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Salmonella and Campylobacter epidemiology
Research Guide
What is Salmonella and Campylobacter epidemiology?
Salmonella and Campylobacter epidemiology is the study of the incidence, distribution, transmission, and control of Salmonella and Campylobacter bacteria as major causes of foodborne illnesses in human populations.
The field encompasses surveillance data showing that 31 major pathogens, including Salmonella and Campylobacter, cause 9.4 million foodborne illness episodes annually in the United States (Scallan et al., 2010). Foodborne diseases from these pathogens contribute to approximately 76 million illnesses, 325,000 hospitalizations, and 5,000 deaths each year in the US (Mead et al., 1999). There are 110,421 works on Salmonella and Campylobacter epidemiology in the literature.
Research Sub-Topics
Salmonella Source Attribution Modeling
This sub-topic develops microbial subtyping and epidemiological models to apportion human salmonellosis cases to animal, food, and environmental reservoirs. Researchers use WGS, PFGE, and outbreak data for quantitative risk attribution.
Campylobacter jejuni Population Genetics
Researchers apply whole-genome sequencing to study genetic diversity, recombination, and host adaptation in C. jejuni lineages from poultry, ruminants, and humans. Analysis reveals transmission dynamics and virulence evolution.
Antimicrobial Resistance in Non-Typhoidal Salmonella
This area tracks resistance plasmids, genes like blaTEM, and multidrug phenotypes in NTS from food animals and clinical cases. Studies quantify fitness costs and transmission via food chains.
Poultry-Associated Campylobacteriosis Outbreaks
Researchers investigate molecular epidemiology of poultry meat-linked Campylobacter outbreaks using MLST, WGS, and traceback investigations. Focus includes flock colonization, processing contamination, and consumer exposure.
Salmonella and Campylobacter Whole Genome Sequencing Surveillance
This sub-topic implements national WGS platforms for real-time outbreak detection, strain tracking, and international comparison. Methodological advances include core genome MLST and metadata integration.
Why It Matters
Salmonella and Campylobacter drive substantial foodborne disease burdens, with Scallan et al. (2010) estimating 9.4 million US cases yearly from 31 pathogens including these bacteria, informing targeted interventions like poultry processing controls. Mead et al. (1999) quantified 76 million illnesses and 5,000 deaths annually, highlighting needs for enhanced surveillance such as the CDC's FoodNet, now scaled back to focus on Salmonella among top contributors to hospitalizations. Recent preprints detail multidrug-resistant Salmonella enterica serotype Infantis (REPJFX01 strain) emergence during 1979-2022 and WGS-based Campylobacter surveillance in Italian chicken meat (2023), while PATH-SAFE Consortium (2025) recommends genomic surveillance using Salmonella as exemplar for outbreak source tracing, as shown in Denmark (2015-2017) linking Campylobacter jejuni patient isolates to sources.
Reading Guide
Where to Start
"Foodborne Illness Acquired in the United States—Major Pathogens" by Scallan et al. (2010), as it provides foundational US incidence estimates for 31 pathogens including Salmonella and Campylobacter from surveillance data, essential for understanding disease burden.
Key Papers Explained
Scallan et al. (2010) builds on Mead et al. (1999) by updating foodborne illness estimates to 9.4 million episodes for 31 pathogens, refining the earlier 76 million illnesses and 5,000 deaths figure with credible intervals from active surveillance. Neidhardt (1996) offers cellular and molecular biology context for Salmonella, complementing epidemiological burdens in Scallan and Mead. Van Boeckel et al. (2015) connects to resistance trends in food animals, relevant for Salmonella and Campylobacter transmission.
Paper Timeline
Most-cited paper highlighted in red. Papers ordered chronologically.
Advanced Directions
Preprints emphasize WGS for Salmonella in African LMICs (446 isolates, 2019-2023) and multidrug-resistant Infantis (REPJFX01, 1979-2022); Campylobacter surveillance in Italy (2023) and Denmark outbreaks (2015-2017). PATH-SAFE (2025) pushes genomic protocols; CDC FoodNet now prioritizes Salmonella amid scaling back.
Papers at a Glance
| # | Paper | Year | Venue | Citations | Open Access |
|---|---|---|---|---|---|
| 1 | Escherichia coli and Salmonella :cellular and molecular biology | 1996 | ASM Press eBooks | 8.2K | ✕ |
| 2 | Foodborne Illness Acquired in the United States—Major Pathogens | 2010 | Emerging infectious di... | 7.5K | ✓ |
| 3 | Food-Related Illness and Death in the United States | 1999 | Emerging infectious di... | 7.2K | ✓ |
| 4 | UNIDENTIFIED CURVED BACILLI IN THE STOMACH OF PATIENTS WITH GA... | 1984 | The Lancet | 5.4K | ✕ |
| 5 | Pathogenic Escherichia coli | 2004 | Nature Reviews Microbi... | 5.3K | ✕ |
| 6 | <i>In Silico</i> Detection and Typing of Plasmids using Plasmi... | 2014 | Antimicrobial Agents a... | 4.5K | ✓ |
| 7 | Escherichia Coli and Salmonella: Typhimurium Cellular and Mole... | 1987 | — | 4.1K | ✕ |
| 8 | Global trends in antimicrobial use in food animals | 2015 | Proceedings of the Nat... | 3.6K | ✓ |
| 9 | Cowan and Steel's Manual for the Identification of Medical Bac... | 1993 | Cambridge University P... | 3.1K | ✕ |
| 10 | TYGS is an automated high-throughput platform for state-of-the... | 2019 | Nature Communications | 2.9K | ✓ |
In the News
Analysis highlights bacterial contamination, multidrug ...
which collects data on enteric bacteria found in people, retail meat samples, and animals at slaughter. NARMS focuses on bacteria that are associated with foodborne illness, such as*Salmonella, Esc...
PATH-SAFE Consortium Recommendations for Genomic Surveillance of Foodborne Diseases, Using Salmonella as an Exemplar | Published in FSA Research and Evidence
Vallejo-Trujillo, A., …Vegvari, C. (2025). PATH-SAFE Consortium - Recommendations for Genomic Surveillance of foodborne diseases, using Salmonella as an exemplar.*FSA Research and
Whole-Genome Sequencing to Detect Numerous Campylobacter jejuni Outbreaks and Match Patient Isolates to Sources, Denmark, 2015–2017
by enhancing outbreak detection, source tracing, and potentially prevention of human infections. RESEARCH public health surveillance of several foodborne pathogens (e.g., Salmonella, Listeria, an...
The CDC quietly scaled back a surveillance program for ...
As of July 1, the Foodborne Diseases Active Surveillance Network (FoodNet) program has reduced surveillance to just two pathogens: salmonella and Shiga toxin-producing E. coli (STEC), a spokesperso...
The CDC Is Scaling Back a Major Food Safety Program ...
As for the decision to keep monitoring*Salmonella*and STEC, the HHS spokesperson said the two pathogens are among the top five contributors to foodborne illnesses, hospitalizations, and deaths in A...
Code & Tools
`SamnTrek` enables rapid integration of NCBI Pathogen Detection (NPD) data to place local _Salmonella_ strains in a global context. Specifically, g...
*epidemics*is an R package that provides modular representations of populations and public health response measures, allowing them to be combined w...
# epiworld epiworld logo This C++ library provides a general framework for epidemiologic simulation. The core principle of`epiworld`is fast epid...
Summer is a Python-based framework for the creation and execution of compartmental (or "state-based") epidemiological models of infectious disease ...
Explore a range of infectious disease models in a consistent framework. The primary aim of `idmodelr` is to provide a library of infectious disease...
Recent Preprints
Using metagenomics and whole-genome sequencing to ...
study, we use whole-genome sequencing (WGS) and metagenomic approaches to characterize enteric pathogens from human, animal, and environmental sources across four African LMICs between 2019 and 202...
(PDF) Public health importance of foodborne pathogens
promote weight gain and elevate risk for diabetes \[16\]. Foodborne Pathogens: The most commonly recognized FBPs include bacteria (e.g. Campylobacter,Salmonella, E. coli,L. monocytogenes,Shigell...
Epidemiology and antimicrobial resistance of Salmonella enterica serotype Infantis in the United States: infections and emergence of a multidrug-resistant strain during 1979-2022 - PubMed
**Background:***Salmonella*infections are a major cause of human illness in the United States.*Salmonella enterica*serotype Infantis has re-emerged as a leading serotype with the emergence of a mul...
WGS-based surveillance for Campylobacter spp. in human infections and chicken meat production in Italy (2023)
*Campylobacter*spp. infections are the most widespread zoonoses affecting humans and represent the leading cause of bacterial food-borne gastroenteritis worldwide [ 1 ] ( https://www.who.int/news-r...
Risk factor analysis of Campylobacter spp., Listeria monocytogenes and Salmonella spp. in the chicken meat value chain
* 5Division of Epidemiology, ICAR-Indian Veterinary Research Institute, Izatnagar, India **Introduction:**A cross-sectional study was conducted to evaluate microbiological risk factors associated w...
Latest Developments
Recent research indicates that as of early 2026, epidemiologic data show ongoing outbreaks of Salmonella, with 45 cases reported in January 2026 across 21 states, and a significant increase in Campylobacter and Salmonella cases in the UK, reaching the highest levels in a decade (CDC, January 2026; GOV.UK, June 2025). Additionally, advances in genomic analysis are being used to attribute Salmonella sources and understand transmission pathways, with studies published in 2024 highlighting the use of whole-genome sequencing to trace food sources and analyze bacteria from poultry production stages (CDC; PMC).
Sources
Frequently Asked Questions
What is the annual burden of foodborne illnesses from Salmonella and Campylobacter in the US?
Scallan et al. (2010) estimated 9.4 million episodes from 31 major pathogens including Salmonella and Campylobacter using active and passive surveillance data. Mead et al. (1999) reported 76 million illnesses, 325,000 hospitalizations, and 5,000 deaths yearly from foodborne diseases encompassing these pathogens.
How does whole-genome sequencing aid Salmonella and Campylobacter epidemiology?
Recent preprints describe WGS characterizing 446 bacterial isolates including Salmonella and Campylobacter from human, animal, and environmental sources in African LMICs (2019-2023). WGS-based surveillance detected Campylobacter spp. in Italian human infections and chicken meat (2023), and matched Campylobacter jejuni outbreaks to sources in Denmark (2015-2017).
What are key risk factors for Salmonella and Campylobacter in food chains?
A cross-sectional study evaluated microbiological risk factors for Salmonella spp., Campylobacter spp., and Listeria monocytogenes along the chicken meat value chain in India. NARMS data highlight bacterial contamination and multidrug resistance in Salmonella, E. coli, and Campylobacter from retail meat and animals.
Why focus surveillance on Salmonella amid program changes?
CDC's FoodNet scaled back to Salmonella and STEC as of July 1, as they rank among top five contributors to US foodborne illnesses, hospitalizations, and deaths. PATH-SAFE Consortium (2025) uses Salmonella as exemplar for genomic surveillance recommendations in foodborne diseases.
What recent strains concern Salmonella epidemiology?
A multidrug-resistant Salmonella enterica serotype Infantis strain (REPJFX01, designated by CDC) has emerged as a leading serotype in US infections during 1979-2022.
Open Research Questions
- ? How can WGS integrate local Salmonella strains into global NCBI Pathogen Detection contexts for improved epidemiology, as enabled by tools like SamnTrek?
- ? What are the transmission dynamics of multidrug-resistant Campylobacter from chicken meat production to human infections, based on Italian 2023 surveillance?
- ? How do risk factors vary for Salmonella, Campylobacter, and Listeria along regional chicken meat value chains, such as in India?
- ? What surveillance gaps arise from CDC FoodNet's reduction to only Salmonella and STEC, impacting Campylobacter tracking?
- ? How effectively does genomic surveillance, using Salmonella exemplars, trace outbreaks for multiple enteric pathogens like Campylobacter?
Recent Trends
CDC FoodNet reduced surveillance to Salmonella and STEC (July 2025), reflecting their top-five status in illnesses and deaths.
Preprints report WGS on 380 Salmonella and Campylobacter genomes from African sources (2019-2023), multidrug-resistant S. Infantis emergence (1979-2022), and Campylobacter in Italian chicken/human cases.
2023PATH-SAFE advances Salmonella genomic surveillance; NARMS notes multidrug resistance in retail meat bacteria.
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