Antimicrobial Resistance in Swine Fecal Specimens Across Different Farm Management Systems

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) gene...

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Main Authors: Suporn Pholwat, Tawat Pongpan, Rattapha Chinli, Elizabeth T. Rogawski McQuade, Iyarit Thaipisuttikul, Parntep Ratanakorn, Jie Liu, Mami Taniuchi, Eric R. Houpt, Suporn Foongladda
Format: Article
Language:English
Published: Frontiers Media S.A. 2020-06-01
Series:Frontiers in Microbiology
Subjects:
AMR
Online Access:https://www.frontiersin.org/article/10.3389/fmicb.2020.01238/full
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spelling doaj-c8af79d6edd3478885b0f80a2fa9899d2020-11-25T03:37:30ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2020-06-011110.3389/fmicb.2020.01238525963Antimicrobial Resistance in Swine Fecal Specimens Across Different Farm Management SystemsSuporn Pholwat0Suporn Pholwat1Tawat Pongpan2Rattapha Chinli3Elizabeth T. Rogawski McQuade4Iyarit Thaipisuttikul5Parntep Ratanakorn6Jie Liu7Mami Taniuchi8Eric R. Houpt9Suporn Foongladda10Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, ThailandDivision of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, United StatesSwine Veterinarian Service, Charoen Pokphand Foods PCL, Bangkok, ThailandDepartment of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, ThailandDivision of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, United StatesDepartment of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, ThailandFaculty of Veterinary Science, Mahidol University, Nakhon Pathom, ThailandDivision of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, United StatesDivision of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, United StatesDivision of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, United StatesDepartment of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, ThailandAntimicrobial 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.https://www.frontiersin.org/article/10.3389/fmicb.2020.01238/fullantimicrobial resistanceAMRswinefarm managementfecal specimens
collection DOAJ
language English
format Article
sources DOAJ
author Suporn Pholwat
Suporn Pholwat
Tawat Pongpan
Rattapha Chinli
Elizabeth T. Rogawski McQuade
Iyarit Thaipisuttikul
Parntep Ratanakorn
Jie Liu
Mami Taniuchi
Eric R. Houpt
Suporn Foongladda
spellingShingle Suporn Pholwat
Suporn Pholwat
Tawat Pongpan
Rattapha Chinli
Elizabeth T. Rogawski McQuade
Iyarit Thaipisuttikul
Parntep Ratanakorn
Jie Liu
Mami Taniuchi
Eric R. Houpt
Suporn Foongladda
Antimicrobial Resistance in Swine Fecal Specimens Across Different Farm Management Systems
Frontiers in Microbiology
antimicrobial resistance
AMR
swine
farm management
fecal specimens
author_facet Suporn Pholwat
Suporn Pholwat
Tawat Pongpan
Rattapha Chinli
Elizabeth T. Rogawski McQuade
Iyarit Thaipisuttikul
Parntep Ratanakorn
Jie Liu
Mami Taniuchi
Eric R. Houpt
Suporn Foongladda
author_sort Suporn Pholwat
title Antimicrobial Resistance in Swine Fecal Specimens Across Different Farm Management Systems
title_short Antimicrobial Resistance in Swine Fecal Specimens Across Different Farm Management Systems
title_full Antimicrobial Resistance in Swine Fecal Specimens Across Different Farm Management Systems
title_fullStr Antimicrobial Resistance in Swine Fecal Specimens Across Different Farm Management Systems
title_full_unstemmed Antimicrobial Resistance in Swine Fecal Specimens Across Different Farm Management Systems
title_sort antimicrobial resistance in swine fecal specimens across different farm management systems
publisher Frontiers Media S.A.
series Frontiers in Microbiology
issn 1664-302X
publishDate 2020-06-01
description 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.
topic antimicrobial resistance
AMR
swine
farm management
fecal specimens
url https://www.frontiersin.org/article/10.3389/fmicb.2020.01238/full
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