
    [Google Scholar]
  70. Sahl JW, Steinsland H, Redman JC, Angiuoli SV, Nataro JP et al. A comparative genomic analysis of diverse clonal types of enterotoxigenic Escherichia coli reveals pathovar-specific conservation. Infect Immun 2011;79:950–960 [CrossRef][PubMed]
    [Google Scholar]
  71. Huang W, Li L, Myers JR, Marth GT. ART: a next-generation sequencing read simulator. Bioinformatics 2012;28:593–594 [CrossRef]
    [Google Scholar]
  72. Edgar RC. Search and clustering orders of magnitude faster than BLAST. Bioinformatics 2010;26:2460–2461 [CrossRef]
    [Google Scholar]
  73. 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 [CrossRef]
    [Google Scholar]
  74. Chain PS, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J et al. Genome project standards in a new era of sequencing. Science 2009;326:236–237 [CrossRef][PubMed]
    [Google Scholar]
  75. Rognes T, Flouri T, Nichols B, Quince C, Mahé F. VSEARCH: a versatile open source tool for metagenomics. PeerJ 2016;4:e2584 [CrossRef]
    [Google Scholar]
  76. Treangen TJ, Salzberg SL. Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet 2012;13:36–46 [CrossRef]
    [Google Scholar]
  77. Nye TMW, Lio P, Gilks WR. A novel algorithm and web-based tool for comparing two alternative phylogenetic trees. Bioinformatics 2006;22:117–119 [CrossRef]
    [Google Scholar]
  78. Price LB, Stegger M, Hasman H, Aziz M, Larsen J et al. Staphylococcus aureus CC398: host adaptation and emergence of methicillin resistance in livestock. MBio 2012;3:e00305-11 [CrossRef][PubMed]
    [Google Scholar]
  79. Hedge J, Wilson DJ. Bacterial phylogenetic reconstruction from whole genomes is robust to recombination but demographic inference is not. MBio 2014;5:e02158-14 [CrossRef][PubMed]
    [Google Scholar]
  80. 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 [CrossRef][PubMed]
    [Google Scholar]
  81. Medini D, Donati C, Tettelin H, Masignani V, Rappuoli R. The microbial pan-genome. Curr Opin Genet Dev 2005;15:589–594 [CrossRef]
    [Google Scholar]
  82. Tettelin H, Masignani V, Cieslewicz MJ, Donati C, Medini D et al. Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci USA 2005;102:13950–13955 [CrossRef][PubMed]
    [Google Scholar]
  83. Georgiades K, Raoult D. Defining pathogenic bacterial species in the genomic era. Front Microbiol 2010;1:151 [CrossRef][PubMed]
    [Google Scholar]
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