Major Pathogens Associated with Poultry: Bacterial, Viral, and Parasitic Threats

Introduction

Poultry production faces constant challenges from a diverse array of infectious agents, including bacteria, viruses, and parasites, which cause significant economic losses and threaten food security globally. The control of these pathogens is complicated by the emergence of antimicrobial resistance (AMR), the evolution of novel viral variants, and the complex ecology of parasitic vectors [1, 100]. This review provides a comprehensive, publication-grade overview of the major bacterial, viral, and parasitic pathogens affecting poultry, with a focus on their pathogenesis, molecular epidemiology, and diagnostic considerations.

Bacterial Pathogens

Avian Pathogenic Escherichia coli (APEC)

Avian pathogenic Escherichia coli (APEC) is the primary etiological agent of colibacillosis, a systemic disease in poultry characterized by airsacculitis, pericarditis, perihepatitis, and septicemia [33, 34, 56]. APEC strains belong predominantly to specific serogroups, including O1, O2, O78, and O125, and harbor a suite of virulence-associated genes (VAGs) such as those encoding fimbriae (e.g., fimC), iron acquisition systems (e.g., iucD, iroN), and protectins (e.g., iss) [38, 45, 94]. The pathogenicity of APEC is modulated by quorum-sensing regulators; for instance, the LsrR regulator directly controls the expression of cysN, influencing bacterial metabolism and virulence [2]. Genome-scale metabolic reconstructions have identified lineage-specific metabolic pathways across different APEC phylogroups, providing insights into their adaptation to the avian host [3]. The global dissemination of multidrug-resistant (MDR) APEC strains, including those harboring plasmid-mediated colistin resistance genes (mcr-1, mcr-5) and extended-spectrum beta-lactamase (ESBL) genes, is a major concern [4, 39, 52, 87]. Biofilm formation is a critical virulence trait in APEC, with strong associations between biofilm production, antimicrobial resistance, and the presence of specific VAGs. Novel therapeutic strategies, including the use of bacteriophages such as vB_EcoM_GXW16, have demonstrated efficacy against drug-resistant APEC strains [5]. Additionally, prebiotic compounds like xylooligosaccharides have been shown to interfere with the APEC cell cycle and reduce antibiotic tolerance.

Salmonella enterica

Non-typhoidal Salmonella enterica serovars, particularly Enteritidis and Typhimurium, are major foodborne zoonotic pathogens associated with poultry products [1, 110]. Salmonella Gallinarum and Pullorum are host-specific serovars causing fowl typhoid and pullorum disease, respectively. The pathogenicity of Salmonella is mediated by a complex array of virulence factors, including the Salmonella pathogenicity islands (SPIs) and the type III secretion system (T3SS). The virulence factor SptP activates the NLRP3/Caspase-1 pathway, inducing pyroptosis and exacerbating intestinal injury in chicks [6]. Genomic analyses of Salmonella Enteritidis from clinical poultry cases have revealed a high degree of genetic diversity and the presence of multiple antimicrobial resistance genes [7, 49]. The emergence of MDR Salmonella serovars, including those resistant to third-generation cephalosporins and fluoroquinolones, is a global phenomenon driven by the horizontal transfer of resistance plasmids [8, 9, 10, 63, 66]. Bacteriophage therapy, using phages such as vB_SalP_NW15, has shown promise in reducing Salmonella colonization in chicken infection models [11, 12, 109]. Phytochemicals, including clove extract and microencapsulated essential oils, have also been investigated for their ability to mitigate Salmonella-induced intestinal dysfunction and control infection [13, 36].

Campylobacter jejuni and Campylobacter coli

Campylobacter jejuni and Campylobacter coli are the leading bacterial causes of human gastroenteritis worldwide, with poultry meat serving as the primary reservoir and source of infection [14, 75, 77]. Campylobacter colonizes the avian intestinal tract, particularly the ceca, reaching high densities without causing clinical disease in the host. The bacterium can enter a viable but non-culturable (VBNC) state under environmental stress, which complicates detection and control. Psychrotolerant spoilage bacteria on refrigerated chicken meat can enhance the culturability of C. jejuni, potentially increasing the risk of human exposure [15]. Campylobacter hepaticus has been identified as the causative agent of spotty liver disease (SLD) in laying hens, with transcriptomic analyses revealing genes involved in SLD pathogenesis [16]. Antimicrobial resistance in Campylobacter is a significant public health concern, with high rates of resistance to fluoroquinolones and tetracyclines reported globally [76, 79]. A comprehensive meta-analysis has evaluated the effectiveness of various interventions for reducing Campylobacter in poultry farms [17]. Bacteriophage cocktails have been shown to reduce C. jejuni and C. coli counts in experimentally infected chickens by approximately 2 log10 CFU/g.

Clostridium perfringens

Clostridium perfringens is a Gram-positive, spore-forming anaerobe that causes necrotic enteritis (NE) in broiler chickens, a disease of major economic importance [48, 60]. The primary virulence factors are the alpha-toxin (CPA) and the NetB toxin, with NetB being essential for the development of NE in chickens. C. perfringens type A and type G (NetB-producing) are the most common types associated with NE [18]. Toxinotyping of isolates from broiler flocks has confirmed the predominance of NetB-positive strains in clinical cases. The bacterium is also a common cause of foodborne illness in humans. The use of bacteriophages, such as ΦCP5(17) and ΦCP17(i), has been explored as a biocontrol strategy against C. perfringens [19]. Probiotics and dietary interventions, including the use of non-bound proteinogenic amino acids, are being investigated to modulate the growth of C. perfringens and other pathogens in the gut [20, 99].

Mycoplasma gallisepticum and Mycoplasma synoviae

Mycoplasma gallisepticum (MG) is the primary etiological agent of chronic respiratory disease (CRD) in chickens and infectious sinusitis in turkeys. Mycoplasma synoviae (MS) causes infectious synovitis and respiratory disease, and is also associated with eggshell apex abnormalities in laying hens. These cell-wall-deficient bacteria are fastidious and require specialized culture media. Molecular detection using PCR is the standard diagnostic method. A multiplex TaqMan real-time PCR assay has been developed for the differential identification of wild-type and vaccine strains of MG, facilitating disease surveillance and control [21]. Co-infections with other respiratory pathogens, such as infectious bronchitis virus (IBV) and Escherichia coli, are common and exacerbate disease severity. Whole-genome association studies have been conducted to identify genetic determinants of antibiotic susceptibility in Mycoplasma anserisalpingitidis, a related species in geese [22].

Pasteurella multocida

Pasteurella multocida is the causative agent of fowl cholera, a highly contagious and often fatal disease in poultry and waterfowl [23, 24]. The bacterium is a Gram-negative coccobacillus that produces a polysaccharide capsule, a key virulence factor. Serotypes A and D are most commonly associated with avian disease. Secondary P. multocida infection can be potentiated by primary viral infections, such as fowl adenovirus serotype 4 (FAdV-4), which enhances bacterial adherence and aggravates pathological damage [23]. Attenuated live vaccines, developed through serial passage, have been evaluated for their efficacy in ducks [24]. The epidemiology of fowl cholera is influenced by environmental factors, including land cover, which can affect the occurrence of outbreaks.

Ornithobacterium rhinotracheale

Ornithobacterium rhinotracheale (ORT) is a Gram-negative bacterium associated with respiratory disease in turkeys and chickens, often presenting as airsacculitis and pneumonia [25, 32]. Whole-genome analysis of ORT isolates from turkeys in Poland has provided insights into the global diversity, virulence gene repertoire, and antimicrobial resistance profiles of this pathogen [25]. Genomic analysis of strains from Austria and Hungary has revealed the presence of two dominant strains with distinct MDR profiles, highlighting the importance of regional surveillance.

Avibacterium paragallinarum

Avibacterium paragallinarum is the etiological agent of infectious coryza, an acute respiratory disease of chickens characterized by facial edema, nasal discharge, and conjunctivitis [26]. The bacterium is a Gram-negative, pleomorphic rod. The use of probiotics combined with berry phenolic extracts has been investigated as a potential alternative to antibiotics for controlling A. paragallinarum infection [26].

Other Bacterial Pathogens

Several other bacterial species are of significance in poultry. Staphylococcus aureus and coagulase-negative staphylococci are associated with bumblefoot, osteomyelitis, and bone lesions in broilers [27, 28, 53, 61]. Methicillin-resistant S. aureus (MRSA) strains have been isolated from poultry, raising concerns about zoonotic transmission. Enterococcus species are opportunistic pathogens and indicators of fecal contamination [61, 112]. Riemerella anatipestifer is a major pathogen of ducks and geese, causing septicemia and serositis. Gallibacterium anatis is associated with salpingitis and peritonitis in laying hens. Pseudomonas aeruginosa has been reported in Japanese quail and is associated with MDR profiles. Acinetobacter baumannii has been isolated from chickens, with whole-genome sequencing revealing a high content of AMR and virulence genes. Listeria monocytogenes is a foodborne pathogen that can contaminate poultry products [81, 86]. Borrelia anserina, transmitted by the tick Argas persicus, causes avian spirochetosis.

Viral Pathogens

Infectious Bronchitis Virus (IBV)

Infectious bronchitis virus (IBV) is a highly contagious coronavirus that causes respiratory disease, nephritis, and reduced egg production in chickens. The virus is characterized by extensive genetic diversity, driven by mutations and recombination events in the spike (S) glycoprotein gene, particularly the S1 subunit. QX-type IBV strains (GI-19 lineage) have emerged as dominant variants globally, often escaping immunity induced by classical vaccine strains. Recombination between circulating field strains and live attenuated vaccine strains can generate novel variants with altered pathogenicity and antigenicity.

Infectious Bursal Disease Virus (IBDV)

Infectious bursal disease virus (IBDV) is a birnavirus that causes immunosuppression in young chickens by targeting the bursa of Fabricius. Very virulent IBDV (vvIBDV) strains cause high mortality, while novel variant IBDV (nVarIBDV) strains are associated with atypical, subclinical disease. Recent epidemiological surveys in China have identified mutated vvIBDV (mvvIBDV) strains that harbor specific mutations in the VP2 hypervariable region and induce atypical IBD symptoms without causing direct mortality.

Fowl Adenovirus (FAdV)

Fowl adenoviruses (FAdVs) are associated with several disease syndromes, including inclusion body hepatitis (IBH), hepatitis-hydropericardium syndrome (HHS), and gizzard erosion [23]. FAdV serotype 4 (FAdV-4) is the primary cause of HHS. Co-infection with FAdV-4 can potentiate secondary bacterial infections, such as those caused by Pasteurella multocida [23].

Gyroviruses

Gyrovirus galga1 (formerly chicken anemia virus, CAV) and Gyrovirus homsa1 are small, single-stranded DNA viruses that cause immunosuppression and anemia in young chickens. A dual fluorescence channel recombinase-aided amplification (RAA)-based CRISPR-Cas12a/Cas13a system has been developed for the highly sensitive detection of these viruses.

Newcastle Disease Virus (NDV) and Avian Influenza Virus (AIV)

Newcastle disease virus (NDV) and avian influenza virus (AIV) are highly contagious viral pathogens with significant zoonotic potential. NDV causes respiratory, nervous, and enteric signs, while AIV, particularly highly pathogenic avian influenza (HPAI) H5N1, causes systemic disease and high mortality. Both viruses are subject to strict surveillance and control programs globally.

Parasitic Pathogens

Ectoparasites

The poultry red mite, Dermanyssus gallinae, is the most significant ectoparasite of laying hens worldwide, causing anemia, stress, reduced egg production, and mortality. D. gallinae also acts as a vector for a range of bacterial and viral pathogens, including E. coli, Salmonella Enteritidis, and Pasteurella multocida [69, 70, 78, 106]. The mite's microbiome, characterized using metaproteomics, includes both symbiotic and potentially pathogenic bacteria. The lesser mealworm beetle, Alphitobius diaperinus, is another important reservoir and vector of poultry bacterial pathogens and AMR genes within poultry houses. Plant-derived phytochemicals, such as phenols, flavonoids, and terpenoids, are being explored as sustainable alternatives to synthetic acaricides for controlling D. gallinae.

Protozoan Parasites

Coccidiosis, caused by several species of Eimeria (e.g., E. tenella, E. necatrix, E. acervulina, E. maxima), is a major parasitic disease of poultry, characterized by intestinal lesions, diarrhea, and reduced performance. Histomonas meleagridis causes blackhead disease (histomoniasis) in turkeys, characterized by necrotic hepatitis and typhlitis. Leucocytozoon species, transmitted by blackflies, cause leucocytozoonosis, a disease affecting the blood and tissues. Avian haemosporidian infections, including Plasmodium and Haemoproteus species, have been detected in domestic chickens.

Helminth Parasites

Ascaridia galli is the largest intestinal nematode of chickens, causing weight loss and intestinal obstruction. Heterakis gallinarum is a cecal worm that is a vector for Histomonas meleagridis. Capillaria species cause capillariasis, affecting the crop, intestine, or ceca. Syngamus trachea (gapeworm) causes respiratory distress in young birds. Davainea proglottina and other cestodes (tapeworms) infect the small intestine, with snails and beetles serving as intermediate hosts.

Diagnostic Approaches

Diagnosis of poultry pathogens relies on a combination of clinical examination, necropsy, histopathology, and laboratory testing. Bacterial culture and isolation remain the gold standard for many bacterial pathogens, followed by biochemical identification and antimicrobial susceptibility testing (AST). Molecular methods, including conventional and real-time PCR, are widely used for the rapid and specific detection of bacterial, viral, and parasitic agents [21, 103]. Whole-genome sequencing (WGS) has become an essential tool for epidemiological surveillance, outbreak investigation, and the characterization of AMR and virulence genes [25, 7, 32, 34, 40, 49]. Metagenomic approaches are increasingly used for the comprehensive profiling of microbial communities and the detection of unculturable or unexpected pathogens [90, 113]. Serological tests, such as ELISA, are used for monitoring flock exposure to specific pathogens. Advanced techniques, including surface-enhanced Raman spectroscopy (SERS) sensors, are being developed for the rapid, multiplex detection of foodborne pathogens in poultry products.

Antimicrobial Resistance

Antimicrobial resistance (AMR) is a critical challenge in poultry production, driven by the extensive use of antibiotics for disease prevention and growth promotion [1, 58, 111]. MDR is prevalent among major poultry pathogens, including APEC, Salmonella, Campylobacter, and Enterococcus [85, 87, 110]. Resistance genes, such as those encoding ESBLs (e.g., blaTEM, blaSHV, blaCTX-M), carbapenemases (e.g., blaNDM), and colistin resistance (e.g., mcr-1), are frequently carried on mobile genetic elements, facilitating their horizontal spread [9, 4, 39, 52, 87]. The use of antimicrobial processing aids (APA) during poultry processing may also contribute to the co-selection of antibiotic-resistant bacteria. Alternative strategies to reduce antibiotic dependence include the use of bacteriophages, probiotics, prebiotics, phytochemicals, and vaccines [12, 58, 60, 99, 107, 109].

Conclusion

The management of infectious diseases in poultry requires a comprehensive understanding of the diverse bacterial, viral, and parasitic pathogens that threaten flock health and food safety. The emergence and dissemination of AMR, coupled with the evolution of novel viral variants, necessitate continuous surveillance, the development of rapid and accurate diagnostic tools, and the implementation of integrated control strategies. A One Health approach, recognizing the interconnectedness of animal, human, and environmental health, is essential for mitigating the risks posed by these pathogens.

References

[1] Sharma S, Kaur S, Naguib M et al. Major Foodborne Bacterial Pathogens in Poultry: Implications for Human Health and the Poultry Industry and Probiotic Mitigation Strategies. Microorganisms. 2025. URL: https://pubmed.ncbi.nlm.nih.gov/41156822/

[2] Nawaz S, Wang Z, Jiang W et al. Quorum-sensing regulator LsrR modulates avian pathogenic Escherichia coli pathogenicity through direct regulation of cysN. Infect Immun. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41313186/

[3] Long H, Mehat JW, Wu H et al. Use of genome-scale metabolic reconstructions of avian pathogenic Escherichia coli (APEC) phylogroups for the identification of lineage-specific metabolic pathways. Microb Genom. 2025. URL: https://pubmed.ncbi.nlm.nih.gov/40961347/

[4] Xedzro C, Shimamoto T, Ahmed AM et al. Genomic insights into multidrug-resistant extraintestinal pathogenic Escherichia coli O4:H12 harboring mcr-5 and blaSHV-12 on conjugative plasmids isolated from chicken meat in Japan. J Appl Microbiol. 2025. URL: https://pubmed.ncbi.nlm.nih.gov/40928475/

[5] Xu T, Yang W, Cao J et al. Isolation and therapeutic potential of phage vB_EcoM_GXW16 against a drug-resistant avian pathogenic Escherichia coli strain. Poult Sci. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41833115/

[6] Zhang B, Li K, Yan H et al. Salmonella virulence factor sptP activates the NLRP3/Caspase-1 pathway to induce pyroptosis and exacerbate intestinal injury in chicks. Vet Microbiol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41539065/

[7] Ma J, Bai X, Wang S et al. Characteristics and genomics study of Salmonella isolates in retail chicken in Shaanxi, China: Focus on comparative genomics analysis of S. Kentucky and S. enteritidis isolates from Shaanxi with those from elsewhere in China. Int J Food Microbiol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41330090/

[8] Cartelo LA, Salhi O, Boumahdi Merad Z et al. Occurrence, antimicrobial resistance and molecular characterization of Salmonella spp. from broiler chickens in Northern Algeria. Braz J Microbiol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42149349/

[9] Salem M, Al-Khalidi AAH, Hammad E et al. Isolation and characterization of Salmonella enterica serovars from poultry in Egypt: a comprehensive genetic analysis of ESBLs, MCR, integron and other resistance genes. BMC Vet Res. 2025. URL: https://pubmed.ncbi.nlm.nih.gov/41272651/

[10] Sripaurya B, Pelyuntha W, Ngasaman R et al. Antibiotic resistance, sequence typing, and virulence gene profiles of Salmonella enterica isolated from the broiler production chain in southern Thailand. Res Vet Sci. 2025. URL: https://pubmed.ncbi.nlm.nih.gov/41014858/

[11] Yang W, Xu T, Li Y et al. Therapeutic efficacy of phage vB_SalP_NW15 and cinnamaldehyde against drug-resistant Salmonella Enteritidis in a chicken infection model. Poult Sci. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41485350/

[12] Muneeb M, Ullah Khan E, Ahmad S et al. A Comprehensive Review of the Application of Bacteriophages Against Enteric Bacterial Infection in Poultry: Current Status, Challenges, and Future Prospects. Antibiotics (Basel). 2025. URL: https://pubmed.ncbi.nlm.nih.gov/41463709/

[13] Feng Y, Lv Y, Chen H et al. Protection of clove extract against Salmonella enteritidis-induced intestinal dysfunction in broilers through JAK2/STAT3-mediated stem cell activation. Poult Sci. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41442916/

[14] Ivanov I, Takkinen HK, Takkinen J et al. Sources of Human Campylobacteriosis Cases in Estonia and the Genomic Associations with Broiler Chicken Meat Isolates. Pathogens. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42198665/

[15] Yan R, Watson SC, Wei X et al. Psychrotolerant spoilage bacteria enhanced Campylobacter jejuni culturability on refrigerated chicken meat. Food Microbiol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41963066/

[16] Bommineni V, Edison LK, Gottapu C et al. Campylobacter hepaticus Transcriptomics Identified Genes Involved in Spotty Liver Disease (SLD) Pathogenesis. Pathogens. 2025. URL: https://pubmed.ncbi.nlm.nih.gov/41156659/

[17] Zefanias O, Gonzales-Barron U, Cadavez V. Effectiveness of Interventions and Control Measures in the Reduction of Campylobacter in Poultry Farms: A Comprehensive Meta-Analysis. Foods. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41596905/

[18] Tran C, Poezevara T, Maladen V et al. Isolation rate, genetic diversity, and toxinotyping of Clostridium perfringens isolated from French cattle, pig or poultry slaughterhouses. Food Microbiol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/40889869/

[19] Naseem H, Haider Z, Mannan S et al. Genomic and physiochemical characterization of two lysogenic bacteriophages, ΦCP5(17) and ΦCP17(i), infecting Clostridium perfringens. Arch Virol. 2025. URL: https://pubmed.ncbi.nlm.nih.gov/41125819/

[20] Chau D, Turni C, Roura E et al. Use of non-bound proteinogenic amino acids to modulate the growth of pathogenic bacteria from broiler chickens. Poult Sci. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41349479/

[21] Xin J, Zhang J, Liang S et al. A multiplex TaqMan real-time PCR assay for differential identification of wild-type and vaccine strains of Mycoplasma gallisepticum. Poult Sci. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41702344/

[22] Kovács ÁB, Wehmann E, Bekő K et al. Genome-wide association study of Mycoplasma anserisalpingitidis strains for antibiotic susceptibility. Sci Rep. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41735391/

[23] Chen Y, Yi G, Huang Y et al. FAdV-4-induced secondary Pasteurella multocida infection potentiates bacterial adherence and aggravates pathological damage in SPF chickens. Vet Microbiol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41764915/

[24] Ji X, Meng Y, Yang H et al. Attenuation mechanisms and vaccine potential of the serial passage-derived Pasteurella multocida strain PMZ8 in ducks. Poult Sci. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41747463/

[25] Blanda M, Kursa O, Kowalczyk J et al. Whole-genome analysis of Ornithobacterium rhinotracheale from turkeys in Poland: Insights into global diversity, virulence, and antimicrobial resistance. Vet Microbiol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/41621167/

[26] Thapa K, Phan A, Lin S et al. Implication of probiotics with berry phenolic extracts against Avibacterium paragallinarum. Microb Pathog. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42097187/

[27] Szafraniec GM, Chrobak-Chmiel D, Adamczyk K et al. Phenotypic and genotypic characterization of antimicrobial resistance in coagulase-negative staphylococci from bone lesions in broiler chickens. BMC Vet Res. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42192425/

[28] Ullah A, Fatima B, Ejaz M et al. Genomic Insights into Poultry-Associated Staphylococcus Aureus from Haripur, Pakistan. Curr Microbiol. 2025. URL: https://pubmed.ncbi.nlm.nih.gov/41160231/

[29] Lafuente I, Sevillano E, Peña N et al. Isolation and characterization of bacteriocin-producing E. coli isolates from a poultry slaughterhouse, and cell-free production and evaluation of native and engineered bacteriocins. Poult Sci. 2025. URL: https://pubmed.ncbi.nlm.nih.gov/41197358/

[30] Wang L, Qiu M, Li X et al. Antimicrobial activity and possible mechanisms of juglone against Escherichia coli, Staphylococcus aureus, and Salmonella pullorum. BMC Microbiol. 2025. URL: https://pubmed.ncbi.nlm.nih.gov/41107751/

Disclaimer: This article is for educational and informational purposes only. It is not intended to substitute for professional veterinary advice, diagnosis, treatment, or regulatory guidance. Always consult a licensed veterinarian or qualified specialist regarding animal health, disease diagnosis, and therapeutic decisions.