新加坡基因组研究所Niranjan Nagarajan研究组的研究绘制三级医院环境中机会病原体和抗生素抗性基因图谱。2020年6月8日，《自然-医学》发表了这一成果。

他们报告了三级医院的微生物群、病原体和抗生素抗性盒的首次广泛的基因组学表征，该研究来自与45张病床相关的179个位点的重复采样（间隔长达1.5年）。深度shotgun宏基因组学揭示了微生物和抗生素抗性基因的独特生态位，其特征在于生物膜形成和受人微生物组影响的环境，并具有相应的时空分布模式。

带有纳米孔测序的准突变基因组学提供了数千个高连续性基因组、噬菌体和质粒序列（新颖性> 60％），从而能够表征医院环境中的抗肿瘤组和运动组多样性以及动态结构。系统发育学鉴定出耐多药菌株广泛分布并且在各个部位稳定定植。与临床分离株的比较表明，这种微生物可以在医院中长期存在（> 8年），从而机会感染患者。

这些发现凸显了表征医院中抗生素耐药性储库的重要性，并确立了进行系统研究以预防感染的目标资源的可行性。

据了解，尽管消毒是控制感染的关键，但医院环境微生物的定植模式和耐药性仍未得到充分研究。

附：英文原文

Title: Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

Author: Kern Rei Chng, Chenhao Li, Denis Bertrand, Amanda Hui Qi Ng, Junmei Samantha Kwah, Hwee Meng Low, Chengxuan Tong, Maanasa Natrajan, Michael Hongjie Zhang, Licheng Xu, Karrie Kwan Ki Ko, Eliza Xin Pei Ho, Tamar V. Av-Shalom, Jeanette Woon Pei Teo, Chiea Chuen Khor, Swaine L. Chen, Christopher E. Mason, Oon Tek Ng, Kalisvar Marimuthu, Brenda Ang, Niranjan Nagarajan

Issue&Volume: 2020-06-08

Abstract: Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely distributed and stably colonizing across sites. Comparisons with clinical isolates indicated that such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections.

DOI: 10.1038/s41591-020-0894-4

Source: https://www.nature.com/articles/s41591-020-0894-4