Chicken farming may influence the gut antibiotic resistome and microbiome of workers: a metagenomic analysis
- 1Department of Epidemiology, School of Public Health, Zhengzhou University, No. 100 of Science Avenue, Zhengzhou, 450001 China
Abstract
In the context of the broad utilization of antibiotics in poultry breeding, an increasing number of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) are accumulating in chicken feces, which presents a latent danger to workers’ health. However, few studies have explored the effect of chicken rearing on the microbial flora of workers. In this study, using metagenomic analysis techniques, a panoramic view of the intestinal microbiome and resistome across 40 chickens, 31 farm workers and 23 control villagers was obtained. The results showed that the chicken gut harbored more pathogens than the human gut. ESKAPE pathogens showed a stepwise increase from villagers to workers to chickens. The level of Streptococcus pneumoniae in workers was higher than that in villagers, indicating potential pathogen exposure risks. Chickens shared more ARGs with workers than villagers. Significantly higher abundances of 125 ARGs were detected in chicken samples compared to human samples. Among these, 22 ARGs were more abundant in worker samples than in villager samples. Metagenome-assembled genome (MAG) analysis revealed that 99 ARGs were annotated in human MAGs, predominantly in Escherichia coli (43 ARGs) and Klebsiella pneumoniae (22 ARGs). Co-occurrences of ARGs and mobile genetic elements (MGEs) were observed in E. coli and K. pneumoniae, with the transposon gene tnpA being carried by multiple bacteria. Co-localization of ARGs (APH(3’’)-Ib, APH(6)-Id) and MGE (IS91) in the MAG (Parasutterella gallistercoris) of workers was detected, while these two ARGs showed increasing abundance from villager to worker to chicken samples. This study indicated that chicken guts serve as important reservoirs of ARB and ARGs, which may influence the gut bacterial health of workers. Therefore, it is necessary to strengthen the management of antibiotic use in chicken farms and the health monitoring of relevant populations.
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s42523-026-00612-2.
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BibTeX
@article{hao2026chicken,
title = {{Chicken farming may influence the gut antibiotic resistome and microbiome of workers: a metagenomic analysis}},
author = {Yuqing Hao and Yuan Li and Ying Wang and Fang Liu and Jinzhao Long and Haiyan Yang},
journal = {Animal Microbiome},
year = {2026},
month = aug,
doi = {10.1186/s42523-026-00612-2},
url = {https://doi.org/10.1186/s42523-026-00612-2},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - JOUR
TI - Chicken farming may influence the gut antibiotic resistome and microbiome of workers: a metagenomic analysis
AU - Yuqing Hao
AU - Yuan Li
AU - Ying Wang
AU - Fang Liu
AU - Jinzhao Long
AU - Haiyan Yang
PY - 2026
DA - 2026/08/06
JO - Animal Microbiome
DO - 10.1186/s42523-026-00612-2
UR - https://doi.org/10.1186/s42523-026-00612-2
AB - In the context of the broad utilization of antibiotics in poultry breeding, an increasing number of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) are accumulating in chicken feces, which presents a latent danger to workers’ health. However, few studies have explored the effect of chicken rearing on the microbial flora of workers. In this study, using metagenomic analysis techniques, a panoramic view of the intestinal microbiome and resistome across 40 chickens, 31 farm workers and 23 control villagers was obtained. The results showed that the chicken gut harbored more pathogens than the human gut. ESKAPE pathogens showed a stepwise increase from villagers to workers to chickens. The level of Streptococcus pneumoniae in workers was higher than that in villagers, indicating potential pathogen exposure risks. Chickens shared more ARGs with workers than villagers. Significantly higher abundances of 125 ARGs were detected in chicken samples compared to human samples. Among these, 22 ARGs were more abundant in worker samples than in villager samples. Metagenome-assembled genome (MAG) analysis revealed that 99 ARGs were annotated in human MAGs, predominantly in Escherichia coli (43 ARGs) and Klebsiella pneumoniae (22 ARGs). Co-occurrences of ARGs and mobile genetic elements (MGEs) were observed in E. coli and K. pneumoniae, with the transposon gene tnpA being carried by multiple bacteria. Co-localization of ARGs (APH(3’’)-Ib, APH(6)-Id) and MGE (IS91) in the MAG (Parasutterella gallistercoris) of workers was detected, while these two ARGs showed increasing abundance from villager to worker to chicken samples. This study indicated that chicken guts serve as important reservoirs of ARB and ARGs, which may influence the gut bacterial health of workers. Therefore, it is necessary to strengthen the management of antibiotic use in chicken farms and the health monitoring of relevant populations. Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1186/s42523-026-00612-2.
SN - 2524-4671
ER -