Genetic Determinants of Resistance to Extended-Spectrum Cephalosporin and Fluoroquinolone in Escherichia coli Isolated from Diseased Pigs in the United States

Shivdeep Singh Hayer; Seunghyun Lim; Samuel Hong; Ehud Elnekave; Timothy Johnson; Albert Rovira; Fabio Vannucci; Jonathan B Clayton; Andres Perez; Julio Alvarez

doi:10.1128/mSphere.00990-20

Genetic Determinants of Resistance to Extended-Spectrum Cephalosporin and Fluoroquinolone in Escherichia coli Isolated from Diseased Pigs in the United States

mSphere. 2020 Oct 28;5(5):e00990-20. doi: 10.1128/mSphere.00990-20.

Authors

Shivdeep Singh Hayer^{1

2}, Seunghyun Lim^{1

3}, Samuel Hong^{1

4}, Ehud Elnekave¹, Timothy Johnson⁵, Albert Rovira^{1

6}, Fabio Vannucci^{1

6}, Jonathan B Clayton^{2

7}, Andres Perez¹, Julio Alvarez^{8

9

10}

Affiliations

¹ Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA.
² Department of Biology, University of Nebraska at Omaha, Omaha, Nebraska, USA.
³ Bioinformatics and Computational Biology Program, University of Minnesota-Rochester, Rochester, Minnesota, USA.
⁴ Department of Microbiology and Immunology, Rega Institute, KU Leuven, Leuven, Belgium.
⁵ Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA.
⁶ Veterinary Diagnostic Laboratory, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA.
⁷ Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.
⁸ Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, Minnesota, USA jalvarez@visavet.ucm.es.
⁹ VISAVET Health Surveillance Center, Universidad Complutense Madrid, Madrid, Spain.
¹⁰ Department of Animal Health, Facultad de Veterinaria, Universidad Complutense Madrid, Madrid, Spain.

Abstract

Fluoroquinolones and cephalosporins are critically important antimicrobial classes for both human and veterinary medicine. We previously found a drastic increase in enrofloxacin resistance in clinical Escherichia coli isolates collected from diseased pigs from the United States over 10 years (2006 to 2016). However, the genetic determinants responsible for this increase have yet to be determined. The aim of the present study was to identify and characterize the genetic basis of resistance against fluoroquinolones (enrofloxacin) and extended-spectrum cephalosporins (ceftiofur) in swine E. coli isolates using whole-genome sequencing (WGS). bla_CMY-2 (carried by IncA/C2, IncI1, and IncI2 plasmids), bla_CTX-M (carried by IncF, IncHI2, and IncN plasmids), and bla_SHV-12 (carried by IncHI2 plasmids) genes were present in 87 (82.1%), 19 (17.9%), and 3 (2.83%) of the 106 ceftiofur-resistant isolates, respectively. Of the 110 enrofloxacin-resistant isolates, 90 (81.8%) had chromosomal mutations in gyrA, gyrB, parA, and parC genes. Plasmid-mediated quinolone resistance genes [qnrB77, qnrB2, qnrS1, qnrS2, and aac-(6)-lb'-cr] borne on ColE, IncQ2, IncN, IncF, and IncHI2 plasmids were present in 24 (21.8%) of the enrofloxacin-resistant isolates. Virulent IncF plasmids present in swine E. coli isolates were highly similar to epidemic plasmids identified globally. High-risk E. coli clones, such as ST744, ST457, ST131, ST69, ST10, ST73, ST410, ST12, ST127, ST167, ST58, ST88, ST617, ST23, etc., were also found in the U.S. swine population. Additionally, the colistin resistance gene (mcr-9) was present in several isolates. This study adds valuable information regarding resistance to critical antimicrobials with implications for both animal and human health.IMPORTANCE Understanding the genetic mechanisms conferring resistance is critical to design informed control and preventive measures, particularly when involving critically important antimicrobial classes such as extended-spectrum cephalosporins and fluoroquinolones. The genetic determinants of extended-spectrum cephalosporin and fluoroquinolone resistance were highly diverse, with multiple plasmids, insertion sequences, and genes playing key roles in mediating resistance in swine Escherichia coli Plasmids assembled in this study are known to be disseminated globally in both human and animal populations and environmental samples, and E. coli in pigs might be part of a global reservoir of key antimicrobial resistance (AMR) elements. Virulent plasmids found in this study have been shown to confer fitness advantages to pathogenic E. coli strains. The presence of international, high-risk zoonotic clones provides worrisome evidence that resistance in swine isolates may have indirect public health implications, and the swine population as a reservoir for these high-risk clones should be continuously monitored.

Keywords: ESBLs; PMQR; PacBio; USA; WGS; antimicrobial resistance; cephalosporin; epidemic plasmids; fluoroquinolone; high-risk clones; long-read sequencing; plasmids; swine.

Publication types

Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Anti-Bacterial Agents / pharmacology
Cephalosporins / pharmacology*
DNA, Bacterial / genetics
Drug Resistance, Multiple, Bacterial / genetics*
Escherichia coli / drug effects*
Escherichia coli / genetics*
Escherichia coli Infections / microbiology
Escherichia coli Infections / veterinary*
Fluoroquinolones / pharmacology*
Global Health
Microbial Sensitivity Tests
Plasmids / genetics
Swine
United States

Substances

Anti-Bacterial Agents
Cephalosporins
DNA, Bacterial
Fluoroquinolones