Open AccessOne year cross-sectional study in adult and neonatal intensive care units reveals the bacterial and antimicrobial resistance genes profiles in patients and hospital surfaces
Author(s) -
Ana Paula Christoff,
Aline Fernanda Rodrigues Sereia,
Giuliano Netto Flores Cruz,
Daniela Carolina de Bastiani,
Vanessa Leitner Silva,
Camila Hernandes,
Ana Paula Metran Nascente,
Ana Andrea dos Reis,
Renata Gonçalves Viessi,
Andrea dos Santos Pereira Marques,
Bianca Silva Braga,
Telma Priscila Lovizio Raduan,
Marinês Dalla Valle Martino,
Fernando Gatti de Menezes,
Luiz Felipe Valter de Oliveira
Publication year - 2020
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0234127
Subject(s) - antibiotic resistance , staphylococcus epidermidis , bacteria , intensive care , biology , microbiome , microbiology and biotechnology , medicine , antibiotics , staphylococcus aureus , bioinformatics , intensive care medicine , genetics
Several studies have shown the ubiquitous presence of bacteria in hospital surfaces, staff, and patients. Frequently, these bacteria are related to HAI (healthcare-associated infections) and carry antimicrobial resistance (AMR). These HAI-related bacteria contribute to a major public health issue by increasing patient morbidity and mortality during or after hospital stay. Bacterial high-throughput amplicon gene sequencing along with identification of AMR genes, as well as whole genome sequencing (WGS), are biotechnological tools that allow multiple-sample screening for a diversity of bacteria. In this paper, we used these methods to perform a one-year cross sectional profiling of bacteria and AMR genes in adult and neonatal intensive care units (ICU and NICU) in a Brazilian public, tertiary hospital. Our results showed high abundances of HAI-related bacteria such as S . epidermidis , S . aureus , K . pneumoniae , A . baumannii complex, E . coli , E . faecalis , and P . aeruginosa in patients and hospital surfaces. Most abundant AMR genes detected throughout ICU and NICU were mecA , bla CTX-M-1 group , bla SHV-like , and bla KPC-like . We found that NICU environment and patients were more widely contaminated with pathogenic bacteria than ICU. Patient samples, despite the higher bacterial load, have lower bacterial diversity than environmental samples in both units. Finally, we also identified contamination hotspots in the hospital environment showing constant frequencies of bacterial and AMR contamination throughout the year. Whole genome sequencing (WGS), 16S rRNA oligotypes, and AMR identification allowed a high-resolution characterization of the hospital microbiome profile.