Microorganisms in Confined Habitats: Microbial Monitoring and Control of Intensive Care Units, Operating Rooms, Cleanrooms and the International Space Station

Abstract

Indoor environments, where people spend most of their time, are characterized by a specific microbial community, the indoor microbiome. Most indoor environments are connected to the natural environment by high ventilation, but some habitats are more confined: intensive care units, operating rooms, cleanrooms and the international space station (ISS) are extraordinary living and working areas for humans, with a limited exchange with the environment. The purposes for confinement are different: a patient has to be protected from infections (intensive care unit, operating room), product quality has to be assured (cleanrooms), or confinement is necessary due to extreme, health-threatening outer conditions, as on the ISS. The ISS represents the most secluded man-made habitat, constantly inhabited by humans since November 2000 – and, inevitably, also by microorganisms. All of these man-made confined habitats need to be microbiologically monitored and controlled, by e.g., microbial cleaning and disinfection. However, these measures apply constant selective pressures, which support microbes with resistance capacities against antibiotics or chemical and physical stresses and thus facilitate the rise of survival specialists and multi-resistant strains. In this article, we summarize the available data on the microbiome of aforementioned confined habitats. By comparing the different operating, maintenance and monitoring procedures as well as microbial communities therein, we emphasize the importance to properly understand the effects of confinement on the microbial diversity, the possible risks represented by some of these microorganisms and by the evolution of (antibiotic) resistances in such environments – and the need to reassess the current hygiene standards.

ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples

“…(Lang et al ., ) as well as in the fascinating research performed by Mora et al . (Mora et al ., ), which compared the ISS, intensive care units, operating rooms and cleanrooms. However, the extent to which the ISS environment here reflected human gastrointestinal microbiome samples surprised the authors.…”

Building upon current knowledge and techniques of indoor microbiology to construct the next era of theory into microorganisms, health, and the built environment

“…Microorganisms can be found in every environment, including built environments-our habitat of buildings, roads, vehicles, and other human-associated spaces-and even in ultra-clean rooms and space stations [28]. Collectively, these factors mold the built environment's microbiome [29][30][31]-all the genetic material of the microbial members present, from which can be derived taxonomic identification and metabolic potential, including activities like nutrient utilization and antimicrobial production [30,32].…”

“…This may be due to the fallibility of typical cleaning behaviors. Common surface cleaning techniques do not remove all microbial biomass from surfaces, where, after just a few days [173], microbial communities are found even in clean rooms or reagents that are considered to be sterile [28,[174][175][176]. Furthermore, the use of cleaning materials which are themselves contaminated with bacteria simply relocate bacteria between surfaces without removing them [177].…”

“…The bacterial community in the gastrointestinal tract of Antarctic visitors decreased in diversity and lost key beneficial members, such as Bifidobacterium [215], both of which can lead to a disrupted intestinal community and risk of disease. Similarly, the sterilization of food and equipment prior to launch, the harsh conditions of space travel, and the isolation from any outside microbial source, contributes to the development of a low-diversity microbial community which is both sparse and tough [28,216,217], and does not make for pleasant company [218][219][220]. The harsh conditions and increase in radiation can contribute to accelerated evolution; a distinct strain of Aspergillus niger was isolated from the International Space Station [221].…”

The influence of bioregenerative life‐support system dietary structure and lifestyle on the gut microbiota: a 105‐day ground‐based space simulation in Lunar Palace 1

“…Hence, one of the major challenges in manned space exploration is protecting astronauts from microbiota dysbiosis. In recent years, with the development of high-throughput sequencing technology for complex microbial communities, both hostderived and environmental microbiome have frequently been studied, either in space stations (Checinska et al, 2015;Moissleichinger et al, 2016;Mora et al, 2016b;Be et al, 2017) or ground-based space simulations Mayer et al, 2016;Sun et al, 2016;Blachowicz et al, 2017;Schwendner et al, 2017;Turroni et al, 2017).…”