Resistance, virulence, and population genomic structure of avian pathogenic Escherichia coli from poultry airsacculitis in South Africa.
- 1Division of Molecular Bacterial Epidemiology & Infectious Diseases, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
- 2V-Tech (Pty) Ltd, Midrand, South Africa; Dunevax Biotech (Pty) Ltd, Windhoek, Namibia.
- 3Division of Molecular Bacterial Epidemiology & Infectious Diseases, Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland. Electronic address: [email protected].
Abstract
A total of 109 avian pathogenic Escherichia coli (APEC) were isolated from poultry with airsacculitis in 21 different farms in South Africa between June 2021 and January 2022. All isolates were sequenced using Illumina technology and one representative strain from each detected sequence type (ST) was sequenced using Oxford Nanopore technology (ONT) to obtain complete genomes for single nucleotide polymorphism (SNP) analysis. Whole genome sequences (WGS) were used for molecular serotyping, sequence typing, virulence and antimicrobial resistance genes detection, core genome multilocus sequence typing (cgMLST)-based phylogeny, and cgSNP. The MICs of 15 antibiotics were tested by broth microdilution. A total of 21 serotypes and 18 STs were detected, with O78:H4-ST117 (n=29), O36:H5-ST5764 (n=10), and O78:H4-ST15549 (n=9) being the most common. Comparative genomic analyses revealed that some strains within the same serotype-ST combinations were genetically closely related (<20 cgSNPs) and were isolated within the same farm and across different farms. Each serotype-ST combination exhibited specific virulence and resistance profiles. Of 172 genes covering 51 virulence factors identified, 15 of them were shared by all strains. Resistance to ampicillin, ciprofloxacin, nalidixic acid, tetracycline, and trimethoprim was most frequent, each occurring in over 50% of the strains. Multidrug resistance to 3-9 antimicrobials was observed in 58.7% of the isolates. Antimicrobial resistance phenotype was associated with the presence of acquired resistance genes and mutations. This study provided an in-depth WGS-based characterization of genomic features revealing a high number of different virulence and antimicrobial resistance genes, also highlighting a possible vertical and horizontal transmission of several APEC lineages in the poultry chain in South Africa.
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BibTeX
@article{wang2026resistance,
title = {{Resistance, virulence, and population genomic structure of avian pathogenic Escherichia coli from poultry airsacculitis in South Africa.}},
author = {Zhuohao Wang and Naima Ameris Guthauser and David Gerber and Vincent Perreten},
journal = {Poultry science},
year = {2026},
month = oct,
doi = {10.1016/j.psj.2026.107885},
url = {https://europepmc.org/article/MED/42892223},
note = {CC BY},
}
RIS
TY - JOUR
TI - Resistance, virulence, and population genomic structure of avian pathogenic Escherichia coli from poultry airsacculitis in South Africa.
AU - Zhuohao Wang
AU - Naima Ameris Guthauser
AU - David Gerber
AU - Vincent Perreten
PY - 2026
DA - 2026/10/05
JO - Poultry science
DO - 10.1016/j.psj.2026.107885
UR - https://europepmc.org/article/MED/42892223
AB - A total of 109 avian pathogenic Escherichia coli (APEC) were isolated from poultry with airsacculitis in 21 different farms in South Africa between June 2021 and January 2022. All isolates were sequenced using Illumina technology and one representative strain from each detected sequence type (ST) was sequenced using Oxford Nanopore technology (ONT) to obtain complete genomes for single nucleotide polymorphism (SNP) analysis. Whole genome sequences (WGS) were used for molecular serotyping, sequence typing, virulence and antimicrobial resistance genes detection, core genome multilocus sequence typing (cgMLST)-based phylogeny, and cgSNP. The MICs of 15 antibiotics were tested by broth microdilution. A total of 21 serotypes and 18 STs were detected, with O78:H4-ST117 (n=29), O36:H5-ST5764 (n=10), and O78:H4-ST15549 (n=9) being the most common. Comparative genomic analyses revealed that some strains within the same serotype-ST combinations were genetically closely related (<20 cgSNPs) and were isolated within the same farm and across different farms. Each serotype-ST combination exhibited specific virulence and resistance profiles. Of 172 genes covering 51 virulence factors identified, 15 of them were shared by all strains. Resistance to ampicillin, ciprofloxacin, nalidixic acid, tetracycline, and trimethoprim was most frequent, each occurring in over 50% of the strains. Multidrug resistance to 3-9 antimicrobials was observed in 58.7% of the isolates. Antimicrobial resistance phenotype was associated with the presence of acquired resistance genes and mutations. This study provided an in-depth WGS-based characterization of genomic features revealing a high number of different virulence and antimicrobial resistance genes, also highlighting a possible vertical and horizontal transmission of several APEC lineages in the poultry chain in South Africa.
SN - 0032-5791
SN - 1525-3171
ER -