Genomic and Phenotypic Characterization of Extensively Drug-Resistant Clinical Klebsiella quasipneumoniae subsp. similipneumoniae ST1929 Isolates

Abstract

Background: Klebsiella quasipneumoniae subsp. similipneumoniae is an emerging member of the K. pneumoniae complex that is often misidentified in routine diagnostics. Its clinical relevance and genomic characteristics remain poorly understood. Methods: Four K. quasipneumoniae subsp. similipneumoniae isolates were collected from hospitalized patients in different wards and identified by whole-genome sequencing. Antimicrobial susceptibility testing was conducted using the broth microdilution method. Phylogenetic, comparative genomic, and plasmid transfer analyses were conducted to elucidate genetic relatedness and resistance mobility. Virulence phenotypes were assessed by measuring capsule production, biofilm formation, serum resistance, and in vivo pathogenicity in a Galleria mellonella infection model. Results: All four isolates belonged to the novel ST1929-KL159 clonotype and exhibited an extensively drug-resistant phenotype, with resistance to β-lactams, carbapenems, fluoroquinolones, tigecycline, and trimethoprim-sulfamethoxazole. Amikacin was the only consistently active agent; one isolate showed high-level resistance to polymyxin B due to a premature stop mutation in mgrB (Gln30*). Genomic analysis revealed the coexistence of blaNDM-1 and the tigecycline resistance cluster tmexC2D2-toprJ2 on a IncU plasmid, which transferred efficiently to E. coli recipients. Comparative genomics demonstrated strong similarity to multidrug-resistant plasmids from diverse Enterobacterales. Phylogenetic analysis confirmed the global distribution of K. quasipneumoniae subsp. similipneumoniae but highlighted the rarity of ST1929, with close relatedness among the four isolates suggesting recent nosocomial transmission. Despite the absence of classical virulence genes, ST1929 exhibited enhanced biofilm formation, moderate capsule production, and intermediate serum resistance, but low virulence in the G. mellonella model. Conclusion: This study provides the first description of K. quasipneumoniae subsp. similipneumoniae ST1929, an extensively drug-resistant lineage harboring blaNDM-1 and the tigecycline resistance cluster tmexC2D2-toprJ2 on a transferable IncU plasmid. The findings underscore the need for accurate detection and surveillance of this rare lineage.