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.
Highlights
Escherichia coli is a commensal facultative anaerobic microorganism that inhabits the lower gastrointestinal tract of mammals and birds shortly after birth and acts as a symbiont involved in the synthesis of necessary vitamins for their hosts [1]
144 dead broilers were subjected to post-mortem examination and 50 thereof (35.0%, 95% confidence intervals (95% CI) 20.4–53.0%) were found having typical lesions of colibacillosis and E. coli isolates were recovered from their organs
A high prevalence of colibacillosis across the broiler production pyramid was found in this study, with approximately one in three deaths being attributable to avian pathogenic E. coli (APEC)-related infections
Summary
Escherichia coli is a commensal facultative anaerobic microorganism that inhabits the lower gastrointestinal tract of mammals and birds shortly after birth and acts as a symbiont involved in the synthesis of necessary vitamins for their hosts [1]. A subset of the latter group, avian pathogenic E. coli (APEC), is a important pathotype for the broiler industry since it causes colibacillosis, a disease with significant economic losses due to the mortality and/or reduced productivity of affected birds. Clinical APEC isolates recovered from cases of colibacillosis are far from limited to these characteristics and usually show exceptional diversity between countries and even within the same flock or disease outbreak, representing a challenge for the prompt diagnosis and prevention of the disease [5]. The VG content of APEC (and ExPEC) is an additional conundrum since specific virulence determinants have not been explicitly associated with colibacillosis and some of those more frequently identified in pathogenic isolates have been recovered from their commensal counterparts (i.e., avian fecal E. coli, AFEC). These findings highlight our incomplete understanding of this important pathotype [8]
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