Molecular characterization of carbapenemase producing enterobacteria (CPE) isolated from a tertiary care teaching hospital in Sri Lanka and validation of a rapid CPE detection protocol

Abstract

INTRODUCTION: The emergence and spread of carbapenem-resistant Enterobacteriaceae (CRE) is in dramatic increase, resulting in failure of almost all the available antibiotics and hence limit the effective therapeutic options. Therefore, accurate and timely detection of carbapenemase-producing enterobacteria (CPE) is essential to streamline the optimum antibiotic therapy. This study was carried out to determine the current status of CRE in Sri Lanka and to evaluate the performances of CPE detection methods. METHODOLOGY: A cross-sectional study was conducted at Colombo North Teaching Hospital during 2017-2018. Extended-spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-PE) and CRE were identified by the disc diffusion method. CRE isolates were identified up to species level using a rapid identification kit. Four CPE detection methods, namely Carba NP test (CNPt), CNPt-direct, modified carbapenem inhibition method (mCIM), and modified hodge test (MHT) were evaluated. The genetic background of CPE was determined by PCR. RESULTS: The estimated overall prevalence of ESBL-PE and CRE were found to be 26.0% and 9.6%, respectively. The highest prevalence of ESBL-PE and CRE were found amongst uropathogenic (30.8%) and respiratory infections producing (20.8%) Enterobacteriaceae, respectively. K. pneumoniae (80.7%), E.coli (5.3%), C.freundii (7.0%), P. rettgeri (3.5%), E. cloacae (1.7%), and E. aerogenes (1.7%) were identified in CRE cohort. OfCRE, 94.7% were found to be CPE. The carbapenemase encoding genes detected were of blaKPc, blCINDM. and blaoXA-48-Iike and, blaoXA-48-Iike (88.9%) was the most prevalent. The overall sensitivity and specificity of CPE detection tests were as; MHT-90.7%, 92.1%, mCIM- 100%, 100%, CNPt-75.9%, I 00%, and CNPt-direct-83.3%, 100%, respectively. Only amikacin showed reasonable sensitivity (>50%) for CRE among the routine antibiotic panel whereas a higher level of susceptibility was noted for fosfomycin (92.9%), ceftazidime-avibactam (85.9%), and colistin (92.9%). CONCLUSION: K pneumoniae was the most prevalent CRE species. Carbapenemases production was the major resistance mechanism in CRE and b/aoXA-48-like was the most prevalent gene type. The first occurrence of blaKPc was recognized in Sri Lanka. MCIM and MHT had higher sensitivity compared to both CNP tests for the detection of CPE. However, when a prompt decision is needed, CNP tests can be a viable option since their results can be obtained within two hours.