Resistance to change: AMR gene dynamics on a commercial pig farm with high antimicrobial usage
Resistance to change: AMR gene dynamics on a commercial pig farm with high antimicrobial usage
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DOI：
10.1038/s41598-020-58659-3
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发表时间：
2020-02-03
影响因子：
4.6
通讯作者：
Corbishley，Alexander
中科院分区：
文献类型：
--
作者：
Pollock，Jolinda;Muwonge，Adrian;Corbishley，Alexander
群体抗菌素管理用于控制牲畜疾病，但我们对这如何影响抗菌素耐药性（AMR）基因动力学知之甚少。在这里，在一个历史上和目前抗菌药物使用率很高的商品猪单位进行了一个单一生产周期的纵向研究。采用定量PCR、16S rRNA基因元条形码和霰弹枪宏基因组测序等方法对粪便AMR基因丰度、多样性和微生物组α多样性进行了追踪。霰弹枪宏基因组测序共鉴定出144个AMR基因，与干母猪相比，仔猪的AMR基因多样性更高。无论饲料中的抗生素治疗或微生物组多样性的变化，AMR基因的平均拷贝数一直很高，其中一些AMR基因的拷贝数与细菌的16S rRNA基因相当。综上所述，无论是在生产周期还是在全群用药后，AMR基因的流行度和丰度都不受抗生素使用的影响。某些基因的高水平表明它们在微生物种群中广泛传播，可能有助于稳定性。尽管对所使用的主要抗菌素的抗性基因水平较高且相对稳定，但这些化合物继续控制着该单位的生产限制疾病。
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.