Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment
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.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Jun 01, 2020
- Source ID
- 10.1038/s41591-020-0894-4
Entities
People
- Abigail Lyons
- Alexandra B. Graf
- Alina Frolova
- Amanda Hui Qi Ng
- Amanda Ng
- Ana M. Cañas
- Andre Kahles
- Angela Jones
- Aspassia D. Chatziefthimiou
- Ben Young
- Beth Mutai
- Brandon Valentine
- Brenda Ang
- Chandrima Bhattacharya
- Chengxuan Tong
- Chenhao Li
- Chiea Chuen Khor
- Christelle Desnues
- Christopher E. Mason
- Daisy Donnellan
- Daniel J. Butler
- Daniela Bezdan
- Danilo Ercolini
- David C. Green
- David Danko
- David Paez-espino
- Denis Bertrand
- Denise Syndercombe Court
- Dimitar I. Vassilev
- Dmitry Meleshko
- Dominique Thomas
- Ebrahim Afshinnekoo
- Eduardo Castro-nallar
- Eileen Png
- Elena Vayndorf
- Eliza Xin Pei Ho
- Emmanuel Dias-neto
- Emmanuel F. Mongodin
- Eran Elhaik
- Francesca De Filippis
- Frank J. Kelly
- Gabriella Mason-buck
- Gregorio Iraola
- Gunnar Rätsch
- Harun Mustafa
- Haruo Suzuki
- Heba Shaaban
- Houtan Noushmehr
- Hugues Richard
- Hwee Meng Low
- Iman Hajirasouliha
- Jeanette Woon Pei Teo
- Jifeng Zhu
- Jochen Hecht
- Jorge L. Sanchez
- Josue Alicea
- Juan A. Ugalde
- Junmei Samantha Kwah
- Kalisvar Marimuthu
- Karrie Kwan Ki Ko
- Kaymisha Knights
- Ken Mcgrath
- Kern Rei Chng
- Klas I. Udekwu
- Le Huu Song
- Leming Shi
- Levy Shawn
- Licheng Xu
- Lynn M. Schriml
- Maanasa Natrajan
- Malay Bhattacharyya
- Manuela Oliveira
- Marcus H. Y. Leung
- Maria A. Sierra
- Marina Nieto-caballero
- Marius Dybwad
- Mark Hernandez
- María M. Zambrano
- Metasub Consortium
- Michael Hongjie Zhang
- Mikhail Karasikov
- Milton Ozorio Moraes
- Nicolas Rascovan
- Nikos C. Kyrpides
- Niranjan Nagarajan
- Olayinka O. Osuolale
- Olga Nikolayeva
- Oon Tek Ng
- Orhan Özcan
- Osman U. Sezerman
- Patrick K. H. Lee
- Paweł P. Łabaj
- Per Ljungdahl
- Ran Blekhman
- Robert W. Crawford
- Russell Y. Neches
- Scott W. Tighe
- Sibo Zhu
- Sofia Ahsanuddin
- Soojin Jang
- Stephan Ossowski
- Swaine L. Chen
- Tamar V. Av-shalom
- Tatyana Nikolayeva
- Thirumalaisamy P. Velavan
- Torsten Semmler
- Xinzhao Tong
- Youping Deng