Section: Avian Bacteria

Antimicrobial Resistance in Avian Pathogenic E. coli: Mechanisms and Alternative Therapies

Introduction

Avian pathogenic Escherichia coli (APEC) is a major cause of colibacillosis in poultry, resulting in significant economic losses and welfare concerns globally. APEC strains harbor a diverse arsenal of virulence factors and antimicrobial resistance (AMR) determinants. The emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) APEC lineages has rendered conventional antibiotic therapy increasingly ineffective. This article provides a detailed examination of the molecular mechanisms underlying AMR in APEC, focusing on extended-spectrum beta-lactamases (ESBLs), AmpC beta-lactamases, and plasmid-mediated colistin resistance mediated by mcr genes. In addition, we critically evaluate alternative therapeutic strategies including bacteriophage therapy, probiotic administration, phytobiotic compounds, and immunomodulatory approaches. The discussion is framed within a One Health context, recognizing the zoonotic potential of APEC and its role as a reservoir of resistance genes.

Avian Pathogenic Escherichia coli (APEC) represents a pathotype of extraintestinal pathogenic E. coli (ExPEC) that causes respiratory and systemic infections in chickens, turkeys, and other avian species. The pathotype is distinguished by the presence of specific virulence-associated genes such as iroN, iss, iucD, and tsh [15]. The iroN gene, encoding a catecholate siderophore receptor, is frequently detected in MDR APEC isolates from poultry and has been proposed as a marker for pathogenic potential [15]. Comprehensive genomic characterization of APEC isolates has revealed a high degree of genetic diversity and the presence of clinically relevant resistance determinants [12].

Mechanisms of Antimicrobial Resistance

Extended-Spectrum Beta-Lactamases and AmpC Beta-Lactamases

ESBLs, particularly CTX-M, SHV, and TEM types, hydrolyze oxyimino-cephalosporins and monobactams, rendering third-generation cephalosporins ineffective. Plasmid-mediated AmpC beta-lactamases (e.g., CMY-2) confer resistance to cephamycins and are often co-transferred with ESBL genes. A systematic review and meta-analysis of ESBL-producing E. coli in food-producing animals, including poultry, found high prevalence rates in Nigeria and other regions, emphasizing the need for surveillance [6]. Co-existence of blaCTX-M and mcr-1 in APEC has been documented, with strains from Southern Xinjiang demonstrating a wide array of AMR genes on conjugative plasmids [11]. The genomic characterization of an XDR APEC strain revealed an accumulation of resistance determinants including blaCTX-M-55, blaTEM-1B, blaCMY-2, and mcr-1, illustrating the convergence of resistance mechanisms in a single isolate [9].

Plasmid-Mediated Colistin Resistance (mcr Genes)

Colistin (polymyxin E) has been a last-resort antibiotic for treating MDR Gram-negative infections. The emergence of plasmid-mediated colistin resistance via mcr genes (mcr-1 to mcr-10) threatens its efficacy. In poultry, mcr-1 is the most commonly reported variant. The mcr-1 gene encodes a phosphoethanolamine transferase that modifies the lipid A moiety of lipopolysaccharide, reducing colistin binding. Co-occurrence of mcr-1 with ESBL genes on the same plasmid facilitates co-selection under beta-lactam pressure [11]. Retail meat studies have confirmed the presence of mcr-positive E. coli of high priority critical importance, underscoring the foodborne transmission risk [13].

Other Resistance Mechanisms and Virulence-Resistance Linkage

APEC isolates often co-carry genes for resistance to tetracyclines (tet), sulfonamides (sul), aminoglycosides (aac, aph), and fluoroquinolones (mutations in gyrA and parC). The toxin-antitoxin system ecnAB modulates APEC virulence by regulating capsular sialic acid biosynthesis, and its presence is associated with increased resistance to host immune clearance [8]. The ecnAB system also affects biofilm formation and may contribute to persistence in antibiotic-treated flocks. Clinical and non-clinical E. coli from chickens exhibit overlapping AMR patterns, indicating that commensal strains can serve as reservoirs for resistance genes and that the distinction between pathogenic and non-pathogenic is increasingly blurred [10].

Surveillance and Genomic Approaches

Whole-genome sequencing (WGS) has become the gold standard for characterizing APEC AMR. Resistome profiling using short-read or long-read sequencing allows identification of known resistance genes and plasmid replicons. APEC has been proposed as a sentinel organism for AMR surveillance in poultry production systems [12]. Genomic surveillance data from retail meat have identified high-risk clones (e.g., ST131, ST10) carrying ESBL and mcr genes, which are shared between poultry and human clinical isolates [13]. Pet birds, including psittacines, are also potential reservoirs of AMR bacteria in digestive and respiratory tracts, highlighting the need for a comprehensive surveillance strategy [4]. In subtropical environments, livestock including poultry harbor significant AMR burdens, with environmental contamination contributing to dissemination [5].

Alternative Therapies

Bacteriophage Therapy

Phage therapy employs lytic bacteriophages to specifically infect and lyse APEC. A key advantage is the ability to target MDR strains without disrupting the normal gut microbiota. However, the presence of temperate bacteriophages in APEC genomes is a concern, as they may carry virulence or resistance genes. Genomic characterization of temperate phages from Brazilian poultry APEC revealed the presence of integrases, recombinases, and potential cargo genes that could enhance bacterial fitness [14]. For therapeutic applications, strictly lytic phages are preferred. Phage cocktails targeting multiple receptors can mitigate the emergence of phage-resistant mutants. In vivo studies in broiler chickens have shown that phage administration reduces APEC colonization and mortality, although efficacy depends on timing, dose, and delivery route.

Probiotics and Gut Homeostasis

Probiotics, particularly Lactobacillus and Bacillus species, compete with APEC for adhesion sites, produce antimicrobial peptides (bacteriocins), and stimulate the host immune response. The administration of probiotics can enhance phagocytic capacity of macrophages and heterophils in layer chickens, thereby reducing antibiotic dependence [2]. Alterations in gut microbiota composition induced by probiotics or prebiotics can limit APEC expansion. Network pharmacology studies of Sihuang Zhili Granules, a traditional Chinese medicine formulation, demonstrated protective effects against APEC O78 challenge by restoring gut homeostasis-related metabolic pathways [7]. This suggests that modulation of the intestinal environment is a viable strategy for controlling APEC infections.

Phytobiotics and Plant Extracts

Plant-derived compounds offer a rich source of antimicrobial and immunomodulatory agents. Myrmecodia sp. extract has been investigated for its effects on APEC-infected broilers. Comparative studies found that Myrmecodia extract and infusion improved organ function biomarkers and lipid metabolism while reducing meat lipid peroxidation, without adverse effects on growth performance [1]. The active phytochemicals, including flavonoids and tannins, may act by disrupting bacterial cell membranes and inhibiting quorum sensing. Standardization of extraction protocols and dosing remains a challenge for commercial application.

Vaccines and Immunomodulation

Vaccination is a cornerstone of APEC control. Traditional bacterins and subunit vaccines have been developed, but efficacy is often limited by serotype diversity. Recent advances include epitope-based and peptide-based vaccines designed using reverse vaccinology and machine learning. A meta-analysis of epitope-based vaccines against APEC identified conserved outer membrane proteins (e.g., OmpA, OmpC, OmpW) as promising targets [3]. Machine learning algorithms predicted immunodominant epitopes that elicit both humoral and cellular responses. In ovo vaccination with peptide cocktails is being explored for early protection. Immunostimulants, such as beta-glucans and CpG oligonucleotides, can enhance phagocytic activity and reduce the severity of colibacillosis [2]. The integration of vaccine strategies with immune profiling using flow cytometry and cytokine assays can inform vaccine design.

Decision Tree for Alternative Therapy Selection

graph TD
    A[APEC outbreak confirmed?], > B{Antimicrobial susceptibility test available?}
    B, >|Yes| C[Identify resistance profile]
    B, >|No| D[Empiric therapy based on regional AMR data]
    C, > E{Effective antibiotics exist?}
    D, > E
    E, >|Yes| F[Use narrow-spectrum antibiotic with stewardship]
    E, >|No| G[Consider alternatives]
    G, > H[Phage therapy: select lytic phages from local bank]
    G, > I[Probiotic + phytobiotic combination]
    G, > J[Vaccination with multi-epitope peptide]
    H & I & J, > K[Monitor clinical response and gut microbiota]
    K, > L{Response adequate?}
    L, >|No| M[Adjust phage cocktail or probiotic strain]
    L, >|Yes| N[Continue management]

Diagnostic Considerations

Accurate identification of APEC and its resistance profile is essential for guiding therapy. Traditional culture and disk diffusion are complemented by molecular methods such as polymerase chain reaction (PCR) for resistance genes and WGS for detailed characterization. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) provides rapid species identification and can detect some resistance markers. For field application, loop-mediated isothermal amplification (LAMP) assays targeting mcr-1 and blaCTX-M are being developed. The integration of these diagnostics with farm management data supports evidence-based decision making.

One Health Implications

APEC AMR is not confined to poultry. Resistant E. coli can be transmitted to humans through direct contact, food consumption, and environmental contamination. The presence of identical resistance plasmids in poultry and human isolates indicates horizontal gene transfer across hosts. Companion birds, including pet psittacines, represent an underrecognized reservoir of AMR bacteria that may bridge household environments and poultry operations [4]. A One Health approach that integrates surveillance across humans, animals, and the environment is critical. Computational modeling of AMR dissemination using genomic and epidemiological data can identify transmission hotspots and inform intervention strategies.

Future Directions

Continued genomic surveillance is needed to track the emergence of novel resistance genes and high-risk clones in APEC. Research on alternative therapies should prioritize rigorous in vivo efficacy trials with standardized endpoints. For phage therapy, the development of stable, regulatory-approved phage cocktails and understanding of phage-bacterium coevolution are necessary. Probiotic formulations should be optimized for poultry production systems, considering compatibility with feed and water additives. Phytobiotics require standardization of bioactive compounds and toxicological assessment. Advances in bioinformatics, including machine learning for epitope prediction and foundation models for protein function prediction, will accelerate vaccine and drug discovery. Finally, antimicrobial stewardship programs in poultry must be strengthened, with emphasis on preventive measures such as biosecurity and flock management.

References

  1. Lisnanti EF, Lokapirnasari WP, Arif MAA, et al. Comparative effects of Myrmecodia sp. extract and infusion on organ function biomarkers, lipid metabolism, and meat lipid profile in avian pathogenic Escherichia coli-infected broiler chickens: Implications for sustainable poultry production within a One Health framework. Vet World. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42245456/

  2. Liu S, Cao J, Wang S, et al. Enhancing phagocytic capacity in layer chickens: a one health approach to sustainable production through improved disease resistance and reduced antibiotic dependence. Front Vet Sci. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42221954/

  3. Waseem M, Kamran Z, Ali A. Advancing poultry health: A meta-analysis of epitope-based and peptide-based vaccines against Avian Pathogenic E. coli with machine learning insights. PLoS One. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42201941/

  4. Crăciun S, Turcu MC, Novac CŞ, et al. Pet Birds as Potential Reservoirs of Antimicrobial-Resistant Bacteria in Digestive and Respiratory Infections. Antibiotics (Basel). 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42192709/

  5. Kanwal B, Asif E, Kalhoro NH, et al. Prevalence of Antimicrobial-Resistant Bacterial Pathogens Among Livestock in Subtropical Environments. Antibiotics (Basel). 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42192683/

  6. Yakubu Y, Gaddafi MS, Hassan UL, et al. Systematic Review and Meta-Analysis of Extended-Spectrum Beta-Lactamase-Producing (ESBL) Escherichia coli in Food-Producing Animals and Animal Products in Nigeria. Antibiotics (Basel). 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42192654/

  7. Guo Z, Wang X, Cai D, et al. Integrative analysis of 16S rRNA sequencing and network pharmacology suggests protective effects of Sihuang Zhili Granules against APEC O78 challenge through gut homeostasis-related changes. Front Vet Sci. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42164768/

  8. Jing Y, Shen X, Yin D, et al. The ecnAB toxin-antitoxin system modulates avian pathogenic Escherichia coli virulence through regulating the capsular sialic acid biosynthesis pathway. Vet Microbiol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42160786/

  9. Ni W, Chen L, Chen H, et al. Genomic and Pathogenic Characterization of an Extensively Drug-Resistant Avian Pathogenic Escherichia coli Strain. Transbound Emerg Dis. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42147456/

  10. de Souza Campos MR, Dias TS, Gonçalves VD, et al. Clinical and non-clinical Escherichia coli from chickens reveal antimicrobial resistance patterns of one health concern. Comp Immunol Microbiol Infect Dis. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42119341/

  11. Yang B, Xing G, Ma W, et al. Co-existence of blaCTX-M and mcr-1 in avian pathogenic Escherichia coli in Southern Xinjiang: current status and antimicrobial resistance characteristics. Folia Microbiol (Praha). 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42090104/

  12. Gaonkar PP, Golden R, Santana-Pereira ALR, et al. Genomic characterization of avian pathogenic Escherichia coli and its potential as a marker organism for antimicrobial resistance. Appl Environ Microbiol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42080571/

  13. Nievas HD, Aurnague C, Helman E, et al. Genomic Diversity and Virulence Potential of High-Priority Critically Important Antimicrobial-Resistant Escherichia coli from Pork and Chicken Retail Meat. Pathogens. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42075768/

  14. Cadamuro RD, Pilati GVT, Elois MA, et al. Genome Characterization of Temperate Bacteriophages and Associated Genetic Features in Avian Pathogenic Escherichia coli from Brazilian Poultry. Animals (Basel). 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42071930/

  15. Keytimu MO, Rahayu U, Wibisono FJ, et al. Detection of the iroN virulence gene in multidrug-resistant Escherichia coli isolated from quails in traditional markets of Surabaya, Indonesia. Vet World. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42046676/