Salmonella Typhimurium

Background: Salmonella enterica subsp. enterica serovar Typhimurium (antigenic formula 1,4,[5],12:i:1,2) is a serovar of the O:4 (B) serogroup. One variant named Salmonella Typhimurium var. Copenhagen, which lacks the factor 5 in the O antigen (1,4,12:i:1,2). The serotype 1,4,[5],12:i:–, which lacks the second-phase H2 flagellar antigen, is a monophasic variant of Salmonella Typhimurium. This serovar was named Typhimurium because it produces Typhi like symptoms in the murine (mouse) model. In humans, it is frequently associated with acute gastroenteritis. S. Typhimurium has been used as model to understand the pathogenicity of Salmonella. Salmonella Typhimurium is the most extensively studied serovar for nontyphoidal salmonellosis and has emerged as the primary model for nontyphoidal Salmonella research. The S. Typhimurium LT2 strain has been particularly well-characterized and remains widely used in research since the 1940s. Both Salmonella Typhimurium and Enteritidis dominate global human salmonellosis cases, despite regional differences in prevalence.

NCBI PD link for serovar Typhimurium: https://www.ncbi.nlm.nih.gov/pathogens/isolates/#(taxgroup_name:%22Salmonella%20enterica%22)%20AND%20computed_types:(%22serotype=Typhimurium%22)

Genetic characteristics:

Salmonella Typhimurium has been found to be polyphyletic with four lineages identified. According to den Bakker et al. (2011) classification, Salmonella Typhimurium belongs to clade A of Salmonella enterica. This serovar is classified according to the susceptibility to typing phages, in definite phage types (DT); one common DT (DT104) has been found to have resistance to ampicillin, chloramphenicol, streptomycin, sulphonamide and tetracycline (ACSSuT resistance type). In England, two outbreaks caused by a multidrug resistant (MDR) strain (ASSuTTm resistant type) of S. Typhimurium DT120 occurred in 2011. A review paper concluded that lineages of S. Typhimurium was associated with different sequence types (STs). While ST19 exhibits a broad host range and commonly causes gastroenteritis in humans, the host-restricted ST313 is predominantly associated with invasive bloodstream infections in sub-Saharan Africa. According to EnteroBase, ST19 accounts for 86% of available S. Typhimurium genomes, whereas ST313 represents only 7%. Epidemic ST19 strains encompass multiple phage types, including DT104 (mainly cattle), DT193/DT120 and U288 (primarily swine), DT8 (ducks/geese), and DT160 (wild birds). Recent advances in genomic classification have introduced a hierarchical clustering (HC) system for Salmonella based on single nucleotide variations (SNVs). At the serotype-defining level (HC900), most S. Typhimurium isolates cluster within HC900_2, with a minority assigned to HC900_6511 and HC900_6910.

Most of the strains of S. Typhimurium contain a plasmid of approx. 90 kb that carry virulence genes (Salmonella virulence plasmid (SVP)). Large resistant plasmids of approx. 200 kb that represented different incompatibility types (e.g., IncHI1), have also been identified in S. Typhimurium. Prophages and genomic islands are important genomic components of serovar Typhimurium; for example, S. Typhimurium str. LT2 has four prophages (Fels-1, Fels-2, Gifsy-1, and Gifsy-2). Pathogenicity islands (SPIs) are found in all S. Typhimurium sequenced to date, this include SPIs-1 to 6, 9, 11 to 14, and 16; being SPI-14 specific to S. Typhimurium. In addition, some genomic islands are strain-specific; for example, S. Typhimurium MDR strain ST1660/06 has three strain-specific genomic islands that encode putative virulence and resistance genes. Genomic islands that encode antibiotic resistance appear to be a common feature of a number of S. Typhimurium MDR strains, these genomic islands include, e.g., Salmonella genomic island 1 (SGI1) described in S. Typhimurium DT104 and genomic island GI-DT12 in S. Typhimurium T000240. The latest genomic island (GI-DT12) contains antibiotic resistance genes (i.e., bla(oxa-30), aadA1, qacEΔ1, and sul1, cat, and tetA) and virulence genes (i.e., the aerobactin iron-acquisition siderophore system (lutA and lucABC), and an iron transporter (sitABCD)). Similarly, another study found that all S. Typhimurium ST313 isolates collected from Nigeria and the Democratic Republic of Congo carried resistance genes, including blaTEM1b, catA1, strA/B, sul1, and dfrA1, along with the aac(6')1aa gene. Phylogenetic analysis showed that Congolese and Nigerian isolates—from both blood and stool—were closely related. Furthermore, comparative genomic analysis uncovered a unique virulence-associated fragment (ST313-TD) shared exclusively by S. Typhimurium ST313 and S. Dublin.

In Sub-Sahara regions of Africa, invasive strains of S. Typhimurium emerged, single nucleotide polymorphism (SNP)-based phylogeny of these invasive strains and strains from other regions, showed two lineages of invasive strains that clustered together. Okoro et al. estimated that these lineages emerged independently around 52 and 35 years ago, closely coinciding with the onset of the current HIV pandemic. The shift from lineage I to lineage II isolates may have been driven by clonal replacement, possibly influenced by chloramphenicol use in treating invasive NTS disease.

Animal reservoir: Serovar Typhimurium is host-generalists that can colonize and cause diseases in multiple animal species, including but not limited to cattle, poultry, swine, wild animals, and insects.

Geographical distribution: Serovar Typhimurium is globally distributed. During the study period from 2001 to 2007, Salmonella Typhimurium were the second most prevalent Salmonella serovars isolated from human in most regions, except in North America and Oceania (Australia and New Zealand). In these two regions, Salmonella Typhimurium was the most frequently reported in humans. Among human Salmonella isolates, serovar Typhimurium accounted for 17.1% of cases (ranging from 15% in 2007 to 18.9% in 2001).

Human outbreaks: Numerous outbreaks have been associated with S. Typhimurium. Human outbreaks have been linked to a number of foods and to contact with animals (chicks, ducklings, and other live animals). Below are some examples.

Year	Location	Associated source	Number of cases
2024-2025	US: multistate	Cucumbers	113
2024	US: multistate	Backyard poultry¹	470
2023-2025	Europe: multi-country	Alfalfa sprouts	509
2018	US: multistate	Chicken salad	265
2018	US: multistate	Dried coconut	14
2013	US: multistate	Live poultry	356
2013	US: multistate	Ground beef	At least 22
2012	Canada	Ground beef	50
2012	US: multistate	Pet hedgehogs	26
2012	US: multistate	Cantaloupe²	261
2011	US: multistate	Ground beef	20
2011	US: multistate	African dwarf frogs	241
2011	England	Hog roast	24
2009-2011	Ireland	Duck eggs	34
2009	England	Unknown	14
2008-2009	US: multistate	Peanut butter	714

¹ Multiple serovars, including Salmonella Altona, Cerro, Enteritidis, Indiana, Infantis, Johannesburg, Mbandaka, and Typhimurium, were linked to this outbreak. The case number represents the total number of cases associated with the outbreak and does not specifically indicate the number of people infected by Salmonella Typhimurium.

² A total of 228 Salmonella Typhimurium and 33 Salmonella Newport infections were reported in 24 states.

Border rejections: Multiple border rejections linked to Salmonella Typhimurium have been reported. The majority of them are associated with poultry and poultry products. Below are some examples.

Year	Exporting country	Importing country	Associated source	Product category
2025	Brazil	Netherlands	Frozen chicken meat	Poultry meat and poultry meat products
2024	Brazil	Portugal	Chicken gizzards	Poultry meat and poultry meat products
2023	Brazil	Netherlands	Fresh chicken meat	Poultry meat and poultry meat products
2021	Brazil	Germany	Black pepper¹	Herbs and spices
2021	Cameroon	Finland	Chilled waterleaves (Talinum triangulare)	Fruits and vegetables
2020	India	Germany	Dog chews (dried tripes)²	Feed materials

¹ Salmonella Gaminara, Agona, Typhimurium, Infantis, Rubislaw, and Saintpaul were found.

² Salmonella Typhimurium and Newport were found.

Recalls: Multiple recalls linked to Salmonella Typhimurium have been reported. They are associated with a variety of food commodities.

Year	Location	Recalled food	Type
2024-2025	US: multistate	Cucumbers¹	Fruits and vegetables
2023-2025	Europe: multi-country	Alfalfa sprouts²	Fruits and vegetables
2023	Romania	Turkey meat from Hungary	Poultry meat and poultry meat products
2022	Ireland	Milled brown flaxseed from UK	Nuts, nut products and seeds
2021	Norway	Pork sides with jaw from Germany	Meat and meat products (other than poultry)
2008-2009	US: multistate	Peanut butter	Nuts, nut products and seeds

¹ This recall was caused by a multistate outbreak described above. Importers issued a recall for American/slicer cucumbers produced by Agrotato, S.A. de C.V. in Sonora, Mexico, which were sold during October and November 2024.

² This recall was caused by a multi-country outbreak in Europe described above.

³ This recall was caused by a multistate outbreak described above. Peanut Corporation of America’s Blakely, GA and TX issued a recall of their commercially distributed peanut butter.

Relevant links:

Page tree

Salmonella Typhimurium