Pangenomic Approach To Understanding Microbial Adaptations within a Model Built Environment, the International Space Station, Relative to Human Hosts and Soil

Blaustein, Ryan A.; McFarland, Alexander; Maamar, Sarah Ben; López, Alberto M.; Castro-Wallace, Sarah L.; Hartmann, Erica M.

doi:10.1128/msystems.00281-18

Cited by 47 publications

(37 citation statements)

References 82 publications

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“…In our study, we confirmed the pangenome-based observation of Blaustein et al . (24), on genomic, but also on isolate and resistance-pattern level that ISS microorganisms are not necessarily more extremophilic or antibiotic resistant than their ground-relatives with respect to growth behavior, or antibiotics resistances, nor their genomic inventory.…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, the given environmental microbial contamination limits (air, surfaces) were exceeded only in a few cases to date, in which appropriate countermeasures succeeded in a timely manner (23). Moreover, a recent genomics-based study could not reveal potentially health-threatening differences in Bacillus and Staphylococcus pangenomes from ISS, compared to human-associated and soil pangenomes (24).…”

Section: Introductionmentioning

confidence: 99%

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The International Space Station selects for microorganisms adapted to the extreme environment, but does not induce genomic and physiological changes relevant for human health

Mora

Wink

et al. 2019

Preprint

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The International Space Station (ISS) is a unique, completely confined habitat for the human crew and co-inhabiting microorganisms. Here, we report on the results of the ISS experiment “EXTREMOPHILES”. We aimed to exploit the microbial information obtained from three surface and air sampling events aboard the International Space Station during increments 51 and 52 (2017) with respect to: i) microbial sources, diversity and distribution within the ISS, ii) functional capacity of microbiome and microbial isolates, iii) extremotolerance and antibiotics-resistance (compared to ground controls), and iv) microbial behavior towards ISS-relevant materials such as biofilm formation, or potential for degradation. We used wipe samples and analyzed them by amplicon and metagenomics sequencing, cultivation, comparative physiological studies, antibiotic resistance tests, genome analysis of isolates and co-incubation experiments with ISS-relevant materials. The major findings were: i) the ISS microbiome profile is highly similar to ground-based confined indoor environments, ii) the ISS microbiome is subject to fluctuations and indicative for the (functional) location, although a core microbiome was present over time and independent from location, iii) the ISS selects for microorganisms adapted to the extreme environment, but does not necessarily induce genomic and physiological changes which might be relevant for human health, iv) cleanrooms and cargo seems to be a minor source of microbial contamination aboard, and v) microorganisms can attach to and grow on ISS-relevant materials. Biofilm formation might be a threat for spacecraft materials with the potential to induce instrument malfunctioning with consequences for mission success. We conclude that our data do not raise direct reason for concern with respect to crew health, but indicate a potential threat towards biofilm formation and material integrity in moist areas.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The International Space Station selects for microorganisms adapted to the extreme environment, but does not induce genomic and physiological changes relevant for human health

Mora

Wink

et al. 2019

Preprint

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“…On the other hand, the accessory genome has genes related to microbial adaptation mechanisms, such as antimicrobial resistance factors, symbiosis, adaptation to the environment, and virulence, which may or may not be acquired via horizontal gene transfer [53,54]. In our study, the accessory genome revealed a total of 26309 genes that may be related to adaptation to the host and are more represented in pathways of carbohydrate and amino acid metabolism, xenobiotic metabolism, and drug resistance.…”

Section: Functional Characterization Through Pan-genome Analysismentioning

confidence: 69%

Pan-resistome insights into the multidrug resistance of Acinetobacter baumannii

Rodrigues

Morais-Rodrigues

Hurtado

et al. 2020

Preprint

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BACKGROUND Acinetobacter baumannii is an important Gram-negative opportunistic pathogen, which is responsible for many nosocomial infections. This etiologic agent has acquired, over the years, multiple mechanisms of resistance to a wide range of antimicrobials and the ability to survive in different environments. In this context, our study aims to elucidate the resistome from the A. baumannii strains based on phylogenetic, phylogenomic, and comparative genomics analyses. In silico analysis of the complete genomes of A. baumannii strains was carried out to identify genes involved in resistance mechanisms and the phylogenetic relationships and grouping of the strains based on the sequence type. RESULTS The strains belonging to the same sequence type (ST) were phylogenomically closer than from distinct STs, and the most prevalent ST was ST 2. The presence of genomic islands containing most of the resistance gene repertoire indicated high genomic plasticity, which probably enabled the acquisition of resistance genes and the formation of a robust resistome. A. baumannii displayed an open pan-genome and revealed a still constant genetic permutation among their strains, similarly to the genera Escherichia, Klebsiella, and Pseudomonas. CONCLUSIONS Our study is the first one to evaluate the resistome of the species A. baumannii using comparative multi-omics methods. Furthermore, the resistance genes suggest a specific profile within the species throughout its evolutionary history. Moreover, the current study performed the screening and characterization of the main genes present in the resistome, which can be used in applied research for the development of new therapeutic methods to control this important bacterial pathogen.

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“…the prevalence of pathogens. Indoor microbial diversity has also been characterized in other confined environments, such as the International Space Station [25][26][27], but without a focus on mobile ARG in these environments. The few such studies have found ARGs with comparable diversities to hospitals or agricultural settings, including tet(W), blaSRT-1, erm(B), qnr, ftsH and mtrAB encoding respectively resistance to tetracycline, beta-lactams, macrolides, fluoroquinolones, aminoglycosides, and multidrug resistance (efflux pumps) [8,9].…”

Section: Introductionmentioning

confidence: 99%

Mobilizable antibiotic resistance genes are present in dust microbial communities

et al. 2020

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The decades-long global trend of urbanization has led to a population that spends increasing amounts of time indoors. Exposure to microbes in buildings, and specifically in dust, is thus also increasing, and has been linked to various health outcomes and to antibiotic resistance genes (ARGs). These are most efficiently screened using DNA sequencing, but this method does not determine which microbes are viable, nor does it reveal whether their ARGs can actually disseminate to other microbes. We have thus performed the first study to: 1) examine the potential for ARG dissemination in indoor dust microbial communities, and 2) validate the presence of detected mobile ARGs in viable dust bacteria. Specifically, we integrated 166 dust metagenomes from 43 different buildings. Sequences were assembled, annotated, and screened for potential integrons, transposons, plasmids, and associated ARGs. The same dust samples were further investigated using cultivation and isolate genome and plasmid sequencing. Potential ARGs were detected in dust isolate genomes, and we confirmed their placement on mobile genetic elements using long-read sequencing. We found 183 ARGs, of which 52 were potentially mobile (associated with a putative plasmid, transposon or integron). One dust isolate related to Staphylococcus equorum proved to contain a plasmid carrying an ARG that was detected metagenomically and confirmed through whole genome and plasmid sequencing. This study thus highlights the power of combining cultivation with metagenomics to assess the risk of potentially mobile ARGs for public health.

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Pangenomic Approach To Understanding Microbial Adaptations within a Model Built Environment, the International Space Station, Relative to Human Hosts and Soil

Cited by 47 publications

References 82 publications

The International Space Station selects for microorganisms adapted to the extreme environment, but does not induce genomic and physiological changes relevant for human health

The International Space Station selects for microorganisms adapted to the extreme environment, but does not induce genomic and physiological changes relevant for human health

Pan-resistome insights into the multidrug resistance of Acinetobacter baumannii

Mobilizable antibiotic resistance genes are present in dust microbial communities

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