A complex approach to a complex problem: the use of whole-genome sequencing in monitoring avian-pathogenic Escherichia coli – a review

Infections associated with Escherichia coli are responsible for immense losses in poultry production; moreover, poultry products may serve as a source of pathogenic and/or resistant strains for humans. As early as during the first hours of life, commercially hatched chickens are colonized with potentially pathogenic E. coli from the environment of hatcheries. The source of contamination has not been quite elucidated and the possibility of vertical spread of several avian pathogenic E. coli (APEC) lineages has been suggested, making the hatcheries an important node where cross-contamination of chicken of different origin can take place. The recent technological progress makes the method of whole-genome sequencing (WGS) widely accessible, allowing high-throughput analysis of a large amount of isolates. Whole-genome sequencing offers an opportunity to trace APEC and extended-spectrum/plasmid-encoded AmpC beta-lactamasesproducing E. coli (ESBL/pAmpC-E.coli) along the poultry processing chain and to recognize the potential pathways of “epidemicˮ sequence types. Data from WGS may be used in monitoring antimicrobial resistance, comparative pathogenomic studies describing new virulence traits and their role in pathogenesis and, above all, epidemiologic monitoring of clonal outbreaks and description of different transmission routes and their significance. This review attempts to outline the complexity of poultry-associated E. coli issues and the possibility to employ WGS in elucidating them. Avian colibacillosis, sequence types, virulence plasmids, hatcheries, poultry production chain Escherichia coli is an intriguing pathogen of poultry. It contributes to several distinct syndromes, commonly referred to as colibacillosis, a cause of non-negligible losses in poultry industry (Nolan et al. 2013). Different forms of colibacillosis affect all production categories; E. coli is the most common cause of increased first-week mortality in chicken due to yolk-sac-infection and septicaemia with or without omphalitis (Olsen et al. 2012; Poulsen et al. 2017), airsacculitis, polyserositis and septicaemia in broilers (Pourbakhsh et al. 1997) and salpingitis/peritonitis or acute septicaemia in layers (Vanderkerchove et al. 2004). Until recently, colibacillosis had been considered merely an opportunistic infection, secondary to several predisposing factors, such as viral and mycoplasmatal respiratory infections, high ammonium concentrations, environmental stress and immunosuppression (Oyetunde et al. 1978; Nakamura et al. 1992; 1994), although its association with several serogroups (O1, O2, O78) had been acknowledged (Sojka and Carnaghan 1961). However, progress in genotyping methods has revealed that strains implicated in poultry E. coli infections are distinct from common commensals, differing in possession of putative virulence-associated sequences (Rodriguez-Siek et al. 2005; Maturana et al. 2011) and presumably forming a specific pathotype – APEC (avian pathogenic E. coli). Nonetheless, this pathotype remains ill-defined. The inherent genomic plasticity, leading to the extreme diversity of colibacillosis-associated strains, as well as high prevalence and economic importance of colibacillosis make effective ACTA VET. BRNO 2020, 89: 273–282; https://doi.org/10.2754/avb202089030273 Address for correspondence: MVDr. Aneta Papoušková Department of Infectious Diseases and Microbiology Faculty of Veterinary Medicine University of Veterinary and Pharmaceutical Sciences Brno Palackého tř. 1946/1, 612 42 Brno, Czech Republic E-mail: papouskovaa@vfu.cz http://actavet.vfu.cz/