Salmonella: A Brief Review

Abstract

Salmonella causes significant illness in humans and animals and is a major public health concern worldwide, contributing to an increased economic burden. Salmonella is usually transmitted through the consumption of contaminated food, such as raw or undercooked meat, poultry, eggs, and dairy products, and water or through contact with infected animals or their environment. The most common symptoms of salmonellosis, the illness caused by Salmonella, include diarrhea, fever, and abdominal cramps; in severe cases, the infection can lead to hospitalization and even death. The classification and taxonomy of Salmonella were historically controversial, but the genus is now widely accepted as composed of two species and over 2600 serovars. Some of these serovars infect a single host, that is, host-restricted, whereas others have a broad host range. Colonization of the host is complex and involves a series of interactions between the Salmonella and the host’s immune system. Salmonella utilizes an array of over 300 virulence factors, mostly present in Salmonella pathogenicity islands (SPIs) to achieve adherence, invasion, immune evasion, and, occasionally, systemic infection. Once colonized, it secretes a number of toxins and inflammatory mediators that cause diarrhea and other symptoms of salmonellosis. The overuse and misuse of antibiotics in human and animal medicine and agriculture have contributed to the development of antimicrobial resistance (AMR) in Salmonella, making AMR strains more severe and difficult to treat and increasing the risk of morbidity and mortality. Various methods are used for the detection of Salmonella, including traditional culture methods, molecular methods such as polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP), and immunological-based assays. Because of its ubiquitous distribution, the prevention and control of Salmonella transmission remain a significant challenge. This chapter briefly covers the history, classification, transmission, pathogenesis and virulence factors, antimicrobial resistance genes, detection, diagnosis, surveillance, prevention, and control pertaining to Salmonella.

1. Introduction

Salmonella is a bacterial genus consisting of many closely related organisms, which remains a major cause of morbidity and mortality worldwide with significant public health implications, contributing to the economic burdens of both developed and economically marginalized countries because of costs associated with monitoring, surveillance, prevention, and treatment of salmonellosis [1, 2, 3, 4, 5, 6, 7]. Karl Joseph Eberth of the University of Zurich, a physician and pathologist, described a bacillus in the abdominal lymph nodes and spleen of a patient who died of typhoid in 1879 [8]. At the time, the bacterium was referred to as Eberth’s Bacillus [9, 10] and followed by the discovery of Bacillus as the cause of human typhoid fever by George Gaffky in 1884 [1, 8, 10]. Nevertheless, the genus “Salmonella” was named after Daniel Elmer Salmon, an American veterinary pathologist and head of the United States Department of Agriculture (USDA) Microorganism Research Program in the late 1800s [1]. Together with Theobald Smith, Salmon isolated Salmonella from the intestines of the pigs that succumbed to the disease known as hog cholera in 1884 [8, 11]. Historians and scientists studying past disease outbreaks have concluded that many catastrophic disease outbreaks of the early ages were likely caused by Salmonella, more specifically, typhoid infections [5, 12]. As early as 430 B.C., a plague, which is now believed to have been typhoid fever, wiped out a third of the population of Athens [1, 5].

Salmonellosis is a common cause of foodborne illness in the world [2, 3, 13]. Symptoms of salmonellosis can include fever, diarrhea, abdominal cramps, and vomiting and can last for several days. According to the World Health Organization (WHO), more than 2 billion people worldwide suffer from diarrheal diseases annually [8], and 1 of 4 of these diseases is caused by Salmonella [4, 7, 8, 14]. Depending on host factors and the serotype of Salmonella, as well as the presence of antimicrobial resistance (AMR) genes, 11–20 million cases of salmonellosis become severe and life-threatening, leading to 161,000 deaths annually [4, 7]. According to the Centers for Disease Control and Prevention (CDC), salmonellosis is one of the most common bacterial foodborne illnesses in the United States, with an estimated 1.35 million cases occurring annually [15]. The Public Health Agency of Canada (PHAC) estimates that there are about 87,500 cases of salmonellosis each year in Canada [16]. According to the European Centre for Disease Prevention and Control (ECDC) in 2021, salmonellosis was the second most common bacterial foodborne infection in Europe, with an estimated 60,050 cases occurring annually [15]. In developing countries, the burden of salmonellosis is usually higher because of the combination of many factors, such as poor hygiene and sanitation conditions, lack of access to safe water and proper food handling practices, lack of proper disease reporting structure, and limited resources for disease surveillance and response [4, 14, 17].

This chapter will briefly review the nomenclature, transmission, pathogenesis, diagnosis and detection, prevention, control, and treatment.

2. The organism

Salmonella is a rod-shaped, Gram-negative bacterium and consists of a cell wall, cell membrane, cytoplasm, ribosomes, plasmids, and nucleoid region. It has a diameter of around 0.7 to 1.5 μm, a length from 2 to 5 μm, and flagella, which allows for motility [18]. Salmonella is a chemoorganotroph, which means it obtains energy from the oxidation of the reduced organic compounds, and is a facultative anaerobe [18]. After colonizing the epithelium, Salmonella reproduces by binary fission, which begins with the replication and attachment of the DNA molecules to the cell membrane. Once the bacterium doubles its original size, the cell membrane begins to pinch inward and a cell wall forms between the two DNA molecules to divide the original cell into two identical daughter cells [18, 19]. Once reproduced, the bacterium either stays within the intestine or enters the bloodstream or lymph tracts [19]. Salmonella can also survive for several weeks outside of a living host in a dry environment and several months in water and is often not destroyed by freezing temperatures. The bacteria will only be destroyed in temperatures above 75°C, which makes raw and undercooked food, together with improperly washed fruits and vegetables, a common source of transmission of the bacterium.

The genome of Salmonella is relatively small, with a size ranging from 4.7 to 5.3 million base pairs [20, 21, 22]. It is a single circular chromosome that encodes a wide range of proteins involved in various cellular processes, including metabolism, regulation, and pathogenicity [22, 23, 24, 25]. Several studies have characterized the genomic features of Salmonella and identified genes that are important for its survival, virulence, and antimicrobial resistance [23, 25, 26, 27, 28, 29]. These include genes encoding toxins and other virulence factors that allow the bacteria to colonize and infect host tissues, as well as genes involved in the uptake and metabolism of nutrients. One of Salmonella’s most well-known genomic features is the presence of prophages, which are bacteriophages (viruses that infect bacteria) that have integrated into the bacterial genome [30, 31]. Prophages can be activated under certain conditions, leading to the production of new phages that can potentially spread to other bacteria. Genomic studies of Salmonella have also identified a number of genes that are involved in antibiotic resistance [32, 33, 34, 35]. These genes can be horizontally transferred among bacteria, leading to the spread of antibiotic resistance among different bacterial species. In recent years, the use of whole-genome sequencing (WGS) to study Salmonella has allowed for a deeper understanding of the organism’s epidemiology, biology, evolution, and population structure [36, 37, 38, 39]. WGS can accurately predict various characteristics and traits of a Salmonella isolate based on its genomic sequence, replacing the need for time-consuming and costly traditional methods [26, 30, 39].

3. Classification

Salmonella belongs to the Kingdom Monera or Eubacteria, phylum Proteobacteria, class Gamma-Proteobacteria, order Enterobacteriales, family Enterobacteriaceae, and the genus Salmonella [40, 41]. The nomenclature of the genus Salmonella has been confusing and controversial and has two systems of nomenclature widely used for the taxonomical assignments of Salmonella. One system, which does not conform to the rules of the Bacteriological Code but has wide acceptance, was proposed in the 1980s by Le Minor and Popoff in 1980 [18, 42], whereas the second system conforms to the rules of the Bacteriological Code and is not widely used [43]. To resolve the discrepancies in the taxonomical system of Salmonella, the Judicial Commission of the International Committee on the Systematics of Prokaryotes issued an Opinion (Opinion 80), with the intention that it should solve these discrepancies [41]. However, Opinion 80 was also limited to matters of nomenclature and meant to provide a clear presentation and interpretation of Salmonella taxonomy of the widely accepted division of the genus Salmonella into two species [41]. There are approximately 2000 similar species of Salmonella, which has caused much confusion in terms of classifying each species. In order to simplify this, the Center for Disease Control and Prevention (CDC) has agreed upon two species of Salmonella, Salmonella enterica and Salmonella bongori. Salmonella enterica is subdivided into six subspecies: S. enterica ssp. enterica (I), S. enterica ssp. salamae (II), S. enterica ssp. arizonae (IIIa), S. enterica ssp. diarizonae (IIIb), S. enterica ssp. houtenae (IV), and S. enterica ssp. Indica [44, 45]. These species and subspecies are further classified into multiple serotypes based on the White–Kauffmann–Le Minor scheme updated by the World Health Organization’s Collaborating Centre for Reference and Research on Salmonella at the Pasteur Institute, Paris, France [45, 46]. The genus Salmonella is made up of approximately 2600 serovars based on antigenic polymorphisms of their somatic O antigens (lipopolysaccharide), H antigens (flagellar proteins), and Vi antigens (capsular polysaccharides; [41, 43]). Most of the serovars belong to S. enterica ssp. enterica (I), and the most common serogroups are A, B, C1, C2, D, and E [43].

To avoid confusion in writing names and differentiate between serovars designation and species-level designation, it is recommended to write them in Roman style starting with a capital letter [43]. The current convention used in scientific writing is to state first the genus name and then the species name, followed by the word “serovar” (which can be abbreviated as “ser.”), and finally the actual name of the serovar [43]. An example, at first, is to write Salmonella. enterica subsp. enterica serovar (or ser.) Typhimurium. To simplify this long written convention and avoid the long nature of nomenclature, the name can be shortened by writing the genus name, followed directly by the serovar name starting with a capital letter; for example, Salmonella. enterica subsp. enterica serovar Typhimurium can be written as Salmonella Typhimurium.

Salmonella has a wide host range, which based on host adaptability, can be divided into three broad groups [47]. Group 1 Salmonella serovars are adapted to humans and higher primates such as Salmonella Typhi, Salmonella Paratyphi A, B, C, and Salmonella Sendai [47]. Group 2 Salmonella are largely adapted to specific animal hosts such as Salmonella Dublin in cattle, Salmonella Gallinarum in poultry, Salmonella Abortusequi in horses, Salmonella Abortusovis in sheep, and Salmonella Choleraesuis in pigs [47]. Group 3 Salmonella have a wide host range including humans, animals, and the environment, such as Salmonella Typhimurium and Salmonella Enteritidis, the two most common serotypes of Salmonella transmitted to humans in most parts of the world [47].

4. Transmission

Salmonella generally resides in the gut of animals, including birds, and is usually transmitted to humans by eating contaminated foods [7, 15]. These contaminated foods are typically from animal origin such as beef, poultry, milk, or eggs, but all food types including vegetables may be contaminated [15, 16]. The bacteria are commonly found in raw eggs and undercooked chicken and eggs. Person-to-person spread is possible in close contact, especially during the acute diarrheal phase of the illness [15, 16, 48]. Salmonella is transmitted by the consumption of raw food that is contaminated with the bacteria, such as vegetables that have not been cooked or washed properly, meat, or eggs. Salmonella can be transferred if the food handler or processor does not use gloves when dealing with food [15, 16]. It can also be transmitted by reptiles or rodents through their feces [49]. If the food is contaminated with a high concentration of Salmonella, the person is more likely to become infected. Children, elderly people, and HIV-positive people are more likely to become infected [7, 16, 49]. Once ingested, Salmonella embeds itself into the intestinal epithelium where it reproduces [50]. The liver, spleen, and especially the gall bladder have a high concentration of Salmonella. If left untreated, the organism can travel through the bloodstream to joints, organs, placenta, and membranes around the brain [50]. The toxins released by the bacteria can damage various organs in the body [51, 52].

5. Diseases

The general term for infections caused by Salmonella is salmonellosis, which is generally is divided into two main types: typhoidal and non-typhoidal. Typhoidal salmonellosis or typhoid fever is caused mainly by Salmonella Typhi, characterized by symptoms such as fever, weakness, abdominal pain, and loss of appetite [1, 4, 53] and typically acquired through the consumption of contaminated food or water and more common in developing countries [4]. However, non-typhoidal salmonellosis is caused by a variety of Salmonella serotypes and mostly causes food poisoning symptoms, such as diarrhea, abdominal cramps, and fever and is more common in developed countries [14, 53, 54]. Most of the people infected with Salmonella will develop diarrhea, abdominal cramps, fever, and vomiting, which can last up to a week [1, 4, 55, 56]. Other symptoms caused by Salmonella infection include the enlargement of the spleen and lymph nodes, accumulation of fluid and blood in organs such as the lungs, and damage to the liver [1, 53, 55]. In chronic cases, arthritis may even occur, known as Reiter’s Syndrome, and can last for months or even years [57, 58]. Different symptoms will occur in different mammals and birds.

6. Pathogenesis and virulence factors

Salmonella uses an array of virulence genes as part of its mechanism of pathogenesis [59]. These genes encode proteins that help the bacteria to evade the host’s immune system, colonize and survive in host tissues, and cause inflammation and tissue damage [55, 60, 61]. Understanding the virulence genes of Salmonella can help researchers to develop strategies for preventing and treating infections caused by these bacteria. Some key virulence genes involved in each step of Salmonella pathogenesis include the following:

• invA: encodes a protein called Invasin, which is involved in the invasion of host cells by Salmonella [60, 62].

• spvC: encodes a protein called SpvC, which is involved in the formation of a specialized structure called the Salmonella-containing vacuole (SCV) within host cells. The SCV helps Salmonella to evade the host’s immune system and establish an intracellular infection [63].

• sopE: encodes a protein called SopE, which is involved in the manipulation of host cell signaling pathways. SopE can activate signaling pathways that promote inflammation and tissue damage, as well as inhibit signaling pathways that would otherwise inhibit bacterial growth [64].

• sseL: encodes a protein called SseL, which is involved in the secretion of toxins into host cells, macrophage killing, and enhancement of virulence [65, 66, 67].

Many of these virulence genes are located on pathogenicity islands known as Salmonella pathogenicity islands (SPIs), which are thought to be acquired by horizontal gene transfer [68, 69]. SPIs are regions of bacterial DNA found in some strains of Salmonella and believed to play a role in the bacteria’s ability to cause diseases [68, 69]. SPIs are typically composed of several genes, including virulence genes that encode proteins involved in the bacterium’s ability to invade host cells, evade the immune system, and survive in different environments [69]. There are a total of 24 SPIs (1–24) recognized in Salmonella so far [70]. Each SPI is believed to have a specific function in the pathogenesis of Salmonella infections [68, 69]. For example, SPI-1 is involved in the bacterium’s ability to invade and replicate within host cells [70], whereas SPI-2 is involved in the production of a toxin that can cause inflammation in the intestinal tract [69]. SPI-1 is a large and complex region of DNA, comprising approximately 40 genes [69]. Many of these genes are involved in the production of proteins called effectors, which are secreted by the bacteria into host cells and function to alter host cell function [70]. For example, some effectors can disrupt the normal functioning of the host cell’s cytoskeleton, enabling the bacteria to move within the host tissue and evade immune cells [69, 70]. Other effectors can interfere with the host cell’s signaling pathways, helping the bacteria to evade detection by the host’s immune system. The type III secretion system (T3SS) encoded by SPI-1 is considered to be the most important virulence factor for Salmonella [68, 69, 70]. SPI-2 is another 40 kb long region of DNA found in certain strains of Salmonella bacteria, which has two distinct regions encoding proteins required to establish and maintain Salmonella-containing vacuole essential for Salmonella replication [71]. SPI-2 encodes a second T3SS, implicated in systemic pathogenesis [72]. The two regions of SPI-2 have unique species-specific distribution; for example, the larger 25 kb region is exclusive to S. enterica, whereas a second 15 kb long region is identified in S. bongori [69]. Like SPI-1, it contains a number of genes that contribute to the pathogenicity of the bacteria; SPI-2 is a smaller and less complex region of DNA than SPI-1 [69].

SPI-3 is a 17 kb long chromosomal DNA region that encodes many proteins involved in adhesion, such as MisL protein, which is vital for the long-term persistence of Salmonella [69]. SPI-3 is thought to be conserved in S. Typhi and S. Typhimurium [69, 73]. Similarly, SPIs 4–24 are involved in various aspects of pathogenesis and functions, all of which are not fully understood yet [69]. However, understanding the role of SPIs in Salmonella pathogenesis is important for the development of vaccines and therapies against the bacteria. Researchers are currently studying the mechanisms by which Salmonella utilizes SPIs to cause diseases, with the goal of finding new ways to prevent or treat infections caused by this bacterium.

Various Salmonella strains also contain plasmids, which have virulence and AMR genes [74, 75, 76, 77]. Salmonella plasmids are usually small, circular pieces of DNA that are found in some strains of Salmonella. However, some strains also carry large Salmonella virulence plasmids [22, 77, 78]. Plasmids are separate from the bacterial chromosome and can carry a variety of genes, including those that confer antibiotic resistance or other traits that can help the bacteria survive and thrive in different environments [22, 79, 80, 81]. Some Salmonella plasmids carry virulence genes, which are responsible for the bacteria’s ability to cause illness in humans and animals. Salmonella plasmids can be transmitted from one bacterium to another through horizontal gene transfer and can contribute to the evolution of new pathogenic strains [74, 82, 83]. Plasmids are an important tool in molecular biology and are often used to introduce new genes into bacterial cells for research or biotechnology purposes. There are several types of Salmonella plasmids that vary in size from 2 to more than 200 kb, which have been identified and characterized. Some of these include the following:

1. Virulence plasmids: These plasmids are usually large and carry genes that are responsible for the bacteria’s ability to cause illness in humans and animals. These genes may encode proteins that help the bacteria evade the host immune system or enzymes that allow the bacteria to produce toxins that damage host cells [77, 78, 84, 85].

2. Antibiotic resistance plasmids: These plasmids carry genes that allow the bacteria to resist the effects of certain antibiotics. This can make the bacteria more difficult to treat and can contribute to the spread of antibiotic resistance [74, 82, 83].

3. Conjugative plasmids: These plasmids can be transferred from one bacterium to another through a process called conjugation. This allows the plasmids to spread through bacterial populations, even between species of bacteria and can contribute to the evolution of new pathogenic strains [75, 86].

4. IncI1 plasmids: These plasmids are a type of conjugative plasmid that is commonly found in Salmonella enterica serovar Typhimurium, a strain of Salmonella that is responsible for many human infections. IncI1 plasmids carry genes that encode proteins that help the bacteria colonize and survive in the host [80, 87, 88].

5. IncF plasmids: These plasmids are another type of conjugative plasmid that is found in many strains of Salmonella. IncF plasmids carry genes that encode proteins that help the bacteria evade the host immune system and colonize the host intestine [89].

7. Antimicrobial resistance genes in Salmonella

Some strains of Salmonella have developed resistance to certain antibiotics, which can make it more difficult to treat infections [90, 91, 92]. These are known as antibiotic-resistant Salmonella or AMR Salmonella. AMR is a growing global health concern because it can make it more difficult to effectively treat bacterial infections, including those caused by Salmonella [92, 93, 94]. The overuse and misuse of antibiotics are major contributing factors to the development of AMR in bacteria [93, 95]. Antibiotic resistance in Salmonella has a long history [96]. Salmonella have been known to cause illness for over a century, and antibiotics have been used to treat Salmonella infections since the 1940s [96, 97]. However, as with many other types of bacteria, Salmonella has developed resistance to many of the antibiotics that have been used for clinical treatment [98]. One of the first reported cases of antibiotic resistance in Salmonella was in the 1950s, when strains of Salmonella that were resistant to streptomycin were identified [96, 97]. Since then, Salmonella’s resistance to other antibiotics, such as tetracycline and ampicillin, has also been reported [55, 99], and some strains are now resistant to multiple antimicrobial drugs or antibiotics.

Some common AMR genes found in Salmonella include the following:

1. blaTEM gene encodes for beta-lactamase, an enzyme that hydrolyzes beta-lactams (e.g., ampicillin, penicillins, and cephalosporins etc.; [100]).

2. sul1 and sul2 genes encode for sulfonamide-resistant dihydropteroate synthases, which when expressed can inactivate sulfonamide antibiotics [101, 102, 103].

3. tetA and tetB genes encode for tetracycline efflux pumps, which can pump tetracycline antibiotics out of the bacterial cell, making the bacteria resistant to these drugs [102, 104].

4. qnr gene encodes for quinolone resistance-determining region, which can make Salmonella resistant to quinolone antibiotics [92, 105, 106].

5. mcr gene encodes phosphoethanolamine transferase, which transfers the phosphatidylethanolamine residue to the lipid A of the cell membrane and provides resistance to colistin, last-resort antibiotics effective against multidrug-resistant Salmonella [107, 108].

The presence of an AMR gene does not necessarily mean that the bacterium will be resistant to the use of the antimicrobial drug [109, 110]. The ability of bacteria to survive antimicrobial treatment depends on many factors, including the specific strain of bacteria, the type and dosage of the drug, and the presence of other AMR genes [95, 110].

Recently, extensively drug-resistant (XDR) or more commonly known as multiple-drug resistant (MDR) Salmonella types, that is, Salmonella resistant to a wide range of antimicrobial drugs including many antibiotics that are typically used to treat Salmonella infections, have been on the rise, especially in developing countries [95, 111, 112, 113]. XDR Salmonella is of particular concern because it can be more difficult to treat and may lead to more severe or even fatal infections [95, 112]. XDR Salmonella can be transmitted through contaminated food, water, or surfaces, as well as through contact with infected animals or people. XDR phenotype in Salmonella arises through the acquisition of multiple AMR genes, which enables the bacteria to survive exposure to multiple drugs [109, 114]. The specific AMR genes present in XDR Salmonella can vary, but they may include genes that confer resistance to antibiotics such as ciprofloxacin, amoxicillin, and ceftriaxone. China has recently reported the first case of a waterborne outbreak caused by XDR S. Typhi in Beijing [113]. Similarly, the World Health Organization (WHO) recorded about 5274 cases of XDR typhoid fever in Pakistan from November 2016 to December 2018 [115, 116]. The prevalence of AMR in Salmonella can vary significantly by region, with some areas having higher rates of AMR than others. For example, studies have shown that the prevalence of AMR in Salmonella isolates from animals and food in the United States is generally low, with most isolates being susceptible to a range of antimicrobial drugs [7].

However, the prevalence of AMR Salmonella isolates from humans in the United States is higher, with some studies reporting resistance rates as high as 30–40% [93]. In other parts of the world, the prevalence of AMR Salmonella may be higher. For example, studies have shown that the prevalence of AMR Salmonella isolates from humans in some European countries is as high as 50–60% [117]. The distribution of AMR Salmonella in developing countries can vary significantly depending on the specific country and region. However, in general, the prevalence of AMR in Salmonella in developing countries tends to be higher than in developed countries [95]. There are several factors that may contribute to the higher prevalence of AMR in Salmonella in developing countries including the following [7]:

1. Limited access to clean water and sanitation: In some developing countries, access to clean water and adequate sanitation facilities is limited, which can increase the risk of bacterial infections, including salmonellosis and the spread of AMR.

2. Poor infection control practices: In certain countries, infection control practices are inadequate, which can increase the risk of Salmonella infections and the spread of AMR.

3. High use of antimicrobial drugs in animals: In some developing countries, there is high and uncontrolled use of antimicrobial drugs in animals, which contribute to the development and spread of AMR.

4. Limited surveillance and monitoring: In developing countries, there is usually limited surveillance and monitoring systems for the presence of Salmonella on food and food-related environment, leading to increased prevalence of infections including Salmonella infections and the spread of AMR Salmonella.

Overall, the frequency distribution of AMR in Salmonella among developing countries can vary significantly, but it is generally considered a major public health concern.

8. Detection and diagnosis

Accurate, sensitive, and specific detection of Salmonella is critical for food safety worldwide. Over the last decade, various other detection methods and techniques such as immunology, molecular biology, mass spectrometry, spectroscopy, optical analysis, and biosensor-based methods have been developed [34, 118, 119]. Generally, these methods can be divided into many categories as follows:

1. Culture methods: One of the most common methods for diagnosing Salmonella is through the use of traditional culture-based techniques, which are usually slow, labor-intensive, and not suitable for on-location or high-volume testing. However, these methods are considered gold standard and are in use since the discovery of enteric fever and have been standardized by the International Organization of Standards [120] for Salmonella detection, which is being used by many regulatory bodies all over the world [118, 121]. Similar standards have been published by FDA’s Bacteriological Analytical Manual (BAM). The first stage in traditional culture methods for most food samples involves pre-enrichment in a nonselective liquid medium, such as buffered peptone water, which is then subcultured into two selective enrichment media, such as Rappaport Vasiliadis Soy broth (RVS) and Muller-Kauffmann Tetrathionate-Novobiocin (MKTTn) broth that inhibit background flora. This is followed by the inoculation on at least two selective differential agar media, such as Brilliant Green Sulfa (BGS), Bismuth Sulfite (BS), BrillianceTM Salmonella Agar, Xylose Lysine Deoxycholate (XLD), Xylose Lysine Tergitol-4 (XLT-4), and others, to allow the growth of Salmonella and distinguish them from other background microbial flora [118]. The last step in traditional culture methods includes the confirmation of presumptive positive Salmonella colonies.

2. Culture-independent diagnostic tests: These methods do not require prior culture enrichments in the media and can achieve sensitive and selective identification of Salmonella. A rapid and sensitive Whole Genome Culture-Independent Diagnostic Test (WG-CIDT) for Salmonella detection in lettuce has been developed, which could also be adapted for other perishable food [122].

3. Immunological assays: These include the enzyme-linked immunosorbent assay (ELISA), latex agglutination assay, and lateral flow and immunochromatography assay [118].

4. DNA detection methods: These include widely used polymerase chain reaction (PCR), mostly using invasin gene A (invA), loop-mediated isothermal amplification (LAMP), nucleic acid sequence-based amplification (NASBA), recombinase polymerase amplification (RPA), DNA microarrays, and others [118, 123].

5. Whole-genome sequencing methods (WGS): WGS has rapidly changed the practice of microbiology and public health surveillance and investigation of foodborne Salmonella illnesses, which allows to sequence and analyze the whole genome and provides a greater level of details. This method can also provide a one-step characterization of bacteria by identifying the species, serotype, genotype, and resistance and virulence genes all within a single laboratory workflow. WGS has been adopted in food safety framework in various countries, including the United States and England [124, 125, 126].

6. Mass spectrometry methods: matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) and liquid chromatography-mass spectrometry (LC-MS) [118].

7. Spectroscopy methods: Raman spectroscopy, near-infrared (NIR) spectroscopy, hyperspectral imaging (HSI), and optical phenotyping with light diffraction technology [118].

8. Sensor-based methods: These include electrochemical sensor- or biosensor-based technologies, which can detect Salmonella from as low as three colony-forming units using potentiometry, conductometry, and impedimetric techniques [119, 127]. Sensing techniques for detecting Salmonella in food are still in the early stages of development, but they hold promise as a way to create portable biosensing platforms. The use of nanomaterials and advanced bioreceptors makes these techniques particularly promising for future use. These methods utilize different targets for sensing Salmonella, including [127] single-stranded DNA/RNA-based probes for sensing of Salmonella, immunoglobulin-based sensing of Salmonella, phage-based sensing of Salmonella, and DNA-based biosensors for sensing Salmonella.

Multiple materials have been tested, which provide varying degrees of selective advantages and have their own limitations. These include magnetic nanoparticles (MNPs)-based electrochemical biosensors, carbon nanoparticles-based electrochemical biosensors, metallic nanoparticles-based electrochemical biosensors, amperometric biosensors, potentiometric biosensors, conductometric biosensors, microfluidics-based biosensing platforms, Internet of Things (IOT)-supported sensing of Salmonella, and clustered regularly interspaced short palindromic repeats (CRISPR)-based electrochemical sensors.

Overall, the choice of diagnostic method for Salmonella will depend on the specific circumstances and resources available, as well as the specific goals of the diagnosis such as identifying the specific strain of Salmonella or determining the severity of the infection.

9. Surveillance, prevention, and control

Many socio-economic factors contribute to the spread of Salmonella. The main factors are poverty and lack of education [7]. Poor environmental conditions contribute to poor hygiene, which ultimately helps spread the disease. Some Salmonella strains can cause serious and sometimes life-threatening infections, particularly in people with compromised immune systems. Different countries have developed regulatory framework for the testing and early detection of Salmonella in food. The US Centers for Disease Control and Prevention (CDC) conducts surveillance for Salmonella in the United States through the National Salmonella Surveillance System. This system tracks cases of Salmonella infection through laboratory testing and reporting by state health departments. CDC has developed a comprehensive national Salmonella surveillance program in the U.S. CDC has several systems for obtaining information about Salmonella, each of which has different purpose and provides information on various features of the organism’s epidemiology, such as the number of outbreaks, antimicrobial-resistant infections, and subtypes. These programs include Laboratory-based Enteric Disease Surveillance (LEDS), National Notifiable Diseases Surveillance System (NNDSS), Foodborne Disease Active Surveillance Network (FoodNet), National Molecular Subtyping Network for Foodborne Disease Surveillance (PulseNet), National Antimicrobial Resistance Monitoring System—enteric bacteria (NARMS), and Foodborne Disease Outbreak Surveillance System (FDOSS; https://www.cdc.gov/). Similarly, in Canada, the surveillance of Salmonella is conducted by the Public Health Agency of Canada (PHAC), which monitors and tracks cases of Salmonella in people through its integrated Salmonella surveillance system, collecting data from the provinces and territories under the National Enteric Surveillance Program (NESP), FoodNet Canada, and Canadian Notifiable Disease Surveillance System (https://www.canada.ca/en/public-health/services/diseases/salmonellosis-). In Europe, the European Centre for Disease Prevention and Control (ECDC) and the European Food Safety Authority (EFSA) are responsible for the surveillance of Salmonella. European Centre for Disease Prevention and Control has framed and adopted Regulation (EC) No 2160/2003 on protecting human health against Salmonella and other specified foodborne zoonotic agents, with the goal of controlling Salmonella at every stage of food production and in animal feed to reduce its prevalence and the risk to public health (https://leap.unep.org/countries/no/national-legislation/regulation-no-1703-control-). The ECDC is responsible for the surveillance of Salmonella infections across the European Union (EU). The organization collects data on Salmonella infections in humans from the EU Member States through the EU Surveillance Network for Communicable Diseases (TESSy) system. This allows the ECDC to track the number of cases, identify outbreaks, and monitor trends in Salmonella infections across the EU. The EFSA, on the other hand, is responsible for food safety and conducts surveillance of Salmonella in food products. It collects data on Salmonella in food from EU Member States and also conducts its own risk assessments on specific food products. The EFSA also provides scientific advice and support to the European Commission and EU Member States on food safety issues, including Salmonella control in the food chain. Additionally, the European Union Reference Laboratory for Salmonella (EURL-Salmonella) also plays an important role in the surveillance of Salmonella in Europe. This laboratory is responsible for coordinating the network of national reference laboratories for Salmonella and providing scientific and technical support for the detection and control of Salmonella in food and animal feed.

Surveillance of Salmonella in the developing world varies from one country to another, but in general, it is less robust and comprehensive compared with that in developed countries [7, 128, 129]. In developing countries, the surveillance of Salmonella is conducted by the national public health department or ministry of health [7, 128]. However, the capacity for laboratory testing and data collection is limited because of the lack of resources and infrastructure. In addition, lack of awareness and education on food safety and good hygiene practices among the population, inadequate sanitation, and poor infrastructure exacerbate the spread of Salmonella in developing countries. However, efforts to improve them through international collaboration and aid programs, education, and capacity building are essential to curb the spread of these bacteria. To control salmonellosis, it is important to follow good hygiene practices, such as washing hands thoroughly with soap and water before handling food and cooking food to a safe temperature to kill Salmonella that may be present. It is also important to store food properly and avoid cross-contamination, for example, by using separate cutting boards and utensils for raw and cooked foods. In addition to these measures, it is important to control the spread of Salmonella in food-producing animals, as they can be a source of contamination. To be successful, Salmonella control requires a focus on the sources of the organism and the means of transmission to humans, which is best achieved through the One Health approach, with adequate attention paid to animal and food sources and the environment that harbors organisms and provides avenues of transmission to humans. Specific measures such as proper animal feeding and husbandry practices, effective disinfection of animal housing and equipment, monitoring wildlife sources especially avian species, and effective food safety practices are required.

10. Conclusion

In conclusion, Salmonella is one of the leading causes of food poisoning in humans. It is commonly found in raw or undercooked meat, poultry, eggs, and dairy products, as well as in fruits and vegetables that have come into contact with contaminated water or soil. Salmonella is a pathogen of great concer, which can cause severe illness and leads to death in some cases. The virulence of Salmonella is determined by a variety of factors including the serotype, presence of specific virulence genes, and the host’s immune response. In addition, the emergence of antibiotic-resistant Salmonella is a significant concern in the field of food safety. Salmonella can acquire AMR genes through horizontal gene transfer, and the presence of these genes makes the treatment of infections more difficult and complicated. Additionally, the emergence of extensively drug-resistant (XDR) Salmonella has become a great public health concern because of its ability to resist multiple classes of antibiotics, leading to a significant public health concern because of prolonged illness and increased health care costs. It is important to limit the use of antibiotics to decrease the risk of antibiotic resistance and implement strategies to prevent the spread of resistant strains of Salmonella, such as proper food handling and sanitation practices. It is also important to develop advanced, fast, and efficient methods to monitor the emergence of antibiotic-resistant Salmonella to quickly detect and respond to outbreaks.