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 the hospital environmental surfaces, staff, and patients. Frequently, these bacteria are related to HAI (healthcare-associated infections) and carry antimicrobial resistance (AMR). These HAI-related bacteria contributes 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 AMR genes identification and whole genome sequencing (WGS) are new biotechnological tools that allow multiple-sample screening for a diversity of bacteria. In this paper, we used these methods to perform an one-year cross sectional profiling of bacteria and AMR genes in adult and neonatal intensive care units (ICU and NICU) in a Brazilian public hospital. Our results showed high abundances of HAI-related bacteria 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. WGS sequencing, 16S rRNA oligotypes and AMR identification allowed a high-resolution data analysis for bacterial characterization and its distributions along the hospital microbiome profile.