New Delhi metallo-β-lactamase and extended spectrum β-lactamases co-producing isolates are high in community-acquired urinary infections in Assam as detected by a novel multiplex polymerase chain reaction assay

Background: The ability of microorganisms to evade antibiotic pressure is challenging in healthcare as patients have little or no drug treatment options. Detection of the prevalence of antibacterial resistance pattern helps towards improved antibiotic policy and empirical treatment. Objectives: We carried out antibiogram profiling and documented the prevalence and co-prevalence of New Delhi metallo-beta-lactamase (NDM) and extended spectrum beta-lactamases (ESBL) encoding genes in urinary Escherichia coli and Klebsiella pneumonia isolates. Materials and Methods: Antibiotic susceptibilities were tested for 241 isolates of E. coli and K. pneumoniae from urine samples collected from out-and hospitalised patients. Polymerase chain reaction (PCR) was carried out on isolates tested positive for phenotypic production of metallo-beta-lactamase and ESBL. A multiplex PCR assay was designed to detect the genes. Results: Multiplex PCR assay designed had a limit of detection of 103 CFU/mL in vitro. NDM detected was significantly higher among K. pneumoniae compared to E. coli (69.2% vs. 18.2%; P = 0.001). Of 17, 14 NDM positive isolates also harboured ESBL genes. The co-production of CTX-M + TEM + NDM (3/9; 33.3% and 5/8; 62.5%) was most common in K. pneumoniae and E. coli, respectively while CTX-M + TEM + SHV + NDM was found in one isolate. Of the 156 phenotypically ESBL producing isolates, CTX-M, TEM and SHV was detected by PCR in 85, 53 and 24 isolates, respectively. Conclusion: NDM and ESBL co-producing isolates were both community (64.7%) and hospital (35.29%) acquired among E. coli. Antibiotic resistance can be effectively evaluated by a cost and time effective molecular method, such as the multiplex PCR used in this study, which complement culture and sensitivity tests.