Examining Different Analysis Protocols Targeting Hospital Sanitary Facility Microbiomes

Abstract

Indoor spaces exhibit microbial compositions that are distinctly dissimilar from one another and from outdoor spaces. Unique in this regard, and a topic that has only recently come into focus, is the microbiome of hospitals. While the benefits of knowing exactly which microorganisms propagate how and where in hospitals are undoubtedly beneficial for preventing hospital-acquired infections, there are, to date, no standardized procedures on how to best study the hospital microbiome. Our study aimed to investigate the microbiome of hospital sanitary facilities, outlining the extent to which hospital microbiome analyses differ according to sample-preparation protocol. For this purpose, fifty samples were collected from two separate hospitals—from three wards and one hospital laboratory—using two different storage media from which DNA was extracted using two different extraction kits and sequenced with two different primer pairs (V1–V2 and V3–V4). There were no observable differences between the sample-preservation media, small differences in detected taxa between the DNA extraction kits (mainly concerning Propionibacteriaceae), and large differences in detected taxa between the two primer pairs V1–V2 and V3–V4. This analysis also showed that microbial occurrences and compositions can vary greatly from toilets to sinks to showers and across wards and hospitals. In surgical wards, patient toilets appeared to be characterized by lower species richness and diversity than staff toilets. Which sampling sites are the best for which assessments should be analyzed in more depth. The fact that the sample processing methods we investigated (apart from the choice of primers) seem to have changed the results only slightly suggests that comparing hospital microbiome studies is a realistic option. The observed differences in species richness and diversity between patient and staff toilets should be further investigated, as these, if confirmed, could be a result of excreted antimicrobials.

Exploring clonality and virulence gene associations in bloodstream infections using whole-genome sequencing and clinical data

“…The notable clustering of ST50 E. quasihormaechei isolates calls for focused investigations, given the escalating local and global issue of sewage-related clonal colonization in hospital sanitary facilities ( Babouee Flury et al., 2016 ; Kehl et al., 2022 ; Stokes et al., 2022 ). Similarly, the recurring identification of ST147 K. pneumoniae and ST235 and ST823 P. aeruginosa isolates, even in wards geographically distant from those assumed to have a contamination source in our setting ( Kehl et al., 2022 ; Neidhöfer et al., 2023a ), urges us to implement transmission dynamics monitoring networks ( Bohl et al., 2022 ; Ko et al., 2022 ; Neidhöfer et al., 2023b ).…”

Hospital sanitary facilities on wards with high antibiotic exposure play an important role in maintaining a reservoir of resistant pathogens, even over many years

“…Our study highlights that, consistently antibiotic-exposed patients might, in interaction with their constantly antibiotic-exposed sanitary facilities form a niche that could be supportive for the emergence of certain nosocomial pathogen populations in the hospital, due to antibiotic-induced selection pressure [ 11 , 39 ]. These highly resistant clones subsequently survive particularly well in the sanitary facilities of those patients who are at highest risk of colonization or infection, i.e., patients who are frequently treated with broad-spectrum antibiotics due to their immunodeficiency, and who have hardly any remaining healthy normal flora able to outcompete the highly resistant clones [ 40 ].…”

ESKAPEE Pathogen Biofilm Control on Surfaces with Probiotic Lactobacillaceae and Bacillus species

“…Despite the generally recognized safety of probiotics and the fact that most were derived from benign edible sources some of which are even consumed in large quantities, the use of these microorganisms in hospitals warrants further investigation to ensure their safety, particularly in dysbiotic, immunocompromised, leukopenic or even agranulocytic patients [172][173][174][175], as these are patient groups that could particularly benefit from such innovative solutions [176][177][178][179][180][181][182][183][184]. It is desirable for these microorganisms, which may be transferred from the environment to the patient, to retain their protective effects in the patient as well.…”