Degree Final Project defended by Irene del Corral Medina

July 20^th, 2023

Escherichia coli is a microorganism found as part of the commensal intestinal microbiota of mammals but can also cause infections with clinical consequences. This bacterium can harbor a large diversity of antimicrobial resistance mechanisms, with the production of extended-spectrum beta-lactamases (ESBL), AmpC beta-lactamases, and carbapenemases being among the most concerning. These enzymes confer resistance to beta-lactams, one of the most widely used antimicrobial families in human and veterinary medicine. The increasing presence of ESBL/AmpC-producing E. coli in humans and animals has led to the need for surveillance and monitoring of this bacterium in different compartments (animals, humans, and the environment). The main objective of this study is to characterize a selection of ESBL/AmpC-producing E. coli strains from samples of production animals, in order to determine the diversity and evolution of their resistance phenotypes and their associated resistance mechanisms. For this purpose, the "ESBL-EC" database from the VISAVET-UCM Center, including information from 2,226 E. coli strains identified as potentially ESBL/AmpC and/or carbapenemase producers, was used. These strains were isolated from cecal content samples of turkey, broiler chicken, pig and cattle between 2014 and 2018. Isolates were classified according to their resistance phenotypes, the complete genome of a selection of isolates was sequenced, and a statistical analysis of the obtained data was performed. The results revealed that a high proportion of isolates (77.7%) exhibited multidrug resistance. Furthermore, the probability of resistance to a particular antibiotic was associated with the host species from which the strain was retrieved (p<0.001), although similar trends were observed for certain antibiotics in cattle-pig and broiler-turkey. The CTX-M family of ESBL genes was the most abundant in the strain collection, although specifically, the blaSHV-12 gene was found in a larger number of isolates. In conclusion, this study shows that the phenotypic and genotypic characteristics of each species are unique but also reveals similarities that could indicate the existence of similar selection phenomena, exposure to common sources of resistant strains, and/or the exchange of isolates between host species