Impacts of Short-Term Antibiotic Withdrawal and Long-Term Judicious Antibiotic Use on Resistance Gene Abundance and Cecal Microbiota Composition on Commercial Broiler Chicken Farms in Québec

Abstract

The ever-increasing problem of antibiotic resistance makes routine use of antibiotics in animal production no longer considered as a reasonable and viable practice. The Chicken Farmers of Canada have developed and are implementing an Antimicrobial Use Reduction Strategy, which has the ultimate goal of eliminating the preventive use of medically important antibiotics in broiler chicken and turkey production. However, very little is known about the real overall impact of an antibiotic use reduction strategy in complex ecosystems, such as the bird intestine or the commercial broiler chicken farm. The main objectives of the present study were to compare the abundance of antibiotic resistance-encoding genes, characterize the intestinal microbiota composition, and evaluate the presence of Clostridium perfringens, in six commercial poultry farms adopting short-term antibiotic withdrawal and long-term judicious use strategy. Implementing an antibiotic-free program over a 15-months period did not reduce the abundance of many antibiotic resistance-encoding genes, whereas the judicious use of antibiotics over 6 years was found effective. The short-term antibiotic withdrawal and the long-term judicious use strategy altered the intestinal microbiota composition, with the Ruminococcaceae and Lachnospiraceae families being negatively impacted. These findings are in agreement with the lower production performance and with the increased C. perfringens populations observed for farms phasing out the use of antibiotics. Adopting a conventional rearing program on commercial broiler chicken farms selected for specific antibiotic resistance-encoding genes in many barns. This study highlights the potential impacts of different rearing programs in poultry production and will help guide future policies in order to reduce the use of antibiotics while maintaining production performance.

Using whole-genome sequence data to examine the epidemiology of Salmonella, Escherichia coli and associated antimicrobial resistance in raccoons (Procyon lotor), swine manure pits, and soil samples on swine farms in southern Ontario, Canada

“…A previous study examining AMR in wild small mammals in a variety of environments in the same study region also found that resistance to tetracyclines (conferred by tetA) was significantly more likely to be identified in generic E. coli from animals trapped on swine farms compared to residential areas [51]. Overall, our findings are consistent with recent mounting evidence that the use of antimicrobials in agriculture is a major driver of AMR in intensive farm environments [52][53][54]. In the future, exploration of enteric bacteria and AMR carried by raccoons in different types of environments, including cities, may contribute valuable information concerning the impact of agricultural and urban environments on the microbiome of these animals.…”

Effect of Enrofloxacin on the Microbiome, Metabolome, and Abundance of Antibiotic Resistance Genes in the Chicken Cecum

“…We found no significant changes in partial PMQR gene abundances at day 14 compared to those at days 7 and 21 ( P > 0.05). This is similar to previous reports showing that the abundance of antibiotic resistance genes is not changed significantly after a period of antibiotic discontinuation ( 55 ). In addition, according to previous reports, the use of antibiotics might cause changes in the abundance of genes conferring resistance to other types of antibiotics ( 56 ).…”

Dose-dependent impact of enrofloxacin on broiler chicken gut resistome is mitigated by synbiotic application

“…However, in vivo evaluation of such optimized doses in broiler chickens is still lacking. The impact of other antimicrobials on the residential microbiota in broilers has been investigated ( Xiong et al, 2018 ; Luiken et al, 2019 ; Turcotte et al, 2020 ), showing a range of effects, including reduction of overall diversity of the bacterial communities, microbiome metabolic shifts, increasing gut susceptibility to colonization, and stimulation of the development of AMR. In medical research, there are indications that alternatives to antibiotics, including dietary prebiotics, probiotics, and synbiotics (products that combine the simultaneous and potentially synergistic use of pre- and probiotics) ( Gibson et al, 2004 ; Markowiak and Śliżewska, 2017 ) can reverse the perturbations induced by antimicrobial administration ( Korpela et al, 2018 ; Abd El-Hack et al, 2020 ).…”