Nationwide genomic surveillance of carbapenem- and colistin-resistant Klebsiella pneumoniae bloodstream isolates in Thailand (2020–2024)

Klebsiella pneumoniae is a major cause of bloodstream infections worldwide and is increasingly associated with multidrug resistance, particularly to carbapenems and colistin, which severely limits treatment options. This study investigated the genomic epidemiology of K. pneumoniae bloodstream infection (BSI) isolates collected in Thailand between 2020 and 2024. A total of 227 K. pneumoniae BSI isolates collected nationwide through the National Antimicrobial Resistance Surveillance Center, Thailand were subjected to antimicrobial susceptibility testing and whole-genome sequencing, followed by multilocus sequence typing, AMR gene detection, plasmid profiling, virulence scoring, phylogenetic analysis, and genotype–phenotype correlation. Among the isolates, 199 were resistant to carbapenems, seven were resistant only to colistin, and 21 were not resistant to either carbapenems or colistin. Three high-risk sequence types (ST) (ST16, ST147, and ST231) predominated in most regions, whereas the south showed greater clonal diversity. ST16 isolates commonly co-harbored bla NDM−1 and bla OXA−232 and had high rates of carbapenem and colistin co-resistance. ST231 isolates exhibited carbapenem resistance along with rmtF1 -mediated aminoglycoside resistance, whereas ST147 isolates demonstrated high genomic plasticity and resistance diversity. Rare ST isolates carrying mcr genes and hypervirulent ST23 and ST268 lineages were also identified, with ST268 resistant to all carbapenems tested. These findings highlight the dissemination of high-risk clones in Thailand and underscore the need for real-time genomic surveillance and molecular diagnostics to inform infection control and national AMR strategies.