Raw sequences of K. pneumoniae

Background. K. pneumoniae is a gram-negative bacillus, facultative, anaerobic, and non-motile. It is a common cause of antimicrobial-resistant opportunistic infections in hospital settings and remains one of the most common nosocomial pathogens in the world. In Colombia, K. pneumoniae has been identified as the third most frequent microorganism (11.5%) causing HAI at the national level, mainly associated with the circulation of isolates belonging to GC258. Aim. to contribute to the knowledge of the genetic diversity and dissemination of K. pneumoniae isolates resistant to carbapenems and susceptible to carbapenems associated with HAI in Colombia. Materials and methods. From 2020 to 2021, a total of 335 K. pneumoniae isolates carbapenem-resistant and carbapenem-susceptible were collected from 26 participating institutions in Colombia. The isolates were characterized by whole-genome sequencing to determine CGs, STs, Serotypes, resistance mechanisms to carbapenems and ESBL, hypervirulence, and possible transmission groups. Results. We found 21 new STs (ST6690 to ST6710) and 112 known sequence types, of which ST11, ST1082, and ST307 were the most frequent. The STs were classified into 96 clonal groups (CGs) and 7 singletons. Carbapenem resistance genes KPC-like were observed with the variants blaKPC-3, blaKPC-2, and blaKPC-19 mainly related to ST11. The NDM-like gen was identified with blaNDM-1 the variant, mostly associated with ST147 and ST307. Other carbapenemases like blaVIM-24 and blaGES-2 were identified in co-production. While blaCTX_M_15, blaSHV-27, and blaSHV-41 were the most frequent ESBL genes in CRKP and CSKP. In addition, some hvKp isolates related to ST23 were identified. Finally, we were able to identify transmission of mostly carbapenem-resistant and ESBL-producing strains within and between hospitals. Conclusion. The present study provides recent epidemiological information on the behavior of CRKP and CSKP in Colombia. Our results demonstrate that CRKP continues to represent a challenge at the in-hospital level, mainly due to its high prevalence in the ICU and hospitalization.