Salmonella in Poultry: Prevalence, Transmission, and Food Safety Implications

By Dr. Zubair Khalid, DVM, MS, PhD · 2026-06-06

Key Takeaways

• Poultry serves as a primary reservoir for Salmonella enterica, a leading cause of global bacterial gastroenteritis, with prevalence varying significantly by region, production system, and sampling point, often exceeding 20% in some African and Asian regions.
• Transmission pathways are multifaceted, including vertical (transovarian) transmission, horizontal fecal-oral contact, environmental persistence in litter and feed, and mechanical vectors, with biosecurity gaps amplifying spread.
• Antimicrobial resistance (AMR) is a critical concern, driven by preharvest antibiotic use and horizontal gene transfer via plasmids, integrons, and transposons, leading to the widespread circulation of multidrug-resistant (MDR) strains like Salmonella Infantis and Kentucky.
• Salmonella-contaminated poultry meat and eggs are major vehicles for human illness, with contamination occurring on-farm, during slaughter, and through post-harvest cross-contamination, necessitating integrated control strategies.
• Control strategies encompass preharvest interventions (biosecurity, probiotics, vaccination), harvest, and postharvest measures, alongside advanced diagnostic tools like whole genome sequencing and CRISPR-SeroSeq for high-resolution subtyping and surveillance.
• Plasmid-mediated colistin resistance (e.g., mcr-1) and extended-spectrum beta-lactamase (ESBL) genes (e.g., *bla*CTX-M) are emerging threats in poultry-associated Salmonella, often carried on conjugative plasmids and contributing to reduced susceptibility to last-resort antibiotics.

Introduction

Salmonella enterica represents a genus of Gram-negative, facultative anaerobic bacilli within the Enterobacteriaceae family that remains a leading cause of bacterial gastroenteritis worldwide, with poultry serving as a primary reservoir for both host-restricted and broad-host-range serovars [<a href="#ref-1">1</a>, <a href="#ref-2">2</a>, <a href="#ref-3">3</a>]. The bacterium colonizes the gastrointestinal tract of chickens, turkeys, ducks, and other avian species, often without inducing clinical disease, thereby facilitating silent dissemination along the production continuum [<a href="#ref-4">4</a>, <a href="#ref-5">5</a>]. Host-adapted serovars such as Salmonella Gallinarum and Salmonella Pullorum cause systemic fowl typhoid and pullorum disease, respectively, while non-typhoidal serovars (e.g., Enteritidis, Typhimurium, Infantis, Kentucky) are of paramount concern for zoonotic foodborne transmission [<a href="#ref-6">6</a>, <a href="#ref-7">7</a>]. The economic and public health burden of poultry-associated salmonellosis justifies sustained investigation into prevalence patterns, transmission mechanics, antimicrobial resistance (AMR) evolution, and intervention strategies [<a href="#ref-8">8</a>, <a href="#ref-9">9</a>].

Global and Regional Prevalence of Salmonella in Poultry

Prevalence estimates for Salmonella in poultry vary markedly by geographic region, production system (commercial vs. backyard), and sampling point (farm, slaughterhouse, retail) [<a href="#ref-10">10</a>, <a href="#ref-11">11</a>, <a href="#ref-12">12</a>]. A continent-wide meta-analysis of African poultry and animal-derived foods reported pooled prevalence rates exceeding 20 % in some regions, with serovar diversity dominated by Enteritidis and Typhimurium [<a href="#ref-13">13</a>]. In Nigeria, prevalence in live bird markets and processing environments reached 15-30 %, with multidrug-resistant (MDR) strains circulating widely [<a href="#ref-1">1</a>, <a href="#ref-14">14</a>]. Similarly, studies in Southeast Asia demonstrate seasonal fluctuations: chicken samples from slaughterhouses and retail markets in Northeast Thailand exhibited prevalence peaks during the rainy season, and serovars such as Enteritidis and Corvallis were predominant [<a href="#ref-5">5</a>, <a href="#ref-15">15</a>]. In South Korea, longitudinal surveillance from 2019-2024 revealed temporal shifts in serovar distribution, with Kentucky and Infantis increasing in frequency alongside plasmid-mediated colistin resistance genes [<a href="#ref-4">4</a>]. The broiler production chain in Algeria and Brazil also reports high carriage rates, with serovars Minnesota and Infantis frequently isolated [<a href="#ref-10">10</a>].

Table 1 summarizes selected prevalence data from recent peer-reviewed studies:

Backyard and free-range poultry operations consistently harbor higher Salmonella prevalence than intensively managed flocks, a pattern linked to reduced biosecurity and increased environmental exposure. In Saint Kitts, seroprevalence of Salmonella in commercial premises was lower than in village chickens, underscoring the impact of housing and hygiene practices [<a href="#ref-8">8</a>]. Egg contamination remains a critical concern: a meta-analysis of Chinese studies reported that 8.7 % of egg samples (shell and/or contents) tested positive, with surface contamination more frequent than internal. The presence of Salmonella in eggs can occur via vertical transmission from infected reproductive tissues or through horizontal penetration of the shell after laying.

Transmission Dynamics within Poultry Populations

Salmonella transmission in poultry follows multiple routes: vertical, horizontal, and environmental. Vertical (transovarian) transmission is particularly relevant for serovar Enteritidis, which colonizes the ovary and oviduct of asymptomatically infected laying hens and is deposited inside the egg before shell formation [<a href="#ref-15">15</a>, <a href="#ref-20">20</a>]. Whole genome sequencing (WGS) studies of breeder flocks have traced clonal expansion of Enteritidis from parent stock to broiler progeny, confirming heritable transmission chains [<a href="#ref-20">20</a>, <a href="#ref-21">21</a>]. Horizontal transmission occurs through fecal-oral contact, ingestion of contaminated feed or water, and via mechanical vectors such as litter beetles and wild birds [<a href="#ref-15">15</a>, <a href="#ref-22">22</a>]. The poultry house environment, including litter, flooring, and ventilation systems, can sustain Salmonella for weeks to months, especially under favorable moisture and temperature conditions [<a href="#ref-2">2</a>]. Transcriptomic analyses indicate that Salmonella Infantis upregulates stress response genes when exposed to poultry litter, enhancing its persistence. Osmotic stress adaptation, mediated by trehalose synthesis and porin regulation, further promotes survival in desiccated feed and fecal matter [<a href="#ref-2">2</a>].

Biosecurity gaps amplify transmission. Risk factor analyses in Burkina Faso and Israel identified shared equipment, lack of footbaths, and multi-age stocking as significant predictors of flock positivity. AI-driven modeling of farm management practices has shown that feeding type, cleaning frequency, and visitor protocols are the most influential variables for Salmonella occurrence. Temporal sampling of commercial turkey flocks revealed that detection at early grow-out stages (week 1-3) strongly predicts later cecal colonization, supporting the need for preharvest monitoring [<a href="#ref-22">22</a>]. The role of contaminated eggshells used as a calcium source in feed was implicated in a nationwide Enteritidis outbreak in the Netherlands, demonstrating how feed ingredients can act as transmission vehicles.

The following Mermaid diagram illustrates the primary transmission pathways and intervention points in the poultry production continuum:

flowchart TD
 A["Parent/Breeder Flocks"] -->|"Vertical transmission"| B["Eggs"]
 A -->|"Fecal shedding"| C["Environment: litter, water, feed"]
 C -->|"Horizontal transmission"| D["Broiler/Layer Flocks"]
 B -->|"Hatchery"| D
 D -->|"Slaughter/Processing"| E["Poultry Meat"]
 D -->|"Egg production"| F["Table Eggs"]
 E -->|"Retail"| G["Consumer Exposure"]
 F -->|"Retail"| G
 C -->|"Contaminated equipment"| D
 D -->|"Biosecurity measures"| H["Intervention"]
 H -->|"Probiotics, vaccines, phage"| D
 H -->|"Preharvest monitoring"| D

Antimicrobial Resistance: Mechanisms and Dissemination

The proliferation of antimicrobial-resistant Salmonella in poultry is driven by preharvest antibiotic use (particularly tetracyclines and penicillins) and the horizontal transfer of resistance genes via plasmids, integrons, and transposons [<a href="#ref-3">3</a>, <a href="#ref-11">11</a>, <a href="#ref-12">12</a>, <a href="#ref-23">23</a>]. Extended-spectrum beta-lactamase (ESBL) genes, notably blaCTX-M, are widespread among poultry isolates and are often carried on conjugative plasmids of the IncI1, IncF, and pESI types [<a href="#ref-7">7</a>, <a href="#ref-13">13</a>]. In retail chicken meat from China, blaCTX-M-65 and blaCTX-M-15 were identified in a high proportion of Infantis and Enteritidis isolates, with chromosomal integration observed in some clonal lineages [<a href="#ref-7">7</a>]. Similarly, South Korean poultry harbored blaCTX-M-15 on hybrid transposons Tn1721/Tn21, facilitating broad host-range dissemination.

Plasmid-mediated colistin resistance (mcr-1 and mcr-3) has emerged in poultry-derived Salmonella across Asia and Europe, posing a critical threat given colistin's role as a last-resort antibiotic [<a href="#ref-4">4</a>, <a href="#ref-16">16</a>]. In Bangladesh, mcr-1-positive strains were recovered from both retail chicken and live bird market sewage, indicating environmental amplification [<a href="#ref-16">16</a>]. The pESI megaplasmid, which carries multiple AMR determinants (aminoglycosides, tetracyclines, sulfonamides) and virulence factors, has been identified as a key driver of the global expansion of MDR Salmonella Infantis [<a href="#ref-24">24</a>]. Poultry populations in Ecuador, the United States, and Mexico harbor pESI-positive Infantis clones with reduced susceptibility to disinfectants [<a href="#ref-24">24</a>, <a href="#ref-25">25</a>].

Fluoroquinolone resistance, primarily arising from mutations in gyrA (e.g., D87Y) and parC, is prevalent in serovars Kentucky and Typhimurium [<a href="#ref-17">17</a>]. Ciprofloxacin-resistant Salmonella Typhimurium has demonstrated cross-tolerance to heat treatments, raising concerns about the efficacy of thermal inactivation in liquid food matrices. In Thailand, clonal spread of MDR Enteritidis with gyrA and aac(6')-Ib-cr was documented in broiler production chains. The convergence of AMR with biofilm formation and virulence genes further complicates control efforts; isolates from Xinjiang, China, harboring multiple efflux pump genes and csgD/bapA, exhibited enhanced biofilm production and surface adherence [<a href="#ref-26">26</a>].

Food Safety Implications and Control Strategies

Salmonella-contaminated poultry meat and eggs are primary vehicles for human salmonellosis worldwide [<a href="#ref-27">27</a>, <a href="#ref-28">28</a>, <a href="#ref-29">29</a>]. Contamination occurs at multiple points: on-farm colonization leads to carcass contamination during slaughter, while cross-contamination in processing plants and retail outlets propagates the pathogen [<a href="#ref-9">9</a>, <a href="#ref-19">19</a>, <a href="#ref-30">30</a>]. The risk is exacerbated by the ability of Salmonella to survive cold storage and form biofilms on stainless steel and plastic surfaces [<a href="#ref-26">26</a>]. Retail chicken nuggets in Turkey were found to harbor biofilm-forming Enteritidis with resistance to multiple antibiotics. Quantitative risk assessment models, such as quantile regression forests, have been developed to predict outbreak likelihood using multi-source surveillance data (e.g., temperature, humidity, retail sampling) [<a href="#ref-31">31</a>].

Interventions against Salmonella in poultry can be categorized as preharvest, harvest, and postharvest strategies. Preharvest approaches include biosecurity enhancement, competitive exclusion using probiotics, synbiotics, or cecal microbiota transplants, and vaccination [<a href="#ref-8">8</a>, <a href="#ref-14">14</a>, <a href="#ref-32">32</a>, <a href="#ref-33">33</a>]. Competitive exclusion with defined bacterial consortiums has demonstrated efficacy in reducing cecal colonization by multiple serovars in broilers. Synbiotic supplementation (prebiotics plus probiotics) decreased Enteritidis shedding and gut inflammation in challenged chickens [<a href="#ref-33">33</a>]. Oregano essential oil administered in feed reduced Enteritidis burden in market-age broilers, likely through disruption of quorum sensing and membrane integrity [<a href="#ref-32">32</a>]. Vaccination strategies include killed whole-cell, conjugate, outer-membrane vesicle, and multi-epitope protein vaccines [<a href="#ref-14">14</a>, <a href="#ref-34">34</a>]. A bivalent live Salmonella vaccine has been developed with a validated disc diffusion method to differentiate vaccine strains from field isolates [<a href="#ref-35">35</a>].

Bacteriophage therapy offers a targeted, non-antibiotic approach. Lytic phages specific to MDR Salmonella have shown activity against biofilm-embedded cells in vitro and reduced cecal colonization in turkey trials [<a href="#ref-36">36</a>]. A phage cocktail applied to commercial turkey farms significantly lowered cecal Salmonella counts compared to untreated controls. Nanoencapsulated antimicrobials (gentamicin, ciprofloxacin, lysozyme) within chitosan-metal-organic frameworks exhibit synergistic activity against drug-resistant strains, though regulatory approval for food animals remains pending [<a href="#ref-37">37</a>]. Postharvest interventions include intense pulsed light treatment for fresh produce that may cross-contaminate poultry products, and optimization of recipe composition to reduce Salmonella survival in tahini-based sauces.

Diagnostic Approaches and Monitoring Tools

Accurate detection and serotyping are fundamental to surveillance and outbreak investigations. Culture-based methods remain the gold standard but are time-consuming [<a href="#ref-22">22</a>, <a href="#ref-35">35</a>]. Indirect ELISA targeting the Sptp protein provides a serological screening tool for flock-level exposure [<a href="#ref-6">6</a>]. High-throughput sequencing techniques, including whole genome sequencing and CRISPR-SeroSeq, allow high-resolution subtyping and serovar discrimination directly from complex samples [<a href="#ref-20">20</a>, <a href="#ref-21">21</a>]. CRISPR-SeroSeq, which amplifies CRISPR spacers, can detect multiple serovars simultaneously in cecal contents, yielding a detailed diversity profile without prior culture. Core-genome multilocus sequence typing (cgMLST) of plasmids (e.g., IncI1) has been used to track geographic and temporal spread of AMR determinants in Canadian poultry [<a href="#ref-13">13</a>].

Machine learning models trained on genomic features (e.g., k-mer frequencies, SNP profiles) can predict host specificity and geographic origin of zoonotic serovars such as Kentucky. These genomic epidemiology approaches are increasingly integrated with traditional production records to quantify the contribution of primary breeders to downstream contamination [<a href="#ref-21">21</a>]. Monitoring programs must account for the intermittent shedding and low within-flock prevalence that challenge preharvest detection [<a href="#ref-22">22</a>]. Chick paper sampling, a non-invasive method, has been employed for One Health surveillance during outbreak investigations linked to backyard poultry.

Conclusion

Salmonella in poultry presents a complex interplay of host adaptation, environmental persistence, and human-driven AMR selection. Prevalence remains substantial across all production types, with MDR clones (Infantis, Kentucky, Enteritidis) expanding globally via plasmid-mediated dissemination. Effective control requires an integrated One Health framework combining biosecurity, vaccination, competitive exclusion, phage therapy, and rigorous genomic surveillance. Continued research into transmission ecology, bacterial stress responses, and novel intervention technologies is necessary to mitigate the food safety burden of poultry-associated salmonellosis.

References

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