Background The rise of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) strains represents a major clinical threat, particularly in Asia. These strains possess both extensive drug resistance and enhanced virulence traits, leading to high morbidity and mortality. This study aimed to characterize the genomic profile of a CR-hvKp isolate (BB-7) obtained from a clinical case in eastern India and to investigate its resistance and virulence mechanisms. Methods K. pneumoniae BB-7 was obtained from the urine sample of a 75-year-old male and identified by using the VITEK2 system and ITS–PCR amplification. Hypervirulence was confirmed through the string test and detection of the iucA gene. The antimicrobial susceptibility (AST) was determined by the Kirby-Bauer disk diffusion method, whereas colistin susceptibility was measured using broth microdilution. Whole-genome sequencing was performed using Illumina NovaSeq, followed by de novo assembly, annotation, and resistome/virulome analysis using tools including PROKKA, CARD, ResFinder, and VFAnalyzer. MLST, plasmid typing, capsular serotyping, phage element, and insertion element were analyzed by using an online database. Phylogenetic analysis was performed using cgMLST and core SNP approaches. Results BB-7 exhibited an extensively drug-resistant (XDR) phenotype, including resistance to β-lactams, fluoroquinolones, aminoglycosides, tetracyclines, and colistin. Resistance genes identified included blaCTX-M-15, blaSHV-28, blaTEM-1, blaOXA-232, blaOXA-1, armA, aadA2, and others. The virulence profile revealed genes such as iucABCD, iutA, iroEN, and T6SS clusters. Plasmid analysis identified IncHI1B, ColKP3, and IncFIB(K), contributing to the convergence of resistance and virulence. The Capsular serotype at K-locus and O-locus is K64 and O2α.1, respectively. The isolate was assigned a novel sequence type, ST7947 (gapA-1, infB-6, mdh-1, pgi-1, phoE-749, rpoB-46, tonB-1), differing from ST2096 by one allele phoE. Phylogenetic analysis revealed that BB-7 was closely related to ST2096 MDR K. pneumoniae isolates from an Indian hospital. Conclusion BB-7 represents a novel CR-hvKp strain with a unique ST7947 genotype, exhibiting co-resistance and hypervirulence, raising concern for public health. The association of high-risk resistance plasmids with virulence factors underscores the urgent need for enhanced genomic surveillance, infection control, and devising specific therapies to restrict the proliferation of such strains.

Genomic insights into novel ST7947 carbapenem-resistant hypervirulent Klebsiella pneumoniae: a threat from an Indian hospital setting

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2025年11月17日

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Birasen Behera,
Sanghamitra Pati,
Bidyutprava Rout,
Saubhagini Sahoo,
Aishwarya Swain,
Rajesh Kumar Sahoo,
Rajashree Panigrahy

摘要

Background

The rise of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) strains represents a major clinical threat, particularly in Asia. These strains possess both extensive drug resistance and enhanced virulence traits, leading to high morbidity and mortality. This study aimed to characterize the genomic profile of a CR-hvKp isolate (BB-7) obtained from a clinical case in eastern India and to investigate its resistance and virulence mechanisms.

Methods

K. pneumoniae BB-7 was obtained from the urine sample of a 75-year-old male and identified by using the VITEK2 system and ITS–PCR amplification. Hypervirulence was confirmed through the string test and detection of the iucA gene. The antimicrobial susceptibility (AST) was determined by the Kirby-Bauer disk diffusion method, whereas colistin susceptibility was measured using broth microdilution. Whole-genome sequencing was performed using Illumina NovaSeq, followed by de novo assembly, annotation, and resistome/virulome analysis using tools including PROKKA, CARD, ResFinder, and VFAnalyzer. MLST, plasmid typing, capsular serotyping, phage element, and insertion element were analyzed by using an online database. Phylogenetic analysis was performed using cgMLST and core SNP approaches.

Results

BB-7 exhibited an extensively drug-resistant (XDR) phenotype, including resistance to β-lactams, fluoroquinolones, aminoglycosides, tetracyclines, and colistin. Resistance genes identified included bla_CTX-M-15, bla_SHV-28, bla_TEM-1, bla_OXA-232, bla_OXA-1, armA, aadA2, and others. The virulence profile revealed genes such as iucABCD, iutA, iroEN, and T6SS clusters. Plasmid analysis identified IncHI1B, ColKP3, and IncFIB(K), contributing to the convergence of resistance and virulence. The Capsular serotype at K-locus and O-locus is K64 and O2α.1, respectively. The isolate was assigned a novel sequence type, ST7947 (gapA-1, infB-6, mdh-1, pgi-1, phoE-749, rpoB-46, tonB-1), differing from ST2096 by one allele phoE. Phylogenetic analysis revealed that BB-7 was closely related to ST2096 MDR K. pneumoniae isolates from an Indian hospital.

Conclusion

BB-7 represents a novel CR-hvKp strain with a unique ST7947 genotype, exhibiting co-resistance and hypervirulence, raising concern for public health. The association of high-risk resistance plasmids with virulence factors underscores the urgent need for enhanced genomic surveillance, infection control, and devising specific therapies to restrict the proliferation of such strains.