Whole Genome Sequencing Differentiates Presumptive Extended Spectrum Beta-Lactamase Producing Escherichia coli along Segments of the One Health Continuum.

Emelia H Adator,Rahat Zaheer,Ron Read,Shaun R Cook,Sherry J Hannon,Noriko Goji,Claudia Narvaez-Bravo,Celine A Nadon,Deirdre Church,Matthew Walker,Lisa Tymensen,Tim A Mcallister,Kingsley Amoako,Calvin W Booker

doi:10.3390/microorganisms8030448

Abstract

Antimicrobial resistance (AMR) has important implications for the continued use of antibiotics to control infectious diseases in both beef cattle and humans. AMR along the One Health continuum of the beef production system is largely unknown. Here, whole genomes of presumptive extended-spectrum β-lactamase E. coli (ESBL-EC) from cattle feces (n = 40), feedlot catch basins (n = 42), surrounding streams (n = 21), a beef processing plant (n = 4), municipal sewage (n = 30), and clinical patients (n = 25) are described. ESBL-EC were isolated from ceftriaxone selective plates and subcultured on ampicillin selective plates. Agreement of genotype-phenotype prediction of AMR ranged from 93.2% for ampicillin to 100% for neomycin, trimethoprim/sulfamethoxazole, and enrofloxacin resistance. Overall, β-lactam (100%; blaEC, blaTEM-1, blaSHV, blaOXA, blaCTX-M-), tetracycline (90.1%; tet(A), tet(B)) and folate synthesis (sul2) antimicrobial resistance genes (ARGs) were most prevalent. The ARGs tet(C), tet(M), tet(32), blaCTX-M-1, blaCTX-M-14, blaOXA-1, dfrA18, dfrA19, catB3, and catB4 were exclusive to human sources, while blaTEM-150, blaSHV-11–12, dfrA12, cmlA1, and cmlA5 were exclusive to beef cattle sources. Frequently encountered virulence factors across all sources included adhesion and type II and III secretion systems, while IncFIB(AP001918) and IncFII plasmids were also common. Specificity and prevalence of ARGs between cattle-sourced and human-sourced presumptive ESBL-EC likely reflect differences in antimicrobial use in cattle and humans. Comparative genomics revealed phylogenetically distinct clusters for isolates from human vs. cattle sources, implying that human infections caused by ESBL-EC in this region might not originate from beef production sources.

Highlights

Infections caused by extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae have been linked to their dissemination through both food and the environment [1,2,3]
The CLSI minimum inhibitory concentration (MIC) ampicillin break-point was used for isolating presumptive ESBL-producing E. coli (ESBL-EC), not all E. coli were resistant to ampicillin based on subsequent disk diffusion susceptibility tests
Comparison of the genotypic and phenotypic characteristics of these isolates along a One Health continuum revealed differences in prevalence of similar antimicrobial resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factors together with phylogenetic differences, implying that ESBL-EC originating from beef cattle may not play a significant role in ESBL-EC infections in humans in southern Alberta

Summary

Introduction

Infections caused by extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae have been linked to their dissemination through both food and the environment [1,2,3]. ESBL-producing bacteria, including E. coli are frequently resistant to multiple antimicrobials including 3rd and 4th generation cephalosporins in addition to quinolones and aminoglycosides [1,2,4]. These bacteria have been designated priority group 1 pathogens for the development of alternative antimicrobial therapies by the World Health Organization [5] as they can cause serious urinary tract [6,7] and bloodstream [8,9,10] infections, occasionally resulting in mortalities [11]. Conventional AMR susceptibility tests have been instrumental in detecting and monitoring AMR status and emergence, but has limitations with regard to the extent that information on phylogeny, mobile genetic elements (MGEs), or virulence traits can contribute to epidemiological investigations [22,23]

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Conclusion