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Salmonella: a common foodchain contaminant frequently isolated from foodborne infection

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Salmonella is a normally motile, Gram-negative, rod-shaped bacterium belonging to the family Enterobacteriaceae


What is Salmonella spp.?

Salmonella is a normally motile, Gram-negative, rod-shaped bacterium belonging to the family Enterobacteriaceae.  The genus Salmonella is divided into two species that can cause illness in humans (salmonellosis), S. enterica and S. bongori.  
Salmonella enterica, which is of the greatest public health concern (WHO, 2015), is comprised of six subspecies, namely enterica, salamae, arizonae, diarizonae, houtenae and indica
Salmonella species (spp.) and subspecies can be distinguished based on differential biochemical characters (Grimont P. & Weill F.X., 2007).
Salmonella isolates are further subdivided into serotypes according to the Kauffmann-White classification based on their flagellar (H) and somatic (O) antigens (Grimont P. & Weill F.X., 2007) or using genome-based serotyping approaches (Banerji S. et al., 2020).  Salmonella spp. are commonly referred to by their serotype names. 
Over 2500 Salmonella serotypes have been referenced (Ibrahim GM and Morin PM, 2018); However, only a few of them, such as Enteritidis and Typhimurium, have proven to be consistent isolates along the food chain and responsible for significant foodborne human infections (EFSA & ECDC, 2021; CDC, 2021). In fact, chromosomal or plasmid-borne virulence and regulatory factors often associated to antimicrobial resistance determinants (Cadel-six S. et al., 2021) confer upon them striking fitness for survival and spread (Chen R.A. et al., 2019; Huang X. et al., 2019; Guillén, S. et al., 2021) within animal feeds, farm animals, food industries, foodstuffs and human beings. 


What are the risks for the consumers?

Healthy persons infected with Salmonella often experience fever, diarrhea, nausea, vomiting and abdominal pain. In rare circumstances, bloodstream infections can produce more severe illnesses especially in young children or elderly people, and others with weakened immune systems.
Mortality is generally less than 1%; However, fatality rate associated to specific serotypes such as S. Enteritidis can surge up to 3.6 % with the elderly being particularly affected. (FDA, 2012). Multidrug resistant Salmonella infections have more serious health outcomes (EFSA & ECDC, 2021b).

Key figures:

In 2020, EU Salmonella reporting recorded the lowest number of human cases since 2007 owing to the impacts of both the withdrawal of the United Kingdom from the EU and the COVID-19 pandemic. 
The number of confirmed cases of human salmonellosis was 52,702, corresponding to an EU notification rate of 13.7 per 100,000 population. This was a decrease of 29.7% and 32.8% compared with the rate in 2019 (19.5 and 20.4 per 100,000 population) with and without the data from the United Kingdom, respectively. Notwithstanding, the overall trend for salmonellosis in 2016–2020 did not show any statistically significant increase or decrease (EFSA-ECDC, 2021).
The proportion of hospitalized cases was 29.9%, which was lower than in 2019, with an EU case fatality rate of 0.19%.
The top five Salmonella serovars involved in human infections overall were S. Enteritidis (48.7%), S. Typhimurium (12.4%), monophasic S. Typhimurium (1,4, [5],12:i:-) (11.1%), S. Infantis (2.5%) and S. Derby (1.2%).
In total, 694 foodborne outbreaks of Salmonella were reported causing 3,686 illnesses, 812 hospitalizations and seven deaths. Salmonella caused 22.5% of all EU foodborne outbreaks in 2020. The majority (57.9%) of the reported foodborne outbreaks of Salmonella were caused by S. Enteritidis.

In the US, during 2020 (CDC, 2021), 26% fewer infections were reported for all pathogens compared with the average annual number reported during 2017–2019. As in the EU, the widespread 2020 interventions associated to the covid-19 pandemic as well as other changes to daily life and hygiene behaviors, including increased handwashing, have likely changed exposures to foodborne pathogens. 
The overall 2020 Salmonellosis incidence in the US was 13.3 per 100,000; The proportion of hospitalized cases was 29 % and the fatality rate, 0,7 %. The seven most common serotypes were Enteritidis (1.6 per 100,000 population), Newport (1.5), Javiana (1.0), Typhimurium (0.9), I 4,[5],12: i: - (0.5), Hadar (0.4), and Infantis (0.3). Most (73%) of the outbreak-associated Salmonella infections during 2020 were caused by three serotypes: Newport (35%), Hadar (21%), and Enteritidis (17%). 


How are Salmonella spp. transmitted?

Salmonella can colonize the intestinal tracts of vertebrates, including livestock, wildlife, domestic pets, and humans. They can also survive for long times in diverse environments (Chen G. et al., 2021). 
It is spread through the fecal-oral route and through contact with contaminated water. It may then contaminate meat, irrigation water (thus contaminating Produce in the field), soil and insects, factory equipment, hands, kitchen surfaces and utensils (FDA, 2012).
Salmonellosis is mostly foodborne (94 % - Scallan E. et al., 2011) but direct contact with live animals and environmental transmission have been identified as potential sources (Pires S.M. et al., 2011).


What are the Food industries affected by Salmonella spp.?

Salmonella is a significant and objectionable concern for most of the food sectors (primary productions and the downstream corresponding food industries). In the US (IFSAC, 2021), more than 75% of Salmonella illnesses were attributed to seven food categories i.e. chicken, fruits, pork, seeded vegetables (such as tomatoes), other Produce (such as nuts), turkey and eggs. In the EU, the three food vehicles most involved in foodborne salmonellosis outbreaks were ‘eggs and egg products’, followed by pig meat and bakery products (EFSA & ECDC, 2021).
Some key serotypes such as Enteritidis or Typhimurium has been more closely associated respectively with laying hens (Pires S.M. et al., 2011) and with the pig reservoir (Pires S.M. et al., 2011; Munk et al., 2020; Arnold et al., 2021).


How can Salmonella spp. be prevented and controlled in the food industry?

Food business operators along the food chain must consider their business specificities, design and implement their tailor-made HACCP- based control systems and Good Hygiene & Manufacturing practices as required by US and EU regulations (FDA 21CFR 1 et al., 2015; 9CFR304 et al., 1996; EU 852/2004).
Salmonella spp. which is consistently a hazard more than reasonably likely to occur shall be part of most of the food industries’ HACCP or food safety plans to prevent the adulteration of foodstuffs (EU 178/2002; Federal Food, Drug & Cosmetic Act, 1938; FDA-FSMA, 2011). Additional regulatory measures for the control of the most public-health significant Salmonella serotypes such as Enteritidis and Typhimurium have been set up in the EU and in the US (read the specific article: Salmonella Enteritidis and Typhimurium factsheet).


How can the presence of Salmonella spp. be detected in the food industry?

EU and US regulations specifically require that food business operators perform microbiological testing as appropriate when they are validating and verifying the effectiveness of their HACCP and GHP -based control systems (EU 852/2004; FDA, 2011).

Salmonella spp. monitoring is specifically put in place i) by regulatory agencies for compliance and surveillance purposes (EU 625/2017; FDA, 2011) and ii) within concerned food sectors by business partners primarily for customer protection but also for the prevention of both mandatory product recall (FDA, 2011; EU 178/2002) and legal prosecution.

Different microbiological methods either traditional or molecular (PCR or Whole Genome sequencing) for the detection of Salmonella spp and/or serotyping of Salmonella Enteritidis or Typhimurium have been described, notably:

- Standardized reference methods,
. the FDA-BAM, 2021,
. the USDA NPIP standard, 2019
. the MLG 4.11, 2021
. the ISO 6579-1:2017 and 2020 amendment, ISO TR 6579-3:2014 (serotyping), ISO/DTS 6579-4 (1,4,[5],12, i:-).

- AOAC or EN ISO 16140-2:2016 or ISO 16140-6:2019 validated alternative methods. Compared to the standard methods, these rapid methods usually bring ease of use as well as reduced times to results which add flexibility to the management of the analytical and business flows.

bioMérieux provides the food safety managers with proven standardized or validated methods for the management of Salmonella spp. or S. Enteritidis & S. Typhimurium along the Food Chain.

Jean-Pierre Facon
Written by
Jean-Pierre FACON

(PhD), Biotech consultant

Picture Isabelle DESFORGES
Written by

Global Marketing Scientific Manager / Scientific Affairs

Food Business Industry Unit, bioMérieux SA, France

French Delegate of Food Microbiology Standardization committees
(AFNOR V08B, ISO/TC 34/SC 9 and CEN/TC 463)


Sample and culture media preparation:

- DILUMAT® gravimetric diluter
- SMASHER®  lab blender
- MASTERCLAVE® automated media preparator
Traditional Culture media:
- large range of traditional and standard culture media: Rappaport Vassiliadis Soy Broth, MKTTn, XLD ISO 6579 

Chromogenic culture media for standard or alternative methods:

- SMS® - Selective medium for the detection of Salmonella 
- SALMA™ (Salmonella One Day) - Selective medium for the detection of Salmonella spp 
- chromID™ Salmonella - Chromogenic medium for the selective isolation and differentiation of the genus Salmonella
- ASAP™ - Chromogenic medium for the isolation of Salmonella
- SALSA™ agar - Bi-plate for the detection of Salmonella and Shigella

List of official validations: (bottom of the page)
Rapid detection solutions: 

VIDAS® Enzyme Linked Fluorescent Assay (ELFA) pathogen detection automated platform:

-VIDAS®  UP Salmonella (SPT)
-VIDAS®  Salmonella (SLM)
-VIDAS®  Salmonella (SLM) Easy Salmonella
-VIDAS®  Immuno-Concentration Salmonella (ICS)

GENE-UP® Molecular pathogen detection automated platform:

-GENE-UP®  Salmonella 2
-GENE‑UP®S. Enteritidis & S. Typhimurium kit (SEST) (Ref.423127)
Real‑time Polymerase Chain Reaction (PCR) assay for the detection of Salmonella Enteritidis and Salmonella Typhimurium in food
(Official validation to come in 2022)

October 19, 2021
List of official validations (for VIDAS® and GENE-UP® methods)
(bottom of pages)

-API®  20E, API®  Rapid 20E
-ID32E, Rapid ID32E

-Salmonella spp Latex

List of official validations
(bottom of the page)

AST (Antibiotic Susceptibility Testing)



Arnold M. et al. Bayesian Source attribution of Salmonella Typhimurium isolates from human patients and farm animals in England and Wales. 2021. Front. Microbiol. 12:579888.

Banerji S. et al. Genome-based Salmonella serotyping as the new gold standard. Nature Research, 2020, 10:4333.

Cadel-Six S. et al. The Spatiotemporal Dynamics and Microevolution Events That Favored the Success of the Highly Clonal Multidrug-Resistant Monophasic Salmonella Typhimurium Circulating in Europe. Front. Microbiol. 2021, 12:651124.

CDC (US Center of Disease Control). Decreased Incidence of Infections Caused by Pathogens Transmitted Commonly Through Food During the COVID-19 Pandemic — Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 2017–2020. MMWR, 2021, 70 (38): 5p.
CHEN G. et al. Induction of a Viable but Nonculturable State, Thermal and Sanitizer Tolerance, and Gene Expression Correlation with Desiccation-Adapted Biofilm and Planktonic Salmonella in Powdered Infant Formula. Journal of Food Protection, 2021, 84 (7), : 1194–1201.<
Cheng RA. et al. Embracing Diversity: Differences in Virulence Mechanisms, Disease Severity, and Host Adaptations Contribute to the Success of Nontyphoidal Salmonella as a Foodborne Pathogen. Front. Microbiol. 2019, 10:1368.

EFSA and ECDC (European Food Safety Authority and European Centre for Disease Prevention and Control). The European Union One Health 2020 Zoonoses Report. EFSA Journal 2021;19 (12):6971, 324 pp.

EFSA and ECDC. The European Union Summary Report on Antimicrobial Resistance in zoonotic and indicator bacteria from humans, animals and food in 2018/2019. EFSA Journal 2021b ;19(4):6490, 179 pp.

EU Regulation 178/2002 laying down the general principles and requirements of food law, establishing the European Food Safety Authority and laying down procedures in matters of food safety: 24 p.

EU Regulation 852/2004 on the hygiene of foodstuffs: 23 p.

EU REGULATION 625/2017 on official controls and other official activities performed to ensure the application of food and feed law. 142 p.

FDA (Food and Drug Administration). Bad Bug Book, Foodborne Pathogenic Microorganisms and Natural Toxins - Salmonella species. Second Edition. 2012: 5 p.

Federal Food, Drug & Cosmetic Act. To prohibit the movement in interstate commerce of adulterated and misbranded food, drugs, devices, and cosmetics, and for other purposes. 1938.

FDA Food Safety Modernization Act (FSMA) – Public Law to amend the Federal Food, Drug, and Cosmetic Act with respect to the safety of the food supply. 2011. 89 p.

FDA. 21CFR Parts 1, 11, 16, 106, 110, 114, 117, 120, 123, 129, 179, and 211. Food Safety Modernization Act. Current Good Manufacturing Practice, Hazard Analysis, and Risk-Based Preventive Controls for Human Food. 2015, 80 (180): 55908-56168.

FDA - BAM (Bacteriological Analytical Manual) - Chapter 5: Salmonella. 2021: 24 p.

Grimont P., and Weill F.X. Antigenic Formulae of the Salmonella Serovars. 9th Edn. Paris: WHO Collaborating Centre for Reference and Research on Salmonella. 2007: 167 p.

Guillén, S. et al. Impact of the Resistance Responses to Stress Conditions Encountered in Food and Food Processing Environments on the Virulence and Growth Fitness of Non-Typhoidal Salmonellae. Foods 2021, 10, 617.

Huang X. et al.  Transcriptional sequencing uncovers survival mechanisms of Salmonella enterica serovar Enteritidis in antibacterial egg white. mSphere, 2019, 4 (1): 19 p.

Ibrahim GM and Morin PM. Salmonella Serotyping Using Whole Genome Sequencing. Front. Microbiol. 2018, 9:2993.

IFSAC (US Interagency Food Safety Analytics Collaboration). Foodborne illness source attribution estimates for 2019 for Salmonella, Escherichia coli O157, Listeria monocytogenes and Campylobacter using multi-year outbreak surveillance data, United States. Department of Health and Human Services, Centers for Disease Control and Prevention and U.S. Food and Drug Administration, U.S. Department of Agriculture’s Food Safety and Inspection Service. Oct 2021. 14 p.

ISO 6579-1 2017. Microbiology of the food chain — Horizontal method for the detection, enumeration and serotyping of Salmonella — Part 1: Detection of Salmonella spp.

ISO 6579-1:2017/AMD 1:2020 - Microbiology of the food chain — Horizontal method for the detection, enumeration and serotyping of Salmonella — Part 1: Detection of Salmonella spp. — Amendment 1: Broader range of incubation temperatures, amendment to the status of Annex D, and correction of the composition of MSRV and SC.

ISO/TR 6579-3:2014. Technical report - Guidance for serotyping of Salmonella spp.

ISO/DTS 6579-4 (expected to be published in 2023) Microbiology of the food chain - Horizontal method for the detection, enumeration and serotyping of Salmonella - Part 4: Identification of monophasic Salmonella Typhimurium (1,4,[5],12,i:-) by polymerase chain reaction (PCR).

ISO 16140-2:2016 - Microbiology of the food chain - Method validation - Part 2: Protocol for the validation of alternative (proprietary) methods against a reference method.

ISO 16140-6:2019 - Microbiology of the food chain - Method validation - Part 6: Protocol for the validation of alternative (proprietary) methods for microbiological confirmation and typing procedures.

Munck N. et al. Application of Whole-Genome Sequences and Machine Learning in Source Attribution of Salmonella Typhimurium. Risk Analysis, Vol. 40, No. 9, 2020: 1693-1705.

Pires, S. M., et al. Technical report submitted to EFSA. Estimation of the relative contribution of different food and animal sources to human Salmonella infections in the European Union. National Food Institute, Technical University of Denmark. EFSA J., 8 (8), 2011: 80 p.

Scallan E., et al. Foodborne illness acquired in the United States, major pathogens. Emerging Infectious Diseases, 2011; 17: 7–15.

USDA-FSIS 9CFR Parts 304, 308, 310, 320, 327, 381, 416, and 417. Pathogen Reduction; Hazard Analysis and Critical Control Point (HACCP) Systems; Final Rule.1996. 185p.

USDA – FSIS. MLG 4.11. Isolation and Identification of Salmonella from Meat, Poultry, Pasteurized Egg, and Siluriformes (Fish) Products and Carcass and Environmental Sponges. 2021: 19 p.

WHO (World Health Organization). WHO estimates of the global burden of foodborne diseases. Epidemiology reference group 2007-2015, 2015: 265p.

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