Open AccessApproaches for characterizing and tracking hospital-associated multidrug-resistant bacteria
Author(s) -
Kevin S Blake,
Joo-Hee Choi,
Gautam Dantas
Publication year - 2021
Publication title -
cellular and molecular life sciences
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.928
H-Index - 223
eISSN - 1420-9071
pISSN - 1420-682X
DOI - 10.1007/s00018-020-03717-2
Subject(s) - antibiotic resistance , antibiotics , horizontal gene transfer , outbreak , biology , multiple drug resistance , transmission (telecommunications) , genome , drug resistance , population , gene , intensive care medicine , computational biology , medicine , microbiology and biotechnology , genetics , virology , environmental health , computer science , telecommunications
Hospital-associated infections are a major concern for global public health. Infections with antibiotic-resistant pathogens can cause empiric treatment failure, and for infections with multidrug-resistant bacteria which can overcome antibiotics of "last resort" there exists no alternative treatments. Despite extensive sanitization protocols, the hospital environment is a potent reservoir and vector of antibiotic-resistant organisms. Pathogens can persist on hospital surfaces and plumbing for months to years, acquire new antibiotic resistance genes by horizontal gene transfer, and initiate outbreaks of hospital-associated infections by spreading to patients via healthcare workers and visitors. Advancements in next-generation sequencing of bacterial genomes and metagenomes have expanded our ability to (1) identify species and track distinct strains, (2) comprehensively profile antibiotic resistance genes, and (3) resolve the mobile elements that facilitate intra- and intercellular gene transfer. This information can, in turn, be used to characterize the population dynamics of hospital-associated microbiota, track outbreaks to their environmental reservoirs, and inform future interventions. This review provides a detailed overview of the approaches and bioinformatic tools available to study isolates and metagenomes of hospital-associated bacteria, and their multi-layered networks of transmission.