Genomic characterization of hypermucoviscous Carbapenem-resistant Klebsiella pneumoniae ST25 isolates from northwest Argentina

DENTICE MAIDANA, STEFANIA; ALBARRACÍN, LEONARDO; ORTIZ MOYANO, RAMIRO; RAYA TONETTI, FERNANDA; ELEAN, MARIANO; JURE, MARIA ANGELA; VILLENA, JULIO

San Miguel de Tucumán

Simposio; 7ma edición del Simposio Argentino de Jóvenes Investigadores en Bioinformática; 2022

Argentine Regional Student Group (RSG-Argentina)

In recent years, an increase in the prevalence hypermucoviscous carbapenem-resistantKlebsiella pneumoniae with sequence type 25 (ST25) was detected in hospitals of Tucuman(Northwest Argentina). In this work, a comparative genomic analysis was performed with twoK. pneumoniae ST25 strains (LABACER 01 and LABACER 27) to characterize the genesassociated with virulence and host´s colonization. The complete genomes of K. pneumoniaeLABACER 01 and LABACER 27 were sequenced with the Illumina MiSeq platform (Illumina Inc.,San Diego, CA, USA) at INDEAR-BIOCERES (Rosario, Argentina), using a 2_150 bp read lengthsequencing protocol. Ribosomal Multilocus Sequence Typing (rMLST) was applied to theKlebsiella genomes and 32/51 genes encoding ribosomal protein subunits (rps) were recoveredfrom the species K. pneumoniae and queried with the other Klebsiella genomes using theBLASTn algorithm. The sequences were concatenated with Mafft software and used forphylogenomic reconstruction with RAxML software. For the reconstruction of the phylogenetictree, the GTR substitution model and 1000 bootstrap replications were used. Virulence factorsassociated with K. pneumoniae infections were retrieved from the NCBI database andcompared across genomes using the BLASTp algorithm. Genomic analysis revealed that K.pneumoniae LABACER01 and LABACER27 possess virulence factors found in other strains thathave been shown to be hypervirulent, including genes required for enterobactin (entABCDEF)and salmochelin (iroDE) biosynthesis. In both strains, the genes of toxin–antitoxin systems, aswell as regulators of the expression of virulence factors and adhesion genes were alsodetected. Comparative genomics studies performed in this work also showed that theLABACER 01 and LABACER 27 strains possess unique virulence factors when compared to eachother, the presence of tamA in the genome of LABACER 01 and not in LABACER 27 could beassociated with the ability of the former to colonize the lungs and spread to the blood ofinfected mice more efficiently. On the other hand, K. pneumoniae LABACER 27 possesses thefimbriae genes yadV2, yadV3, and bfpA, associated with the ability of pathogenic E. coli strainsto colonize abiotic surfaces, as well as to adhere to epithelial cells and even inhibit thephagocytic activity of macrophages. Our genomic study also detected the presence of therfaH, copA, and aroE genes in the K. pneumoniae LABACER 27 genome, were rfaH and aroEare necessary to resist the microbicidal action of the complement system and copA to preventthe bactericidal effect of copper. Studies on the genetic potential of multiresistant K.pneumoniae strains as well as their cellular and molecular interactions with the host are offundamental importance to assess the association of certain virulence factors with theintensity of the inflammatory response. In this sense, this work explored the virulence profilebased on genomic and in vivo studies of hypermucoviscous carbapenem-resistant K.pneumoniae ST25 strains, expanding the knowledge of the biology of the emerging ST25 clonein Argentina.