Prevalence and Characterisation of Antimicrobial Resistance, Virulence Factors and Multilocus Sequence Typing (MLST) of Escherichia coli Isolated from Broiler Caeca

This study was undertaken to determine the effect of bird age and administering either <i>Lactococcus lactis</i> ssp. lactis 1 (LL) or <i>Limosilactobacillus fermentum</i> 1 (LF) in the drinking water on the prevalence of antimicrobial resistance by phenotypic test, multilocus sequence typing (MLST) and virulence genes of <i>Escherichia coli</i> (<i>E. coli</i>) isolated from broiler caeca by whole-genome sequencing (WGS) analysis. Male (Ross 308) day-old chicks (240) were reared for 28 days. Water was provided either untreated (CON) or with LL (10⁷/mL) or LF (10⁷/mL) via a nipple drinker on three days each week during the starter phase (days 1, 3, 5, 7, 9 and 11 d) in eight replicate pens per treatment, with initially ten chicks per pen. One chick from each pen was sacrificed when LL or LF was added to the water, and again on d 14 and 28. There was no evidence that LL and LF had any effect on the prevalence of antimicrobial resistance and virulence genes in <i>E. coli</i> isolates. The population density of <i>Lactobacillus</i> sp. and coliforms decreased with age (<i>p</i> < 0.001). The high resistance of <i>E. coli</i> to ampicillin and tetracycline was maintained throughout the life of the broilers. The prevalence of virulence genes was greatest during the starter phase but declined when birds were 28 days of age (<i>p</i> < 0.05). In birds < 14 d of age, <i>E. coli</i> MLST 457, 1640, 1485 and 155 were dominant, and these carried <i>iuc</i>D, <i>irp</i>2, <i>ast</i>A, <i>iut</i>A and <i>iro</i>N genes. When birds were 28 d of age, MLST 1286, 1112 and 973 predominated, and these carried few virulence genes. This suggests that young birds were more susceptible to putative pathogenic <i>E. coli</i> than older birds. Supporting the development of a healthy microbiome that might control the proliferation of potentially pathogenic <i>E. coli</i> is an area of future research.