Section: Avian Bacteria

Antimicrobial Resistance in Poultry: Current Status and Alternative Strategies

Introduction

Antimicrobial resistance (AMR) represents a critical challenge to global poultry production, undermining the efficacy of therapeutic and prophylactic antibiotic use. The selective pressure exerted by intensive farming practices, including subtherapeutic administration of growth promoters, has accelerated the emergence and dissemination of resistant bacterial populations within poultry flocks. These resistant bacteria, including extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli, fluoroquinolone-resistant Campylobacter species, and methicillin-resistant Staphylococcus aureus (MRSA), can persist along the food chain and contaminate poultry products, posing risks within a One Health framework. This review examines the current status of AMR among key poultry pathogens and evaluates alternative strategies, including probiotics, bacteriophages, essential oils, and vaccination, to reduce reliance on conventional antibiotics.

Current Status of Antimicrobial Resistance in Poultry

ESBL-producing Escherichia coli

Avian pathogenic Escherichia coli (APEC) causes colibacillosis, a major economic burden in broiler and layer operations. ESBL-producing APEC strains have been increasingly reported worldwide, with CTX-M-type enzymes predominating. Plasmid-mediated horizontal transfer of blaCTX-M genes is a primary dissemination mechanism. Sheng et al. [10] documented the prevalence of blaCTX-M genes in Salmonella isolates from retail chicken and pork meats in China, demonstrating both plasmid transmission and chromosomal integration events. Such genetic mobility facilitates the spread of resistance across bacterial species within the poultry gut microbiome.

Subinhibitory concentrations of polyether ionophores, commonly used as anticoccidials, can enhance plasmid transfer. Yang et al. [8] showed that ionophore exposure transiently perturbed the broiler gut resistome and increased the frequency of resistance plasmid conjugation. This finding highlights unintended consequences of in-feed additives on AMR dynamics.

Campylobacter Species

Campylobacter jejuni and Campylobacter coli are leading causes of foodborne gastroenteritis, and poultry serves as a major reservoir. Fluoroquinolone resistance in Campylobacter is well established, largely driven by the use of enrofloxacin in poultry. Macrolide resistance, although less frequent, is emerging. Surveillance programs that integrate culture-based methods with molecular techniques are essential for monitoring resistance trends. Otto et al. [1] compared culture, long-read metagenomics, and recombinase polymerase amplification for detecting respiratory bacteria and AMR determinants in feedlot cattle; analogous approaches are being adapted for poultry Campylobacter surveillance.

Other Pathogens

Salmonella enterica serovars, including Typhimurium and Enteritidis, frequently carry multidrug resistance determinants. Zhang et al. [3] conducted seasonal surveillance of Salmonella prevalence and AMR in chickens from slaughterhouses and retail markets in Northeast Thailand, revealing high rates of resistance to tetracyclines and sulfonamides. In South Korea, a 12-year nationwide study by Lee et al. [9] characterized MRSA from livestock carcasses, including poultry, identifying livestock-associated lineages with resistance to beta-lactams and tetracyclines.

Linezolid, a critically important antibiotic for human medicine, has been used sparingly in poultry, yet non-susceptible Enterococcus spp. have been recovered. Kerek et al. [4] phenotypically and genomically characterized linezolid non-susceptible, multidrug-resistant Enterococcus from poultry in Hungary, identifying mutations in 23S rRNA and acquisition of the cfr gene. The detection of the mobilized colistin resistance gene mcr-1.1 in Salmonella Kentucky ST198 from a captive houbara bustard in the United Arab Emirates, with genetic links to local broiler poultry, underscores the transboundary spread of resistance [13].

Residues of antibiotics in poultry meat further compound the issue. Bhatta et al. [15] detected tetracycline and colistin residues in broiler meat samples from Nepal, indicating ongoing non-compliant usage.

Diagnostic Surveillance

Accurate AMR surveillance relies on robust diagnostic methods. For example, Jimenez et al. [5] described a European ring test for differentiating wild-type Mycoplasma synoviae from the MS-H vaccine strain, employing real-time PCR and high-resolution melt analysis. Similar molecular tools can discriminate resistant from susceptible bacterial subpopulations. Antimicrobial usage data from farms, as reported by Silwamba et al. [12] in Zambian broiler flocks, complement laboratory surveillance to identify drivers of resistance.

Alternative Strategies to Reduce Antimicrobial Use

Given the accelerating AMR crisis, a range of non-antibiotic interventions has been investigated to maintain poultry health and productivity. These strategies target pathogen exclusion, immune modulation, and direct antimicrobial activity.

Probiotics and Paraprobiotics

Probiotics are live microorganisms that confer health benefits by competing with pathogens, enhancing gut barrier function, and modulating immune responses. Lactobacillus, Bacillus, and Enterococcus species are commonly used. Wang et al. [11] conducted a comprehensive review of paraprobiotics (inactivated probiotic cells) in modern broiler production, emphasizing their stability, safety, and multifunctional benefits, including improved growth performance and reduced intestinal pathogen load.

Liu et al. [7] demonstrated that dietary supplementation with specific probiotics enhanced phagocytic capacity in layer chickens, improving disease resistance and reducing antibiotic dependence. This approach aligns with sustainable production objectives.

Bacteriophages

Bacteriophages offer highly specific lytic activity against bacterial pathogens. Phage cocktails targeting E. coli and Campylobacter have shown efficacy in reducing colonization in poultry. Phage therapy can be administered via drinking water or feed. Advantages include self-limiting replication, minimal disruption to commensal microbiota, and the ability to target antibiotic-resistant strains. Challenges include narrow host range, requirement for periodic cocktail updates, and potential immune clearance.

Essential Oils and Phytobiotics

Plant-derived compounds, including essential oils and extracts, possess antimicrobial and anti-inflammatory properties. Lisnanti et al. [2] evaluated the effects of Myrmecodia sp. extract and infusion on organ function biomarkers and meat lipid profiles in APEC-infected broiler chickens. The phytobiotic treatment improved lipid metabolism and meat quality while reducing infection-induced organ damage, suggesting a role as an antibiotic alternative.

Kober et al. [6] investigated the antibacterial and cytotoxic activities of five hop (Humulus lupulus) isolates. They observed mixture-dependent correlation patterns; specific hop fractions exhibited potent activity against Gram-positive poultry pathogens, though cytotoxicity to host cells requires careful dose optimization.

Vaccination

Vaccination against key poultry pathogens reduces the need for therapeutic antibiotics. For APEC, both bacterins and recombinant vaccines have been developed. Waseem et al. [14] performed a meta-analysis of epitope-based and peptide-based vaccines against APEC, incorporating machine learning insights to predict immunogenic epitopes. Such computational approaches accelerate vaccine design and can target conserved virulence factors across multiple serotypes.

Other vaccines, including live attenuated Salmonella vaccines and autogenous vaccines for E. coli, are used in the field. Vaccination programs should be integrated with biosecurity and management practices to maximize efficacy.

Diagnostic and Intervention Workflow

A structured decision framework for implementing alternative strategies is presented in the Mermaid diagram below. The workflow begins with sample collection from poultry flocks, followed by pathogen isolation and AMR phenotyping. Genomic characterization (e.g., whole-genome sequencing, plasmid typing) informs the selection of targeted alternatives. Probiotics, bacteriophages, or essential oils can be deployed based on pathogen profile, while vaccination is recommended for recurring infections.

flowchart TD
    A[Sample Collection from Poultry Flocks], > B{Pathogen Isolation}
    B, >|Positive| C[AMR Phenotyping & Genotyping]
    C, > D{Resistance Pattern}
    D, >|ESBL/MDR| E[Consider Bacteriophages or Phytobiotics]
    D, >|Susceptible| F[Antibiotic Therapy if needed]
    D, >|Recurring| G[Vaccination Program]
    B, >|No Pathogen| H[Probiotic Maintenance]
    E, > I[Monitor Clinical Outcome & AMR]
    G, > I
    H, > I
    I, > A

Regular monitoring of AMR trends using both phenotypic and genomic methods is necessary to adapt intervention strategies. Data integration platforms, such as those described in Cloud-Based Diagnostic Data Integration for Herd Health Management, facilitate real-time decision-making.

Conclusion

Antimicrobial resistance in poultry is a multifactorial problem driven by antibiotic usage patterns, microbial genetics, and farm management practices. ESBL-producing E. coli and Campylobacter remain priority targets for intervention. Alternative strategies, including probiotics, paraprobiotics, bacteriophages, essential oils, and vaccination, offer viable tools to reduce antibiotic dependence. Their successful implementation requires rigorous diagnostic surveillance, evidence-based selection, and ongoing evaluation. An integrated One Health approach, combining these alternatives with improved biosecurity and husbandry, is essential for sustainable poultry production and the preservation of antibiotic efficacy.

References

  1. Otto SJG, McLeod L, McCarthy EL, et al. Laboratory tests for bovine respiratory bacteria and antimicrobial resistance in commercial feedlot cattle: comparing culture, long-read metagenomics, and recombinase polymerase amplification. Front Microbiol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42245511/
  2. 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/
  3. Zhang Z, Suksawat F, Pulsrikarn C, et al. Seasonal surveillance of Salmonella prevalence, antimicrobial resistance, and genetic relatedness in chickens from slaughterhouses and retail markets in Northeast Thailand. Vet World. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42245451/
  4. Kerek Á, Radnai L, Tornyos G, et al. Phenotypic and genomic characterization of linezolid non-susceptibility in poultry-derived multidrug-resistant Enterococcus spp. from Hungary. Front Vet Sci. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42238789/
  5. Jimenez CM, Kreizinger Z, Gyuranecz M, et al. European ring test on the differentiation of wild-type Mycoplasma synoviae and the MS-H vaccine strains in clinical samples. Poult Sci. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42235157/
  6. Kober L, von Karger L, Castiglione K. Mixture dependent correlation patterns in antibacterial and cytotoxic activities of five hop isolates. Sci Rep. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42225839/
  7. 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/
  8. Yang J, Shi T, Du Z, et al. Sub-inhibitory polyether ionophores enhance resistance plasmid transfer and transiently perturb the broiler gut resistome. J Antimicrob Chemother. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42219901/
  9. Lee YH, Ali MS, Moon BY, et al. Longitudinal surveillance and molecular characterization of methicillin-resistant Staphylococcus aureus (MRSA) from livestock carcasses in South Korea: a 12-year nationwide study (2013-2024). Food Microbiol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42215217/
  10. Sheng H, Suo J, Yan Y, et al. Prevalence, plasmid transmission, and chromosomal integration of blaCTX-M genes in Salmonella isolated from retail chicken and pork meats in China. Food Res Int. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42215089/
  11. Wang X, Shaukat A, Al-Rasheed M, et al. Paraprobiotics in modern broiler production: stability, safety, and multifunctional benefits – a comprehensive review. Probiotics Antimicrob Proteins. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42207421/
  12. Silwamba I, Muma JB, Mainda G, et al. Antimicrobial usage in broiler poultry farms in Zambia. Front Vet Sci. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42205807/
  13. Carrasco Muñoz M, Pérez de Vargas A, Alhebshi M, et al. Genomic characterization of mcr-1.1-positive Salmonella Kentucky ST198 from a captive Asian houbara bustard reveals links to broiler poultry in the United Arab Emirates. Front Vet Sci. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42205805/
  14. 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/
  15. Bhatta NP, Rijal S, Sapkota RC, et al. Detection of tetracycline and colistin residue in broiler meat of Siddharthanagar Municipality, Rupandehi, Nepal. Vet Med Int. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42199640/