Antimicrobial Resistance in Swine Fecal Specimens Across Different Farm Management Systems.

Tawat Pongpan,Eric R. Houpt,Parntep Ratanakorn,Iyarit Thaipisuttikul,Rattapha Chinli,Mami Taniuchi,Suporn Pholwat,Jie Liu,Suporn Foongladda,Elizabeth T. Rogawski McQuade

doi:10.3389/fmicb.2020.01238

Abstract

Antimicrobial use in agricultural animals is known to be associated with increases in antimicrobial resistance. Most prior studies have utilized culture and susceptibility testing of select organisms to document these phenomena. In this study we aimed to detect 66 antimicrobial resistance (AMR) genes for 10 antimicrobial agent classes directly in swine fecal samples using our previously developed antimicrobial resistance TaqMan array card (AMR-TAC) across three different swine farm management systems. This included 38 extensive antimicrobial use (both in treatment and feed), 30 limited antimicrobial use (treatment only), and 30 no antimicrobial use farms. The number of resistance genes detected in extensive antimicrobial use farms was higher than in limited and no antimicrobial use farms (28.2 genes ± 4.2 vs. 24.0 genes ± 4.1 and 22.8 genes ± 3.6, respectively, p < 0.05). A principal component analysis and hierarchical clustering of the AMR gene data showed the extensive use farm samples were disparate from the limited and no antimicrobial use farms. The prevalence of resistance genes in extensive use farms was significantly higher than the other farm categories for 18 resistance genes including blaSHV, blaCTX–M1 group, blaCTX–M9 group, blaVEB, blaCMY2–LAT, aac(6′)-lb-cr, qnrB1, gyrA83L-E. coli, armA, rmtB, aac(3)-IIa, mphA, 23S rRNA 2075G-Campylobacter spp., mcr-1, catA1, floR, dfrA5-14, and dfrA17. These genotypic findings were supported by phenotypic susceptibility results on fecal E. coli isolates. To examine the timing of AMR gene abundance in swine farms, we also performed a longitudinal study in pigs. The results showed that AMR prevalence occurred both early, presumably from mothers, as well as after weaning, presumably from the environment. In summary, detection of AMR genes directly in fecal samples can be used to qualitatively and quantitatively monitor AMR in swine farms.

Highlights

Antimicrobial resistance (AMR) in bacteria is driven by the selective pressure of antibiotics and exerts an enormous disease burden and increased economic costs (Founou et al, 2017)
The samples were from 38 extensive antimicrobial use farms (Exf) (n = 190), 30 limited antimicrobial use farms (Li-f) (n = 150), and 30 no antimicrobial use farms (No-f) (n = 150)
ESBL producing Enterobacteriaceae (ESBL-PE) are of critical global public health importance (Maslikowska et al, 2016; Ahn et al, 2017; Flokas et al, 2017) and these pathogens have dramatically increased worldwide including in Thailand (Sawatwong et al, 2019)

Summary

Introduction

Antimicrobial resistance (AMR) in bacteria is driven by the selective pressure of antibiotics and exerts an enormous disease burden and increased economic costs (Founou et al, 2017). While the use of antimicrobial agents as feed additives is prohibited in some countries, it is commonly practiced in many Southeast Asian countries (Nhung et al, 2016; Zellweger et al, 2017). This overuse of antimicrobial agents in livestock is one likely driver of the high AMR burden in Southeast Asia, including high rates of extended spectrum β-lactamase (ESBL) and CTX-M enzymes (Zellweger et al, 2017). AMR in food animals can impact human health by the direct introduction of AMR pathogens into the food chain, by promoting horizontal transfer of resistance determinants to other bacterial pathogens (Munita and Arias, 2016), and by indirect spread to other animals and humans via water and soil (Marshall and Levy, 2011; Woolhouse et al, 2015)

Objectives

Methods

Results

Conclusion