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

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.     

长期有机/无机肥配施对褐土细菌群落及抗生素抗性基因赋存的影响

为探明长期有机/无机肥配施对土壤细菌及抗生素抗性基因多样性的影响，以山西寿阳褐土长期定位试验为依托，采集5个有机/无机肥配施处理（N₀P₀M₀，N₂P₁M₁，N₄P₂M₂，N₃P₂M₃和N₀P₀M₆）0~20 cm土层土壤样品，采用宏基因组测序技术研究有机/无机肥配施条件下褐土中细菌群落和抗生素抗性基因的差异。结果表明：长期有机/无机肥配施显著改变了土壤细菌及抗生素抗性基因的多样性，细菌优势门为变形菌门、酸杆菌门、放线菌门、芽单胞菌门和绿弯菌门。不同处理土壤共同抗性基因亚型有256个，土壤特有抗生素抗性基因亚型随施肥量的增加均呈现先增加后降低的趋势，且在N₃P₂M₃处理中达到最高。土壤中丰度较高的抗生素抗性基因种类有大环内酯类、多药类、万古霉素类、四环素类、氯霉素类，其中含量最高的抗性基因亚型为MacB、BcrA、MexW、MexF和pbp1a。皮尔森相关性分析表明：土壤理化性质直接或间接地影响着细菌群落及ARGs的组成和变异，冗余分析进一步表明，抗生素抗性基因的变化受细菌群落结构的影响。抗生素抗性基因已经成为威胁人类健康的潜在污染物，农业生产中施用畜禽粪污时应充分腐熟并与化肥配合施用，以保障生态环境安全。