Oral and parenteral treatment with a third-generation cephalosporin promotes the proliferation of diverse ESBL-producing <i>Escherichia coli</i> in the chicken intestinal tract

The global rise of antimicrobial resistance is a major public health threat, with <i>Escherichia coli</i> facilitating the spread of extended-spectrum beta-lactamase (ESBL) genes like <i>bla</i>_CTX-M, which confer resistance to third-generation cephalosporins (3GCs). This study examines the impact of 3GC treatment on resistant <i>E. coli</i> clones and horizontal gene transfer (HGT) of ESBL genes in broiler chickens in Quito, Ecuador. Fifteen-day-old Ross broilers were divided into three groups: oral ceftriaxone (100 mg/kg), parenteral ceftriaxone (100 mg/kg intramuscular), and control (no treatment). The study included three phases: baseline, antimicrobial administration (5 days), and recovery (15 days). Fecal cultures on McConkey agar, with and without ceftriaxone (2 µg/mL), measured the ratio of 3GC-resistant lactose fermenters. Regardless of the administration route, ceftriaxone significantly increased resistant coliforms (>80%). Five <i>E. coli</i> colonies per animal and time point were analyzed using single-gene typing, with clonal candidates subjected to whole-genome sequencing. Clonal analysis revealed high genetic diversity, averaging three distinct clones per animal. A unique lineage (H34) emerged exclusively during treatment, and new clones appeared post-treatment. The <i>bla</i>_CTX-M-55 variant was the most abundant ESBL gene, persisting despite fluctuations in other <i>bla</i>_CTX-M variants. Comparative plasmid analysis suggested <i>bla</i>_CTX-M-55 HGT, as plasmids were identified in two genetically distinct <i>E. coli</i> isolates from the same host. Most plasmids belonged to IncFII, with IncX1 and IncN also present. These findings highlight how 3GC treatments rapidly impact ESBL-producing <i>E. coli</i> diversity in the intestine.IMPORTANCEThe global rise of antimicrobial resistance (AMR) poses a critical public health challenge, with <i>Escherichia coli</i> playing a central role in the spread of extended-spectrum beta-lactamase (ESBL) genes like <i>bla</i>_CTX-M, which confer resistance to third-generation cephalosporins (3GCs). This study highlights the significant impact of 3GC treatment on the frequency and diversity of 3GC-resistant <i>E. coli</i> clones and horizontal gene transfer of ESBL genes in the intestinal microbiota of broiler chickens. Understanding how antimicrobial treatments drive resistance dynamics in animal populations is crucial for developing strategies to mitigate AMR in both human and veterinary settings.