Detection of antimicrobial resistance genes associated with the International Space Station environmental surfaces

Urbaniak, Camilla; Sielaff, Aleksandra Checinska; Frey, K. G.; Allen, Jonathan; Singh, Nitin Kumar; Jaing, Crystal; Wheeler, Kevin; Venkateswaran, Kasthuri

doi:10.1038/s41598-017-18506-4

Cited by 92 publications

(106 citation statements)

References 48 publications

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“…Spaceflight could affect the drug resistance phenotype of bacteria and a profound drug resistance capacity of ISS microorganisms against environmental stresses was detected during these years (Mora et al, ; Singh et al, ; Urbaniak et al, ). It has been demonstrated that the increased antibiotic tolerance of Escherichia coli in human spaceflight environment might be attributed to the upregulation of genes related to oxidative stress response (Aunins et al, ).…”

Section: Discussionmentioning

confidence: 99%

“…Red spots represent upregulated genes, blue spots represent downregulated genes, and gray spots represent the genes that did not change significantly F I G U R E 7 Hierarchical clustering analysis of DEGs for the SEG and SES strains. Blue bars represent the downregulated genes, red bars represent the upregulated genes, and white bars represent the genes that did not change significantly Spaceflight could affect the drug resistance phenotype of bacteria and a profound drug resistance capacity of ISS microorganisms against environmental stresses was detected during these years (Mora et al, 2016;Singh et al, 2018;Urbaniak et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

“…For instance, some microbial isolates were collected from astronauts and filter debris during orbital spaceflights on the International Space Station (ISS) (Checinska et al, 2015;Venkateswaran et al, 2014). It has been reported that the space environment can alter the microbial growth rate, virulence, and antibiotic susceptibility (Kim et al, 2013;Klaus & Howard, 2006;Mora et al, 2016;Rosenzweig, Ahmed, Eunson, & Chopra, 2014;Taylor, 2015;Urbaniak et al, 2018;Wilson et al, 2007). In addition, many studies have shown that the extreme environment of space plays an important role in dysregulation of the human immune system (Crucian et al, 2018;Kaur, Simons, Castro, Ott, & Pierson, 2005;Taylor, 2015).…”

Section: Introductionmentioning

confidence: 99%

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Increased growth rate and amikacin resistance of Salmonella enteritidis after one‐month spaceflight on China’s Shenzhou‐11 spacecraft

et al. 2019

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China launched the Tiangong‐2 space laboratory in 2016 and will eventually build a basic space station by the early 2020s. These spaceflight missions require astronauts to stay on the space station for more than 6 months, and they inevitably carry microbes into the space environment. It is known that the space environment affects microbial behavior, including growth rate, biofilm formation, virulence, drug resistance, and metabolism. However, the mechanisms of these alternations have not been fully elucidated. Therefore, it is beneficial to monitor microorganisms for preventing infections among astronauts in a space environment. Salmonella enteritidis is a Gram‐negative bacterial pathogen that commonly causes acute gastroenteritis in humans. In this study, to better understand the effects of the space environment on S. enteritidis, a S. enteritidis strain was taken into space by the Shenzhou‐11 spacecraft from 17 October 2016 to 18 November 2016, and a ground simulation with similar temperature conditions was simultaneously performed as a control. It was found that the flight strain displayed an increased growth rate, enhanced amikacin resistance, and some metabolism alterations compared with the ground strain. Enrichment analysis of proteome revealed that the increased growth rate might be associated with differentially expressed proteins involved in transmembrane transport and energy production and conversion assembly. A combined transcriptome and proteome analysis showed that the amikacin resistance was due to the downregulation of the oppA gene and oligopeptide transporter protein OppA. In conclusion, this study is the first systematic analysis of the phenotypic, genomic, transcriptomic, and proteomic variations in S. enteritidis during spaceflight and will provide beneficial insights for future studies on space microbiology.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Increased growth rate and amikacin resistance of Salmonella enteritidis after one‐month spaceflight on China’s Shenzhou‐11 spacecraft

et al. 2019

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“…Other publications also focused on the detection of antimicrobial resistance genes aboard the ISS and evaluated the potential risk these genes might represent in a closed spacecraft environment (20). Singh et al assessed the succession and persistence of microbial communities and the associated antimicrobial resistance and virulence properties based on metagenomic reads obtained from samples of three flights.…”

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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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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“…From this panel, we only used the first primer pool targeting the ARGs. The second panel used was the Ion AmpliSeq™ Antimicrobial Resistance (AMR) Research panel that also consisted of two primer pools comprising a total of 815 amplicons targeting 478 known ARGs 32 . Both primer pools were used from this panel.…”

Section: Methodsmentioning

confidence: 99%

A preliminary investigation of major bacterial antibiotic resistance genes present in Australian fecal samples using shotgun metagenomics and targeted sequencing

Guernier

Chamings

Collier

et al. 2020

Preprint

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24The gut microbiota is an immense reservoir of antimicrobial resistance genes (ARGs); however, in 25 Australia the profile of the gut 'resistome', or ensemble of ARGs, has not been investigated. This 26 study provides a first preliminary mapping of the major bacterial ARGs present in human, domestic 27 dog and wild duck fecal samples collected from south-eastern Victoria, Australia; and evaluates 28 the use of shotgun metagenomics sequencing (SMS) and targeted amplification of ARGs. We 29 analysed SMS data using an in-house method and web-based bioinformatics tools: ResFinder and 30 KmerResistance. We examined targeted sequences using One Codex or the PanBacterialAnalysis 31 Torrent Suite plugin. All methods detected ARGs in all samples, with resistance to up to 13 32 classes of antibiotics detected overall. ARGs were more abundant in the human and dog samples 33 than the duck samples. They mostly conferred resistance to three classes of antibiotics that are 34 the most frequently prescribed in Australia: tetracycline, b-lactams and MLSB (macrolide, 35 lincosamide, streptogramin B). Targeted sequencing significantly improved sensitivity for detection 36 of ARGs included in the panel; however, SMS provided quantitative information and allowed 37 tentative identification of the host bacteria. For SMS, web-based and in-house methods gave 38 comparable results, with discrepancies mostly due to different reference databases. The in-house 39 method allowed manually checking results and potential errors, while web-based methods were 40 user-friendlier and less time-consuming. More samples need to be investigated to fully describe 41 the resistome in humans and animals in Australia. 43Antimicrobial resistance (AMR) occurs naturally in bacteria and other microorganisms, but 48 increases when antimicrobials (antibiotics, antivirals, antifungals) are used 1 . According to WHO, 49AMR accounts for an estimated 700,000 deaths per year and is one of the ten threats to global 50 health in 2019 2 . Reservoirs of multi drug-resistant (MDR) bacteria are ubiquitous, and the concept 51 of an "antibiotic resistome" was first coined to describe the large collection of bacterial 52 antimicrobial resistance genes (ARGs) found in a specific environment 3 . Although AMR is most 53 clinically relevant in pathogenic bacteria, ARGs exist in both pathogenic and non-pathogenic 54 bacteria, and large reservoirs of these genes exist in all ecosystems, including in commensals at 55 all sites of the human or animal body 4 . 57The adult human gastrointestinal tract harbours up to 1,000 molecular species or phylotypes often 58 referred to as operational taxonomic units (OTUs) in 16S rRNA metagenomics 5,6 . This vast array 59 of resident bacteria responds to environmental conditions inside the host, including altered dietary 60 intake and antibiotic-induced disturbances. That can result in modifications in the microbial 61 community structure and genetics, including the enrichment of ARGs within the gut microbiota. 62Recent studies have suggested pot...

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Detection of antimicrobial resistance genes associated with the International Space Station environmental surfaces

Cited by 92 publications

References 48 publications

Increased growth rate and amikacin resistance of Salmonella enteritidis after one‐month spaceflight on China’s Shenzhou‐11 spacecraft

Increased growth rate and amikacin resistance of Salmonella enteritidis after one‐month spaceflight on China’s Shenzhou‐11 spacecraft

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

A preliminary investigation of major bacterial antibiotic resistance genes present in Australian fecal samples using shotgun metagenomics and targeted sequencing

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