Asghar Muhammad Umer, Zhai Yuting, Liu Ting, Fan Peixin, Ain Noor Ul, Zaidi Arsalan Haseeb, Tariq Muhammad, Mainar-Jaime Raul C, Jeong Kwangcheol C
Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA; Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA; National Probiotic Lab, National Institute for Biotechnology and Genetic Engineering-College, Faisalabad 38000, Pakistan; Pakistan Institute of Engineering & Applied Sciences, Nilore, Islamabad 45650, Pakistan.
Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611, USA; Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA.
J Hazard Mater. 2025 Sep 15;496:139384. doi: 10.1016/j.jhazmat.2025.139384. Epub 2025 Jul 29.
Hospital environments are critical yet underexamined reservoirs for hazardous antimicrobial resistance (AMR), particularly in lower-middle-income countries (LMICs) where resource constraints often hinder comprehensive surveillance. In this study, we employed 16S rRNA gene sequencing and shotgun metagenomics to characterize the microbiome, resistome, and potential transmission routes across five clinical environments within a hospital in Pakistan: the intensive care unit (ICU), surgical ward (SW), cardiac surgery ward (CSW), cardiac ward (CW), and operating theater (OT). Microbial community analysis revealed compositional similarities among the ICU, SW, and OT, with the ICU emerging as a primary source of microbial dissemination. Species-level profiling identified hospital-associated pathogens such as Acinetobacter baumannii, Klebsiella pneumoniae, and Enterobacter cloacae, and metagenome-assembled genome (MAG) analysis enabled the linkage of antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) to specific bacterial hosts. ARGs and MGEs displayed setting-specific patterns, with the SW harboring the highest abundance of ARGs, particularly those conferring resistance to β-lactams and biocides. Insertion sequences were the most prevalent MGEs and were commonly linked to ARGs, indicating potential horizontal gene transfer. Co-occurrence network analysis identified Staphylococcus, Enterococcus, and Escherichia as central hub taxa within the microbial communities of the ICU, SW, and OT, indicating their critical roles in potential ARG transmission. These findings provide critical insights into the environmental transmission dynamics of AMR in LMIC healthcare settings and underscore the urgent need for metagenomics-informed infection control strategies.
医院环境是有害抗菌药物耐药性（AMR）的关键但未得到充分研究的储存库，尤其是在中低收入国家（LMICs），资源限制往往阻碍全面监测。在本研究中，我们采用16S rRNA基因测序和鸟枪法宏基因组学来表征巴基斯坦一家医院内五个临床环境中的微生物组、耐药组和潜在传播途径：重症监护病房（ICU）、外科病房（SW）、心脏外科病房（CSW）、心脏病房（CW）和手术室（OT）。微生物群落分析揭示了ICU、SW和OT之间的组成相似性，ICU成为微生物传播的主要来源。物种水平分析确定了医院相关病原体，如鲍曼不动杆菌、肺炎克雷伯菌和阴沟肠杆菌，宏基因组组装基因组（MAG）分析能够将抗菌药物耐药基因（ARGs）和移动遗传元件（MGEs）与特定细菌宿主联系起来。ARGs和MGEs呈现出特定环境的模式，SW中ARGs的丰度最高，尤其是那些赋予对β-内酰胺类和杀菌剂耐药性的基因。插入序列是最常见的MGEs，通常与ARGs相关联，表明潜在的水平基因转移。共现网络分析确定葡萄球菌、肠球菌和大肠杆菌是ICU、SW和OT微生物群落中的核心枢纽分类群，表明它们在潜在的ARG传播中起关键作用。这些发现为中低收入国家医疗环境中AMR的环境传播动态提供了关键见解，并强调了基于宏基因组学的感染控制策略的迫切需求。
