Exploratory Genomic Characterisation of the Resistome, Virulome and Molecular Epidemiology of Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates from Four Peruvian Regions

Quispe Oré K.; Salazar-Granara A.; Cueva Távara M.; Huancachoque Molina J.; Segura-Loayza D.; Obispo Achallma D.; Liendo Aguirre G.; Burgos Espejo A.; Briones Alejos A.; Lifonzo Mucha S.; Alarcón-Castillo T.; Marcos-Carbajal P. · Microorganisms (2026) · DOI: 10.3390/microorganisms14071573

Resumen

Multidrug-resistant (MDR) Klebsiella pneumoniae is a critical cause of nosocomial infections associated with high mortality. Of particular concern is the genomic convergence of multidrug resistance and hypervirulence (MDR-hvKP), which represents a severe public health threat. This study characterised the resistome, virulome, and population structure of seven clinical MDR K. pneumoniae isolates collected between 2024 and 2025 across four Peruvian regions (Moquegua, Ucayali, Loreto, and Lima) using whole-genome sequencing (WGS). Genomic analysis identified six distinct sequence types, with the high-risk clone ST307 being the most prevalent (2/7 isolates), consistently associated with the KL102 capsular locus. Remarkably, one isolate from Loreto (oph_54) exhibited a convergent MDR-hvKP genomic profile (ST218, KL57, virulence score 4), carrying yersiniabactin, salmochelin (iro), and aerobactin (iuc) loci alongside multiple resistance determinants. The isolates presented a robust resistome dominated by the extended-spectrum beta-lactamase gene blaCTX-M-15 (5/7) and blaOXA-1, coupled with aac(6′)-Ib-cr and fosA6 genes. Plasmid analysis revealed a predominance of IncFIB(K) replicons. Although exploratory, these findings demonstrate the regional presence of high-risk ST307 lineages and the emergence of convergent MDR-hvKP genomic profiles within the analysed Peruvian hospitals. Immediate and continuous genomic surveillance is urgently required to monitor the potential spread of these highly dangerous, MDR bacterial lineages within these healthcare environments.

Instituciones: Universidad Nacional Mayor de San Marcos; Universidad de San Martín de Porres; Universidad Nacional Intercultural de la Amazonia