Genetic Diversity and Antimicrobial Resistance of Extraintestinal E. coli Populations Pre- and Post-Antimicrobial Therapy on Broilers Affected by Colisepticemia

SIMPLE SUMMARY: Although the use of antimicrobials and the related selection of antimicrobial-resistant (AMR) pathogens are recognized worldwide, limited or no information is available on the effect of the antibiotic treatment on the genetic structure as well as the dissemination and persistence of plasmids carrying AMR genetic determinants. This is of particular interest for bacterial pathogens like Avian Pathogenic Escherica coli (APEC), which have the potential to persist and be transmitted from broilers to humans through the food chain as well as for their AMR genetic determinants, which have the potential to be mobilized and spread. With a genomic approach, results of the present study revealed that during the enrofloxacin treatment of broilers, initial strains of extraintestinal E. coli disappeared, being substituted by new clones. Plasmid-mediated fluoroquinolone resistance did not appear to disseminate or persist among observed genomes, confirming that QRDR mutations rather than plasmids are the main drivers of quinolone resistance. Interestingly, plasmids carrying other AMR genes than quinolone-determinant ones were disseminated and persistent since they were found in different clones both before and after the treatment. The persistence of plasmids without a direct antimicrobial selective pressure, if confirmed with further studies, might give insights on the so-called plasmid paradox. ABSTRACT: The aim of the present study was to investigate the genetic diversity and antimicrobial resistance (AMR) of E. coli during enrofloxacin therapy in broilers affected by colisepticemia. Three unrelated farms with ongoing colibacillosis outbreaks were sampled at day 1 before treatment and at days 5, 10 and 24 post-treatment. A total of 179 E. coli isolates were collected from extraintestinal organs and submitted to serotyping, PFGE and the minimum inhibitory concentration (MIC) against enrofloxacin. PFGE clusters shifted from 3–6 at D1 to 10–16 at D5, D10 and D24, suggesting an increased population diversity after the treatment. The majority of strains belonged to NT or O78 and to ST117 or ST23. PFGE results were confirmed with SNP calling: no persistent isolates were identified. An increase in resistance to fluoroquinolones in E. coli isolates was observed along the treatment. Resistome analyses revealed qnrB19 and qnrS1 genes along with mutations in the gyrA, parC and parE genes. Interestingly, despite a fluoroquinolone selective pressure, qnr-carrying plasmids did not persist. On the contrary, two conjugative AMR plasmid clusters (AB233 and AA474) harboring AMR genes other than qnr were persistent since they were identified in both D1 and D10 genomes in two farms. Further studies should be performed in order to confirm plasmid persistence not associated (in vivo) to antimicrobial selective pressure.