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) is a major public health concern, particularly in Sri Lanka. 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 PheonixTM automated system. The presence of eight carbapenemase genes; blaKPC, blaNDM, blaVIM, blaIMP, blaOXA-23, blaOXA-48, blaOXA-51, and blaOXA-58, among 97 CROs was detected by a multiplex PCR kit. Results: Out of 99 urinary CROs, K. pneumoniae (33/99, 33.3%) was the most common species. A single gene was detected in 35.05 % (34/97), whereas two or more genes co-occurred in 39.18% (38/97). The highest occurrence was blaOXA-51 (47.4%), followed by blaOXA-58 (41.2%). The education level of the patients was significantly associated with the presence of carbapenemase genes (p<0.05). The majority of the patients (95.74%; n=90/97) clinically improved within seven days of treatment. However, majority (74.20%; n=69/93) experienced one or more mild UTI episodes during the next three months. Four deaths (4/10, 40%) occurred during the hospital stay, and six deaths (6/10, 60%) during the follow-up period, but none were due to UTIs. Conclusion: 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.