Distribution and co-occurrence of carbapenemase, quinolone resistance, and 16S rRNA methyltransferase genes among carbapenem-resistant Klebsiella pneumoniae clinical isolates in a Thai tertiary care hospital

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a major public health concern because of extensive antimicrobial resistance and limited treatment options. However, data on the co-occurrence of carbapenemase, quinolone-resistance, and 16s rRNA methyltransferase (16s-RMTase) genes among CRKP isolates in Thailand remain limited, and targeted gene detection may not correspond to phenotypic carbapenemase activity or antimicrobial susceptibility. This study characterized these genes and examined their co-occurrence and genotype–phenotype relationships among CRKP clinical isolates from a Thai tertiary care hospital. We analyzed 218 CRKP clinical isolates collected during matched four-month periods (March–June) in 2023 and 2024. The same months were selected to provide comparable sampling windows rather than because of anticipated seasonal or epidemiological differences. Antimicrobial susceptibility was evaluated using routine hospital testing and disk diffusion for selected reserve agents. Meropenem, ciprofloxacin, and amikacin MICs were determined by broth microdilution. Carbapenemase production was assessed using the modified and EDTA-modified carbapenem inactivation methods and commercial combined disk tests. Selected resistance genes were detected by PCR. All isolates were multidrug resistant, and 199/218 (91.3%) were extensively drug resistant. bla OXA−48−like was detected alone or with bla NDM in 81.2% of isolates, whereas bla NDM was detected alone or with bla OXA−48−like in 30.3%; both genes were co-detected in 42/218 (19.3%) isolates. Carbapenemase genes frequently co-occurred with quinolone-resistance and 16s-RMTase determinants. Meropenem MIC distributions differed across the defined genotype–phenotype categories ( p < 0.001). The dual-gene-positive, phenotype-confirmed group had descriptive MIC₅₀ and MIC₉₀ values of 128 µg/mL, while the genotype–phenotype-discordant group had corresponding values of 1 and 16 µg/mL. Cefiderocol disk diffusion categorized 198/218 (90.8%) isolates as susceptible, including all nine isolates with a routine-panel pandrug-resistant phenotype. CRKP isolates exhibited extensive resistance and frequent co-detection of selected resistance genes. Variation in meropenem MICs across genotype–phenotype categories indicates that targeted gene detection alone may not fully characterize the resistance phenotype and supports its interpretation alongside phenotypic carbapenemase and antimicrobial susceptibility testing. Genomic investigations are needed to determine the genetic contexts and relatedness of these isolates.