One year cross-sectional study in adult and neonatal intensive care units reveals the bacterial and antimicrobial resistance genes profiles in patients and hospital surfaces

• Published in: PloS one Vol. 15; no. 6; p. e0234127
• Main Authors: Christoff, Ana Paula, Sereia, Aline Fernanda Rodrigues, Cruz, Giuliano Netto Flores, Bastiani, Daniela Carolina de, Silva, Vanessa Leitner, Hernandes, Camila, Nascente, Ana Paula Metran, Reis, Ana Andrea Dos, Viessi, Renata Gonçalves, Marques, Andrea Dos Santos Pereira, Braga, Bianca Silva, Raduan, Telma Priscila Lovizio, Martino, Marines Dalla Valle, Menezes, Fernando Gatti de, Oliveira, Luiz Felipe Valter de
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 03-06-2020; Public Library of Science (PLoS)
• Subjects: Adult; Analysis; Anti-Bacterial Agents - pharmacology; Anti-Infective Agents - pharmacology; Antimicrobial agents; Antimicrobial resistance; Bacteria; Bacteria - drug effects; Bacteria - genetics; Bacteria - isolation & purification; Bacterial genetics; Bacterial infections; Bacterial Load; Biology and Life Sciences; Biotechnology; Brazil; Characterization; Contamination; Criminal investigation; Cross infection; Cross Infection - microbiology; Cross Infection - pathology; Cross-Sectional Studies; Deoxyribonucleic acid; Disease hot spots; DNA; DNA sequencing; Drug resistance; Drug Resistance, Bacterial - drug effects; Drug Resistance, Bacterial - genetics; E coli; Einstein, Albert (1879-1955); Escherichia coli; Escherichia coli - drug effects; Escherichia coli - genetics; Escherichia coli - isolation & purification; Gene sequencing; Genes; Genetic aspects; Genetic testing; Genomes; Genomics; Hospitals; Humans; Infant, Newborn; Infection; Intensive care; Intensive Care Units; Intensive Care Units, Neonatal; Library collections; Medical laboratories; Medicine and Health Sciences; Methods; Microbial drug resistance; Microbiology; Microbiomes; Microorganisms; Morbidity; Mortality; Neonatal intensive care; Neonates; Newborn babies; Newborn infants; Nosocomial infections; Pathogens; Patients; Pneumonia; Public health; Public health movements; Research and Analysis Methods; RNA; RNA, Ribosomal, 16S - chemistry; RNA, Ribosomal, 16S - genetics; RNA, Ribosomal, 16S - metabolism; rRNA 16S; Staphylococcus aureus - drug effects; Staphylococcus aureus - genetics; Staphylococcus aureus - isolation & purification; Tertiary Care Centers; Whole Genome Sequencing; Brazil; United States > US
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0234127

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, blaCTX-M-1 group, blaSHV-like, and blaKPC-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.