Sequence type-associated carbapenemase genes in sewage-derived Klebsiella pneumoniae and characterization of a tigecycline-resistant ST34 strain

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a high-priority pathogen that severely limits clinical treatment options. Sewage systems serve as critical interfaces for the dissemination of antimicrobial resistance (AMR). However, the clonal distribution and evolutionary dynamics of CRKP co-harboring carbapenemases and tigecycline resistance genes in these environments remain insufficiently characterized. This study investigated CRKP resistance mechanisms in sewage using whole-genome sequencing. A total of 143 CRKP strains were isolated from 30 sewage samples (hospital, community, and livestock farm). Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) identified 22 representative strains belonging to 6 sequence types (STs), with ST11 being the predominant clone across all sources. All isolates exhibited carbapenem resistance, and 27.3% carried tigecycline resistance. The carbapenemase genes bla KPC-2 and bla NDM-1 exhibited ST-specific genetic environments. Complete genome sequencing of ST34 strain JD_E1, which carried tmexCD-toprJ , bla NDM-1 , and bla KPC-2 , revealed that these genes were located on conjugative IncHI5-like/IncU and IncFIB(pQil)/IncFII(Yp) plasmids. These plasmids demonstrated high transferability and stability without antibiotic selection. Plasmid pE1_NDM underwent insertion sequence (IS)-mediated structural streamlining via the deletion of non-essential segments while preserving core resistance modules. These findings suggest that sewage environments are reservoirs for multidrug-resistant CRKP clones, providing molecular epidemiological evidence for integrated infection control strategies.