Genomic characterization of multidrug-resistant Klebsiella pneumoniae from an outbreak in Northeastern Brazil: mechanisms of virulence and resistance

Klebsiella pneumoniae is an important nosocomial pathogen, considered a critical threat to public health, but its genomic data are scarce in Brazil. Therefore, the aim of this study was to identify the mechanisms of virulence and antimicrobial resistance and to evaluate the molecular epidemiology of K. pneumoniae isolates from an outbreak in a university hospital in Brazil. The DNA of the 25 isolates was sequenced, the functional annotation of the genome was performed in Prokka, for virulence and resistance analyses PanViTa was used, and for Multilocus Sequence Typing analyses pyMLST was used. The isolates presented several virulence genes such as those of the fim operon, ecp operon, and T6SS (identified in all isolates), which are related to adhesion, biofilm formation, and toxin delivery. Other predicted virulence genes involve nutritional/metabolic factors, effector delivery systems, and immune modulation, while resistance genes mainly involve efflux (AcrAB-TolC, KpnGH-TolC, OqxAB, and KpnEF), antibiotic target alteration, reduced permeability, and antibiotic inactivation. In addition, the resistance genes identified in K. pneumoniae isolates are related to a total of 28 antimicrobials from different classes. The sequence types (ST) 11, 273, 395, 5209 and 636 were identified, this being the first report of the ST636 in Brazil. Genomic analysis confirmed the presence of complex virulence and antimicrobial resistance mechanisms, highlighting the threat these pathogens pose and raising concerns about the introduction of ST636 into Brazil, emphasizing the complexity of local strains and the need for continuous surveillance.