从粪便宏基因组深入了解脉冲式抗生素给药对鸡肠道和菌群的影响

doi:10.1016/j.jia.2022.11.006

Journal of Integrative Agriculture ›› 2023, Vol. 22 ›› Issue (6): 1857-1869.DOI: 10.1016/j.jia.2022.11.006

从粪便宏基因组深入了解脉冲式抗生素给药对鸡肠道和菌群的影响

收稿日期:2022-08-15 修回日期:2022-11-24 接受日期:2022-10-14 出版日期:2023-06-20 发布日期:2022-10-14

Insights into the effects of pulsed antimicrobials on the chicken resistome and microbiota from fecal metagenomes

ZHAO Ruo-nan^{1, 2, 3*}, CHEN Si-yuan^{1, 2, 3*}, TONG Cui-hong^{1, 2, 3}, HAO Jie^{1, 2, 3}, LI Pei-si^{1, 2, 3}, XIE Long-fei^{1, 2, 3}, XIAO Dan-yu^{1, 2, 3}, ZENG Zhen-ling^{1, 2, 3#}, XIONG Wen-guang^{1, 2, 3#}

¹Guangdong Provincial Key Laboratory of Veterinary Pharmaceutics Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P.R.China
²Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, P.R.China
³National Laboratory of Safety Evaluation (Environmental Assessment) of Veterinary Drugs, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, P.R.China

Received:2022-08-15 Revised:2022-11-24 Accepted:2022-10-14 Online:2023-06-20 Published:2022-10-14
About author:ZHAO Ruo-nan, E-mail: zrn_327@163.com; CHEN Si-yuan, E-mail: 1394974930@qq.com; #Correspondence ZENG Zhen-ling, E-mail: zlzeng@scau.edu.cn; XIONG Wen-guang, E-mail: xiongwg@scau.edu.cn * These authors contributed equally to this study.
Supported by:
This work was supported by the Laboratory of Lingnan Modern Agriculture Project, China (NT2021006), the Foundation for Innovative Research Groups of the National Natural Science Foundation of China (32121004), and the Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program, China (2019BT02N054).

摘要/Abstract

摘要：

抗生素耐药性已成为威胁人类健康的全球性问题。抗生素被广泛应用于肉鸡养殖从而影响它们的肠道微生物组和耐药组。为了更好地了解对农场动物持续性给药是如何改变微生物生态的变化，我们采用宏基因组的方法，研究脉冲式抗生素给药对肉鸡粪便微生物群、耐药基因（ARGs）及其宿主的影响。肉鸡分别接受三次连续五天的阿莫西林、金霉素、氟苯尼考单独给药和三种药的联合给药。结果显示，给药氟苯尼考能显著增加耐药基因floR和mcr-1的丰度，而给药阿莫西林则显著增加编码AcrAB-tolC外排泵的相关基因，如marA、soxS、sdiA、rob、evgS and phoP。这三种抗生素给药都显著增加微生物群中变形菌门的丰度。我们推测，耐药基因宿主埃希菌属丰度的上升，主要是由于在脉冲式抗生素给药下，其携带了β-内酰胺类、氯霉素和四环素耐药基因。这些结果表明，脉冲式阿莫西林、金霉素、氟苯尼考或三种药物的联合给药都能显著提高微生物群中变形菌门的丰度，而且会增加特定耐药基因的丰度。耐药基因大类主要由多重耐药基因组成，并且在抗生素处理的组别中，多重耐药基因的丰度与耐药基因总丰度具有很强的相关性。本研究对经脉冲式抗生素给药的鸡的粪便微生物群和耐药组的改变提供了全面的见解。

Abstract:

Antimicrobial resistance has become a global problem that poses great threats to human health. Antimicrobials are widely used in broiler chicken production and consequently affect their gut microbiota and resistome. To better understand how continuous antimicrobial use in farm animals alters their microbial ecology, we used a metagenomic approach to investigate the effects of pulsed antimicrobial administration on the bacterial community, antibiotic resistance genes (ARGs) and ARG bacterial hosts in the feces of broiler chickens. Chickens received three 5-day courses of individual or combined antimicrobials, including amoxicillin, chlortetracycline and florfenicol. The florfenicol administration significantly increased the abundance of mcr-1 gene accompanied by floR gene, while amoxicillin significantly increased the abundance of genes encoding the AcrAB-tolC multidrug efflux pump (marA, soxS, sdiA, rob, evgS and phoP). These three antimicrobials all led to an increase in Proteobacteria. The increase in ARG host, Escherichia, was mainly attributed to the β-lactam, chloramphenicol and tetracycline resistance genes harbored by Escherichia under the pulsed antimicrobial treatments. These results indicated that pulsed antimicrobial administration with amoxicillin, chlortetracycline, florfenicol or their combinations significantly increased the abundance of Proteobacteria and enhanced the abundance of particular ARGs. The ARG types were occupied by the multidrug resistance genes and had significant correlations with the total ARGs in the antimicrobial-treated groups. The results of this study provide comprehensive insight into pulsed antimicrobial-mediated alteration of chicken fecal microbiota and resistome.

Key words: metagenomic , chicken , antimicrobials , resistome , microbial community

ZHAO Ruo-nan, CHEN Si-yuan, TONG Cui-hong, HAO Jie, LI Pei-si, XIE Long-fei, XIAO Dan-yu, ZENG Zhen-ling, XIONG Wen-guang. 从粪便宏基因组深入了解脉冲式抗生素给药对鸡肠道和菌群的影响[J]. Journal of Integrative Agriculture, 2023, 22(6): 1857-1869.

ZHAO Ruo-nan, CHEN Si-yuan, TONG Cui-hong, HAO Jie, LI Pei-si, XIE Long-fei, XIAO Dan-yu, ZENG Zhen-ling, XIONG Wen-guang. Insights into the effects of pulsed antimicrobials on the chicken resistome and microbiota from fecal metagenomes[J]. Journal of Integrative Agriculture, 2023, 22(6): 1857-1869.

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从粪便宏基因组深入了解脉冲式抗生素给药对鸡肠道和菌群的影响

Insights into the effects of pulsed antimicrobials on the chicken resistome and microbiota from fecal metagenomes

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