Multiplex PCR-Based Detection of Eight Carbapenemase Genes and Their Clinical Characteristics in Urinary Tract Infections

Background: The emergence and spread of urinary carbapenem-resistant organisms (CROs) are a major public health concern, particularly in Sri Lanka. Therefore, we aimed to detect and genotypically characterize CROs in urinary tract infections (UTIs) and their clinical outcomes. Methods: Urinary CROs were collected from two hospitals in Sri Lanka from January to December, 2023. Among 7640 urine samples, 100 CROs were identified by disk diffusion method, and 99 were detected by BD Pheonix^TM automated system. The presence of eight carbapenemase genes; bla_KPC, bla_NDM, bla_VIM, bla_IMP, bla_OXA-23, bla_OXA-48, bla_OXA-51, and bla_OXA-58, among 97 CROs was detected by a multiplex PCR kit. Results: Out of 99 urinary CROs, K. pneumoniae (33.3%; n = 33/97) was the most common species. Among the 97 isolates tested by PCR, a single carbapenemase gene was detected in 35.05% (34/97), while two or more genes co-occurred in 39.18% (38/97). The most frequently identified gene was bla_OXA-51 (47.4%), followed by bla_OXA-58 (41.2%). Most patients (95.74%; n = 90/97) showed clinical improvement within seven days of treatment. Among the 93 patients discharged and followed for three months, 74.20% (n = 69/93) experienced at least one mild UTI recurrence. A total of 10 patients died during the study period. Of which, four (40%) during hospitalization and six (60%) during follow-up, though none of the deaths were attributed to UTIs. Conclusions: K. pneumoniae, showed the highest carbapenemase gene diversity. Recurrent UTIs were observed during the follow-up period. Continuous surveillance and implementation of targeted infection control programs are needed to minimize further emergence and spread of carbapenemase genes.