Salmonella: Properties, Enteric Fever, and Laboratory Diagnosis

A young adult comes in with a fever that has climbed higher each day for a week, a headache, and a dull ache in the abdomen. There is no cough and no burning micturition. In many parts of the world, this slow, step-by-step fever has one classic cause: Salmonella Typhi, the organism behind typhoid fever.

Overview

Salmonella is one of the most common causes of foodborne infection worldwide. Some strains cause a brief bout of diarrhea and vomiting. One strain, S. Typhi, does something more dangerous: it enters the bloodstream and causes enteric fever, an illness that can last weeks and turn fatal if missed. This page is about how Salmonella causes disease and how the laboratory identifies it, starting with the test that matters most, blood culture.

Salmonella is a Gram-negative, motile rod of the family Enterobacteriaceae. It swims using flagella spread over its whole surface (peritrichous). The genus has two species, Salmonella enterica and Salmonella bongori, and almost all human disease is caused by S. enterica. Within that species, there are more than 2,500 serotypes (serovars), named by their surface antigens, for example S. Typhi and S. Typhimurium.

Classification of Salmonella

The naming of Salmonella confuses almost everyone at first, because the everyday names (Salmonella Typhi, Salmonella Typhimurium) are not species names. Getting the levels straight makes the rest of the topic easier.

Two species. The genus Salmonella has only two species: Salmonella enterica and Salmonella bongori. Almost all human disease is caused by S. enterica.

Six subspecies. S. enterica is divided into six subspecies, of which subspecies enterica (subspecies I) contains nearly all the serotypes that infect humans.

More than 2,500 serotypes (serovars). Within the species, organisms are divided into over 2,500 serotypes based on their surface antigens (the O and H antigens). The familiar names are serotypes, not species: Salmonella Typhi, Salmonella Typhimurium, and Salmonella Enteritidis are all serotypes of S. enterica.

This is why the correct written form is Salmonella Typhi (or S. Typhi), with the genus italicized and the serotype name in roman type with a capital letter, not Salmonella typhi in italics as though "typhi" were a species. The serotype is not a species, so it is not written like one.

For everyday purposes, the level that matters clinically is the serotype, because the serotype is what determines whether the organism causes enteric fever or gastroenteritis, which is the split covered next.

Typhoidal vs non-typhoidal Salmonella

Salmonella serotypes split into two clinically different groups. Getting this split clear is the single most useful thing on this page, because it decides what illness the organism causes and how you approach it.

Typhoidal Salmonella (S. Typhi and S. Paratyphi A, B, C). These are adapted to humans only. They do not stay in the gut; they invade through the intestinal wall, enter the bloodstream, and cause enteric fever (typhoid and paratyphoid), a systemic illness lasting weeks. Blood culture, not stool culture, is how you catch them.

Fig: Salmonella classification based on their serotype

Non-typhoidal Salmonella (NTS, such as S. Typhimurium and S. Enteritidis). These come from animals and food. In most healthy people they cause gastroenteritis: diarrhea, vomiting, and fever that resolves on its own in a few days. Stool is the specimen. But in infants, the elderly, and immunocompromised people (including those with HIV or sickle cell disease), NTS can invade the blood and cause septicemia and seed distant sites, causing osteomyelitis, especially in sickle cell disease.

So the same genus causes two very different pictures: a prolonged systemic fever with few gut symptoms (typhoidal), and an acute self-limited diarrhea (non-typhoidal) that occasionally turns invasive in a vulnerable host.

The main diseases at a glance

• Enteric fever (typhoid, paratyphoid): typhoidal Salmonella, systemic, blood culture.
• Gastroenteritis (enterocolitis): non-typhoidal, self-limited diarrhea, stool culture.
• Septicemia: invasive NTS in vulnerable hosts.
• Osteomyelitis: a known complication, classically in sickle cell disease.

Salmonella is one of the world's most common causes of foodborne infection. It lives in the intestines of many animals, including cattle, poultry, pigs, and reptiles. One serotype is different: S. Typhi lives only in humans. This single fact shapes typhoid control, because there is no animal reservoir to worry about; the source of a new infection is always another human, often a chronic carrier.

How people get infected:

• Eating contaminated meat, poultry, or eggs.
• Drinking or eating food and water contaminated with human or animal feces.
• Contact with infected animals or their environment (reptiles are a notable source).
• Food handled by an infected person, including a chronic carrier who feels well.

What Salmonella looks like, and what that tells you

Salmonella is a Gram-negative, motile, non-lactose-fermenting rod of the family Enterobacteriaceae. A few features do the identification work and each rules something in or out.

It does not ferment lactose, so it is pale on MacConkey agar. This is the first sorting step in a stool culture. Salmonella, like Shigella, stays colorless while normal gut flora such as E. coli turn pink. So a pale colony is the one worth chasing.

It produces H₂S. Most salmonellae make hydrogen sulfide gas from sulfur-containing amino acids. On selective stool media such as SS agar and Hektoen enteric agar, this shows as a black center in the colony. That black color is the Salmonella signature on a stool plate and is the main visible feature that separates it from Shigella, which does not make H₂S and stays pale. The culture media that show this are covered in the media used for Salmonella isolation, SS agar, and Hektoen enteric agar articles.

It is motile. Unlike Shigella, which is non-motile, Salmonella swims. Motility plus H₂S are the two features that separate the two pale stool pathogens.

Surface antigens

Three antigens define a Salmonella serotype and are the basis of both serotyping and the Widal test:

• O antigen (cell wall lipopolysaccharide): heat-stable.
• H antigen (flagellar protein): heat-labile.
• Vi antigen (capsular): found on S. Typhi. "Vi" means virulence. It coats the organism, can hide the O antigen from antibody, and helps the organism resist immune attack.

Virulence factors and how Salmonella causes disease

Salmonella is built to survive being swallowed and then to invade. Each factor below is tied to what it does.

Acid tolerance. To reach the gut, the organism must survive the stomach. Salmonella has acid-tolerance systems that let enough organisms pass the stomach alive. This is why a larger dose is more likely to cause disease, and why low-acid states (antacids, young age) increase risk.

Invasion of the gut wall (Type III secretion system). Salmonella injects proteins into the intestinal lining cells using a needle-like Type III secretion system. These proteins force the cell to take the organism in. This is the step that separates Salmonella from organisms that stay on the surface: it gets inside the wall.

Survival inside macrophages. Once through the wall, Salmonella is engulfed by macrophages, but instead of being killed, it survives and multiplies inside them. This is the key to enteric fever. The macrophage becomes a vehicle that carries the organism through the lymphatics and into the blood, spreading it to the liver, spleen, and bone marrow.

Vi capsule (S. Typhi). The Vi antigen coats S. Typhi, helping it resist being killed by complement and antibody and reducing the immune response against it. This contributes to the organism's ability to cause a prolonged systemic infection.

Endotoxin (LPS). As organisms grow and die in the blood, LPS drives the sustained fever and the systemic features of enteric fever.

Putting it together: how enteric fever develops

The sequence explains the illness. The organism is swallowed and survives the stomach. It invades the small intestine wall using its Type III secretion system. It is taken up by macrophages but survives inside them, and is carried through the lymphatics into the blood (the first bacteremia). This seeds the liver, spleen, and bone marrow, where it multiplies and re-enters the blood in a larger second bacteremia, which is when the patient becomes ill with sustained fever. Because the organism is inside cells and in the blood rather than in the gut lumen, the illness is a systemic fever with few diarrheal symptoms early on, and blood culture, not stool, is what detects it. This is the single fact that ties the mechanism to the diagnosis.

Non-typhoidal strains, by contrast, mostly stay at the gut wall and trigger a brisk local inflammation, which is why they cause diarrhea rather than a prolonged fever, except in vulnerable hosts where they too invade the blood.

Laboratory diagnosis

Why blood culture, and when

For enteric fever, blood culture is the mainstay. The reason follows from the pathogenesis above: the organism is in the blood and inside cells, not in the gut lumen, so stool culture is unreliable early on. A few practical points that change the yield:

• Take blood before antibiotics. Even one dose lowers the chance of growing the organism.
• Volume matters. More blood gives a higher yield, because the number of organisms per milliliter is low. Follow your blood culture system's recommended volume. Children need less blood than adults but carry more organisms per milliliter. The general principles are covered in the blood culture article.
• Timing. Yield is highest in the first week of fever.
• Bone marrow culture is more sensitive than blood and can stay positive even after antibiotics have started, which is useful in a patient already treated.

Stool and duodenal aspirate culture are used in specific situations, and stool is the specimen for detecting chronic carriers, who continue to shed S. Typhi long after recovery.

Identifying the isolate

On the plate.

• MacConkey agar: pale (non-lactose-fermenting) colonies.
• Blood agar: non-hemolytic, smooth white colonies.
• SS and Hektoen enteric agar: colonies with black centers, from H₂S. See the SS agar and Hektoen enteric agar articles.

The identification panel. Each result below states what it means. For the method of any one test, follow its link.

The TSI and screening pattern for typhoidal Salmonella

This is the high-yield table for enteric fever. The key contrasts are H₂S and gas.

Two things students are tested on: S. Typhi makes only a little H₂S and no gas, while S. Paratyphi A makes no H₂S but does produce gas. That single contrast (weak H₂S/no gas vs no H₂S/gas) separates the two most important typhoidal serotypes on a TSI tube.

Serotyping

A confirmed isolate is serotyped by testing its O and H antigens with specific antisera. The typhoidal serotypes and their antigen formulas:

The Widal test

The Widal test measures agglutinating antibodies against the O and H antigens of S. Typhi. It is widely used where culture is not available, but it has real limits: it can be negative in culture-proven cases, and false positives occur in malaria, other infections, and past exposure or vaccination, because S. Typhi shares antigens with other organisms. A single Widal result should never be read as proof of typhoid on its own. The full principle, procedure, and interpretation are in the Widal test article.

Treatment and the resistance problem

Enteric fever needs antibiotics; untreated typhoid can be fatal. The choice of drug has been reshaped by resistance, which is why this is worth understanding rather than memorizing.

Historically, typhoid was treated with chloramphenicol, then with ampicillin and co-trimoxazole. Widespread resistance to all three produced multidrug-resistant (MDR) typhoid. Fluoroquinolones then became first-line, but fluoroquinolone resistance is now common in South Asia. Third-generation cephalosporins (such as ceftriaxone) and azithromycin are the mainstays where fluoroquinolone resistance is present. Extensively drug-resistant (XDR) typhoid, resistant to most oral options including fluoroquinolones and third-generation cephalosporins, has emerged and is a serious regional concern.

The practical point for a student: the right drug depends on local resistance patterns, and susceptibility testing matters. Doses and durations are clinical decisions and are not covered here. Two typhoid vaccines (Vi polysaccharide and Vi conjugate) exist and are used in high-burden areas; they reduce but do not eliminate risk.

How to remember

Black center means Salmonella. On a stool plate (SS or Hektoen agar), Salmonella colonies have a black center from H₂S. Picture the black dot. Its H₂S-negative neighbor Shigella stays pale. Ask yourself: two pale non-lactose colonies on MacConkey, how do I tell them apart on selective media? The one with the black center and that moves is Salmonella; the pale, still one is Shigella.

Typhi is shy with gas, Paratyphi is not. On TSI, S. Typhi makes weak H₂S and no gas; S. Paratyphi A makes no H₂S but does make gas. A memory hook: Typhi produces the "smell" (H₂S) but not the "bubbles" (gas); Paratyphi A is the reverse.

Why blood, not stool. Enteric fever lives in the blood and inside cells, not in the gut lumen. That is why you culture blood. Tie it to the mechanism: the organism rides inside macrophages into the bloodstream, so that is where you look for it.

Vi means virulence. The Vi antigen of S. Typhi is literally named for virulence. It hides the organism from antibody. Same three letters, same idea.

Key exam facts in one table

Where students get confused

Salmonella species vs serotype. There are only two species (S. enterica, S. bongori), but over 2,500 serotypes. S. Typhi and S. Typhimurium are serotypes of S. enterica, not separate species. Write them as S. Typhi (serotype not italicized), not Salmonella typhi.

Typhoidal vs non-typhoidal. These cause different diseases from different sources. Typhoidal (human-only) causes systemic enteric fever, diagnosed by blood culture. Non-typhoidal (animal source) causes self-limited diarrhea, diagnosed by stool. Mixing them up is the most common error.

Blood vs stool culture. For enteric fever, blood is the specimen, not stool, because the organism is systemic. Students often assume a gut infection means a stool sample. Stool is for gastroenteritis and for detecting carriers.

S. Typhi H₂S is weak. Most salmonellae are strong H₂S producers, but S. Typhi makes only a little. Reading a S. Typhi TSI and expecting a strongly black butt can mislead. Weak H₂S and no gas is the S. Typhi pattern.

The Widal test is not proof. A positive Widal is supportive at best and is frequently wrong in both directions. It does not replace culture. This is a heavily tested point.

Salmonella Typhi vs Shigella on a pale plate. Both are pale non-lactose fermenters on MacConkey. The separators are H₂S (Salmonella positive, black center on selective media; Shigella negative) and motility (Salmonella motile, Shigella non-motile).

References

1. Tille, P. M. (2022). Bailey & Scott's Diagnostic Microbiology (15th ed.). Elsevier.
2. Procop, G. W., et al. (2017). Koneman's Color Atlas and Textbook of Diagnostic Microbiology (7th ed.). Wolters Kluwer.
3. Coburn, B., Grassl, G. A., & Finlay, B. B. (2007). Salmonella, the host and disease: a brief review. Immunology and Cell Biology, 85(2), 112–118. https://doi.org/10.1038/sj.icb.7100007
4. Crump, J. A., Sjölund-Karlsson, M., Gordon, M. A., & Parry, C. M. (2015). Epidemiology, clinical presentation, laboratory diagnosis, antimicrobial resistance, and antimicrobial management of invasive Salmonella infections. Clinical Microbiology Reviews, 28(4), 901–937. https://doi.org/10.1128/CMR.00002-15