摘要
      肺炎克雷伯菌（Kp）等细菌病原体抗微生物耐药性（AMR）的上升是一个紧迫的公共卫生和经济问题。“一个健康”框架认识到，有效管理AMR需要在农业和临床环境中进行监测，特别是在巴基斯坦等资源匮乏地区。在这里，我们使用全基因组测序来表征49个Klebisella spp.分离株（包括43 Kp）和2个推定的Providencia rettgeri分离株，它们是从巴基斯坦奎达（n=29）、费萨拉巴德（n=19）和萨戈达（n=3）3个城市附近的奶牛场回收的。43个Kp分离株对应于38个序列类型（ST），其中35个ST仅观察到一次。这种高度多样性表明在地方尺度上频繁的混合和有限的克隆传播。在49株克雷伯菌中，41株（84%）不含任何临床相关的抗微生物耐药性基因（ARGs），我们也没有检测到任何预测编码碳青霉烯类或粘菌素耐药性的ARGs。然而，四个Kp谱系包含多个ARG：ST11（n=2）、ST1391-1LV（n=1）、ST995（n=一）和ST985（n=1）。ST 11、1391-1LV和995共享一个由五个ARG组成的核心集合，包括blaCTX-M-15，它们携带在不同的AMR质粒上。ST985携带一组不同的16个抗性基因，包括blaCTX-M-55。两个推定的雷氏疟原虫分离株也含有多种ARG。最后，在我们的数据集中，四种最常见的不携带ARG的质粒在区域之间非随机分布，这表明质粒的局部扩增独立于宿主细菌谱系。关于奶牛场如何促进AMR在巴基斯坦的出现和传播的证据，对于负责卫生、农业和环境以及工业发展的公共当局和组织来说是有价值的。
Abstract
The rise of antimicrobial resistance (AMR) in bacterial pathogens such as Klebsiella pneumoniae (Kp) is a pressing public health and economic concern. The ‘One-Health’ framework recognizes that effective management of AMR requires surveillance in agricultural as well as clinical settings, particularly in low-resource regions such as Pakistan. Here, we use whole-genome sequencing to characterise 49 isolates of Klebisella spp. (including 43 Kp) and 2 presumptive Providencia rettgeri isolates recovered from dairy farms located near 3 cities in Pakistan—Quetta (n = 29), Faisalabad (n = 19), and Sargodha (n = 3). The 43 Kp isolates corresponded to 38 sequence types (STs), and 35 of these STs were only observed once. This high diversity indicates frequent admixture and limited clonal spread on local scales. Of the 49 Klebsiella spp. isolates, 41 (84%) did not contain any clinically relevant antimicrobial resistance genes (ARGs), and we did not detect any ARGs predicted to encode resistance to carbapenems or colistin. However, four Kp lineages contained multiple ARGs: ST11 (n = 2), ST1391-1LV (n = 1), ST995 (n = 1) and ST985 (n = 1). STs 11, 1391-1LV and 995 shared a core set of five ARGs, including blaCTX-M-15, harboured on different AMR plasmids. ST985 carried a different set of 16 resistance genes, including blaCTX-M-55. The two presumptive P. rettgeri isolates also contained multiple ARGs. Finally, the four most common plasmids which did not harbour ARGs in our dataset were non-randomly distributed between regions, suggesting that local expansion of the plasmids occurs independently of the host bacterial lineage. Evidence regarding how dairy farms contribute to the emergence and spread of AMR in Pakistan is valuable for public authorities and organizations responsible for health, agriculture and the environment, as well as for industrial development.

https://www.mdpi.com/2079-6382/12/3/539