Genomics of Hospital-Associated Brazilian Multidrug-Resistant Klebsiella pneumoniae: Abundance of Resistance and Virulence Genes and Mosaicism of the blaKPC−2 Genetic Context Among Enterobacterales

Abstract

The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a critical threat to global public health due to limited therapeutic options. This situation is magnified by CRKP strains with elevated virulence. This study aimed to characterize the virulome, resistome, and bla KPC genetic context of CRKP strains exhibiting increased virulence from hospital-associated infections in southeastern Brazil, focusing on their molecular evolution and clinical impact. Despite being classified as classical variants, the strains displayed a dense virulome, averaging 14 ± 0.55 virulence genes, many linked to mobile genetic elements and co-occurring with heavy metal resistance genes. Notably, the colicin-encoding cci gene, reported for the first time in ST147, illustrates unique adaptations in this lineage. Diversity was observed in K- and O-loci, including the rare K-locus 150, identified in an ST11 strain featuring a rearrangement involving the virulence-associated fucose synthesis gene gmb . The pan-resistome included 51 acquired resistance genes (ARGs), with an average of 14.7 ± 2.8 per strain, enabling resistance to multiple antibiotic classes. The colocalization of ARGs suggests horizontal gene transfer as a driver of resistance dissemination. All bla KPC−2 -carrying strains also contained ESBL genes, with the bla KPC−2 gene typically located on IncN or IncM1-type plasmids within Tn 4401 , a conserved genetic context. However, an unusual bla KPC−2 context, associated with Tn 5403 and suggesting a putative recombination event between plasmids from different Proteobacteria, was found in an ST11 (CC258) strain. These findings highlight the urgent need for genomic surveillance in hospitals to monitor and understand the evolution of resistance and virulence in CRKP.

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