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

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...

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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
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Summary:	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.
Bibliography:	Competing Interests: I have read the journal's policy and the authors of this manuscript have the following competing interests: APC, AFRS, GNFC, DCB, VLS, and LFVO are currently full-time employees of BiomeHub (SC, Brazil), a research and consulting company specialized in microbiome technologies. This does not alter our adherence to PLOS ONE policies on sharing data and materials.
ISSN:	1932-6203 1932-6203
DOI:	10.1371/journal.pone.0234127