Global epidemiology and resistance-related mutations of ceftazidime-avibactam-resistant Klebsiella pneumoniae strains

Xinya Xie¹Jiali Chen²Lihua Qi³Yue Yuan⁴Jiamin Long¹Xuelian Wu¹Yuan Liu¹Jinpeng Guo⁵Changjun Wang⁵Xiangzhao Meng^6*Xiong Liu^5*Yong Chen^5*Jie Liu^3*

• ¹China Medical University, Shenyang, China
• ²Nankai University School of Medicine, Tianjin, China
• ³The Seventh Medical Center of PLA General Hospital, Beijing, China
• ⁴5th Medical Center of Chinese PLA General Hospital, Beijing, China
• ⁵Chinese PLA Center for Disease Control and Prevention, Beijing, China
• ⁶Beijing Aerospace General Hospital, Beijing, China

Objective: Understanding the molecular epidemiological characteristics and resistance-related mutations of global CAZ/AVI-R K. pneumoniae strains. Methods: Non-repetitive K. pneumoniae strains isolated from clinical and sewage samples were subjected to antimicrobial susceptibility testing and whole-genome sequencing (WGS). According to the E-test results, 37 and 11 CAZ/AVI-R K. pneumoniae strains were included from clinical and sewage samples, respectively. After applying the inclusion and exclusion criteria, 253 CAZ/AVI-R K. pneumoniae strains with complete genome sequences were retrieved from public databases. Sequence types (STs) and serotypes were identified using Kleborate. Antimicrobial resistance genes (ARGs), virulence factors, and plasmids were annotated using Abricate. Prokka, Roary, and IQtree2 were used for annotation, core gene alignment, and phylogenetic analysis, respectively. Mutations in outer membrane porins (OmpK35 and OmpK36) and efflux pumps (AcrA and AcrB) were analyzed and visualized using Miniprot and BioAider. Results: Through comprehensive annotation, we identified 43 STs, 37 capsular (K) serotypes, 5 O antigen serotypes, 27 plasmid types and 22 ISs, 135 virulence genes, and 10 macromolecular secretion systems were annotated. Prophages carrying ARGs were annotated in 106 strains. In total, 128 distinct ARGs were identified among 301 strains. The ARGs associated with CAZ/AVI resistance in K. pneumoniae strains mainly included the class B metallo-beta-lactamases (MBLs) genes, blaKPC-2, and blaKPC-3 variants. Analysis of porin mutations revealed that in OmpK35, the most common substitution among all strains from three collection sources was at position 28 (*aaK). OmpK36 exhibited the highest number of mutations among strains from three sources, with frequent changes at position 136 (T136G), 137 (-gacacc), and 349 (H349R). Some porin mutations were identified exclusively in strains isolated from hospital clinical samples by our research team. OmpK35 had a substitution at position 132 (E132K). OmpK36 had substitutions at positions 2 (K2S), 3 (V3L), and 146 (R146H), respectively. AcrA and AcrB had substitutions at positions 188 (T188A) and 716 (R716L), respectively. Conclusion: The combination of multiple drug resistance-related mutations leads to resistance to CAZ/AVI. The most common resistance-related mutations in strains from both public databases and those collected by our team are the coexistence of porins and efflux pump mutations, and carriage of MBLs genes.