Bacterial Infections in Chickens: A Comprehensive Guide to Salmonellosis, Colibacillosis, and Other Common Pathogens

Introduction

Bacterial infections represent a major source of morbidity, mortality, and economic loss in commercial and backyard poultry operations worldwide. The major chicken diseases caused by bacteria include salmonellosis, colibacillosis, necrotic enteritis, fowl cholera, and campylobacteriosis [1, 2]. Understanding the pathogenesis, clinical presentation, diagnostic modalities, and control measures for these pathogens is essential for veterinary practitioners and poultry health specialists.

The intestinal and respiratory tracts of chickens harbor complex microbial communities that can become disrupted by pathogenic bacteria, leading to systemic disease [3, 4]. In poultry production, the question of does all chicken have salmonella is frequently posed; while not every chicken carries Salmonella, the organism can colonize asymptomatically in a significant proportion of flocks, and contamination of meat and eggs is a well-documented food safety concern [5, 6]. Regulatory agencies such as the FSIS have established monitoring programs for fsis poultry salmonella to reduce the burden of this pathogen in raw poultry meat [7].

This article provides an exhaustive review of the most important bacterial pathogens affecting chickens, with emphasis on salmonellosis, colibacillosis, and other prevalent agents. The epidemiology of chicken salmonella uk and global patterns of antimicrobial resistance are addressed through recent genomic and phenotypic data [8, 9].

Salmonellosis in Chickens

Etiology and Epidemiology

Salmonellosis is caused by infection with Salmonella enterica subsp. enterica, which includes both non-typhoidal serovars (e.g. Enteritidis, Typhimurium) and host-adapted serovars such as Gallinarum and Pullorum [6, 10]. The question of salmonella chicken only reflects the host specificity of certain serovars: S. Gallinarum and S. Pullorum cause disease almost exclusively in poultry, whereas S. Enteritidis and S. Typhimurium are zoonotic [1, 34]. The epidemiology of salmonella chicken baby (i.e. infection in young chicks) is dominated by vertical transmission through infected breeder flocks and contaminated hatchery environments [1].

The prevalence of Salmonella in broiler and layer flocks varies by region and production system. Studies from Canada have identified IncI1 plasmid types associated with specific production years and geographical regions [11]. In Bangladesh, high levels of antimicrobial resistance have been documented among S. Gallinarum and S. Pullorum isolates [6]. Similarly, a survey from Algeria reported significant antimicrobial resistance among broiler-derived Salmonella spp. [10]. The chicken salmonella uk situation is influenced by biosecurity measures and vaccination programs implemented over the past two decades [5, 8].

Clinical Signs and Pathology

Clinical manifestations depend on serovar, age of the bird, and route of infection. In young chicks, infection with S. Pullorum causes white diarrhea, lethargy, and high mortality, a condition known as pullorum disease [1, 7]. Gallinarum infection (fowl typhoid) in older birds results in acute or chronic septicemia with anorexia, depression, and greenish diarrhea [6, 34].

Non-typhoidal serovars such as S. Enteritidis and S. Typhimurium often produce subclinical intestinal colonization that can persist for weeks [30]. However, under stress or concurrent infection, clinical enteritis may develop [3, 12]. Single-cell transcriptomic profiling has revealed that S. Enteritidis infection triggers an expansion of innate-like cytotoxic intraepithelial lymphocytes in the chicken gut [3].

Postmortem lesions in acute salmonellosis include hepatomegaly, splenomegaly, necrotic foci in the liver and spleen, typhlitis, and caseous cecal cores [7, 13]. In chronic cases, pericarditis and peritonitis may be observed.

Diagnostics

Laboratory diagnosis of salmonellosis relies on bacterial culture, serotyping, and molecular methods. Traditional culture from cloacal swabs, fecal samples, or internal organs using selective media remains the gold standard [10]. Serological detection using indirect ELISA targeting the Sptp protein has been developed and evaluated for poultry [7].

Molecular techniques, including PCR and whole-genome sequencing, provide high-resolution typing and antimicrobial resistance gene profiling [1, 11]. Core-genome multilocus sequence typing (cgMLST) of plasmids has been applied to understand the spread of resistance determinants among Salmonella serovars [11]. Shotgun metagenomic sequencing can detect unidentified pathogens in clinical samples, including hepatic necrosis in Samgye chickens [8].

Treatment and Control

Antimicrobial therapy is indicated in clinical outbreaks, but resistance is a growing concern [2, 14]. The emergence of extended-spectrum beta-lactamase (ESBL) producing strains and colistin resistance mediated by the mcr-1 gene has been documented in chickens [2, 5, 15]. Phage therapy has shown promise as an alternative to antibiotics for S. Pullorum infection in chickens [16].

Vaccination is a key component of control programs. Live attenuated Salmonella vaccines are available for S. Enteritidis, S. Typhimurium, and S. Gallinarum, and different vaccination schedules have been evaluated in layer hens [34]. Experimental conjugate and whole-cell killed vaccines for S. Typhimurium have also been developed [13]. Novel approaches include recombinant attenuated S. Enteritidis vectors expressing Clostridium perfringens antigens for dual protection against salmonellosis and necrotic enteritis [17, 18].

Control on the farm requires comprehensive biosecurity, including cleaning and disinfection of hatcheries, rodent control, and monitoring of feed and water [1, 10]. Pre-harvest interventions such as oregano essential oil have been shown to reduce S. Enteritidis in market-age broilers [19]. Bamboo polyphenols protect against S. Enteritidis by modulating inflammation, barrier integrity, and gut microbiota [12]. Dietary Bacillus subtilis supplementation reduces infection with S. Pullorum in broilers [20]. Phytochemicals like esculetin can restore colistin susceptibility in MCR-positive bacteria [2]. Houttuynia cordata extract inhibits Salmonella infection by targeting type III secretion system 1 [29].

The question of salmonella chicken washing is relevant to food safety: washing raw chicken in the kitchen is discouraged because it can spread Salmonella to surfaces and other foods through aerosolization and cross-contamination. Proper cooking to an internal temperature sufficient to kill Salmonella is the only reliable method to render contaminated meat safe.

A summary of key Salmonella serovars affecting chickens is provided in Table 1.

Table 1. Major Salmonella serovars in chickens, their host adaptation, and clinical significance.

Colibacillosis

Etiology and Pathogenesis

Colibacillosis is caused by avian pathogenic Escherichia coli (APEC). These strains possess specific virulence factors enabling them to colonize the respiratory and intestinal tracts and cause systemic disease [9, 21, 22]. The chicken e coli or salmonella distinction is clinically important because both pathogens can produce similar signs, but their epidemiology and control differ.

APEC infections often occur secondary to environmental stress, viral infections (e.g. H9N2 avian influenza), or immunosuppression [4]. Direct interaction between APEC and H9N2 virus promotes bacterial adhesion, suggesting that viral co-infection exacerbates colibacillosis [4]. The ecnAB toxin-antitoxin system modulates APEC virulence by regulating the capsular sialic acid biosynthesis pathway [9]. Small RNAs such as RyfA and TimR also orchestrate stress resistance and virulence in APEC [22].

Clinical Signs and Pathology

Common presentations include airsacculitis, pericarditis, perihepatitis, peritonitis, and salpingitis in layers [9, 21, 31]. In broilers, colibacillosis often manifests as colisepticemia, leading to sudden death or chronic debilitation. E coli on raw chicken is a food safety concern, but can you get e coli from chicken is answered affirmatively: APEC strains can cause human illness, although the primary foodborne E. coli concern is with Shiga toxin-producing E. coli (STEC) from other sources [23, 24].

Postmortem lesions include fibrinopurulent polyserositis, fibrinous pericarditis (often described as "bread and butter" pericardium), and enlarged, congested livers [21, 31]. Intestinal injury induced by APEC involves the TLR4/MyD88/NF-kB signaling pathway and is ameliorated by luteolin [31].

Antimicrobial Resistance in APEC

APEC strains frequently carry multidrug resistance determinants. Genomic characterization of APEC has revealed the presence of mcr-1, ESBL genes, and other acquired resistance elements [5, 21, 15, 23]. An extensively drug-resistant (XDR) APEC strain has been characterized from clinical cases in poultry [21]. Resistance to critically important antimicrobials is also found in E. coli from retail chicken meat, with implications for food safety [24].

Treatment

Antimicrobial therapy guided by culture and susceptibility testing is recommended. The use of colistin in poultry is under scrutiny due to the spread of mcr-1 genes [2, 15]. Alternatives being explored include plant extracts such as liposomal formulations of cinnamon, oregano, and clove [25]. Probiotic approaches using lactic acid bacteria may help reduce APEC colonization, but clinical evidence remains limited.

Other Common Bacterial Pathogens

Necrotic Enteritis (Clostridium perfringens)

Necrotic enteritis is an important chicken bacteria disease caused by Clostridium perfringens type A and type G (formerly type C). The disease is often triggered by dietary factors or concurrent coccidiosis [33]. C. perfringens produces NetB toxin, which is essential for pathogenesis. Spore load in the environment correlates with farm-level occurrence of necrotic enteritis [33].

Clinical signs include depression, diarrhea, and sudden death. Postmortem findings include a friable, necrotic small intestinal mucosa covered by a pseudomembrane [17, 18]. Diagnosis is confirmed by histopathology, anaerobic culture, and toxin typing.

Control involves management of predisposing factors, ionophore anticoccidials, and vaccination. Recombinant Salmonella vectors expressing Clostridium antigens have been developed for dual protection [17, 18].

Fowl Cholera (Pasteurella multocida)

Fowl cholera is caused by Pasteurella multocida, a Gram-negative coccobacillus. The bacterium can cause acute septicemia or chronic localized infections. P. multocida induces liver pyroptosis in broilers through the MAPK-NLRP3-GSDMD signaling pathway [26]. Clinical signs include fever, mucoid discharge, cyanosis of the comb and wattles, and high mortality. Vaccines (bacterins and live attenuated strains) are available for prevention [26].

Other Pathogens

Chicken bacteria toxins produced by Clostridium perfringens, Staphylococcus aureus, and others can cause enteritis or toxemia. The question of pathogens is most common in raw poultry meat is addressed by multiple surveys: Salmonella, Campylobacter, and Escherichia coli are the three most frequently isolated bacterial contaminants in raw poultry [24, 25]. Chicken neck bacteria and chicken breast bacteria reflect the distribution of contamination on different carcass parts, with skin and neck areas often harboring higher bacterial loads due to handling during processing.

Campylobacter jejuni is a leading cause of human gastroenteritis and is commonly carried asymptomatically in chickens. Although less frequently reported in clinical poultry disease, its foodborne significance is substantial. Ornithobacterium rhinotracheale causes respiratory disease in turkeys and occasionally in chickens. Mycoplasma gallisepticum is a chronic respiratory pathogen that can be complicated by secondary bacterial infections such as APEC.

Diagnostics and Laboratory Workflow

Accurate diagnosis of bacterial infections in chickens requires an integrated approach combining clinical examination, necropsy, histopathology, microbial culture, and molecular methods. The diagnostic workflow is outlined in the Mermaid diagram below.

flowchart TD
    A[Clinical signs: respiratory, enteric, or systemic], > B[Necropsy and gross lesion evaluation]
    B, > C[Sample collection: swabs, tissues, blood]
    C, > D{Bacterial culture}
    D, >|Aerobic culture| E[Selective media for Salmonella, E. coli, Pasteurella]
    D, >|Anaerobic culture| F[Clostridium perfringens isolation]
    E, > G[Biochemical identification and serotyping]
    F, > G
    G, > H{Antimicrobial susceptibility testing}
    H, > I[Phenotypic AST (disk diffusion, MIC)]
    H, > J{Genotypic detection}
    J, > K[PCR: virulence and resistance genes]
    J, > L[Whole-genome sequencing / cgMLST]
    J, > M[Shotgun metagenomics for mixed infections]
    I, > N[Clinical interpretation and treatment recommendation]
    K, > N
    L, > N
    M, > N
    N, > O[Implementation of control measures]

Figure 1. Diagnostic workflow for bacterial infections in chickens.

Serological tools such as indirect ELISA for Salmonella Sptp protein are valuable for flock-level screening [7]. In cases where conventional culture fails, metagenomics can identify unexpected pathogens, as demonstrated in hepatic necrosis cases [8].

Treatment Strategies and Antimicrobial Stewardship

Antimicrobial therapy must be based on accurate diagnosis and susceptibility data to minimize the selection of resistant strains. The emergence of mcr-1-positive colistin-resistant E. coli in poultry farms [5, 15] and XDR APEC [21] underscores the urgency of judicious antibiotic use. Alternative strategies include phage therapy [16], organic acids that impede Salmonella infection by modulating itaconate gene expression in HD11 macrophages [27], and dietary interventions such as Bacillus subtilis [20], esculetin [2], oregano essential oil [19], and bamboo polyphenols [12].

Vaccination plays a central role in preventing salmonellosis [34]. The development of conjugate and whole-cell killed vaccines [13] and recombinant attenuated Salmonella vectors [17, 18] continues to advance. Dietary interactions with vaccination (e.g. iron source from SQM Iron) can shape the poultry gut microbiota and influence vaccine efficacy [32].

Control and Prevention on Farm

Effective control of bacterial infections requires a multi-faceted approach:

• Biosecurity: all-in/all-out management, disinfection of housing between flocks, rodent and insect control [1, 33].
• Hatchery hygiene: reduction of vertical transmission by monitoring breeder flocks and disinfection of eggs [1].
• Vaccination: targeted programs for Salmonella, Pasteurella, and Clostridium species [26, 34].
• Feed and water management: use of organic acids, probiotics, and phytogenics to reduce intestinal pathogen load [27, 12, 20].
• Antimicrobial stewardship: restricted use of critically important antibiotics, routine susceptibility monitoring [14, 23].

Consumer food safety practices such as salmonella chicken washing are not recommended; instead, cooking chicken to a safe internal temperature (75°C in the thickest part) kills bacterial pathogens. The FSIS uses a risk-based inspection system to enforce fsis poultry salmonella standards, and salmonella chicken uk surveillance is conducted by the UK Health Security Agency and the Food Standards Agency.

Conclusion

Bacterial infections remain a significant challenge in poultry production worldwide. Salmonellosis and colibacillosis are the most prevalent chicken diseases caused by bacteria, but other pathogens such as Clostridium perfringens, Pasteurella multocida, and Campylobacter jejuni also require attention. The question does all chicken have salmonella is answered by prevalence data: while not universal, asymptomatic carriage is common, and the organism can be found on raw poultry meat. Understanding the mechanisms of chicken bacteria toxins and the host response at the cellular level, as revealed by transcriptomics [3] and virulence gene profiling [22], provides a foundation for developing novel interventions.

Molecular diagnostics, including whole-genome sequencing and metagenomics, have revolutionized the characterization of bacterial pathogens and their resistance profiles [1, 8, 11, 23]. Continued surveillance of antimicrobial resistance in APEC and Salmonella [6, 10, 14] is essential to inform treatment guidelines and control policies. Integrated control strategies combining vaccination, biosecurity, dietary modification, and responsible antimicrobial use are the most effective means of reducing the burden of bacterial infections in chickens.

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.

References

[1] Eidaroos NH, Khafagy AR, Eldein AE, et al. Virulence and Antimicrobial Resistance Gene Profiling of Salmonella Isolated from Dead-in-Shell Eggs and Hatchery Environments with Emphasis on Class 1 Integron Gene Cassette Sequencing in XDR Strains. Microb Pathog. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42331072/

[2] Guo L, Ren X, Zhang Y, et al. Esculetin restores colistin susceptibility in MCR-positive bacteria through multiple mechanisms, thereby combating drug-resistant bacterial infections in chickens. Bioorg Chem. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42322908/

[3] Majeed S, Shah BR, Aryal B, et al. Single-cell transcriptomic profiling reveals innate-like cytotoxic intraepithelial lymphocyte expansion during Salmonella Enteritidis infection in chickens. Front Immunol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42317345/

[4] Li Y, Xue Y, Quan Y, et al. Direct interaction between avian pathogenic Escherichia coli and H9N2 avian influenza virus promotes bacterial adhesion during their infections. Microbiol Spectr. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42294695/

[5] Xu J, Yan B, Fu Q, et al. Prevalence and Genomic Characterization of mcr-1-Positive Escherichia coli from Livestock in Hunan Province, China (2016-2021). Curr Microbiol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42283845/

[6] Kingshuk MMR, Alam SB, Rahman MS, et al. The Landscape of Salmonella enterica Serovar Gallinarum-Pullorum Antimicrobial Resistance in Bangladesh's Poultry Industry: A Combined Phenotypic and Molecular Study. Microbiologyopen. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42271175/

[7] Xie L, Xia Y, Shen R, et al. Establishment of an indirect ELISA method for detecting Salmonella infection based on Sptp protein in poultry. J Microbiol Methods. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42219045/

[8] Kim Y, Kim JK, Her M, et al. Shotgun Metagenomic Diagnosis of Unidentified Pathogens in Hepatic Necrosis Samples from Samgye Chickens. Avian Pathol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42212564/

[9] 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/

[10] 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/

[11] Hetman B, Pearl D, Reid-Smith R, et al. Core-genome multilocus sequence types of the IncI1 plasmids identified in Salmonella enterica subsp. Enterica serovars Heidelberg and Kentucky from Canadian poultry production are associated with factors related to production, year, and geographical region. Can J Microbiol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42091221/

[12] Liao Q, Zheng L, Huang J, et al. Bamboo Polyphenols Protect Against Salmonella Enteritidis in Chickens by Modulating Inflammation, Barrier Integrity, and Microbiota. Animals (Basel). 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42121711/

[13] Ahmad A, Yousaf Z, Naeem M, et al. Preparation and comparative evaluation of conjugate and whole-cell killed vaccine candidates against Salmonella enterica serovar Typhimurium. Vaccine. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42090745/

[14] Nath S, Habib M, Banerjee J, et al. Understanding antimicrobial resistance dynamics of non-typhoidal Salmonella in chickens and ducks - a prospective study from West Bengal, India. Braz J Microbiol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42113384/

[15] Kirat H, Barraud O, Rahab H, et al. Persistence of MCR-1-Positive Colistin-Resistant E. coli ST162, ST93, and ST3941 Clones in Poultry Farms, Algeria. Microb Drug Resist. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42117676/

[16] Zhao H, You S, Fu J, et al. Phage therapy: A novel strategy to combat drug-resistant Salmonella Pullorum infection in chickens. Vet Microbiol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42061220/

[17] Li W, Li YA, Liu X, et al. Oral immunization with attenuated Salmonella enterica serovar Enteritidis expressing dual-toxin antigen induces protective immunity against avian necrotic enteritis. Vaccine. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42105397/

[18] Li W, Li YA, Liu X, et al. Recombinant Attenuated Salmonella Enteritidis Vector Enhances the Immunogenicity of Clostridium perfringens EntB Antigen for Effective Prevention of Avian Necrotic Enteritis. Biomolecules. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42072696/

[19] Swaggerty CL, Sasia S, Cabrera MD, et al. Oregano essential oil: a pre-harvest tool to reduce Salmonella enterica serovar Enteritidis in market-age broilers. Poult Sci. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42061244/

[20] Chen Y, Li H, Zhang X, et al. Dietary Bacillus subtilis Group Reduces the General Infection of Salmonella Pullorum in Broiler Chicken. Antibiotics (Basel). 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42041352/

[21] 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/

[22] Anamalé C, Bessaiah H, Ng Kwan Lim E, et al. Orchestrating infection: the impact of RyfA and TimR sRNAs on stress resistance and virulence in avian pathogenic Escherichia coli in chickens. Appl Environ Microbiol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42053318/

[23] 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/

[24] 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/

[25] El-Hamid MIA, ELTarabili RM, Ibrahim GA, et al. Emergence of virulent ESBL-producing Escherichia coli in meat with human health implications and control using liposomal cinnamon, oregano, and clove within a One Health framework. Sci

[26] Yan D, Xu G, Cheng Y, et al. Pasteurella multocida causes liver pyroptosis in broilers through the MAPK-NLRP3-GSDMD signaling pathway. Vet Microbiol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42139792/

[27] Marcu D, Balta I, Gundogdu O, et al. Organic acids impede Salmonella infection of chicken macrophage-like cell line (HD11) by modulating itaconate gene expression. Avian Pathol. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42159720/

[28] Liu S, Gao Q, Zhang J, et al. SIRT1 Attenuates Host Resistance to Salmonella Infection by Negatively Regulating the Immune Responses. FASEB J. 2026. URL: https://pubmed.ncbi.nlm.nih.gov/42033180/