is a human-adapted lineage in the ’ complex Open Access

Abstract

is an enterohepatic that causes bacteremia and other diseases in humans. While -like strains are isolated from animals, including dog isolates belonging to a recently proposed , little is known about the genetic differences between and these animal isolates. Here, we sequenced 43 or -like strains isolated from humans, hamsters, rats and dogs and collected 81 genome sequences of , and other enterohepatic strains from public databases. Genomic comparison of these strains identified four distinct clades (clades I–IV) in ’ (HCCM) complex. Among these, clade I corresponds to and represents a human-adapted lineage in the complex. We identified several genomic features unique to clade I. They include the accumulation of antimicrobial resistance-related mutations that reflects the human association of clade I and the larger genome size and the presence of a CRISPR-Cas system and multiple toxin-antitoxin and restriction-modification systems, both of which indicate the contribution of horizontal gene transfer to the evolution of clade I. In addition, nearly all clade I strains but only a few strains belonging to one minor clade contained a highly variable genomic region encoding a type VI secretion system (T6SS), which could play important roles in gut colonization by killing competitors or inhibiting their growth. We also developed a method to systematically search for sequences in large metagenome data sets based on the results of genome comparison. Using this method, we successfully identified multiple HCCM complex-containing human faecal metagenome samples and obtained the sequence information covering almost the entire genome of each strain. Importantly, all were clade I strains, supporting our conclusion that is a human-adapted lineage in the HCCM complex.

Funding
This study was supported by the:
  • Japan Society for the Promotion of Science (Award JP21K07026)
    • Principle Award Recipient: YasuhiroGotoh
  • Kurozumi Medical Foundation
    • Principle Award Recipient: YasuhiroGotoh
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2022-05-10
2024-03-28
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References

  1. Totten PA, Fennell CL, Tenover FC, Wezenberg JM, Perine PL et al. Campylobacter cinaedi (sp. nov.) and Campylobacter fennelliae (sp. nov.): two new Campylobacter species associated with enteric disease in homosexual men. J Infect Dis 1985; 151:131–139 [View Article] [PubMed]
    [Google Scholar]
  2. Araoka H, Baba M, Okada C, Kimura M, Sato T et al. Risk factors for recurrent Helicobacter cinaedi bacteremia and the efficacy of selective digestive decontamination with kanamycin to prevent recurrence. Clin Infect Dis 2018; 67:573–578 [View Article] [PubMed]
    [Google Scholar]
  3. Kawamura Y, Tomida J, Morita Y, Fujii S, Okamoto T et al. Clinical and bacteriological characteristics of Helicobacter cinaedi infection. J Infect Chemother 2014; 20:517–526 [View Article] [PubMed]
    [Google Scholar]
  4. Araoka H, Baba M, Okada C, Kimura M, Sato T et al. First evidence of bacterial translocation from the intestinal tract as a route of Helicobacter cinaedi bacteremia. Helicobacter 2018; 23: [View Article] [PubMed]
    [Google Scholar]
  5. Gotoh Y, Taniguchi T, Yoshimura D, Katsura K, Saeki Y et al. Multi-step genomic dissection of a suspected intra-hospital Helicobacter cinaedi outbreak. Microb Genom 2018; 4:10 [View Article] [PubMed]
    [Google Scholar]
  6. Vandamme P, Harrington CS, Jalava K, On SL. Misidentifying helicobacters: the Helicobacter cinaedi example. J Clin Microbiol 2000; 38:2261–2266 [View Article] [PubMed]
    [Google Scholar]
  7. Oyama K, Khan S, Okamoto T, Fujii S, Ono K et al. Identification of and screening for human Helicobacter cinaedi infections and carriers via nested PCR. J Clin Microbiol 2012; 50:3893–3900 [View Article] [PubMed]
    [Google Scholar]
  8. Taniguchi T, Sekiya A, Higa M, Saeki Y, Umeki K et al. Rapid identification and subtyping of Helicobacter cinaedi strains by intact-cell mass spectrometry profiling with the use of matrix-assisted laser desorption ionization-time of flight mass spectrometry. J Clin Microbiol 2014; 52:95–102 [View Article] [PubMed]
    [Google Scholar]
  9. Solcà NM, Bernasconi MV, Piffaretti JC. Mechanism of metronidazole resistance in Helicobacter pylori: comparison of the rdxA gene sequences in 30 strains. Antimicrob Agents Chemother 2000; 44:2207–2210 [View Article] [PubMed]
    [Google Scholar]
  10. Kawamura Y, Tomida J, Miyoshi-Akiyama T, Okamoto T, Narita M et al. Proposal of Helicobacter canicola sp. nov., previously identified as Helicobacter cinaedi, isolated from canines. Syst Appl Microbiol 2016; 39:307–312 [View Article]
    [Google Scholar]
  11. Goto T, Ogura Y, Hirakawa H, Tomida J, Morita Y et al. Complete genome sequence of Helicobacter cinaedi strain PAGU611, isolated in a case of human bacteremia. J Bacteriol 2012; 194:3744–3745 [View Article] [PubMed]
    [Google Scholar]
  12. Miyoshi-Akiyama T, Takeshita N, Ohmagari N, Kirikae T. Complete genome sequence of Helicobacter cinaedi type strain ATCC BAA-847. J Bacteriol 2012; 194:5692 [View Article] [PubMed]
    [Google Scholar]
  13. Rimbara E, Mori S, Kim H, Suzuki M, Shibayama K. Mutations in genes encoding penicillin-binding proteins and efflux pumps play a role in β-lactam resistance in Helicobacter cinaedi. Antimicrob Agents Chemother 2018; 62:e02036-17 [View Article] [PubMed]
    [Google Scholar]
  14. Misawa N, Kawashima K, Kondo F, Kushima E, Kushima K et al. Isolation and characterization of Campylobacter, Helicobacter, and Anaerobiospirillum strains from a puppy with bloody diarrhea. Vet Microbiol 2002; 87:353–364 [View Article] [PubMed]
    [Google Scholar]
  15. Kajitani R, Yoshimura D, Ogura Y, Gotoh Y, Hayashi T et al. Platanus_B: an accurate de novo assembler for bacterial genomes using an iterative error-removal process. DNA Res 2020; 27:dsaa014 [View Article] [PubMed]
    [Google Scholar]
  16. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  17. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
    [Google Scholar]
  18. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014; 9:e112963 [View Article] [PubMed]
    [Google Scholar]
  19. Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 2018; 34:1037–1039 [View Article] [PubMed]
    [Google Scholar]
  20. Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Anal Methods 2016; 8:12–24 [View Article]
    [Google Scholar]
  21. 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] [PubMed]
    [Google Scholar]
  22. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article] [PubMed]
    [Google Scholar]
  23. Darriba D, Posada D, Kozlov AM, Stamatakis A, Morel B et al. ModelTest-NG: A New and Scalable Tool for the Selection of DNA and Protein Evolutionary Models. Mol Biol Evol 2020; 37:291–294 [View Article] [PubMed]
    [Google Scholar]
  24. Cheng L, Connor TR, Sirén J, Aanensen DM, Corander J. Hierarchical and spatially explicit clustering of DNA sequences with BAPS software. Mol Biol Evol 2013; 30:1224–1228 [View Article] [PubMed]
    [Google Scholar]
  25. Ohtsubo Y, Ikeda-Ohtsubo W, Nagata Y, Tsuda M. GenomeMatcher: a graphical user interface for DNA sequence comparison. BMC Bioinformatics 2008; 9:376 [View Article] [PubMed]
    [Google Scholar]
  26. Kuijper EJ, Stevens S, Imamura T, De Wever B, Claas ECJ. Genotypic identification of erythromycin-resistant campylobacter isolates as helicobacter species and analysis of resistance mechanism. J Clin Microbiol 2003; 41:3732–3736 [View Article] [PubMed]
    [Google Scholar]
  27. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol 2011; 7:539 [View Article] [PubMed]
    [Google Scholar]
  28. Feldgarden M, Brover V, Haft DH, Prasad AB, Slotta DJ et al. Validating the AMRFinder tool and resistance gene database by using antimicrobial resistance genotype-phenotype correlations in a collection of isolates. Antimicrob Agents Chemother 2019; 63:e00483-19 [View Article] [PubMed]
    [Google Scholar]
  29. Abby SS, Cury J, Guglielmini J, Néron B, Touchon M et al. Identification of protein secretion systems in bacterial genomes. Sci Rep 2016; 6:23080 [View Article] [PubMed]
    [Google Scholar]
  30. Russel J, Pinilla-Redondo R, Mayo-Muñoz D, Shah SA, Sørensen SJ. CRISPRCasTyper: automated identification, annotation, and classification of CRISPR-Cas Loci. CRISPR J 2020; 3:462–469 [View Article] [PubMed]
    [Google Scholar]
  31. 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] [PubMed]
    [Google Scholar]
  32. Schwengers O, Barth P, Falgenhauer L, Hain T, Chakraborty T et al. Platon: identification and characterization of bacterial plasmid contigs in short-read draft assemblies exploiting protein sequence-based replicon distribution scores. Microb Genom 2020; 6:10 [View Article] [PubMed]
    [Google Scholar]
  33. Antipov D, Raiko M, Lapidus A, Pevzner PA. Plasmid detection and assembly in genomic and metagenomic data sets. Genome Res 2019; 29:961–968 [View Article] [PubMed]
    [Google Scholar]
  34. Akhter S, Aziz RK, Edwards RA. PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Res 2012; 40:e126 [View Article] [PubMed]
    [Google Scholar]
  35. Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv preprint 2013arXiv:1303.3997
    [Google Scholar]
  36. Wickham H. Ggplot2. Wiley Interdiscip Rev Comput Stat 2011; 3:180–185 [View Article]
    [Google Scholar]
  37. Team RC. R: A language and environment for statistical computing; 2019
  38. Traverso FR, Bohr URM, Oyarzabal OA, Rohde M, Clarici A et al. Morphologic, genetic, and biochemical characterization of Helicobacter magdeburgensis, a novel species isolated from the intestine of laboratory mice. Helicobacter 2010; 15:403–415 [View Article] [PubMed]
    [Google Scholar]
  39. Rimbara E, Mori S, Matsui M, Suzuki S, Wachino J-I et al. Molecular epidemiologic analysis and antimicrobial resistance of Helicobacter cinaedi isolated from seven hospitals in Japan. J Clin Microbiol 2012; 50:2553–2560 [View Article] [PubMed]
    [Google Scholar]
  40. Tomida J, Morita Y, Shibayama K, Kikuchi K, Sawa T et al. Diversity and microevolution of CRISPR loci in Helicobacter cinaedi. PLoS One 2017; 12:e0186241 [View Article] [PubMed]
    [Google Scholar]
  41. Cianfanelli FR, Monlezun L, Coulthurst SJ. Aim, Load, Fire: The Type VI Secretion System, a Bacterial Nanoweapon. Trends Microbiol 2016; 24:51–62 [View Article] [PubMed]
    [Google Scholar]
  42. Nukui Y, Chino T, Tani C, Sonobe K, Aiso Y et al. Molecular epidemiologic and clinical analysis of Helicobacter cinaedi bacteremia in Japan. Helicobacter 2020; 25:e12675 [View Article] [PubMed]
    [Google Scholar]
  43. Katsuma A, Yamamoto I, Tsuchiya Y, Kawabe M, Yamakawa T et al. Helicobacter cinaedi bacteremia with cellulitis in a living-donor kidney transplant recipient identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry: a case report. BMC Res Notes 2017; 10:87 [View Article] [PubMed]
    [Google Scholar]
  44. Toyofuku M, Tomida J, Kawamura Y, Miyata I, Yuza Y et al. Helicobacter cinaedi bacteremia resulting from antimicrobial resistance acquired during treatment for X-linked agammaglobulinemia. J Infect Chemother 2016; 22:704–706 [View Article] [PubMed]
    [Google Scholar]
  45. Chow J, Tang H, Mazmanian SK. Pathobionts of the gastrointestinal microbiota and inflammatory disease. Curr Opin Immunol 2011; 23:473–480 [View Article] [PubMed]
    [Google Scholar]
  46. Vandamme P, Falsen E, Pot B, Kersters K, De Ley J. Identification of Campylobacter cinaedi isolated from blood and feces of children and adult females. J Clin Microbiol 1990; 28:1016–1020 [View Article] [PubMed]
    [Google Scholar]
  47. Gallegos-Monterrosa R, Coulthurst SJ. The ecological impact of a bacterial weapon: microbial interactions and the Type VI secretion system. FEMS Microbiol Rev 2021; 45:fuab033 [View Article] [PubMed]
    [Google Scholar]
  48. Bartonickova L, Sterzenbach T, Nell S, Kops F, Schulze J et al. Hcp and VgrG1 are secreted components of the Helicobacter hepaticus type VI secretion system and VgrG1 increases the bacterial colitogenic potential. Cell Microbiol 2013; 15:992–1011 [View Article] [PubMed]
    [Google Scholar]
  49. Yachida S, Mizutani S, Shiroma H, Shiba S, Nakajima T et al. Metagenomic and metabolomic analyses reveal distinct stage-specific phenotypes of the gut microbiota in colorectal cancer. Nat Med 2019; 25:968–976 [View Article]
    [Google Scholar]
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