Table_9_Prevalence and distribution of extended-spectrum β-lactamase and AmpC-producing Escherichia coli in two New Zealand dairy farm environments.DOCX

Antimicrobial resistance (AMR) is a global threat to human and animal health, with the misuse and overuse of antimicrobials being suggested as the main driver of resistance. In a global context, New Zealand (NZ) is a relatively low user of antimicrobials in animal production. However, the role antimicrobial usage on pasture-based dairy farms, such as those in NZ, plays in driving the spread of AMR within the dairy farm environment remains equivocal. Culture-based methods were used to determine the prevalence and distribution of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Escherichia coli from farm environmental samples collected over a 15-month period from two NZ dairy farms with contrasting management practices. Whole genome sequencing was utilised to understand the genomic epidemiology and antimicrobial resistance gene repertoire of a subset of third-generation cephalosporin resistant E. coli isolated in this study. There was a low sample level prevalence of ESBL-producing E. coli (faeces 1.7%; farm dairy effluent, 6.7% from Dairy 4 and none from Dairy 1) but AmpC-producing E. coli were more frequently isolated across both farms (faeces 3.3% and 8.3%; farm dairy effluent 38.4%, 6.7% from Dairy 1 and Dairy 4, respectively). ESBL- and AmpC-producing E. coli were isolated from faeces and farm dairy effluent in spring and summer, during months with varying levels of antimicrobial use, but no ESBL- or AmpC-producing E. coli were isolated from bulk tank milk or soil from recently grazed paddocks. Hybrid assemblies using short- and long-read sequence data from a subset of ESBL- and AmpC-producing E. coli enabled the assembly and annotation of nine plasmids from six E. coli, including one plasmid co-harbouring 12 antimicrobial resistance genes. ESBL-producing E. coli were infrequently identified from faeces and farm dairy effluent on the two NZ dairy farms, suggesting they are present at a low prevalence on these farms. Plasmids harbouring several antimicrobial resistance genes were identified, and bacteria carrying such plasmids are a concern for both animal and public health. AMR is a burden for human, animal and environmental health and requires a holistic “One Health” approach to address.

抗菌素耐药性（Antimicrobial Resistance, AMR）对人类与动物健康构成全球性威胁，抗菌素的误用与过度使用被认为是耐药性产生的主要驱动因素。在全球范围内，新西兰（New Zealand, NZ）的动物生产中抗菌素使用量相对较低。然而，以牧场为基础的奶牛场（如新西兰的此类牧场）的抗菌素使用，在推动奶牛场环境内AMR传播中所扮演的角色仍不明确。本研究采用培养法，对来自两家管理模式迥异的新西兰奶牛场、历时15个月采集的农场环境样本中，产超广谱β-内酰胺酶（Extended-Spectrum β-Lactamase, ESBL）和AmpC酶的大肠埃希氏菌（Escherichia coli）的流行率与分布特征进行检测。利用全基因组测序技术，对本次研究分离获得的部分第三代头孢菌素耐药大肠埃希氏菌的基因组流行病学特征及其抗菌素耐药基因谱进行解析。产ESBL的大肠埃希氏菌样本流行率较低（粪便样本中为1.7%；4号奶牛场的农场奶牛场废水中为6.7%，1号奶牛场未检出），但两家农场中产AmpC酶的大肠埃希氏菌分离率更高：粪便样本中1号农场为3.3%、4号农场为8.3%，农场奶牛场废水中1号农场为38.4%、4号农场为6.7%。产ESBL和AmpC酶的大肠埃希氏菌于春季和夏季（即抗菌素使用水平存在波动的月份）在粪便与农场奶牛场废水中被检出，但从未在散装罐牛奶或近期放牧牧场的土壤样本中分离得到。本研究对部分产ESBL和AmpC酶的大肠埃希氏菌的短读长与长读长测序数据进行混合组装，成功完成了6株大肠埃希氏菌携带的9种质粒的组装与注释，其中1种质粒同时携带12种抗菌素耐药基因。在这两家新西兰奶牛场的粪便与农场奶牛场废水中，产ESBL的大肠埃希氏菌检出率较低，表明此类细菌在该类牧场中的流行率处于较低水平。本研究鉴定出携带多种抗菌素耐药基因的质粒，携带此类质粒的细菌对动物健康与公共卫生均构成潜在风险。抗菌素耐药性是人类、动物与环境健康的共同负担，需采用整体性的“同一健康（One Health）”策略加以应对。