1887

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
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2022-05-10
2022-05-24
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