Habib Samia, Gibbon Marjorie J, Couto Natacha, Kakar Khadija, Habib Safia, Samad Abdul, Munir Asim, Fatima Fariha, Mohsin Mashkoor, Feil Edward J
The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath BA2 7AY, UK.
Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford OX3 7LF, UK.
Antibiotics (Basel). 2023 Mar 8;12(3):539. doi: 10.3390/antibiotics12030539.
The rise of antimicrobial resistance (AMR) in bacterial pathogens such as (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 spp. (including 43 Kp) and 2 presumptive isolates recovered from dairy farms located near 3 cities in Pakistan-Quetta ( = 29), Faisalabad ( = 19), and Sargodha ( = 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 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 ( = 2), ST1391-1LV ( = 1), ST995 ( = 1) and ST985 ( = 1). STs 11, 1391-1LV and 995 shared a core set of five ARGs, including , harboured on different AMR plasmids. ST985 carried a different set of 16 resistance genes, including . The two presumptive 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.
肺炎克雷伯菌（Kp）等细菌病原体中抗菌药物耐药性（AMR）的上升是一个紧迫的公共卫生和经济问题。“同一健康”框架认识到，有效管理AMR需要在农业以及临床环境中进行监测，特别是在巴基斯坦等资源匮乏地区。在此，我们使用全基因组测序来表征从巴基斯坦三个城市附近的奶牛场分离出的49株肺炎克雷伯菌属菌株（包括43株Kp）和2株推测的肺炎克雷伯菌分离株——奎达（n = 29）、费萨拉巴德（n = 19）和萨戈达（n = 3）。这43株Kp分离株对应38种序列类型（STs），其中35种STs仅被观察到一次。这种高度多样性表明在局部范围内频繁混合且克隆传播有限。在49株肺炎克雷伯菌属分离株中，41株（84%）不包含任何临床相关的抗菌药物耐药基因（ARGs），并且我们未检测到任何预测编码对碳青霉烯类或黏菌素耐药的ARGs。然而，四个Kp谱系包含多个ARGs：ST11（n = 2）、ST1391 - 1LV（n = 1）、ST995（n = 1）和ST985（n = 1）。STs 11、1391 - 1LV和995共享一组包含五个ARGs的核心基因，包括blaCTX - M，这些基因位于不同的AMR质粒上。ST985携带一组不同的16个耐药基因，包括blaNDM - 1。这两株推测的肺炎克雷伯菌分离株也包含多个ARGs。最后，我们数据集中四个最常见的不携带ARGs的质粒在不同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发生。关于奶牛场如何在巴基斯坦促成AMR的出现和传播的证据，对于负责卫生、农业和环境的公共当局和组织以及工业发展而言是有价值的。
