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Research Article | 07 Sep 2026

First comprehensive analysis of virulence-associated gene profiles and co-occurrence patterns of avian pathogenic Escherichia coli isolated from chickens in northern Vietnam

Van Truong Le1 ORCID , Quang Lam Truong2 ORCID , Thi Huong Giang Tran1 ORCID , Thi My Le Huynh1 ORCID , Thi Ngoc Vu1 ORCID , Thi Trang Le2 ORCID , and Huu Anh Dang1 ORCID Show more
VETERINARY WORLD | Article No. 1 | pg no. 3864-3882 | Vol. 19, Issue 9 | DOI: 10.14202/vetworld.2026.3864-3882
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ABSTRACT

                      
Background and Aim: Avian pathogenic Escherichia coli (APEC), a major cause of colibacillosis in poultry, possesses diverse virulence-associated genes (VAGs) that contribute to extraintestinal pathogenicity. However, comprehensive information on VAG combinations and co-occurrence patterns among APEC isolates in Vietnam remains limited. This study aimed to characterize VAG prevalence, combination profiles, and co-occurrence patterns in APEC and non-pathogenic E. coli (NPEC) isolates from chickens in northern Vietnam.
Materials and Methods: From August 2023 to August 2025, 515 spleen samples were collected from healthy and non-healthy chickens on 35 commercial poultry farms in Hanoi, Hai Phong, Phu Tho, Bac Ninh, and Thai Nguyen. A total of 200 E. coli isolates were recovered and screened by multiplex polymerase chain reaction for 19 VAGs: fimC, eaeA, papC, tsh, sfa_foc, iucD, iutA, irp2, fyuA, iucA, iroN, vat, hlyA, hlyF, astA, ompT, iss, cva/cvi, and colV. Isolates carrying ≥5 of nine selected APEC-associated VAGs were classified as APEC; the remainder were classified as NPEC. We compared gene prevalence, combination profiles, and pairwise co-occurrence using appropriate statistical tests and Jaccard similarity analysis.
Results: Among 200 isolates, 121 (60.5%) were classified as APEC and 79 (39.5%) as NPEC. APEC isolates most frequently carried hlyF (100%), fimC and iutA (96.7% each), ompT and iucD (95.9% each), iss (90.1%), irp2 (79.3%), and iroN (65.3%). APEC isolates contained up to 19 VAGs, whereas NPEC isolates contained up to 14. Twenty-three distinct VAG combination profiles were identified among APEC isolates, and 103/121 (85.1%) harbored >8 VAGs. In contrast, NPEC isolates displayed 13 less complex profiles containing 3–6 VAGs. Most VAGs were significantly more prevalent in APEC than in NPEC isolates, while papC, fyuA, and eaeA occurred exclusively in APEC. Co-occurrence analyses demonstrated greater complexity and stronger VAG associations among APEC isolates.
Conclusion: APEC isolates from northern Vietnam exhibited extensive VAG diversity and complex co-occurrence patterns distinct from those of NPEC isolates. These findings provide a molecular basis for improved APEC characterization, epidemiological surveillance, and targeted control of poultry colibacillosis.
                      
Keywords: avian pathogenic Escherichia coli, chickens, colibacillosis, gene co-occurrence, northern Vietnam, poultry, virulence-associated genes, virulence profiles.