Genomic analysis of Escherichia coli strains isolated from diseased chicken in the Czech Republic

Abstract

Background: Avian pathogenic Escherichia coli (APEC) can cause various extraintestinal infections in poultry, resulting in massive economic losses in poultry industry. In addition, some avian E. coli strains may have zoonotic potential, making poultry a possible source of infection for humans. Due to its extreme genetic diversity, this pathotype remains poorly defined. This study aimed to investigate the diversity of colibacillosis-associated E. coli isolates from Central European countries with a focus on the Czech Republic. Results: Of 95 clinical isolates subjected to preliminary characterization, 32 were selected for whole-genome sequencing. A multi resistant phenotype was detected in a majority of the sequenced strains with the predominant resistance to β-lactams and quinolones being associated with TEM-type beta-lactamase genes and chromosomal gyrA mutations respectively. The phylogenetic analysis confirmed a great diversity of isolates, that were derived from nearly all phylogenetic groups, with predominace of B2, B1 and C phylogroups. Clusters of closely related isolates within ST23 (phylogroup C) and ST429 (phylogroup B2) indicated a possible local spread of these clones. Besides, the ST429 cluster carried blaCMY-2, -59 genes for AmpC beta-lactamase and isolates of both clusters were generally well-equipped with virulence-associated genes, with considerable differences in distribution of certain virulence-associated genes between phylogenetically distant lineages. Other important and potentially zoonotic APEC STs were detected, incl. ST117, ST354 and ST95, showing several molecular features typical for human ExPEC. Conclusions: The results support the concept of local spread of virulent APEC clones, as well as of zoonotic potential of specific poultry-associated lineages, and highlight the need to investigate the possible source of these pathogenic strains.

Genomic diversity, pathogenicity and antimicrobial resistance of Escherichia coli isolated from poultry in the southern United States

“…Whole genome phylogenic tree shows that the 10 isolates in this study were close to those APEC downloaded from public database. Analysis of the virulence and resistance genes is another important and most used methods for APEC studies [14,52], including genes of adhesins, invasions, protectins, iron acquisition systems, toxins, and resistant to drug. Those genes were found in our 10 isolates.…”

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

“…2 (Plate VIII), WGS is applicable in epidemiologic studies tracing outbreak-associated high-risk sequence types to reveal their transmission routes. Several studies have chosen this complex approach to assess the diversity of APEC isolates (Cordoni et al 2016;Ronco et al 2017;Cummins et al 2019;Rafique et al 2020;Poulsen et al 2020;Papouskova et al 2020). Others have focused on ESBL/AmpC producing E. coli and their spread through the production chain (Daehre et al 2017;Projahn et al 2018;Oikarainen et al 2019) and their presence in poultry products (Pietsch et al 2018).…”