Animal and Veterinary Sciences, Scotland's Rural College (SRUC), Edinburgh, United Kingdom.
The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom.
Sci Rep. 2020 Feb 3;10(1):1708. doi: 10.1038/s41598-020-58659-3.
Group antimicrobial administration is used to control disease in livestock, but we have little insight into how this impacts antimicrobial resistance (AMR) gene dynamics. Here, a longitudinal study was carried out during a single production cycle on a commercial pig unit with high historic and current antimicrobial usage. Quantitative PCR, 16S rRNA gene metabarcoding and shotgun metagenomic sequencing were used to track faecal AMR gene abundance and diversity and microbiome alpha diversity. Shotgun metagenomic sequencing identified 144 AMR genes in total, with higher AMR gene diversity present in young pigs compared to dry sows. Irrespective of in-feed antibiotic treatment or changes in microbiome diversity, mean AMR gene copy number was consistently high, with some AMR genes present at copy numbers comparable to the bacterial 16S rRNA gene. In conclusion, AMR gene prevalence and abundance were not influenced by antibiotic use, either during the production cycle or following whole-herd medication. The high levels of certain genes indicate they are widely disseminated throughout the microbial population, potentially aiding stability. Despite the high and relatively stable levels of resistance genes against the main antimicrobials used, these compounds continue to control production limiting diseases on this unit.
群体抗菌药物管理被用于控制牲畜疾病，但我们对其如何影响抗菌药物耐药性（AMR）基因动态知之甚少。在这里，在一个具有高历史和当前抗菌药物使用量的商业养猪场的单个生产周期中进行了一项纵向研究。使用定量 PCR、16S rRNA 基因代谢组学和 shotgun 宏基因组测序来跟踪粪便 AMR 基因丰度和多样性以及微生物组 α 多样性。Shotgun 宏基因组测序共鉴定出 144 个 AMR 基因，与干母猪相比，幼猪中 AMR 基因多样性更高。无论是否进行饲料抗生素治疗或微生物组多样性的变化，平均 AMR 基因拷贝数始终很高，一些 AMR 基因的拷贝数与细菌 16S rRNA 基因相当。总之，抗生素的使用，无论是在生产周期中还是在全群用药后，都没有影响 AMR 基因的流行和丰度。某些基因的高水平表明它们在整个微生物群中广泛传播，可能有助于其稳定性。尽管对主要抗菌药物的耐药基因水平较高且相对稳定，但这些化合物仍能继续控制该单位中限制生产的疾病。
