Abstract
The hospital environment significantly contributes to the onset of healthcare associated infections (HAIs), representing the most frequent and severe complications related to health care. The monitoring of hospital surfaces is generally addressed by microbial cultural isolation, with some performance limitations. Hence there is need to implement environmental surveillance systems using more effective methods. This study aimed to evaluate next-generation sequencing (NGS) technologies for hospital environment microbiome characterization, in comparison with conventional and molecular methods, in an Italian pediatric hospital. Environmental samples included critical surfaces of randomized rooms, surgical rooms, intensive care units and delivery rooms. The resistome of the contaminating population was also evaluated. NGS, compared to other methods, detected with higher sensitivity the environmental bacteria, and was the only method able to detect even unsearched bacteria. By contrast, however, it did not detect mycetes, nor it could distinguish viable from dead bacteria. Microbiological and PCR methods could identify and quantify mycetes, in addition to bacteria, and PCR could define the population resistome. These data suggest that NGS could be an effective method for hospital environment monitoring, especially if flanked by PCR for species identification and resistome characterization, providing a potential tool for the control of HAI transmission.
Highlights
Introduction of next-generation sequencing (NGS) in EnvironmentalSurveillance for Healthcare-Associated Infection ControlManola Comar 1,2,†, Maria D’Accolti 3,4,†, Carolina Cason 1,2, Irene Soffritti 3,4, Giuseppina Campisciano 1, Luca Lanzoni 4, Matteo Bisi 4, Antonella Volta 4, Sante Mazzacane 4 and Elisabetta Caselli 3,4,*Received: 15 November 2019; Accepted: 13 December 2019; Published: 16 December 2019 AbstractThe hospital environment significantly contributes to the onset of healthcare associated infections (HAIs), representing the most frequent and severe complications related to health care
We recently showed that abating microbial contamination and its antimicrobial resistance (AMR) in the hospital environment, using a cleaning procedure, was associated with a significant reduction of HAI incidence [19] suggesting that it could be used as a potential strategy for infection control and prevention
Plates were incubated as described in the Materials and Methods section based on the type of microorganism, and colony forming units (CFU) were enumerated
Summary
Introduction of NGS in EnvironmentalSurveillance for Healthcare-Associated Infection ControlManola Comar 1,2,†, Maria D’Accolti 3,4,†, Carolina Cason 1,2, Irene Soffritti 3,4 , Giuseppina Campisciano 1 , Luca Lanzoni 4, Matteo Bisi 4, Antonella Volta 4, Sante Mazzacane 4 and Elisabetta Caselli 3,4,*Received: 15 November 2019; Accepted: 13 December 2019; Published: 16 December 2019 AbstractThe hospital environment significantly contributes to the onset of healthcare associated infections (HAIs), representing the most frequent and severe complications related to health care. Microbiological and PCR methods could identify and quantify mycetes, in addition to bacteria, and PCR could define the population resistome These data suggest that NGS could be an effective method for hospital environment monitoring, especially if flanked by PCR for species identification and resistome characterization, providing a potential tool for the control of HAI transmission. HAIs are known to be responsible for significant excess morbidity and mortality, lengthening the duration of stays, as well as imposing additional costs on health systems [5] They are frequent in several ward types, including pediatric wards, as children are susceptible to infections due to several factors, including an immature immune system, the presence of acquired or congenital immunodeficiencies, effects caused by anti-cancer therapy, etc. AMR is strongly associated with HAI severity, as many HAIs are caused by multidrug resistant (MDR) or even pan-drug resistant (PDR) microbes [7,8]
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