Genomic Characterization of Multidrug-Resistant Pathogenic Enteric Bacteria from Healthy Children in Osun State, Nigeria

Abstract

Antimicrobial resistance (AMR) is responsible for the spread and persistence of bacterial infections. Surveillance of AMR in healthy individuals is usually not considered, though these individuals serve as reservoirs for continuous disease transmission. Therefore, it is essential to conduct epidemiological surveillance of AMR in healthy individuals to fully understand the dynamics of AMR transmission in Nigeria. Thirteen multidrug-resistant <i>Citrobacter</i> spp., <i>Enterobacter</i> spp., <i>Klebsiella pneumoniae</i>, and <i>Escherichia coli</i> isolated from stool samples of healthy children were subjected to whole genome sequencing (WGS) using Illumina and Oxford nanopore sequencing platforms. A bioinformatics analysis revealed antimicrobial resistance genes such as the <i>pmrB_Y358N</i> gene responsible for colistin resistance detected in <i>E. coli</i> ST219, virulence genes such as <i>senB</i>, and <i>ybtP&Q</i>, and plasmids in the isolates sequenced. All isolates harbored more than three plasmid replicons of either the Col and/or Inc type. Plasmid reconstruction revealed an integrated <i>tetA</i> gene, a toxin production <i>caa</i> gene in two <i>E. coli</i> isolates, and a <i>cusC</i> gene in <i>K. quasivariicola</i> ST3879, which induces neonatal meningitis. The global spread of AMR pathogenic enteric bacteria is of concern, and surveillance should be extended to healthy individuals, especially children. WGS for epidemiological surveillance will improve the detection of AMR pathogens for management and control.