Biocide-Resistant Escherichia coli ST540 Co-Harboring ESBL, dfrA14 Confers QnrS-Dependent Plasmid-Mediated Quinolone Resistance

Abstract

Emerging sequence types of pathogenic bacteria have a dual ability to acquire resistance islands/determinants, and remain renitent towards disinfection practices; therefore, they are considered “critical risk factors” that contribute significantly to the global problem of antimicrobial resistance. Multidrug-resistant Escherichia coli was isolated, its genome sequenced, and its susceptibilities characterized, in order to understand the genetic basis of its antimicrobial resistance.The draft genome sequencing of E. coli ECU32, was performed with Illumina NextSeq 500, and annotated using a RAST server. The antibiotic resistome, genomic island, insertion sequences, and prophages were analyzed using bioinformatics tools. Subsequently, analyses including antibiotic susceptibility testing, E-test, bacterial growth, survival, and efflux inhibition assays were performed.The draft genome of E. coli ECU32 was 4.7 Mb in size, the contigs were 107, and the G+C content was 50.8%. The genome comprised 4658 genes, 4543 CDS, 4384 coding genes, 115 RNA genes, 88 tRNAs, and 3 CRISPR arrays. The resistome characterization of ST540 E. coli ECU32 revealed the presence of ESBL, APH(6)-Id, APH(3′)-IIa, dfrA14, and QnrS1, with broad-spectrum multidrug and biocide resistance. Comparative genome sequence analysis revealed the presence of transporter and several virulence genes. Efflux activity and growth inhibition assays, which were performed with efflux substrates in the presence of inhibitor PAβN, exhibited significant reduced growth relative to its control.This study discusses the genotypic and phenotypic characterization of the biocide-tolerant multidrug-resistant E. coli O9:H30 strain, highlighting the contributory role of qnrS-dependent plasmid-mediated quinolone resistance, in addition to innate enzymatic modes of multidrug resistance mechanisms.