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