PDF(Pubmed)
Abstract：
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).
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.
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. Video Abstract.
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.
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. Video Abstract.
摘要：
治疗和促进生长的抗生素经常用于肉鸡生产。间接证据表明，这些做法与抗菌素耐药性（AMR）的扩散有关，抗生素抗性细菌从食用动物传播到人类，和环境，但是缺乏全面的实验数据来支持这一点。我们研究了在生产周期期间，生长促进剂（杆菌肽）和治疗性（恩诺沙星）抗生素给药对肉鸡AMR的影响，使用整合文化依赖和文化独立方法的整体方法。我们特别关注有病原体的家族(肠杆菌科，肠球菌科,和葡萄球菌科）。
抗生素抗性细菌和抗生素抗性基因在鸡泄殖腔和垫料中普遍存在，无论使用何种抗生素。环境（泄殖腔与凋落物）和生长阶段是微生物群和抗性体变化的主要驱动因素，随着年龄的增长，细菌多样性增加，病原体携带家庭的丰度普遍减少。杆菌肽饲喂组的杆菌肽抗性基因和耐万古霉素的肠球菌科较高（总肠球菌科计数不高）。尽管宏基因组分析将28-76％的肠球菌科归类为共生人类病原体粪肠球菌和粪肠球菌，基于培养的分析表明，大约98％的耐万古霉素的肠球菌科是禽类而不是与人类相关的，表明抗性和非抗性菌株的分类学特征存在差异。恩诺沙星治疗有不同的效果，但通常促进了耐多药肠杆菌科菌株的相对丰度增加，主要是大肠杆菌。宏基因组方法揭示了多种葡萄球菌属。,但在培养或宏基因组分析中未检测到条件致病菌金黄色葡萄球菌和耐甲氧西林基因.在泄殖腔样本中，樟脑杆菌科明显更丰富，尤其是在恩诺沙星治疗的鸡中，其中鉴定了具有氟喹诺酮和β-内酰胺抗性基因的宏基因组组装的空肠杆菌基因组。
在“从农场到叉子”中，一个健康的角度，考虑到杆菌肽和恩诺沙星用于家禽生产可以选择耐药性的证据，我们建议对其使用进行监管。此外，我们建议对ESBL大肠杆菌进行常规监测，耐万古霉素粪肠球菌和屎肠球菌，和耐氟喹诺酮的空肠弯曲菌菌株，考虑到其致病性和向环境传播AMR的能力。视频摘要。
抗生素抗性细菌和抗生素抗性基因在鸡泄殖腔和垫料中普遍存在，无论使用何种抗生素。环境（泄殖腔与凋落物）和生长阶段是微生物群和抗性体变化的主要驱动因素，随着年龄的增长，细菌多样性增加，病原体携带家庭的丰度普遍减少。杆菌肽饲喂组的杆菌肽抗性基因和耐万古霉素的肠球菌科较高（总肠球菌科计数不高）。尽管宏基因组分析将28-76％的肠球菌科归类为共生人类病原体粪肠球菌和粪肠球菌，基于培养的分析表明，大约98％的耐万古霉素的肠球菌科是禽类而不是与人类相关的，表明抗性和非抗性菌株的分类学特征存在差异。恩诺沙星治疗有不同的效果，但通常促进了耐多药肠杆菌科菌株的相对丰度增加，主要是大肠杆菌。宏基因组方法揭示了多种葡萄球菌属。,但在培养或宏基因组分析中未检测到条件致病菌金黄色葡萄球菌和耐甲氧西林基因.在泄殖腔样本中，樟脑杆菌科明显更丰富，尤其是在恩诺沙星治疗的鸡中，其中鉴定了具有氟喹诺酮和β-内酰胺抗性基因的宏基因组组装的空肠杆菌基因组。
在“从农场到叉子”中，一个健康的角度，考虑到杆菌肽和恩诺沙星用于家禽生产可以选择耐药性的证据，我们建议对其使用进行监管。此外，我们建议对ESBL大肠杆菌进行常规监测，耐万古霉素粪肠球菌和屎肠球菌，和耐氟喹诺酮的空肠弯曲菌菌株，考虑到其致病性和向环境传播AMR的能力。视频摘要。
