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Background <p>Colibacillosis is an important epidemiological and economic issue in poultry farming and breeding. A common problem with avian pathogenic <i>Escherichia coli</i> strains (APEC) that cause this disease is a lack of an uniform identification system, resulting from a variety of serotypes, phylogenetic groups, sequence types and combinations of virulence factors. There are no clearly defined features that can be associated with pathogenicity. Therefore, without precise identification of pathogenic strains and differentiation from commensal strains, there is no possibility of appropriate selection of targeted therapy.</p> <p>The widespread use of whole genome sequencing (WGS) in recent years creates new possibilities in diagnostics. Therefore, the purpose of this study was to select features defining the APEC pathotype, based on next generation sequencing (NGS), and design a diagnostic test based on selected factors.</p> Results <p>A PCR diagnostic test is proposed. Three predictors of virulence were chosen according to in silico analysis: two virulence genes: <i>iroC</i> and <i>hlyF,</i> as well as one molecular marker of O78 serotype (<i>wzx</i>—O-antigen flippase of the O78 serotype). A choice of markers was supported by a chicken embryo model.</p> Conclusions <p>Whole genome sequencing of <i>E. coli</i> genomes allowed for the development of a rapid diagnostic method identifying pathogenic strains for poultry: APEC. The developed test can support field observations connected with the strain isolation source and clinical symptoms of the disease.</p>

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A rapid detection of Avian Pathogenic Escherichia coli (APEC) strains based on minimal number of virulence markers identified by whole genome sequencing

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年3月17日

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  • Joanna Kazimierczak,
  • Karolina Pospiech,
  • Patrycja Sowińska,
  • Anna Pękala,
  • Paulina Borówka,
  • Ewelina A. Wójcik,
  • Błażej Marciniak,
  • Marcin W. Lis,
  • Dominik Strapagiel,
  • Jarosław Dastych

摘要

Background

Colibacillosis is an important epidemiological and economic issue in poultry farming and breeding. A common problem with avian pathogenic Escherichia coli strains (APEC) that cause this disease is a lack of an uniform identification system, resulting from a variety of serotypes, phylogenetic groups, sequence types and combinations of virulence factors. There are no clearly defined features that can be associated with pathogenicity. Therefore, without precise identification of pathogenic strains and differentiation from commensal strains, there is no possibility of appropriate selection of targeted therapy.

The widespread use of whole genome sequencing (WGS) in recent years creates new possibilities in diagnostics. Therefore, the purpose of this study was to select features defining the APEC pathotype, based on next generation sequencing (NGS), and design a diagnostic test based on selected factors.

Results

A PCR diagnostic test is proposed. Three predictors of virulence were chosen according to in silico analysis: two virulence genes: iroC and hlyF, as well as one molecular marker of O78 serotype (wzx—O-antigen flippase of the O78 serotype). A choice of markers was supported by a chicken embryo model.

Conclusions

Whole genome sequencing of E. coli genomes allowed for the development of a rapid diagnostic method identifying pathogenic strains for poultry: APEC. The developed test can support field observations connected with the strain isolation source and clinical symptoms of the disease.