Genome Analysis of Multidrug-Resistant <i>Escherichia coli</i> Isolated from Poultry in Nigeria

Abstract

<i>Escherichia coli</i> is one of the most common commensal bacteria of the gastrointestinal tract of humans and warm-blooded animals. Contaminated poultry can lead to disease outbreaks in consumers causing massive economic losses in the poultry industry. Additionally, commensal <i>E. coli</i> can harbor antibiotic resistance genes that can be transferred to other bacteria, including pathogens, in a colonized human host. In a previous study on antimicrobial resistance of <i>E. coli</i> from food animals from Nigeria, multidrug-resistant <i>E. coli</i> were detected. Three of those isolates were selected for further study using whole-genome sequencing due to the extensive drug resistance exhibited. All of the isolates carried the extended-spectrum β-lactamase (ESBL) genes, <i>bla</i>_CTX-M15 and <i>bla</i>_TEM-1, whereas one isolate harbored an additional ESBL, <i>bla</i>_OXA-1. All of the tetracycline-resistant isolates carried <i>tet</i>(A). The genes <i>aac3-IIa</i> and <i>aacA4</i>, conferring resistance to aminoglycosides, were identified in an <i>E. coli</i> isolate resistant to gentamicin and tobramycin. In two <i>E. coli</i> isolates, <i>dfrA14</i>, <i>qnrS1</i>, and <i>sulII</i>, were detected conferring resistance to trimethoprim, fluoroquinolones, and sulfonamides, respectively. The third isolate carried <i>dfrA17</i>, no fluoroquinolone resistance gene, an additional <i>sulI</i> gene, and a chloramphenicol resistance gene, <i>catB3.</i> Mutations in candidate genes conferring resistance to fosfomycin and fluoroquinolones were also detected. Several efflux systems were detected in all the <i>E. coli</i> isolates and virulence-associated genes related to serum resistance, motility, and adhesion. <i>E. coli</i> and non-<i>E. coli</i> origin prophages were also identified in the isolates. The results underline the higher resolution power of whole-genome sequencing for investigation of antimicrobial resistance, virulence, and phage in <i>E. coli</i>.