Open research questions in Salmonella and Campylobacter epidemiology

What the literature leaves open

• Introduction Non-typhoidal Salmonella (NTS) is a leading cause of bacterial gastroenteritis worldwide, yet the pathogenic differences among co-circulating dominant clones remain poorly understood.

  Genomic and transcriptomic analyses reveal a Gifsy-1 prophage-encoded virulence module associated with enhanced epithelial adhesion of Salmonella ST34 in Huzhou, China · 2026 · DOI

• STRENGTHS AND LIMITATIONS OF THIS STUDYO_LIThis study will apply molecular diagnostics to identify Shigella and Campylobacter infections in a closely-followed cohort of index children and their families in a high-burden setting while contemporaneously sampling the household environment to identify potential sources of exposure.

  Sources and transmission dynamics of Campylobacter and Shigella using culture-independent molecular methods in Tanzania (SCAT): a protocol for a prospective observational cohort study · 2026 · DOI

• Long-term OIDD patterns, spatiotemporal distribution, and future trends in such dense urban settings are poorly understood, and insights from Beijing can provide valuable guidance for similar cities worldwide.

  Spatiotemporal patterns and 2025 forecasting of other infectious diarrheal diseases in Beijing, China: a 21-year population-based study (2004-2024) · 2026 · DOI

• Enteritidis lacking both ESSI-2 phage and IncX1 plasmid harbored parallel mutations in genes linked to DNA topology, antimicrobial peptide resistance, and virulence.

  The fitness of <i>Salmonella</i> Enteritidis in poultry is strongly shaped by interactions between bacteriophages, plasmids, and the microbial community · 2026 · DOI

• Our findings reveal that an underreported bacteriophage named ESSI-2 and IncX1 plasmids strongly influenced whether strains carried the gyrA mutations associated with decreased ciprofloxacin susceptibility.

  The fitness of <i>Salmonella</i> Enteritidis in poultry is strongly shaped by interactions between bacteriophages, plasmids, and the microbial community · 2026 · DOI

• Background Non-typhoidal Salmonella (NTS) is a leading foodborne pathogen in China, yet the transmission dynamics linking retail wet markets, food handlers, and hospitalised patients remain poorly characterised.

  Retail wet markets, food handlers, and hospitalised patients as nodes in a shared non-typhoidal Salmonella ecosystem: a one health molecular epidemiological pilot study in Wuhan, China · 2026 · DOI

• Although greater genetic diversity is expected in outbreaks linked to animal contact (24), the reasons for the proportionate heterogeneity of AR among isolates within BYPAS outbreaks warrants further study.

  Antimicrobial resistance in nontyphoidal Salmonella associated with multistate outbreaks linked to backyard poultry, United States, 2018–2023 · 2026 · DOI

• While this umbrella review provides a synthesis of research into the prevalence of Campylobacter on broiler farms, there are several limitations which limit the interpretation of results. Due to variabilities in study design, methodologies and outcomes measured across the included reviews, the synthesis presented is qualitative. Further quantitative meta-analysis may be possible, giving further insights into the data and allowing more robust conclusions to be drawn. in this umbrella review Of the quantitative data that were available, the heterogeneity of results and overlap in primary sources between systematic reviews mean that results should be interpreted and compared cautiously. Heterogeneity (I2) is a measure of the degree of variability in effect estimates between studies which cannot be attributed to chance. Of the 55 estimates in this umbrella review with heterogeneity estimates, 9 had “substantial” I2 values (61-75%) and 34 had “considerable” (>75%) I2 values. The high I2 values in this umbrella review therefore reflect high variability in study parameters between primary sources, which limits the confidence in pooled estimates. I2 may also be underestimated when the sample size is small due to low statistical power. Of the 57 estimates in this umbrella review based on more than one study, 22 had a sample size of ≤5 studies. The lack of standardisation between studies and the small number of studies contributing to many estimates means that the pooled prevalence estimates and their confidence intervals should be interpreted cautiously. A second limitation of the quantitative results in this umbrella review is the overlap in primary sources between systematic reviews. The corrected covered area (CCA) for the three systematic reviews with quantitative data was 26%. While some overlap between systematic reviews is expected, a CCA of >15% is typically interpreted as “very high” (Kirvalidze et al., 2023). This suggests that while the overall evidence base is relatively diverse, there is still a notable degree of duplication among studies. The presence of frequently cited foundational studies may disproportionately influence FSA Research and Evidence 37 Risk Factors for Campylobacter on Broiler Farms the perceived effectiveness of certain interventions. It is also worth noting that there is also likely to be substantial overlap between primary sources for the systematic reviews where a full list of primary references was not available (Newell et al., 2011; Pessoa et al., 2021). Agreement between reviews should therefore be interpreted with caution, considering this overlap. Furthermore, comparisons between risk factor groups from different systematic reviews may be affected by different classification assumptions. For example, more prevalence estimates are available from Agunos et al. (2014), as their breakdown of categories was generally more granular than the other reviews. A third limitation of this umbrella review is that interactions between risk factors have not been accounted for. For example, biosecurity measures may be less effective in preventing flock colonisation if the prevalence of Campylobacter is very high in the external environment. Finally, there was a particular absence of quantitative data for the intervention category of farm management and biosecurity, despite this being a key risk factor highlighted by all systematic reviews. Overall, risk prioritisation should consider the underlying data quality and variability presented in this umbrella review.

  Risk Factors for <i>Campylobacter</i> on Broiler Farms · 2026 · DOI

• Despite the valuable insights provided by the current pharmacotherapeutic assessment of three major infectious disorders, certain limitations of the study included a retrospective analysis, including the data extracted from hospital records of case profiles that might be associated with poor documentation quality, potential recall errors, and incomplete diagnostic or therapeutic profiles. Though 300 profiles have been observed, some intervening factors, such as socioeconomic and nutritional factors, and previous utilization or adherence to antimicrobials, have not been accurately covered. Secondly, the data was including JIH collected from two hospitals only, (Abbottabad) and DHQ hospital (Haripur), which may not represent the entire regional population, leading to potential bias due to differences in demographic and clinical outcomes of the patients belonging to regional or rural health care centers. The selection of broader and more diverse health care settings might enhance generalizability. Similarly, the micro-organism’s susceptibility and resistance pattern towards the selected antimicrobial medicaments were not evaluated in the current study, which might be correlated to check the pathogen-specific therapeutic efficacy of antimicrobial drugs. The study could be more from inclusion of microbial cultures and antibiograms to effectively check the therapeutic efficacy of prescribed antibiotics, particularly against the resistant bacterial strains (such as S. Typhi, E. coli, and S. Pneumoniae). Though sex disaggregated prevalence was included, particularly sex specific therapeutic variabilities were not assessed in detail. Similarly, gender associated socio- cultural determinants were not measured quantitatively, limiting their impact on risk of disease occurrence, progression, and therapeutic outcome. Furthermore, the study only covered Drug-Drug interactions, while not quantifying the pharmacokinetic variations among cases of variable age groups or patients with comorbidities leading to variable therapeutic responses, particularly among the geriatric and mal- nourished population.

  Pharmacotherapeutic Assessment of Three Major Infectious Disorders in District Abbottabad and Haripur · 2026 · DOI

• Controlling these infections requires a concerted effort between different actors (governments, the Ministry of Public Health and Prevention of Chad, basic humanitarian services and the population), suggesting the need for future implementation and evaluation of coordinated public health interventions.

  Biochemical and antibiotic resistance profile of Salmonella isolated from stool in N'Djamena, Chad: associated risk factors · 2026 · DOI

• There was no statistically significant relationship between isolated bacteria and the antibiotics used in bacterial diarrhea (p > 0.05), indicating a need for further investigation into why antibiotic therapy was mostly non-probabilistic and not based on antibiogram results.

  Biochemical and antibiotic resistance profile of Salmonella isolated from stool in N'Djamena, Chad: associated risk factors · 2026 · DOI

• The persistent dominance of non-typhoidal Salmonella and Campylobacter as leading foodborne pathogens is a powerful reflec- tion of their successful adaptation to the realities of modern, The author(s) declared that financial support was received for this work and/or its publication. This work were supported by Role of Regional Environmental Exposures in Membranous Nephropathy: A Guangxi-Based Study (GuiKe: AB24010219); Preliminary Project of the Guangxi Bureau of Geology & Mineral Prospecting & Exploitation (GXDK202643); Young Elite Scientists Sponsorship Program by GXAST (GXYESS2025085).

  Epidemiology, antimicrobial resistance transmission, and One Health–based prevention of non-typhoidal Salmonella and Campylobacter infections: an updated literature review · 2026 · DOI

• Environmental surveillance (ES) of <ns3:italic>Salmonella</ns3:italic> Typhi in sewage and wastewater using molecular methods may offer a low-cost alternative, but its performance in comparison with clinical surveillance has not been assessed.

  Environmental surveillance for Salmonella Typhi as a tool to estimate the incidence of typhoid fever in low-income populations. · 2023 · DOI

• <ns3:p> <ns3:bold>Background:</ns3:bold> The relationship between asymptomatic <ns3:italic>Salmonella</ns3:italic> exposure within the gastrointestinal tract and <ns3:italic>Salmonella</ns3:italic> bacteraemia is poorly understood, in part due to the low sensitivity of stool culture and the lack of validated molecular diagnostic tests for the detection of <ns3:italic>Salmonella</ns3:italic> in the stool.

  Performance of molecular methods for the detection of Salmonella in human stool specimens · 2021 · DOI

• Due to the specificity, and the demanding features of Campylobacter, as well as poorly equipped microbiological laboratories, campylobacteriosis is insufficiently studied in our country.

  Participation of some campylobacter species in the etiology of enterocolitis · 2004 · DOI

• The reason for the decline in protection remains unknown, but suggests that changes are needed to the vaccination schedule to improve the long-term protective efficacy of TCVs.

  Development of an 8-valent Salmonella and Shigella MAPS vaccine · 2026 · DOI

• Organic acid mixtures are widely employed as feed additives to suppress enteric pathogens, yet their mechanisms of host protection at the intestinal epithelium remain unclear.

  Future-ready antimicrobials: harnessing organic acids to override Ca2+-driven barrier failure during Salmonella infection · 2026 · DOI

• Although individual risk factors are well described, ecological determinants such as private well water use and proximity to animal feeding operations remain understudied.

  An ecological study of sociodemographic, agricultural and environmental factors associated with laboratory confirmed campylobacteriosis cases in Tennessee · 2026 · DOI

• coli and the limited available data regarding the effect of apramycin use on apramycin resistance highlight the gaps in evidence and challenges in interpreting the role of apramycin use in apramycin resistance of human or animal pathogens.

  Apramycin resistance in bacteria isolated from animals: A systematic review and meta-analysis · 2026

• However, interventional studies to reduce exposure to these pathogens have been ineffective, and evidence that identifies putative sources and species transmission dynamics between humans, animals and the environment is scarce.

  Sources and transmission dynamics of Campylobacter and Shigella using culture-independent molecular methods in Tanzania (SCAT): a protocol for a prospective observational cohort study · 2026 · DOI

• These findings emphasize the importance of mechanistic epidemiologic models for informing public health responses amidst outbreaks with foodborne potential and highlight the need for additional research into raw milk consumption patterns to better understand this exposure pathway.

  Quantitative Microbial Risk Assessment of Human H5N1 Infection From Consumption of Fluid Cow's Milk · 2026 · DOI

• Early microbial exposure during embryogenesis may shape post-hatch gut development in poultry, yet the effects of sublethal pathogenic exposure and in ovo synbiotics remain unclear.

  Establishment of In Ovo Salmonella Enteritidis Infection and Synbiotic Delivery Models in Chick Embryos and Their Effects on Early Gut Health · 2026 · DOI

• Current limited literature suggests that these emerging atypical Salmonella serovars pose a unique threat to human health due to their novel host adaptations, antimicrobial resistance profiles, epidemiology and infection sources.

  New strains, new threats : the rise of atypical non-typhoidal salmonella serovars and what it means for global health · 2026

• This emerging resistance mechanism may be underpinned by multiple genetic determinants, yet it has not been systematically characterized or elucidated until now.

  The synergistic action of reduced membrane permeability and antibiotic sequestration as a novel mechanism for carbapenem resistance in <i>Campylobacter</i> · 2026 · DOI

• Typhimurium, analogous mechanisms remain to be explored. Future studies are needed to determine whether similar localization or substrate-targeting features contribute to its non-lytic secretion of chitinase.

  Non-lytic protein secretion by virulence-associated Type 10 Secretion Systems in Salmonella enterica · 2026 · DOI

Most-cited papers in Salmonella and Campylobacter epidemiology

• The European Union summary report on antimicrobial resistance in zoonotic and indicator bacteria from humans, animals and food in 2021–2022 · EFSA Journal · 2024 · 112 citations
• Preliminary Incidence and Trends of Infections Caused by Pathogens Transmitted Commonly Through Food — Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 2016–2021 · MMWR Morbidity and Mortality Weekly Report · 2022 · 63 citations
• Application of Whole‐Genome Sequences and Machine Learning in Source Attribution of <i>Salmonella</i> Typhimurium · Risk Analysis · 2020 · 63 citations
• The global burden of enteric fever, 2017–2021: a systematic analysis from the global burden of disease study 2021 · EClinicalMedicine · 2024 · 53 citations
• Fresh vegetables and fruit as a source of <i>Salmonella</i> bacteria · Annals of Agricultural and Environmental Medicine · 2022 · 50 citations
• Salmonella, Shigella, and Campylobacter: Common Bacterial Causes of Infectious Diarrhea · Pediatric Annals · 1994 · 28 citations
• A quantitative prevalence of <i>Escherichia coli</i><scp>O157</scp> in different food samples using real‐time <scp>qPCR</scp> method · Food Science & Nutrition · 2022 · 23 citations
• Biofilm Production Potential of <i>Salmonella</i> Serovars Isolated from Chickens in North West Province, South Africa · Polish Journal of Microbiology · 2020 · 17 citations
• Environmental surveillance for Salmonella Typhi as a tool to estimate the incidence of typhoid fever in low-income populations. · Wellcome Open Research · 2023 · 15 citations
• Performance of molecular methods for the detection of Salmonella in human stool specimens · Wellcome Open Research · 2021 · 10 citations

Most recent work

• Epidemiology, antimicrobial resistance transmission, and One Health–based prevention of non-typhoidal Salmonella and Campylobacter infections: an updated literature review · Frontiers in Microbiology · 2026
• Molecular diversity and phylogenetic characterization of the invA gene in non-typhoidal Salmonella from domestic animals and wildlife in Zambia · Veterinary World · 2026
• Biochemical and antibiotic resistance profile of Salmonella isolated from stool in N'Djamena, Chad: associated risk factors · Journal of Drug Delivery and Therapeutics · 2026
• Large outbreak of <i>Salmonella</i> Muenchen linked to dried coconut pieces, September 2020 to July 2021, Germany · Epidemiology and Infection · 2026
• Disseminated multidrug-resistant Salmonella enterica serovar Dublin infection associated with plasmid-borne CMY-2 gene in a patient with travel to a farm in Mexico · European Journal of Clinical Microbiology & Infectious Diseases · 2026
• Genomic characterization of Salmonella enterica isolates causing typhoid among Ghanaian patients · PLOS One · 2026
• Retail wet markets, food handlers, and hospitalised patients as nodes in a shared non-typhoidal Salmonella ecosystem: a one health molecular epidemiological pilot study in Wuhan, China · European Journal of Clinical Microbiology & Infectious Diseases · 2026
• Challenges in the Diagnosis and Management of Campylobacter fetus subsp. venerealis in Bovine Genital Campylobacteriosis: Resistance and Control Strategies · Pakistan Veterinary Journal · 2026
• Genomic surveillance captures resistance evolution in Salmonella enterica ST376 during prolonged disseminated infection in an immunocompromised patient from the United Arab Emirates · Journal of Infection and Public Health · 2026
• Antimicrobial Resistance in Veterinary Bacterial Pathogens: Resistance Patterns, Zoonotic Risks and One Health Implications · Pathogens · 2026

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