The Endophytic Strain Klebsiella michiganensis Kd70 Lacks Pathogenic Island-Like Regions in Its Genome and Is Incapable of Infecting the Urinary Tract in Mice

Abstract

Klebsiella spp. have been isolated from many different environmental habitats but have mainly been associated with nosocomial acquired diseases in humans. Although there are many recently published sequenced genomes of members of this genus, there are very few studies on whole genome comparisons between clinical and non-clinical isolates, and it is therefore still an open question if a strain found in nature is capable of infecting humans/animals. Klebsiella michiganensis Kd70 was isolated from the intestine of larvae of Diatraea saccharalis but genome analysis revealed multiple genes associated with colonization and growth promotion in plants suggesting an endophytic lifestyle. Kd70 cells labeled with gfp confirmed capability of root colonization and soil application of Kd70 promoted growth in greenhouse grown sugarcane. Further genomic analysis showed that the Kd70 genome harbored fewer mammalian virulence factors and no pathogen island-like regions when compared to clinical isolates of this species, suggesting attenuated animal/human pathogenicity. This postulation was corroborated by in vivo experiments in which it was demonstrated that Kd70 was unable to infect the mouse urinary tract. This is to the best of our knowledge the first experimental example of a member of a pathogenic Klebsiella spp. unable to infect a mammalian organism. A proteomic comparison deduced from the genomic sequence between Kd70 and several other K. michiganensis strains showed a high similarity with isolates from many different environments including clinical strains, and demonstrated the existence of conserved genetic lineages within this species harboring members from different ecological niches and geographical locations. Furthermore, most genetic differences were found to be associated with genomic islands of clinical isolates, suggesting that evolutionary adaptation of animal pathogenicity to a large extent has depended on horizontal gene transfer. In conclusion our results demonstrate the importance of conducting thorough in vivo pathogenicity studies before presupposing animal/human virulence of non-clinical bacterial isolates.

Phenol Removal Capacity of the Common Duckweed (Lemna minor L.) and Six Phenol-Resistant Bacterial Strains From Its Rhizosphere: In Vitro Evaluation at High Phenol Concentrations

“…The fact that both Klebsiella oxytoca strains used in this study (strain 9 and 14) formed biofilms in vitro, but only one (strain 14) formed intimate connections with the root system of duckweed, implied a higher level of biological specificity of the tested bacteria-plant interactions, which is also supported by similar studies [32,34].…”

“…Micrographs containing K. oxytoca (strain 14) suggest that this strain inhabited the interior of the cell, as is the case with multiple identified non-clinical isolates of K. oxytoca, which are described as endophytes [34]. This trait explains, at least in part, the phenol removal efficiency of the strain (the plant provides both biological and mechanical protection to the endophytic bacteria) and the positive effect on multiplication rates of duckweed.…”

“…There is a scientific consensus that bacteria tend to adhere to any available immobile surface, organic or inorganic, and form biofilms, and that this process is often stimulated in the presence of various noxious agents [33]. Moreover, in the recent bioremediation studies, it is becoming increasingly clear that the biological "platforms" are advantageous to the inorganic surfaces as a source of nutrients and a physical barrier, which simultaneously enhances the PGP properties of the bacteria [34]. In this study, we observed bacterial microcolonies in the intercellular crevices between epidermal root cells, which is a form of bacterial organization known to correspond to the early stages of biofilm formation [35].…”

Genomic characterization and computational phenotyping of nitrogen-fixing bacteria isolated from Colombian sugarcane fields

“…2). Our results are corroborated by a previous study of Klebsiella michiganensis Kd70 isolated from the intestine of larvae of Diatraea saccharalis , for which the genome was shown to contain multiple genes associated with plant growth promotion and root colonization, but lacked pathogenicity islands in its genome (15). In order to shed further light on this problem, we extended our study of environmental isolates from Colombian sugarcane to comparisons with genomes of Klebsiella clinical isolates associated with opportunistic infections in humans along with a number other environmental isolates with available genome sequences (Fig.…”

“…2A). The absence of pathogenicity islands in the genome of the endophytic nitrogen-fixer K. michiganensis Kd70 was associated with an inability to infect the urinary tract in mice (15). Our results indicate that nitrogen-fixing K. pneumoniae environmental isolates from Colombian sugarcane fields do not pose a health risk compared to clinical and environmental isolates that have previously been associated with pathogenicity.…”