Genomic and Phenotypic Characterisation of Multi-Drug ResistantEscherichia coli carried by meat handlers and slaughterhouse meat from North-Western Tanzania

Our research is part of a larger project Supporting the National Action Plan on Antimicrobial Resistance (SNAP-AMR) in Tanzania. The aspect of this work is to determine the AMR carriage and associated mobile genetic elements of extended spectrum β-lactamase (ESBL) producing Escherichia coli within the community of Mwanza, in North-Western Tanzania. From 54 slaughterhouses a total of 322 E. coli isolates were obtained from raw meat, with 210 originating from meat handlers. Initial antimicrobial susceptibility testing identified 71 (22%) and 27 (13%) of the meat and meat handler isolates, respectively, as being ESBL E. coli. ST2852 was the most abundant MLST, followed by globally disseminated and ESBL associated ST38. Whole genome sequencing and phenotypic analysis revealed 88% of our isolates were resistant to three or more antimicrobial classes. On average, our isolates carried at least 10 different AMR associated genes, with 80% having one or more AMR conferring chromosomal mutation. In relation to ESBL, 88 out of 98 of the isolates carried the globally disseminated allotype blaCTX-M-15, with over 55% of the isolates encoding blaCTX-M-15on multi-drug resistant (MDR) plasmids. The remaining strains encoded one of three different blaCTX-Mallotypes. Our data highlights high prevalence of MDR ESBL E. coli within the community and its potential risk of transmission through the food chain. In our future work, we will combine these community carriage data with our work on ESBL Enterobacteriaceae carriage and infection within healthcare settings, to evaluate the genomic epidemiology of ESBL organisms in this region.