摘要
出身背景
2022年，欧盟禁止在生猪生产中预防性使用抗菌剂和氧化锌（ZnO），因为抗菌剂和重金属的使用与抗微生物耐药性（AMR）之间存在潜在联系，以及对环境污染的担忧。然而，它们的使用对商业养猪场细菌AMR谱的影响仍不完全清楚，之前对ZnO影响的研究报告了对比结果。本研究的目的是检验抗菌剂和氧化锌的使用对商业养猪场AMR的影响。在10个爱尔兰商业农场采集粪便和环境样本，其中5个农场定期使用氧化锌和抗菌药物（阿莫西林或磺胺嘧啶甲氧苄啶）预防疾病。其他5个农场没有使用ZnO或任何其他形式的预防措施。使用未补充和补充的胰蛋白酶-胆汁X-葡萄糖醛酸琼脂对所有样品的大肠杆菌数量进行定量。
后果
总共对351个分离株进行了表型分析，并使用全基因组测序对来自4个农场的44个产生AmpC/ESBL的大肠杆菌分离株的基因组进行了表征。表型分析表明，使用预防措施的农场中有更多的耐多药（MDR）大肠杆菌分离株。此外，使用预防措施的农场与更高数量的对安普霉素、甲氧苄啶、四环素、链霉素和氯霉素具有耐药性的分离株有关，而对环丙沙星的耐药性与不使用任何预防措施的牧场更相关。44株产AmpC/ESBL的大肠杆菌中有34株携带blaCTX-M-1耐药基因，具有多药耐药性（MDR）。此外，质粒的网络分析和整合子的分析表明，抗微生物和杀生物剂抗性基因经常位于可移动的遗传元件上，这表明在抗微生物或杀生物剂使用过程中进行共同选择的可能性是AMR在农场发生和持续的原因。
结论
本研究结果表明，断奶后对猪进行抗菌和ZnO处理有利于AMR和MDR大肠杆菌的选择和发展。观察到抗性基因在可移动遗传元件上的共定位。这项研究通过测序和微生物学方法相结合，证明了表型和基因型检测抗微生物耐药性的有用性。
Abstract
Background
The prophylactic use of antimicrobials and zinc oxide (ZnO) in pig production was prohibited by the European Union in 2022 due to potential associations between antimicrobial and heavy metal usage with antimicrobial resistance (AMR) and concerns regarding environmental pollution. However, the effects of their usage on the bacterial AMR profiles on commercial pig farms are still not fully understood and previous studies examining the effect of ZnO have reported contrasting findings. The objective of this study was to examine the effects of antimicrobial and ZnO usage on AMR on commercial pig farms. Faecal and environmental samples were taken on 10 Irish commercial farms, of which 5 farms regularly used ZnO and antimicrobials (amoxicillin or sulphadiazine-trimethoprim) for the prevention of disease. The other 5 farms did not use ZnO or any other form of prophylaxis. Escherichia coli numbers were quantified from all samples using non-supplemented and supplemented Tryptone Bile X-glucuronide agar.

Results
In total 351 isolates were phenotypically analysed, and the genomes of 44 AmpC/ESBL-producing E. coli isolates from 4 farms were characterised using whole-genome sequencing. Phenotypic analysis suggested higher numbers of multi-drug resistant (MDR) E. coli isolates on farms using prophylaxis. Furthermore, farms using prophylaxis were associated with higher numbers of isolates resistant to apramycin, trimethoprim, tetracycline, streptomycin, and chloramphenicol, while resistance to ciprofloxacin was more associated with farms not using any prophylaxis. Thirty-four of the 44 AmpC/ESBL-producing E. coli strains harboured the blaCTX-M-1 resistance gene and were multi drug resistant (MDR). Moreover, network analysis of plasmids and analysis of integrons showed that antimicrobial and biocide resistance genes were frequently co-located on mobile genetic elements, indicating the possibility for co-selection during antimicrobial or biocide usage as a contributor to AMR occurrence and persistence on farms.

Conclusions
The results of this study showed evidence that antimicrobial and ZnO treatment of pigs post-weaning can favour the selection and development of AMR and MDR E. coli. Co-location of resistance genes on mobile genetic elements was observed. This study demonstrated the usefulness of phenotypic and genotypic detection of antimicrobial resistance by combining sequencing and microbiological methods.

https://gutpathogens.biomedcentral.com/articles/10.1186/s13099-023-00534-3