Comparative genomics reveals the evolution of antimicrobial resistance in Bacteroides nordii

Vikas Sharma; Anshul Sood; Pallab Ray; Archana Angrup

doi:10.1016/j.micpath.2022.105811

Comparative genomics reveals the evolution of antimicrobial resistance in Bacteroides nordii

Microb Pathog. 2022 Dec;173(Pt A):105811. doi: 10.1016/j.micpath.2022.105811. Epub 2022 Sep 29.

Authors

Vikas Sharma¹, Anshul Sood², Pallab Ray³, Archana Angrup⁴

Affiliations

¹ Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India. Electronic address: vikas.sharma.biotech@mail.com.
² Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India. Electronic address: anshulsood02@gmail.com.
³ Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India. Electronic address: drpallabray@gmail.com.
⁴ Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research (PGIMER), Chandigarh, 160012, India. Electronic address: archanaangrup@yahoo.com.

PMID: 36183960
DOI: 10.1016/j.micpath.2022.105811

Abstract

Bacteroides nordii, is an understudied member of the pathogenic B. fragilis group which comprises several multidrug-resistant (MDR) strains. Thus, it is of great interest to study the genome biology of Bacteroides nordii. However, no detailed study is available that characterized B. nordii at the genetic level and explored its role as a potential pathogen. We isolated an MDR strain viz., B. nordii PGMM4098 from the pus sample and subjected it to whole genome sequencing using Illumina technology. The draft genome was de-novo assembled and annotated, followed by comprehensive comparative genomics analyses using the publicly available genome dataset of B. nordii. The pan-genome analysis revealed the open nature of B. nordii, indicating the continuous accumulation of novel genes in non-core components leading to the emergence of new strains of this species. The thirteen antimicrobial resistance (AMR) genes identified in the genomes of all B. nordii strains were part of the non-core component of the pan-genome. Of these, four AMR genes, nimE, aadS, mef(En2), and ermB/F/G were found to be acquired via the process of horizontal gene transfer (HGT) from anaerobic Bacteroidetes. Importantly, the nimE gene conferring metronidazole resistance was found to be present only in B. nordii PGMM4098, which harbors five other AMR genes encoded in its genome. Of these, nimE (metronidazole resistance), ermB/F/G (macrolide-lincosamide-streptogramin B resistance), and cfxA2/A3 (class A β-lactam resistance) genes were further validated using targeted polymerase chain reaction assay. Notably, these three genes were also found to be under the operation of positive selective pressure suggesting the diversification of these genes, which might lead to the emergence of new MDR strains of B. nordii in the near future. Our study reported and characterized the genome of the first MDR strain of B. nordii and revealed the AMR evolution in this species using a comprehensive comparative genomics approach.

Keywords: Antimicrobial resistance; Bacteroides nordii; Comparative genomics; Horizontal gene transfer; Pan-genome; Selective pressure.

MeSH terms

Anti-Bacterial Agents* / pharmacology
Anti-Infective Agents* / pharmacology
Drug Resistance, Bacterial / genetics
Drug Resistance, Multiple, Bacterial
Genomics
Metronidazole

Substances

Anti-Bacterial Agents
Metronidazole
Anti-Infective Agents

Supplementary concepts

Bacteroides nordii