A molecular epidemiological study on Escherichia coli in young chicks with colibacillosis identified two possible outbreaks across farms.

Avian pathogenic Escherichia coli (APEC) is the cause of colibacillosis outbreaks in young poultry chicks, resulting in acute to peracute death. The high morbidity and mortality caused by colibacillosis results in poor animal welfare, reduced sustainability and economical loss worldwide. To advance the understanding of the molecular epidemiology, genomic relatedness and virulence traits of APEC, we performed systematic sampling from 45 confirmed colibacillosis broiler flocks with high first week mortality (FWM) during 2018-2021. From these flocks, 219 APEC isolates were whole genome sequenced (WGS) and bioinformatic analyses were performed. The bioinformatic analyses included sequence typing (ST), serotyping, detection of virulence-associated genes (VAGs) and phylogenetic analysis. Our results showed a high prevalence of ST23, ST429 and ST95 among APEC isolates from Norwegian broiler flocks, and identified ST23, ST429, ST117 and ST371 to cause disease more often alone, compared to ST95, ST69 and ST10. Phylogenetic analyses, together with associated metadata, identified two distinct outbreaks of colibacillosis across farms caused by ST429 and ST23 and gave insight into expected SNP distances within and between flocks identified with the same ST. Further, our results highlighted the need for combining two typing methods, such as serotyping and sequence typing, to better discriminate strains of APEC. Ultimately, systematic sampling of APEC from multiple birds in a flock, together with WGS as a diagnostic tool is important to identify the disease-causing APEC within a flock and to detect outbreaks of colibacillosis across farms.

High sequence similarity between avian pathogenic E. coli isolates from individual birds and within broiler chicken flocks during colibacillosis outbreaks.

Avian pathogenic E. coli (APEC) cause high first week mortality (FWM) in broiler chickens worldwide. In order to investigate the epidemiologic aspects of colibacillosis in broiler flocks it is important to develop reliable and cost-effective sampling guidelines. In this context, it is particularly important to define the minimum number of samples required to reliably identify the causative APEC clone during outbreaks of colibacillosis. This study describes the diversity of E. coli isolates between and within three flocks with high FWM due to colibacillosis. Each flock was represented by five animals, showing typical lesions of colibacillosis, and spleen, liver and one other organ from each animal was sampled for APEC. A total of 47 E. coli isolates, one per organ, and approximately 15 isolates per flock were whole genome sequenced and compared by multilocus sequence typing (MLST), serotyping and phylogenetic analysis to deduce their relationship. The results revealed that within individual birds there was little or no sequence type (ST) or serotype diversity between APEC isolates from different organs. Based on phylogenetic analysis, isolates belonging to the same ST and serotype showed a low number of single nucleotide polymorphisms (SNPs) across more than 95 % of the genome. Isolates from the liver always represented the major disease-causing APEC in individual birds, even when more than one ST was detected within an individual bird and flock. This study guides us towards an economically efficient way of sampling for future epidemiological studies on colibacillosis, by determining the causative APEC-clone at flock level.