Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment.
Kern Rei ChngChenhao LiDenis BertrandAmanda Hui Qi NgJunmei Samantha KwahHwee Meng LowChengxuan TongMaanasa NatrajanMichael Hongjie ZhangLicheng XuKarrie Kwan Ki KoEliza Xin Pei HoTamar V Av-ShalomJeanette Woon Pei TeoChiea Chuen Khornull nullSwaine L ChenChristopher E MasonOon Tek NgKalisvar MarimuthuBrenda AngNiranjan NagarajanPublished in: Nature medicine (2020)
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.
Keyphrases
- antibiotic resistance genes
- wastewater treatment
- microbial community
- multidrug resistant
- gram negative
- healthcare
- anaerobic digestion
- escherichia coli
- end stage renal disease
- pseudomonas aeruginosa
- endothelial cells
- newly diagnosed
- ejection fraction
- chronic kidney disease
- drug resistant
- prognostic factors
- antimicrobial resistance
- drinking water
- cross sectional
- adverse drug
- climate change
- crispr cas
- peritoneal dialysis
- acute care
- risk assessment
- single cell
- staphylococcus aureus
- cystic fibrosis
- emergency department
- dna methylation
- patient reported outcomes
- genome wide
- induced pluripotent stem cells