Comparative Genomic and Resistance Analysis of ST859-KL19 and ST11 Carbapenem-Resistant Klebsiella pneumoniae with Diverse Capsular Serotypes.

Background: In China, Carbapenem-resistant Klebsiella pneumoniae (CRKP) is dominated by sequence type 11 (ST11) harbouring KPC-2, with KL64 displacing KL47 and KL25 emerging. ST859 (ST11 variant) has caused outbreaks, but its epidemiology is unclear. Materials and Methods: A total of 99 non-duplicate CRKP isolates were collected from June to December 2024. Antimicrobial susceptibility was determined by broth microdilution. The genomic sequences of the strains were obtained using next-generation sequencing technology. Resistance genes, virulence loci, and plasmid replicons were identified with Kleborate, Abricate, and MOB-suite, respectively. Results: ST11 accounted for 63.64% and ST859 for 15.15%. All ST859 were KL19, while ST11 were mainly KL25 (60.32%) and KL64 (26.98%). 76.8% co-harbored carbapenemase and extended-spectrum beta-lactamase (ESBL) genes, with KPC-2 and CTX-M-65 being the predominant types. Susceptibility rates were 100% to tigecycline, and 78.79% to ceftazidime/avibactam. ST859 CRKP isolates exhibited higher phenotypic resistance to tetracycline and colistin than ST11 CRKP isolates (p < 0.05), and carrying LAP-2, QnrS1, QnrS10, and tet(A) more frequently. ST11-KL25 showed higher resistance to amikacin, gentamicin, and chloramphenicol, with increased prevalence of CTX-M-65, TEM-1, rmtB, catA2, and dfrA14 compared to ST11-KL64 (p < 0.05). IncF was the most prevalent replicon and both ST859 and ST11 CRKP carry conjugative resistance plasmids, and the host range is predominantly Enterobacterales. Conclusions: ST859-KL19 ranks second to ST11 with higher resistance to tetracyclines and colistin. ST11-KL25 may have already displaced ST11-KL64 as the predominant capsular type in Shanghai, with distinct resistance profiles between KL variants. Long-term, multicenter surveillance is urgently needed to delineate the evolutionary trajectory and clinical impact of these emerging clones.