Complete genome sequence of a commensal bacterium, Hafnia alvei CBA7124, isolated from human feces

Abstract

Background: Members of the genus Hafnia have been isolated from the feces of mammals, birds, reptiles, and fish, as well as from soil, water, sewage, and foods. Hafnia alvei is an opportunistic pathogen that has been implicated in intestinal and extraintestinal infections in humans. However, its pathogenicity is still unclear. In this study, we isolated H. alvei from human feces and performed sequencing as well as comparative genomic analysis to better understand its pathogenicity.

Results: The genome of H. alvei CBA7124 comprised a single circular chromosome with 4,585,298 bp and a GC content of 48.8%. The genome contained 25 rRNA genes (9 5S rRNA genes, 8 16S rRNA genes, and 8 23S rRNA genes), 88 tRNA genes, and 4043 protein-coding genes. Using comparative genomic analysis, the genome of this strain was found to have 72 strain-specific singletons. The genome also contained genes for antibiotic and antimicrobial resistance, as well as toxin-antitoxin systems.

Conclusions: We revealed the complete genome sequence of the opportunistic gut pathogen, H. alvei CBA7124. We also performed comparative genomic analysis of the sequences in the genome of H. alvei CBA7124, and found that it contained strain-specific singletons, antibiotic resistance genes, and toxin-antitoxin systems. These results could improve our understanding of the pathogenicity and the mechanism behind the antibiotic resistance of H. alvei strains.

Keywords: Comparative genomics; Complete genome sequence; Gut microbiota; Hafnia alvei CBA7124.

Fig. 1

Circular genome map of Hafnia alvei CBA7124. From outer to inner rings, the individual circles indicate rRNAs and tRNAs, reverse CDSs, forward CDSs, GC skew, and GC ratio

Fig. 2

Heat map of strain CBA7124 with the related Hafnia alvei strains, constructed based on the presence or absence of POGs. The presence and absence of POGs are indicated by blue and red, respectively