Assessing Carbapenemase Resistant Enterobacteriaceae Prevalence Using a Combined Antibiotic Resistance Gene Assay and Surveillance Cultures in Hospitalized Patients

Abstract

Background. The actual prevalence of carbapenem-resistant Enterobacteriaceae (CRE) in hospitalized patients is unknown. Methods. We performed a cross-sectional CRE prevalence study over 3 days in 2016 at a tertiary care center alongside the city-wide Healthcare Antibiotic Resistance Prevalence- DC Study (HARP DC). Peri-anal swabs were collected from consenting adults. RT-PCR was used to identify the presence of 10 antibiotic resistance associated genes using the Acuitas MDRO Gene Test (OpGen). In parallel, peri-anal swabs were cultured on CRE chromogenic agar medium. Those with microbiologic growth were further tested using the Acuitas Resistome Test (OpGen), which detects up to 46 antibiotic resistance genes. Data was viewed in the Acuitas Lighthouse MDRO Management System (OpGen). Results. A total of 179 of 277 (64.6%) patients participated of which 39.6% were in the ICU, 72.2% had antibiotic exposure within previous 6 months. CRE prevalence using combined culture and molecular testing was 6.1% (11 of 179). Six of 11 (54.6%) had hospitalizations in the past 6 months, 5 of 11 (45.5%) were transferred from an outside hospital or nursing home, 8 of 11 (81.8%) had been in the ICU during the current admission, and the average current length of stay was 39 days. All had antibiotic exposure within the past 6 months with 3 of 11 (27%) to carbapenems, 4 of 11 (36%) to piperacillin/tazobactam, and 6 of 11 (55%) to cephalosporins. MDRO gene screen revealed 8 of 179 (4.5%) had the following CRE genes: 6 KPC alone, 1 KPC/ OXA-23, 1KPC/OXA-48. Growth on the CRE plates occurred in 9 of 179 (5%) with 6 K. pneumonia, 1 C. koseri, 1 E. coli, and 1 E. cloacae. Three of 9 grew only on the CRE plates but had no identifiable CRE genes and were not identified on the MDRO gene screen. Two of 8 identified on the MDRO gene screen did not grow on the CRE plate (1 was KPC and OXA-48 positive and 1 KPC positive). The MIC for imipenem was >16 in 6 specimens (6 of 6 with KPC gene), 3 additional specimens had meropenem MIC = 1 (0 of 3 with KPC gene). Conclusion. We identified over 5% prevalence of CRE colonization using a combined molecular and culture-based approach. Routine surveillance including comprehensive testing with both MDRO gene testing and culture should be considered to identify CRE colonization and help limit the spread of CRE.