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Examining Different Analysis Protocols Targeting Hospital Sanitary Facility Microbiomes

  • 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.

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Document Type:Article
Author:Claudio Neidhöfer, Esther Sib, Al-Harith Benhsain, Christina Mutschnik-Raab, Anna Schwabe, Alexander Wollkopf, Nina Wetzig, Martin A. Sieber, Ralf Thiele, Manuel Döhla, Steffen Engelhart, Nico T. Mutters, Marijo Parčina
Parent Title (English):Microorganisms
Article Number:185
Number of pages:11
Place of publication:Basel
Publishing Institution:Hochschule Bonn-Rhein-Sieg
Date of first publication:2023/01/11
Copyright:© 2023 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license
Funding:This research received no external funding.
Keyword:16S rRNA gene sequencing; NGS; built environment; high-throughput DNA sequencing; hospital environment; hospital-acquired infections; microbial ecology; microbiome
Departments, institutes and facilities:Fachbereich Informatik
Fachbereich Angewandte Naturwissenschaften
Institut für funktionale Gen-Analytik (IFGA)
Dewey Decimal Classification (DDC):5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 579 Mikroorganismen, Pilze, Algen
Entry in this database:2023/01/19
Licence (German):License LogoCreative Commons - CC BY - Namensnennung 4.0 International