Neidhöfer Claudio, Sib Esther, Benhsain Al-Harith, Mutschnik-Raab Christina, Schwabe Anna, Wollkopf Alexander, Wetzig Nina, Sieber Martin A, Thiele Ralf, Döhla Manuel, Engelhart Steffen, Mutters Nico T, Parčina Marijo
Institute of Medical Microbiology, Immunology and Parasitology, University Hospital Bonn, Venusberg-Campus 1, 53127 Bonn, Germany.
Institute for Hygiene and Public Health, University of Bonn, 53127 Bonn, Germany.
Microorganisms. 2023 Jan 11;11(1):185. doi: 10.3390/microorganisms11010185.
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 ), 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.
室内空间呈现出彼此之间以及与室外空间截然不同的微生物组成。在这方面独特且最近才成为焦点的是医院的微生物群。虽然确切了解哪些微生物在医院中如何传播以及在何处传播对于预防医院获得性感染无疑是有益的，但迄今为止，尚无关于如何最佳研究医院微生物群的标准化程序。我们的研究旨在调查医院卫生设施的微生物群，概述根据样本制备方案医院微生物群分析的差异程度。为此，从两家不同的医院——三个病房和一个医院实验室——采集了五十个样本，使用两种不同的存储介质，从中使用两种不同的提取试剂盒提取DNA，并使用两对不同的引物对（V1-V2和V3-V4）进行测序。样本保存介质之间没有可观察到的差异，DNA提取试剂盒之间检测到的分类群存在微小差异（主要涉及），而V1-V2和V3-V4这两对引物之间检测到的分类群存在很大差异。该分析还表明，从厕所到水槽再到淋浴间，以及不同病房和医院之间，微生物的出现和组成可能有很大差异。在外科病房，患者厕所的物种丰富度和多样性似乎低于工作人员厕所。对于哪些评估而言哪些采样点是最佳的，应进行更深入的分析。我们所研究的样本处理方法（除了引物的选择）似乎仅对结果产生了轻微影响，这一事实表明比较医院微生物群研究是一个现实的选择。患者和工作人员厕所之间观察到的物种丰富度和多样性差异应进一步研究，因为如果得到证实，这些差异可能是抗菌剂排泄的结果。
