Complete genome sequence of a commensal bacterium, Hafnia alvei CBA7124, isolated from human fecesReport as inadecuate




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Gut Pathogens

, 9:41

First Online: 27 July 2017Received: 17 February 2017Accepted: 06 July 2017

Abstract

BackgroundMembers 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.

ResultsThe 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.

ConclusionsWe 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.

KeywordsHafnia alvei CBA7124 Complete genome sequence Gut microbiota Comparative genomics AbbreviationsCDSprotein coding gene

COGclusters of orthologous groups

POGpan-genome orthologous group

orthoANIorthologous average nucleotide identity

RASTrapid annotation using subsystem technology

TAtoxin–antitoxin

Electronic supplementary materialThe online version of this article doi:10.1186-s13099-017-0190-0 contains supplementary material, which is available to authorized users.

Young-Do Nam and Seong Woon Roh contributed equally to this work

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Author: Hye Seon Song - Joon Yong Kim - Yeon Bee Kim - Myeong Seon Jeong - Jisu Kang - Jin-Kyu Rhee - Joseph Kwon - Ju Suk Ki

Source: https://link.springer.com/



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