Occurrence of Colibacillosis in Broilers and Its Relationship With Avian Pathogenic Escherichia coli (APEC) Population Structure and Molecular Characteristics

Ilias Apostolakos; Andrea Laconi; Lapo Mughini-Gras; Özlem Şahan Yapicier; Alessandra Piccirillo

doi:10.3389/fvets.2021.737720

Occurrence of Colibacillosis in Broilers and Its Relationship With Avian Pathogenic Escherichia coli (APEC) Population Structure and Molecular Characteristics

Front Vet Sci. 2021 Sep 8:8:737720. doi: 10.3389/fvets.2021.737720. eCollection 2021.

Authors

Ilias Apostolakos¹, Andrea Laconi¹, Lapo Mughini-Gras^{2

3}, Özlem Şahan Yapicier⁴, Alessandra Piccirillo¹

Affiliations

¹ Department of Comparative Biomedicine and Food Science, University of Padua, Legnaro, Italy.
² Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands.
³ Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands.
⁴ Republic of Turkey Ministry of Agriculture and Forestry Veterinary Control, Central Research Institute, Bacteriology Diagnostic Laboratory, Ankara, Turkey.

Abstract

Avian pathogenic Escherichia coli (APEC) causes colibacillosis, the disease with the highest economic loss for the broiler industry. However, studies focusing on the prevalence and population structure of APEC in the broiler production pyramid are scarce. Here, we used genotyping and serotyping data to elucidate the APEC population structure and its changes in different broiler production stages along with whole-genome sequencing (WGS) in a subset of APEC isolates to determine transmission patterns amongst dominant APEC sequence types (STs) and characterize them in detail. Comparison of genotypes encountered in both APEC and avian fecal E. coli (AFEC) provided further insights. Overall, APEC-related mortality, as the proportion of the total sampled mortality in the broiler production, was high (35%), while phylogroup C and serogroup O78 were predominant amongst APEC isolates. We found a low (34.0%) and high (53.3%) incidence of colibacillosis in chicks and end-cycle broilers, respectively, which may be related to a shift in APEC genotypes, suggesting a trend from commensalism to pathogenicity across different broiler production stages. Despite considerable APEC genotypic diversity, there was substantial genotype overlap (40.9%, overall) over the production stages and convergence of STs to the four clusters. Within these clusters, WGS data provided evidence of clonal transmission events and revealed an enriched virulence and resistance APEC repertoire. More specifically, sequenced APEC were assigned to defined pathotypes based on their virulence gene content while the majority (86%) was genotypically multi-drug resistant. Interestingly, WGS-based phylogeny showed that a subset of APEC, which are cephalosporin-resistant, may originate directly from cephalosporin-resistant AFEC. Finally, exploration of the APEC plasmidome indicated that the small fraction of the APEC virulome carried by IncF plasmids is pivotal for the manifestation of the APEC pathotype; thus, plasmid exchange can promote pathogenicity in strains that are at the edge of the commensal and pathogenic states.

Keywords: IncF plasmid; ST11689; WGS (whole genome sequencing); antimicrobial resistance (AMR); avian fecal Escherichia coli (AFEC); avian pathogenic E. coli (APEC); broiler-chicken; colibacillosis.