2025/03/04 by Aoxiao Chen, H.X. Wang, Jing Zhang +3 · 1 voice
Biochemistry, Genetics and Molecular Biology · #Antibiotic Resistance in Bacteria #Infections and bacterial resistance #Bacterial Identification and Susceptibility Testing
paper · doi:10.1093/jacamr/dlaf048
openalex publication_date 2025/03/04 · openalex created_date 2025/04/08 · openalex updated_date 2026/07/31
Sir, The ST11 clone is the most prevalent lineage among hypervirulent Klebsiella pneumoniae (hvKP) and carbapenem-resistant K. pneumoniae (CRKP) worldwide,1 with blaKPC-2 playing a pivotal role in the development of CR-hvKP and hv-CRKP.2 According to the Comprehensive Antibiotic Resistance Database, 242 blaKPC variants have been identified globally, with blaKPC-2 and blaKPC-3 being the most widespread.3 blaKPC-12, a rare variant of blaKPC-2, is characterized by an L169M substitution in the Ω-loop, which may influence the resistance to ceftazidime/avibactam.4 Between 2017 and 2024, the NCBI database reported 22 K. pneumoniae strains carrying blaKPC-12, 21 of which were from China and 1 from Greece. Given the rarity of reports on blaKPC-12 and the lack of documented fatal cases, we present a detailed analysis of a fatal infection caused by a hvKP strain harbouring blaKPC-12, focusing on its genetic context, resistance genes and virulence factors. In January 2024, a K. pneumoniae strain (KP2414) was isolated from the blood culture of a 67-year-old female patient who had undergone heart valve surgery. The patient had been hospitalized in the intensive care unit for 3 months due to elevated postoperative inflammatory markers and several high-risk infection factors. During hospitalization, sputum cultures repeatedly tested positive for CRKP. The patient ultimately died from septic shock, despite treatment with the following combination of antibiotics sequentially: ceftazidime/avibactam, cefoperazone/sulbactam and ceftazidime/avibactam. Antimicrobial susceptibility test revealed that KP2414 was susceptible only to ceftazidime/avibactam (MIC = 4/4 mg/L), tigecycline (1 mg/L) and polymyxin (≤0.5 mg/L), as detailed in Table S1 (available as Supplementary data at JAC-AMR Online). One possible explanation for its susceptibility to ceftazidime/avibactam is that the isolate has not yet undergone the induction required for resistance, as resistance to ceftazidime/avibactam in KPC-12 has been shown to develop after multiple passages under drug pressure.4 Genome sequencing analysis of KP2414 (Supplementary method) revealed that it belongs to the ST11, K19 type. It carries several virulence genes such as iucA, rmpA and rmpA2, as well as multiple resistance genes, including fosA6 (fosfomycin resistance), qnrS1 (quinolone resistance), tet(A) (tigecycline resistance), aadA2 and rmtB (aminoglycoside resistance) and carbapenem resistance genes including blaKPC-12. Compared with the reference strain ATCC13883, KP2414 showed no differences in OmpK35. However, a glycine and aspartic acid insertion were found in the extracellular Loop 3 region of OmpK36, which likely increases the resistance to carbapenem antibiotics. After four to five generations of passaging, KP2414 regained sensitivity to meropenem, most likely due to the increased fitness cost associated with the insertion of an amino acid in the L3 loop of OmpK36.5 The genetic environment of blaKPC-12 in the Tn6929 transposon on the plasmid was analysed, as shown in Figure 1(b). Tn6929 is the most commonly reported transposon carrying blaKPC in China.6 The genetic environment of KP2414 consists of ▵Tn1755-5′-repB-orf-klcA-orf-korC-ISKpn6-blaKPC-12-▵Tn6376(ISKpn27). Insertions of 3-bp inverted repeat sequences were found in the flanking regions of ▵ISKpn27 and ▵Tn1755-5′, and six TGGACC insertion repeat sequences were identified at both the 5′ and 3′ ends of the entire genetic environment. Upstream of blaKPC-12, G and C nucleotide promoter-binding sites were identified at 39 and 250 bp, respectively. The −35/−10 elements of P1 and P2 promoter regions (TAATCC/TTACAT and TTGAC/AATAAT) is consistent with the transcriptional environment of blaKPC-2, as previously reported by Wang et al.7 (a) Phylogenetic tree based on core genome SNPs of 38 K. pneumoniae clinical isolates carrying blaKPC-2 and blaKPC-12. Blue squares represent isolates from Greece, while all other isolates are from China. Red circles indicate cases with fatal outcomes, while outcomes for other isolates remain unspecified. (b) Genetic environments comparison of KP2414 and KP048 (carrying blaKPC-2). Regions with >99.0% homology are shaded in grey. Red arrows indicate blaKPC-2 and blaKPC-12; blue arrows represent genes with unknown or other functions; purple arrows indicate genes encoding transposase functions (e.g. tnpA and tnpR); yellow arrows represent insertion sequences, with triangles marking inverted repeat sequences. Phylogenetic analysis included 15 ceftazidime/avibactam-resistant K. pneumoniae strains carrying blaKPC-2,8 22 strains of K. pneumoniae carrying blaKPC-12 from the NCBI database and KP2414 (Figure 1a). Among the 17 hvKP strains analysed, six were found to carry blaKPC-12. Notably, blaKPC-12 was detected in both the patient and hospital wastewater, underscoring the potential risk of full-chain transmission. hvKP is known for its propensity to cause bloodstream infections, and its co-occurrence with blaKPC-12 poses severe challenges for clinical treatment. To the best of our knowledge, KP2414 represents the first reported case of blaKPC-12-carrying hvKP from bloodstream infection in China. Therefore, while blaKPC-2 and blaKPC-3 remain globally prevalent, the complex transposon-mediated resistance structure of blaKPC-12 and its emerging prevalence in China, coupled with its full-chain transmission potential, represent significant threats to both public health and clinical management. This work was supported by the National Key Research and Development Program of China (no: 2022YFD1800400) and the National Natural Science Foundation of China (grant number: 81971987). None to declare. The genome assemblies of KP2414 have been deposited in the NCBI and are registered under BioProject accession NO. PRJNA1203937. All data are available from the corresponding authors upon reasonable request. Ethical permission for this study was agreed by the Ethics Committee of The Second Affiliated Hospital Zhejiang University School of Medicine (2024-1040). Table S1 is available as Supplementary data at JAC-AMR Online.