Long-read whole genome sequencing and comparative analysis of six strains of the human pathogen Orientia tsutsugamushi.

Publisher: Public Library of Science Country of Publication: United States NLM ID: 101291488 Publication Model: eCollection Cited Medium: Internet ISSN: 1935-2735 (Electronic) Linking ISSN: 19352727 NLM ISO Abbreviation: PLoS Negl Trop Dis Subsets: MEDLINE

Original Publication: San Francisco, CA : Public Library of Science

Genome, Bacterial* ; Sequence Analysis, DNA* ; Whole Genome Sequencing*; Orientia tsutsugamushi/*genetics; Gene Duplication ; Genotype ; Humans ; Orientia tsutsugamushi/classification ; Orientia tsutsugamushi/pathogenicity ; Phylogeny ; Scrub Typhus/microbiology

Background: Orientia tsutsugamushi is a clinically important but neglected obligate intracellular bacterial pathogen of the Rickettsiaceae family that causes the potentially life-threatening human disease scrub typhus. In contrast to the genome reduction seen in many obligate intracellular bacteria, early genetic studies of Orientia have revealed one of the most repetitive bacterial genomes sequenced to date. The dramatic expansion of mobile elements has hampered efforts to generate complete genome sequences using short read sequencing methodologies, and consequently there have been few studies of the comparative genomics of this neglected species.
Results: We report new high-quality genomes of O. tsutsugamushi, generated using PacBio single molecule long read sequencing, for six strains: Karp, Kato, Gilliam, TA686, UT76 and UT176. In comparative genomics analyses of these strains together with existing reference genomes from Ikeda and Boryong strains, we identify a relatively small core genome of 657 genes, grouped into core gene islands and separated by repeat regions, and use the core genes to infer the first whole-genome phylogeny of Orientia.
Conclusions: Complete assemblies of multiple Orientia genomes verify initial suggestions that these are remarkable organisms. They have larger genomes compared with most other Rickettsiaceae, with widespread amplification of repeat elements and massive chromosomal rearrangements between strains. At the gene level, Orientia has a relatively small set of universally conserved genes, similar to other obligate intracellular bacteria, and the relative expansion in genome size can be accounted for by gene duplication and repeat amplification. Our study demonstrates the utility of long read sequencing to investigate complex bacterial genomes and characterise genomic variation.
Competing Interests: PD is Founder, Director, and Executive Officer of Genomics plc and a Partner of Peptide Groove LLP. CC and RL are employees of Pacific Biosciences.

Nat Rev Microbiol. 2011 Nov 08;10(1):13-26. (PMID: 22064560)
Bioinformatics. 2009 Jun 1;25(11):1422-3. (PMID: 19304878)
Bioinformatics. 2015 Nov 15;31(22):3691-3. (PMID: 26198102)
PLoS Genet. 2010 Jan 15;6(1):e1000815. (PMID: 20084105)
PLoS Negl Trop Dis. 2015 Aug 28;9(8):e0004009. (PMID: 26317517)
Genome Res. 2009 Sep;19(9):1639-45. (PMID: 19541911)
Nucleic Acids Res. 2002 Jan 1;30(1):281-3. (PMID: 11752315)
Vector Borne Zoonotic Dis. 2013 Nov;13(11):825-9. (PMID: 24107204)
mBio. 2016 Jun 21;7(3):. (PMID: 27329757)
Am J Trop Med Hyg. 2003 Nov;69(5):519-24. (PMID: 14695089)
Bioinformatics. 2004 Jan 22;20(2):289-90. (PMID: 14734327)
Proc Natl Acad Sci U S A. 1996 Apr 2;93(7):2873-8. (PMID: 8610134)
Bioinformatics. 2012 Dec 1;28(23):3150-2. (PMID: 23060610)
Bioinformatics. 2006 Jul 1;22(13):1658-9. (PMID: 16731699)
FEMS Microbiol Lett. 1999 Nov 15;180(2):163-9. (PMID: 10556707)
PLoS Negl Trop Dis. 2012 Jan;6(1):e1466. (PMID: 22253938)
N Engl J Med. 2016 Sep 8;375(10):954-61. (PMID: 27602667)
Vector Borne Zoonotic Dis. 2013 Jun;13(6):367-75. (PMID: 23590326)
PLoS Negl Trop Dis. 2015 Aug 28;9(8):e0004024. (PMID: 26317624)
Microbiol Immunol. 1984;28(8):873-82. (PMID: 6438448)
Mol Syst Biol. 2011 Oct 11;7:539. (PMID: 21988835)
Genom Data. 2017 Mar 28;12:84-88. (PMID: 28393016)
J Bacteriol. 2006 Apr;188(7):2533-42. (PMID: 16547041)
J Exp Med. 1948 Apr 1;87(4):339-51. (PMID: 18904219)
Am J Trop Med Hyg. 2010 Sep;83(3):658-63. (PMID: 20810835)
PLoS Biol. 2004 Mar;2(3):E69. (PMID: 15024419)
Proc Natl Acad Sci U S A. 2007 May 8;104(19):7981-6. (PMID: 17483455)
Bioinformatics. 2014 May 1;30(9):1312-3. (PMID: 24451623)
Vector Borne Zoonotic Dis. 2010 Mar;10(2):191-3. (PMID: 19492945)
Lancet Glob Health. 2015 Feb;3(2):e104-12. (PMID: 25617190)
J Clin Microbiol. 1990 Apr;28(4):685-8. (PMID: 2110179)
Bioinformatics. 2006 Mar 1;22(5):616-7. (PMID: 16377612)
Biol Rev Camb Philos Soc. 2011 May;86(2):379-405. (PMID: 20716256)
Infect Genet Evol. 2013 Apr;15:25-34. (PMID: 20854933)
Trends Genet. 2007 Oct;23(10):511-20. (PMID: 17822801)
PLoS Negl Trop Dis. 2010 Jul 20;4(7):e752. (PMID: 20651929)
Infect Genet Evol. 2015 Apr;31:1-8. (PMID: 25577986)
Clin Microbiol Infect. 2009 May;15(5):488-95. (PMID: 19416296)
J Bacteriol. 2012 Jan;194(2):376-94. (PMID: 22056929)
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402. (PMID: 9254694)
DNA Res. 2008 Aug;15(4):185-99. (PMID: 18508905)
PLoS One. 2014 Nov 19;9(11):e112963. (PMID: 25409509)
Trop Med Infect Dis. 2018 Jan 17;3(1):. (PMID: 30274407)
Bioinformatics. 2011 Feb 15;27(4):592-3. (PMID: 21169378)
Genome Res. 2011 Jun;21(6):936-9. (PMID: 20980556)
J Bacteriol. 2008 Nov;190(21):6970-82. (PMID: 18723615)
DNA Res. 2010 Oct;17(5):281-91. (PMID: 20682628)
FEMS Immunol Med Microbiol. 2008 Apr;52(3):335-42. (PMID: 18312580)
Bioinformatics. 2014 Jul 15;30(14):2068-9. (PMID: 24642063)
J Clin Microbiol. 2010 Dec;48(12):4404-9. (PMID: 20926708)
PLoS Negl Trop Dis. 2017 Sep 25;11(9):e0005838. (PMID: 28945755)

United Kingdom WT_ Wellcome Trust; MR/N012380/1 United Kingdom MRC_ Medical Research Council

Date Created: 20180607 Date Completed: 20180711 Latest Revision: 20230926

20250114

PMC6005640

10.1371/journal.pntd.0006566

29874223