Study of carbapenem-resistant Pseudomonas aeruginosa (CRPA) by phenotypic and molecular approaches

Abstract

Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is a prominent healthcare-associated pathogen causing public health concerns worldwide. Different resistant mechanisms, either carbapenemase-producing or non-carbapenemaseproducing, such as porin loss and efflux pump, may require different treatment approaches. In addition, the distribution of strains and resistant genes varies among global regions. A limited number of reports regarding this issue have been published in Thailand. Therefore, this study aimed to establish the information on the bacterial strains, resistant genes, and their correlation using the molecular approaches, as well as establishing the efficacy of the modified Carbapenem Inactivation Method (mCIM) for detecting carbapenemase-producing strain. In this study, 164 CRPA isolates were tested for carbapenemase genes by the direct flow chip kits covering 17 carbapenemresistant genes. Of these isolates, five families of carbapenemase genes, including blaIMP, blaVIM, blaNDM, blaGES, and blaSIM, were detected in 83 isolates, while 81 were negative for carbapenemase genes. The blaIMP was the most prevalent, followed by blaVIM and blaNDM. Only 68/83 (83.13%) of carbapenemase gene-positive isolates were positive by the mCIM assay. Of the fifteen mCIM-negative isolates, six (40%) and four (26.67%) isolates contained blaVIM-2 and blaIMP-62, respectively; however, onewas found to co-exist with two genes. Five (33.33%) carried blaGES-5, and one isolate with blaVIM-63. A total of 53 sequence types (STs) and four unmatched STs of CRPA were found in this study. Of these 53 STs, only twelve (22.64%) were associated with carbapenemase genes. The ST235, ST357, and ST964 were the top three most common sequence types containing carbapenemase genes, while ST244 was the most common non-carbapenemase-producing CRPA. Although the resistant genes found in these STs varied, each ST had predominant genes. The blaIMP was dominant in ST235, while blaVIM and a combination of blaNDM plus blaIMP were dominant in ST357 and ST964, respectively. Among 83 carbapenemase-producing P. aeruginosa (CPPA), 81.93% carried a single resistant gene. However, 66.67% of ST964 contained a combination of blaIMP and blaNDM. Interestingly, four carbapenemase genes were detected in an isolate of ST235. The antimicrobial susceptibility profile of CRPA revealed that of 20 tested antibiotics, the MIC50 of only four antibiotics, including amikacin, netilmicin, cefiderocol, and cefepime-zidebactam, was in the susceptible category. Only cefepime-zidebactam showed the MIC90 within susceptible breakpoint, while the MIC90 of cefiderocol was in the intermediate range. Interestingly, the MIC50 and MIC90 of colistin remained in the intermediate breakpoint. The other fifteen antibiotics showed no effect against CRPA. Among the three most common STs of CPPA, ST357, in which most of the isolates contained blaVIM, had the strongest resistant activity. Only amikacin had the MIC90 in the susceptible range, and cefepime-zidebactem and netilmicin remained at the intermediate level. The data of this project revealed the distribution of CRPA strains, the association of STs and carbapenemase genes, and the antimicrobial susceptibility profiles. The results also indicated that minimal antibiotic choices are good candidates for treating CRPA infection