Antimicrobial Resistance in Swine Fecal Specimens Across Different Farm Management Systems

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 bla SHV , bla CTX−M1 group, bla CTX−M9 group, bla VEB , bla CMY2−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.

Antimicrobial resistance in fecal Escherichia coli from different pig production systems

“…The disc diffusion method was carried out to detect antimicrobial resistance. The high antimicrobial-resistant level in this study was amoxicillin (comparable to ampicillin and penicillin), doxycycline (comparable to tetracycline) and trimethoprim-sulfamethoxazole following earlier reports [5,16,17]. This agreement with earlier studies might be because these earlier reports were conducted during a recent period for starting a campaign for reducing antimicrobial use in pig production in Thailand.…”

“…When pig age was classified into 3 age classes (sow, nursery and starter pig, and grower and finisher pig), it was rather obvious that the grower and finisher pigs played a crucial role in the difference in the number of antimicrobial resistance agents between the pigs in the CO and the DE farms. The highest value of number of antimicrobial resistance agents in all study farms with the highest in the CO farm in the northeastern region indicated a similar trend to the results of earlier reports [5]. In this report, a likely higher antimicrobial-resistant gene found in 3-week-old weaning piglets than their sows and 24 weeks old at the finishing stage, consistent with the higher number of E. coli, indicating the diversity of the microbiome which shifted over time during production stages.…”

“…Gruel et al [21] also reported the rate of ampicillin resistance occurrence at 100.0% for ampicillin resistance in ESBL-E. coli versus 14.4% in non-ESBL-E. coli, although βlactams were used by half of the pig farmers. This report would support the high rate of amoxicillin resistance in E. coli for the current study, apart from extensive antimicrobial use [5,15,22] in the past. The absence of or very low level of colistin and enrofloxacin resistance was a positive sign of a very low resistance rate occurring in these two antimicrobials.…”

“…However, there was a cross-sectional sampling in this study, which made it hard to explain the studied results because of various possible confounding factors, such as weaned piglets housed in a particular pen possibly came from sows with differently carried resistant genes. When comparing the results of the number of antimicrobial resistance agents for the pigs from the DE system in the current study with the longitudinal study in the earlier report [5], there were consistent results. This could be explained by the fact that weaned piglets born from a specific sow were regularly housed in a specific pen without including weaned piglets born from different sows and were then housed in a specific pen for starter, grower, and finisher periods.…”

“…Increasing disease pressure is a possible explanation for the higher use of antimicrobials in feed for medium-scale pig farms when compared with small-scale pig farms [3]. For large-scale or industrial pig farms, disease pressure was reduced by better management procedures in these farms [4] and high safety level from farm biosecurity, resulting in no antimicrobial use in some pig herds [5]. Higher the limit of stock density for pigs has been proven to lower production performance and increase the risk of getting infections among pigs through altering immune systems [4].…”