A transversal overview of Intensive Care Units environmental microbiome and antimicrobial resistance profile in Brazil

Introduction: Infections acquired during healthcare setting stay pose significant public health threats. These infections are known as Healthcare-Associated Infections (HAI), mostly caused by pathogenic bacteria, which exhibit a wide range of antimicrobial resistance. Objective: Characterize the microbiome and antimicrobial resistance genes present in high-touch Intensive Care Unit (ICU) surfaces, and to identify the potential contamination of the sanitizers/processes used to clean hospital surfaces. Methods: In this national, multicenter, observational, and prospective cohort, bacterial profiles and antimicrobial resistance genes from 41 hospitals across 16 Brazilian states were evaluated. Using high-throughput 16S rRNA amplicon sequencing and real-time PCR, the bacterial abundance and resistance genes presence were analyzed in both ICU environments and cleaning products. Results: We identified a wide diversity of microbial populations with a recurring presence of HAI-related bacteria among most of the hospitals. The median bacterial positivity rate in surface samples was high (88.24%), varying from 21.62% to 100% in different hospitals. Hospitals with the highest bacterial load in samples were also the ones with highest HAI-related abundances. Streptococcus spp, Corynebacterium spp, Staphylococcus spp, Bacillus spp, Acinetobacter spp, and bacteria from the Flavobacteriaceae family were the microorganisms most found across all hospitals. Despite each hospital particularities in bacterial composition, clustering profiles were found for surfaces and locations in the ICU. Antimicrobial resistance genes mecA, blaKPC-like, blaNDM-like, and blaOXA-23-like were the most frequently detected in surface samples. A wide variety of sanitizers were collected, with 19 different active principles in-use, and 21% of the solutions collected showed viable bacterial growth with antimicrobial resistance genes detected. Conclusion: This study demonstrated a diverse and spread pattern of bacteria and antimicrobial resistance genes covering a large part of the national territory in ICU surface samples and in sanitizers solutions. This data should contribute to the adoption of surveillance programs to improve HAI control strategies and demonstrate that large-scale epidemiology studies must be performed to further understand the implications of bacterial contamination in hospital surfaces and sanitizer solutions. ### Competing Interest Statement D.C.B., A.P.C., G.N.F.C. and L.F.V.O are currently full-time employees of BiomeHub (SC, Brazil), a research and consulting company specialized in microbiome technologies. BiomeHub funded the study design and analysis. ### Funding Statement This study was funded by the Brazilian Ministry of Health, by the Institutional Development Support Program (Programa de Apoio ao Desenvolvimento Institucional do Sistema Unico de Saude / PROADI-SUS), project number 25000.030652/2018-37 - 27/06/2019, and BiomeHub (SC, Brazil). ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: The study was approved by the Hospital Israelita Albert Einstein (HIAE) - São Paulo - Brazil Ethics Committee (approval number 4.122.595), and also by the Hospital do Coração (HCor) - São Paulo - Brazil Ethics committee (approval number 4.040.974). I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All sequence data are deposited in NCBI BioProject SUB13793553