Diversity of Plasmids and Genes Encoding Resistance to Extended-Spectrum β-Lactamase in Escherichia coli from Different Animal Sources.

Abasiofiok Ibekwe,Brian Fanelli,Hiren Karathia,Charlene R Jackson,Adelumola Oladeinde,Lisa Durso,Tom Moorman,Amarachukwu Obayiuwana,Thomas F Ducey,John P Brooks,Robert Dungan,Jonathan G Frye,Nur Hasan

doi:10.3390/microorganisms9051057

Abstract

Antimicrobial resistance associated with the spread of plasmid-encoded extended-spectrum β-lactamase (ESBL) genes conferring resistance to third generation cephalosporins is increasing worldwide. However, data on the population of ESBL producing E. coli in different animal sources and their antimicrobial characteristics are limited. The purpose of this study was to investigate potential reservoirs of ESBL-encoded genes in E. coli isolated from swine, beef, dairy, and poultry collected from different regions of the United States using whole-genome sequencing (WGS). Three hundred isolates were typed into different phylogroups, characterized by BOX AIR-1 PCR and tested for resistance to antimicrobials. Of the 300 isolates, 59.7% were resistant to sulfisoxazole, 49.3% to tetracycline, 32.3% to cephalothin, 22.3% to ampicillin, 20% to streptomycin, 16% to ticarcillin; resistance to the remaining 12 antimicrobials was less than 10%. Phylogroups A and B1 were most prevalent with A (n = 92, 30%) and B1 (87 = 29%). A total of nine E. coli isolates were confirmed as ESBL producers by double-disk synergy testing and multidrug resistant (MDR) to at least three antimicrobial drug classes. Using WGS, significantly higher numbers of ESBL-E. coli were detected in swine and dairy manure than from any other animal sources, suggesting that these may be the primary animal sources for ESBL producing E. coli. These isolates carry plasmids, such as IncFIA(B), IncFII, IncX1, IncX4, IncQ1, CollRNAI, Col440I, and acquired ARGs aph(6)-Id, aph(3″)-Ib, aadA5, aph(3′)-Ia, blaCTX-M-15, blaTEM-1B, mphA, ermB, catA1, sul1, sul2, tetB, dfrA17. One of the E. coli isolates from swine with ST 410 was resistant to nine antibiotics and carried more than 28 virulence factors, and this ST has been shown to belong to an international high-risk clone. Our data suggests that ESBL producing E. coli are widely distributed in different animal sources, but swine and dairy cattle may be their main reservoir.

Highlights

Extended-spectrum β-lactamases (ESBLs) are plasmid-encoded enzymes providing resistance to third-generation cephalosporins, which are a class of β-lactam antibiotics that can be used for the treatment of human infections caused by Gram-negative bacteria, especially Escherichia coli [1]
We investigate agricultural E. coli as a potential reservoir of antibiotic resistance genes, including AmpC and ESBL-encoding genes, and compared resistance profiles across phylogroups and commodities using traditional and whole genome sequencing (WGS) methods
300 isolates of E. coli were typed by PCR into phylogroups, characterized by BOX AIR-1 PCR (Supplementary Table S1B), and evaluated phenotypically for antibiotic resistance to a panel of 18 antibiotics (Supplementary Figure S1A,B)

Summary

Introduction

Extended-spectrum β-lactamases (ESBLs) are plasmid-encoded enzymes providing resistance to third-generation cephalosporins, which are a class of β-lactam antibiotics that can be used for the treatment of human infections caused by Gram-negative bacteria, especially Escherichia coli [1]. E. coli isolates producing extended-spectrum β-lactamases (ESBLs) have rendered the use of third generation cephalosporins increasingly ineffective against this pathogen [2]. ESBL-encoding plasmids frequently carry genes encoding resistance to other drug classes, such as fluoroquinolones, aminoglycosides, sulfa derivatives, and trimethoprim [3,4]. ESBL production has been observed mostly in Enterobacteriaceae, E. coli and Klebsiella pneumoniae, but all other clinically relevant Enterobacteriaceae species are potential ESBL-producers. Since the use of antibiotics provides selection pressure for the development of resistant microorganisms, farms are an important location for monitoring of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs), including genes in commensal bacteria [5]

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Results