Microbial communities profiling in intensive care units expose limitations in current sanitary standards

Ribeiro, L. F.; Lopes, E. M.; Kishi, L. T.; Ribeiro, L. F. C.; Menegueti, M. G.; Gaspar, G. G.; Silva-Rocha, R.; Guazzaroni, M.-E.

doi:10.1101/633404

bioRxiv · 10.1101/633404

Microbial communities profiling in intensive care units expose limitations in current sanitary standards

Ribeiro, L. F.·Lopes, E. M.·Kishi, L. T.·Ribeiro, L. F. C.·Menegueti, M. G.·Gaspar, G. G.·Silva-Rocha, R.·Guazzaroni, M.-E.

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Abstract

Hospital-associated infections (HAIs) are the leading cause of morbidity and mortality in intensive care units (ICUs) and neonatal intensive care units (NICUs). Organisms causing these infections are often present on surfaces around the patient. Given that microbiotas may vary across different ICUs, the HAI-related microbial signatures within these units remain underexplored. In this study, we use deep-sequencing analyses to explore and compare the structure of bacterial communities at inanimate surfaces of the ICU and NICU wards of The Medical School Clinics Hospital (Brazil). The data revealed that NICU presents higher biodiversity than ICU and surfaces closest to the patient showed a peculiar microbiota, distinguishing one unit from the other. Several facultative anaerobes or obligate anaerobes HAI-related genera were classified as biomarkers for the NICU, whereas Pseudomonas was the main biomarker for ICU. Correlation analyses revealed a distinct pattern of microbe-microbe interactions for each unit, including bacteria able to form multi-genera biofilms. Furthermore, we evaluated the effect of concurrent cleaning over the ICU bacterial community. The results showed that, although some bacterial populations decreased after cleaning, various HAI-related genera were quite stable to sanitization, suggesting being well-adapted to the ICU environment. Overall, these results enabled identification of discrete ICU and NICU reservoirs of potentially pathogenic bacteria and provided evidence for the presence of a set of biomarkers that distinguish these units. Moreover, the study exposed the inconsistencies of the routine cleaning to minimize HAI-related genera contamination.\n\nIMPORTANCEDue to the high impact of HAIs, there is an urgent need for the development of robust policies on microbial surveillance to help guide procedures, improving infection control. To the best of our knowledge, this is the first comprehensive study, using a high-throughput approach, focused on comparing the microbiota peculiarities of the ICU and NICU in one of the largest public hospitals in Brazil. The work highlighted bacteria associated with nosocomial infections, identifying the most potent reservoirs of contamination, and evaluated the microbiota changes related to the cleaning procedure. Therefore, this study contributes to increase the knowledge about (N)ICUs microbiomes and may help to reduce health-care-associated infections, especially in developing countries.

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Ribeiro, L. F., Lopes, E. M., Kishi, L. T., Ribeiro, L. F. C., Menegueti, M. G., Gaspar, G. G., Silva-Rocha, R., Guazzaroni, M.-E.. 2019-05-09. Microbial communities profiling in intensive care units expose limitations in current sanitary standards. https://doi.org/10.1101/633404

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