Refining the definition of the avian pathogenic Escherichia coli (APEC) pathotype through inclusion of high-risk clonal groups

Timothy J. Johnson, Elizabeth A. Miller, Cristian Flores-Figueroa, Jeannette Munoz-Aguayo, Carol Cardona, Katie Fransen, Megan Lighty, Eric Gonder, Jill Nezworski, Adam Haag, Michelle Behl, Michelle Kromm, Ben Wileman, Marissa Studniski, Randall S. Singer

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

Colibacillosis in poultry is a unique disease manifestation of Escherichia coli in the animal world, as one of the primary routes of entry is via the respiratory tract of birds. Because of this, a novel extraintestinal pathogenic E. coli (ExPEC) subpathotype coined avian pathogenic E. coli (or APEC) has been described. Like other ExPEC, this pathotype has been challenging to clearly define, and in the case of APEC, its role as an opportunistic pathogen has further complicated these challenges. Using 3,479 temporally matched genomes of poultry-source isolates, we show that the APEC plasmid, previously considered a defining trait of APEC, is highly prevalent in clinical isolates from diseased turkeys. However, the plasmid is also quite prevalent among cecal E. coli isolates from healthy birds, including both turkeys and broilers. In contrast, we identify distinct differences in clonal backgrounds of turkey clinical versus cecal strains, with a subset of sequence types (STs) dominating the clinical landscape (ST23, ST117, ST131, ST355, and ST428), which are rare within the cecal landscape. Because the same clinical STs have also dominated the broiler landscape, we performed lethality assays using strains from dominant STs from clinical or cecal landscapes in embryonated turkey and chicken eggs. We show that, irrespective of plasmid carriage, dominant clinical STs are significantly more virulent than dominant cecal STs. We present a revised APEC screening tool that incorporates APEC plasmid carriage plus markers for dominant clinical STs. This revised APEC pathotyping tool improves the ability to identify high-risk APEC clones within poultry production systems, and identifies STs of interest for mitigation targets.

Original languageEnglish (US)
Article number102009
JournalPoultry science
Volume101
Issue number10
DOIs
StatePublished - Oct 2022

Bibliographical note

Funding Information:
The authors wish the thank the turkey growers of the United States for their participation in this study. The authors also thank Drs. Patrick McDermott and Errol Strain at the US Food and Drug Administration for helpful input regarding this manuscript. This work is supported by Agricultural and Food Research Initiative (AFRI) grants 2018-68003-27464 and 2020-67015-31678 from the USDA National Institute of Food and Agriculture. Bioinformatics was supported using tools available from the University of Minnesota's Minnesota Supercomputing Institute. Additional resources were provided for this study from the Mid-Central Research and Outreach Center in Willmar, Minnesota. The authors declare no conflicts of interest.

Funding Information:
The authors wish the thank the turkey growers of the United States for their participation in this study. The authors also thank Drs. Patrick McDermott and Errol Strain at the US Food and Drug Administration for helpful input regarding this manuscript. This work is supported by Agricultural and Food Research Initiative (AFRI) grants 2018-68003-27464 and 2020-67015-31678 from the USDA National Institute of Food and Agriculture. Bioinformatics was supported using tools available from the University of Minnesota's Minnesota Supercomputing Institute. Additional resources were provided for this study from the Mid-Central Research and Outreach Center in Willmar, Minnesota.

Publisher Copyright:
© 2022 The Authors

Keywords

  • APEC
  • Escherichia coli
  • colibacillosis
  • pathotype
  • poultry

PubMed: MeSH publication types

  • Journal Article

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