Longitudinal study on the effects of growth-promoting and therapeutic antibiotics on the dynamics of chicken cloacal and litter microbiomes and resistomes

Abstract

Background Therapeutic and growth-promoting antibiotics are frequently used in broiler production. Indirect evidence indicates that these practices are linked to the proliferation of antimicrobial resistance (AMR), the spread of antibiotic-resistant bacteria from food animals to humans, and the environment, but there is a lack of comprehensive experimental data supporting this. We investigated the effects of growth promotor (bacitracin) and therapeutic (enrofloxacin) antibiotic administration on AMR in broilers for the duration of a production cycle, using a holistic approach that integrated both culture-dependent and culture-independent methods. We specifically focused on pathogen-harboring families (Enterobacteriaceae, Enterococcaceae, and Staphylococcaceae). Results Antibiotic-resistant bacteria and antibiotic resistance genes were ubiquitous in chicken cloaca and litter regardless of antibiotic administration. Environment (cloaca vs. litter) and growth stage were the primary drivers of variation in the microbiomes and resistomes, with increased bacterial diversity and a general decrease in abundance of the pathogen-harboring families with age. Bacitracin-fed groups had higher levels of bacitracin resistance genes and of vancomycin-resistant Enterococcaceae (total Enterococcaceae counts were not higher). Although metagenomic analyses classified 28–76% of the Enterococcaceae as the commensal human pathogens E. faecalis and E. faecium, culture-based analysis suggested that approximately 98% of the vancomycin-resistant Enterococcaceae were avian and not human-associated, suggesting differences in the taxonomic profiles of the resistant and non-resistant strains. Enrofloxacin treatments had varying effects, but generally facilitated increased relative abundance of multidrug-resistant Enterobacteriaceae strains, which were primarily E. coli. Metagenomic approaches revealed a diverse array of Staphylococcus spp., but the opportunistic pathogen S. aureus and methicillin resistance genes were not detected in culture-based or metagenomic analyses. Camphylobacteriaceae were significantly more abundant in the cloacal samples, especially in enrofloxacin-treated chickens, where a metagenome-assembled C. jejuni genome harboring fluoroquinolone and β-lactam resistance genes was identified. Conclusions Within a “farm-to-fork, one health” perspective, considering the evidence that bacitracin and enrofloxacin used in poultry production can select for resistance, we recommend their use be regulated. Furthermore, we suggest routine surveillance of ESBL E. coli, vancomycin-resistant E. faecalis and E. faecium, and fluoroquinolone-resistant C. jejuni strains considering their pathogenic nature and capacity to disseminate AMR to the environment.

Metatranscriptomic Analysis of the Chicken Gut Resistome Response to In-Feed Antibiotics and Natural Feed Additives

“…However, on Day 21, bacitracin administration at a high dose (AB) resulted in a detectable increase in the relative expression of the bacitracin ARG class, which was even higher than the high background resistance, although the gut resistome diversity had mostly recovered after 2 weeks of antibiotic withdrawal. A study from Gupta et al ( Gupta et al, 2021 ) found an increase in the relative abundance of bacitracin resistance in hens given bacitracin, which is consistent with our findings.…”

“…Additionally, antibiotic combination with phytogenics (AGP + PFA; AB + PFA) showed no unique ARG transcripts over the feeding trial. These findings are supported by those from previous studies and indicate that administration of AGP (low-dose antibiotics) in feed causes an accumulation of ARGs in complex ecosystems ( Butaye et al, 2003 ; You and Silbergeld, 2014 ; Salaheen et al, 2017 ; Gupta et al, 2021 ). Overall, the most expressed ARG classes in our study (aminoglycosides, MLS, tetracyclines) are known to be prevalent in the chicken gut resistome ( Li B. et al, 2015 ; Wang et al, 2020 ; Wang Y. et al, 2021 ).…”

“…Overall, the most expressed ARG classes in our study (aminoglycosides, MLS, tetracyclines) are known to be prevalent in the chicken gut resistome ( Li B. et al, 2015 ; Wang et al, 2020 ; Wang Y. et al, 2021 ). However, the results from another study by Gupta et al (2021) indicated that multidrug and beta-lactam ARGs were most abundant. In our study we did not observe high expression of these ARG classes.…”

Effects of Dietary Antimicrobial Growth Promoters on Performance Parameters and Abundance and Diversity of Broiler Chicken Gut Microbiome and Selection of Antibiotic Resistance Genes

“…PCR and qPCR analysis confirmed the presence of some of the ARGs identified through shotgun analysis. Earlier, Gupta et al (2021) observed that although antibiotic resistance genes were ubiquitous in chicken cloaca and litter, bacitracin fed groups had higher levels of bacitracin resistance genes, and vancomycin-resistant bacteria and enrofloxacin treatments generally facilitated increased abundance of multidrug-resistant bacteria. In contrast, Danzeisen et al (2011) did not observe any significant difference in antimicrobial resistance gene counts in the cecal content of chicken on supplementing with monensin, tylosin, and virginiamycin.…”

Antibiotic Resistance of Bacterial Isolates from Smallholder Poultry Droppings in the Guinea Savanna Zone of Nigeria

“…Poultry production has been identified as a hot-spot for the development of antimicrobial resistance (AMR), and transfer of drug-resistant micro-organisms between food-producing animals and humans [ 4 , 5 , 6 , 7 ]. This is due to the high and chronic use of antibiotics, especially at sub-therapeutic levels, in commercial poultry.…”