Emerging carbapenem-resistant Klebsiella pneumoniae in a tertiary care hospital in Lima, Peru

The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a significant public health threat, particularly in low- and middle-income countries (LMICs) with limited surveillance and treatment options. This study examines the genetic diversity, resistance patterns, and transmission dynamics of 66 CRKP isolates recovered over 5 years (2015-2019) after the first case of CRKP was identified at a tertiary care hospital in Lima, Peru. Our findings reveal a shift from bla(KPC-2) to bla(NDM-1) as the dominant carbapenemase gene after 2017. Lineage ST45 was the most prevalent and persisted for multiple years, followed by high-risk clones ST11 and ST147. The bla(NDM-1) gene was carried almost exclusively by a Tn125-like transposon, similar to the one reported in previous studies from two Peruvian hospitals. Long-read sequencing revealed nearly identical bla(NDM)-carrying plasmids across the four assessed lineages. A comparative analysis of 1,023 South American CRKP genomes confirmed a unique pattern in Peru, where bla(NDM-1) (81.4%) outpaced bla(KPC-2), which remained dominant (59.4%) elsewhere. In addition, emerging clones ST45 and ST348 found in Peru were rarely found elsewhere in South America, suggesting potential regional adaptation. In conclusion, our study provides a comprehensive picture of the intra-hospital dynamics of these emerging pathogens and provides a framework for studying their genomic diversity in the understudied South American region. IMPORTANCE This study provides novel insights into the transmission and genetic diversity of carbapenem-resistant Klebsiella pneumoniae, a bacteria responsible for severe infections, with limited treatment options. By examining isolates recovered over 5 years at a major hospital in Lima, Peru, we demonstrated a shift from one type of resistance gene, bla(KPC), to another, bla(NDM), which is more challenging to treat. Our findings reveal that specific bacterial lineages carrying the bla(NDM) gene in a specific plasmid are emerging in Peru, including well-known high-risk strains and others rarely found elsewhere in South America. This pattern highlights an urgent need for targeted surveillance and infection control as these strains pose a significant challenge to healthcare systems. Our study provides crucial data on Klebsiella pneumoniae in Peru, contributing to broader efforts to monitor and control antibiotic-resistant infections in South America and globally.