病院廃水システムのマイクロバイオームと感染患者からの臨床分離株の大規模な特性解析:多剤耐性微生物種のプロファイリング。 Large-scale characterisation of hospital wastewater system microbiomes and clinical isolates from infected patients: profiling of multidrug-resistant microbial species.
Stephen A. Kelly, Nuala H. O’Connell, Thomas P. Thompson, Lucy Dillon, Jiaqi Wu, Chris Creevey, Patrick Kiely, Barbara Slevin, James Powell, Brendan F. Gilmore, Colum P. Dunne
Journal of Hospital Infection Available online: 9 September 2023
Hospital-acquired infection (HAI) and infectious agents exhibiting antimicrobial resistance (AMR) are challenges globally. Environmental patient-facing wastewater apparatus including handwashing sinks, showers and toilets are increasingly identified as sources of infectious agents and AMR genes.
We performed large-scale metagenomic analysis of the wastewater system in a large teaching hospital in the Republic of Ireland experiencing multidrug-resistant HAI outbreaks. Immediately prior to refurbishment of a medical ward where HAI has been endemic, wastewater pipe sections (n=20) were removed. These comprised toilet u-bends, sink and shower drains and, following DNA extraction, each underwent metagenomic analysis. Diverse taxonomic and resistome profiles were observed, with members of phyla Proteobacteria and Actinobacteria dominating (38.23 ± 5.68% and 15.78 ± 3.53%, respectively). Genomes of five clinical isolates were analysed. These antimicrobial-resistant bacterial isolates were from patients >48 hours post-admission to the ward. Genomic analysis determined that the isolates bore a high number of antimicrobial resistance genes (ARGs). Comparison of resistome profiles of these isolates and wastewater pipe metagenomes revealed a high degree of similarity, with many identical ARGs shared between clinical isolates and the wastewater environment, suggesting probable acquisition post-admission. The highest numbers of ARGs observed were those encoding resistance to significant clinically- and commonly-used antibiotic classes. Average nucleotide identity analysis confirmed presence of highly similar or identical genomes in the clinical isolates and wastewater pipes. These unique large-scale analyses reinforce the need for regular cleaning and decontamination of patient-facing hospital wastewater pipes and effective infection control policies to prevent the transmission of nosocomial infection and emergence of AMR within potential wastewater reservoirs.