Identification of β-Lactamase-Encoding (bla) Genes in Phenotypically β-Lactam-Resistant Escherichia coli Isolated from Young Calves in Belgium

The bla genes identification present in 94 phenotypically resistant Escherichia coli isolated from feces or intestinal contents of young calves with diarrhea or enteritis in Belgium was performed by microarrays (MA) and whole genome sequencing (WGS). According to their resistance phenotypes to 8 beta-lactams at the disk diffusion assay these 94 E. coli produced a narrow-spectrum-beta-lactamase (NSBL), an extended-spectrum-beta-lactamase (ESBL) or a cephalosporinase (AmpC). All ESBL-encoding genes identified by MA and WGS belonged to the bla(CTX-M) family, with a majority to the bla(CTX-M-1) subfamily. Two different genes encoding an AmpC, bla(CMY-2), and bla(DHA-1) were detected in isolates with an AmpC phenotype. The bla(TEM-1) and the bla(OXA-1) were detected alone in isolates with a NSBL phenotype or in combination with ESBL-/AmpC-encoding bla genes. Furthermore, the WGS identified mutations in the ampC gene promoter at nucleotides -42 (C>T) and/or -18 (G>A) that could not be identified by MA, in several isolates with an AmpC-like resistance phenotype. No carbapenemase-encoding gene was detected. To our knowledge this is the first survey on the identification of bla genes in E. coli isolated from young diarrheic or septicemic calves in Belgium.