Genomic epidemiology of avian pathogenic Escherichia coli in two broiler colibacillosis outbreaks in Finland.

In Finland, notable colibacillosis outbreaks occurred in 2015 and 2021, impacting numerous flocks across the country. Diagnostic examinations of broiler carcasses revealed classical colibacillosis indicators such as polyserositis, cellulitis, and femoral head necrosis. Avian pathogenic Escherichia coli (APEC) isolates were mainly collected from the bone marrow of diseased birds for molecular typing by PCR. Typing was conducted for 375 and 217 APEC isolates from 64 and 91 flocks from the years 2015 and 2021, respectively. Typing consisted of determination of the E. coli phylogeny group, O-serogroup, and eight virulence-associated genes. Two predominant APEC types were detected in the 2015 outbreak and one in the 2021 outbreak. These predominant types were present in the majority of investigated flocks (47 out of 64 flocks (73 %) in 2015 and 75 out of 91 flocks (81 %) in 2021). Subsequent whole-genome sequencing (WGS) analysis of a subset of APEC isolates of these predominant types revealed them to be ST117 O78:H4 and ST117 O53:H4 in 2015 and ST23 O78:H4 in 2021. The isolates represented three distinct clonal lineages with small genetic differences. In addition, APEC isolates belonging to the same clonal lineages were detected in other Nordic countries at the same time. The affected flocks were epidemiologically linked by common ancestral parent and grandparent flocks. This study underscores that certain APEC strains with a high virulence potential can trigger severe colibacillosis outbreaks affecting multiple farms in several countries by vertical transmission from ancestral flocks to offspring. PCR typing emerged as a cost-effective and reliable method for promptly detecting the APEC clonal lineages responsible for colibacillosis outbreaks, and subsequent WGS analysis provided more detailed epidemiological and genetic information. The results of this study could also be used in assessing sampling methods and determining genetic differences between APEC isolates in the diagnosis of potential colibacillosis outbreaks.