First Report of Pathogenic Bacterium Kalamiella piersonii Isolated from Urine of a Kidney Stone Patient: Draft Genome and Evidence for Role in Struvite Crystallization

Rekha, P. D.; Hameed, Asif; Manzoor, Muhammed A.P.; Suryavanshi, Mangesh V.; Ghate, Sudeep D.; Arun, A. B.; Rao, Sneha S.; Athmika,; Bajire, Sukesh Kumar; Mujeeburahiman, M; Young, Chiu-Chung

doi:10.3390/pathogens9090711

Cited by 21 publications

(13 citation statements)

References 60 publications

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“…This comparison exhibited the same genetic composition, which con rms that the MAGs might have originated from the living cells. In addition, the comparative genomic analysis of the uropathogenic strain of K. piersonii strain YU22, isolated from human urine (45), revealed no SNVs. SSU Ribosomal Protein S7p.…”

Section: Gene-based Functional Analysismentioning

confidence: 99%

Characterization of Metagenome Assembled Genomes from the International Space Station

Singh

Wood

Patané

et al. 2022

Preprint

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Background Several investigations on the microbial diversity and functional properties of the International Space Station (ISS) environment were carried out to understand the influence of spaceflight conditions on the microbial population. However, metagenome-assembled genomes (MAGs) of ISS samples are yet to be generated and subjected to various genomic analyses, including phylogenetic affiliation, predicted functional pathways, antimicrobial resistance, and virulence characteristics. Results In total, 46 MAGs were assembled from 21 ISS environmental metagenomes, in which metaSPAdes yielded 20 MAGs and metaWRAP generated 26 MAGs. Among 46 MAGs retrieved, 18 bacterial species were identified, including one novel genus/species combination (Kalamiella piersonii) and one novel bacterial species (Methylobacterium ajmalii). In addition, four bins exhibited fungal genomes; this is the first-time fungal genomes were assembled from ISS metagenomes. Variations in the antimicrobial resistant (AMR) and virulence genes of the selected 20 MAGs were characterized to predict the ecology and evolution of biosafety level (BSL) 2 microorganisms in space. Since microbial virulence increases in microgravity, AMR gene sequences of MAGs were compared with genomes of respective ISS isolates and corresponding type strains. Among these 20 MAGs characterized, AMR genes were more prevalent in the Enterobacter bugandensis MAG, which has been predominantly isolated from clinical samples. MAGs were further used to analyze if genes involved in AMR and biofilm formation of viable microbes in ISS have variation due to generational evolution in microgravity and radiation pressure. Conclusions Comparative analyses of MAGs and whole genome sequences of related ISS isolates and their type strains were characterized to understand the variation related to the microbial evolution under microgravity. The Pantoea/Kalamiella strains have the maximum single nucleotide polymorphisms found within the ISS strains examined. This may suggest that Pantoea/Kalamiella strains are much more subjective to microgravity changes. The reconstructed genomes will enable researchers to study the evolution of genomes under microgravity and low dose irradiation compared to the evolution of microbes here on Earth.

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Section: Gene-based Functional Analysismentioning

confidence: 99%

Characterization of Metagenome Assembled Genomes from the International Space Station

Singh

Wood

Patané

et al. 2022

Preprint

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“…3 c). Of note, the K. piersonii strain closely related to one found at the ISS has been associated to human urinary tract infection [ 40 ]. The potentially very pathogenic microbe E. bugandensis was found in location 2 (forward side panel wall of the Waste and Hygiene Compartment) in Flight 1, presenting more than 40 ARGs.…”

Section: Resultsmentioning

confidence: 99%

“…Therefore, PathogenFinder [17] results in Singh et al [45] suggesting K. piersonii as a non-human pathogen should be treated with caution. Furthermore, the strain YU22 (closest match is IIIF1SW-P2 T detected as ISS) isolated in urine microbiome of a kidney stone patient has shown to be an uropathogenic bacteria, showing many virulence factors that are needed for host cell invasion and colonization [40].…”

Section: Discussionmentioning

confidence: 99%

Machine learning algorithm to characterize antimicrobial resistance associated with the International Space Station surface microbiome

et al. 2022

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Background Antimicrobial resistance (AMR) has a detrimental impact on human health on Earth and it is equally concerning in other environments such as space habitat due to microgravity, radiation and confinement, especially for long-distance space travel. The International Space Station (ISS) is ideal for investigating microbial diversity and virulence associated with spaceflight. The shotgun metagenomics data of the ISS generated during the Microbial Tracking–1 (MT-1) project and resulting metagenome-assembled genomes (MAGs) across three flights in eight different locations during 12 months were used in this study. The objective of this study was to identify the AMR genes associated with whole genomes of 226 cultivable strains, 21 shotgun metagenome sequences, and 24 MAGs retrieved from the ISS environmental samples that were treated with propidium monoazide (PMA; viable microbes). Results We have analyzed the data using a deep learning model, allowing us to go beyond traditional cut-offs based only on high DNA sequence similarity and extending the catalog of AMR genes. Our results in PMA treated samples revealed AMR dominance in the last flight for Kalamiella piersonii, a bacteria related to urinary tract infection in humans. The analysis of 226 pure strains isolated from the MT-1 project revealed hundreds of antibiotic resistance genes from many isolates, including two top-ranking species that corresponded to strains of Enterobacter bugandensis and Bacillus cereus. Computational predictions were experimentally validated by antibiotic resistance profiles in these two species, showing a high degree of concordance. Specifically, disc assay data confirmed the high resistance of these two pathogens to various beta-lactam antibiotics. Conclusion Overall, our computational predictions and validation analyses demonstrate the advantages of machine learning to uncover concealed AMR determinants in metagenomics datasets, expanding the understanding of the ISS environmental microbiomes and their pathogenic potential in humans.

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“…Since its first report in 2019, a few clinical cases of K. piersonii have been reported in humans including bacteraemia, meningitis and kidney stones disease amongst others. 110 , 111 Preliminary genomic analysis of this novel species has identified that all strains examined so far exhibit a multidrug resistant (MDR) phenotype and genotype along with a hypervirulence associated (Hv) genotype. The Hv genotype relates to the presence of a 262 Kbp non mobilizable plasmid encoding for the aerobactin gene cluster ( iucA-D/iutA ) along with the vibriobactin utilisation protein ( viuB ) and the virulence transcriptional regulator ( virB ).…”

Section: Spaceflightmentioning

confidence: 99%

Medical Astro-Microbiology: Current Role and Future Challenges

et al. 2023

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The second and third decades of the twenty-first century are marked by a flourishing of space technology which may soon realise human aspirations of a permanent multiplanetary presence. The prevention, control and management of infection with microbial pathogens is likely to play a key role in how successful human space aspirations will become. This review considers the emerging field of medical astro-microbiology. It examines the current evidence regarding the risk of infection during spaceflight via host susceptibility, alterations to the host’s microbiome as well as exposure to other crew members and spacecraft’s microbiomes. It also considers the relevance of the hygiene hypothesis in this regard. It then reviews the current evidence related to infection risk associated with microbial adaptability in spaceflight conditions. There is a particular focus on the International Space Station (ISS), as one of the only two crewed objects in low Earth orbit. It discusses the effects of spaceflight related stressors on viruses and the infection risks associated with latent viral reactivation and increased viral shedding during spaceflight. It then examines the effects of the same stressors on bacteria, particularly in relation to changes in virulence and drug resistance. It also considers our current understanding of fungal adaptability in spaceflight. The global public health and environmental risks associated with a possible re-introduction to Earth of invasive species are also briefly discussed. Finally, this review examines the largely unknown microbiology and infection implications of celestial body habitation with an emphasis placed on Mars. Overall, this review summarises much of our current understanding of medical astro-microbiology and identifies significant knowledge gaps. Graphical Abstract

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First Report of Pathogenic Bacterium Kalamiella piersonii Isolated from Urine of a Kidney Stone Patient: Draft Genome and Evidence for Role in Struvite Crystallization

Cited by 21 publications

References 60 publications

Characterization of Metagenome Assembled Genomes from the International Space Station

Characterization of Metagenome Assembled Genomes from the International Space Station

Machine learning algorithm to characterize antimicrobial resistance associated with the International Space Station surface microbiome

Medical Astro-Microbiology: Current Role and Future Challenges

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