Polyclonal spread of blaCTX-M-15 through high-risk clones of Escherichia coli at a tertiary hospital in Ethiopia.

Abstract Objective The burden of antimicrobial resistance and spread of epidemic clones are rarely reported from low-income countries. We aimed to investigate genome-based epidemiology of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-EC) at a tertiary hospital in Jimma, Ethiopia. Methods Bacteria were isolated from clinical specimens obtained from Jimma Medical Center and subjected to species identification (MALDI-TOF), antibiotic susceptibility testing (disk diffusion), and whole genome sequencing (Illumina HiSeq2500). Genomic data analysis was performed using the Enterobase and Center for Genomic Epidemiology bioinformatics pipelines. A maximum likelihood tree was generated using FastTree/2.1.8 based on SNPs in shared genomic regions to identify transmission clusters. Result E. coli isolates (n=261) were collected from 1,087 single non-repeat clinical specimens over a period of five months in 2016. The prevalence of ESBL-EC was (54.7%, 143/261), and 96% of these isolates were resistant to multiple classes of antibiotics. ESBL-gene blaCTX-M-15 was present in 88.4.% of the isolates (122/138). Genes conferring resistance to aminoglycosides and ciprofloxacin – aac(6’)-Ib-cr (62.3%, 86/138), phenicols - catB3 (56.5%, 78/138), sulfonamides - sul1 (68.1%, 94/138), trimethoprim - dfrA17 (57.9%, 80/138) and macrolides - mph(A) (67.3%, 93/138) were detected. The most prevalent sequence types were ST410 (23%), ST648 (17%), ST131 (10%), and ST167 (7%). Isolates of same sequence type collected from different units of the hospital were highly similar in SNP-analysis. Conclusion A high prevalence of ESBL, and dissemination of blaCTX-M-15 through multiple high-risk clones of E. coli, was detected. The nosocomial spread of multidrug-resistant ESBL-EC within the hospital puts vulnerable patients at risk for difficult-to-treat infections.