Molecular characteristics of carbapenem-resistant Enterobacteriaceae isolated from clinical infection and fecal survey samples in Southern China

Abstract Background: The identified rate of carbapenem-resistant Enterobacteriaceae (CRE) have been increasingly in the clinical infections. Here, a study of analysing the relationship of clinical infectious CRE and fecal carried CRE was performed.Methods: Clinical CRE and fecal CRE were collected from hosiptal in China. Polymerase chain reaction (PCR)-based amplification and sequencing were performed to analyse the carriage of drug-resistant genes and mobile genetic elements (MGEs), Enterobacterial Repetitive Intergenic Consensus (ERIC) technology and whole genome sequencing (WGS) were used to analysis the characteristic of genetic structure of CRE isolates.Results: 99 clinical CRE and 30 fecal CRE were collected, respectively. The top three strains present in the highest proportions were K. pneumoniae (86; 66.67%), E. cloacae (22; 17.05%), and E. coli (11; 8.53%). Most of the isolates were susceptible to colistin (98.45%) and tigecycline (98.45%). blaKPC−2 (96.03%) was the dominant carbapenemase gene in clinical CRE and fecal CRE, followed by blaNDM (52.7%); co-existence of the blaKPC−2 and blaNDM genes was detected in 63 (50.00%) strains. One K. pneumoniae isolate co-producing NDM-5 and mcr-1, and one E. coli isolate co-producing KPC-2, IMP-4, and mcr-1 were detected. Two novel gene cassettes of intI2 were dectected. ERIC genotyping and genomic analysis revealed that K. pneumoniae isolated from clinical infections and fecal survey samples were same clone.Conclusions: This is the first report of comparing the molecular characteristics of CRE isolated from clinical infection and fecal survey samples. we found that fecal carried CRE were closely related to CRE which caused infections.