Genomic analysis reveals the presence of emerging pathogenic Klebsiella lineages aboard the International Space Station.

Abstract

Klebsiella species, including Klebsiella pneumoniae, Klebsiella aerogenes, and Klebsiella quasipneumoniae, are opportunistic pathogens that are known to cause infections in humans. Hypervirulent Klebsiella pneumoniae (hvKP) is a subgroup of K. pneumoniae that has gained attention due to its global dissemination and its ability to cause invasive infections in community settings amongst immunocompetent individuals as well as its increasing levels of antibiotic resistance. Our study reports the first complete genotypic analysis including mobile genetic elements (MGEs) of Klebsiella isolates from the International Space Station (ISS). The genomes of K. pneumoniae, K. aerogenes, and K. quasipneumoniae provided valuable insights into their antimicrobial resistance, virulence, thermotolerance, disinfectant resistance, and MGEs. All isolates belonged to emerging lineages with pathogenic potential, with K. quasipneumoniae ST138 presenting spatial and temporal persistence aboard the ISS, possibly due to its genotypic profile encoding for numerous resistance genes to disinfectants and heavy metals. We also report on the isolation of a yersiniabactin encoding K. pneumoniae, belonging to the emerging high-risk ST101 clone, aboard the ISS. Potential dissemination of hvKp strains on ISS could pose a putative risk to the immunocompromised crew. The presence of MGEs containing virulent loci could facilitate horizontal gene transfer to other benign microorganisms on the ISS, potentially increasing their virulence. In addition, genetic divergence from their respective lineages for some Klebsiella genomes was predicted and hypothesized to be due to the unique spaceflight environmental pressures. These findings highlight the importance of monitoring problematic microbial communities in space to understand their surviving abilities and potential impact on human health. ImportanceThe International Space Station (ISS) is a unique hermetically sealed environment that poses environmental pressures not encountered on Earth, including microgravity and radiation While the adaptability of bacteria during spaceflight is not fully understood, recent research has suggested that it may be species and even clone specific. Given the spaceflight-induced suppression of the human immune system, it is essential to understand the genomics of potential human pathogens in spaceflight. Such understanding could provide valuable insights into species and lineages of medical astromicrobiological importance. Here, we used hybrid assembly approaches and comparative genomics to provide the first comprehensive genomic characterisation of 10 Klebsiella isolates retrieved from the ISS. Our findings revealed that K. quasipneumoniae ST138 exhibits spatial and temporal persistence aboard the ISS, with evidence of genomic divergence from the ST138 lineage on Earth. Additionally, we characterized plasmids from Klebsiella species of ISS origin, which encoded disinfectant and thermoresistance genes suggesting that these might aid adaptability. Furthermore, we identified an MGE containing a hypervirulence-associated locus belonging to a Klebsiella pneumoniae isolate of the "high risk" ST101 clone. Our work provides valuable insights into the adaptability and persistence of Klebsiella species during spaceflight, highlighting the importance of understanding the behaviour of potential pathogenic bacteria in space.