Common Pathogenic Bacteria Found in Stool

Stool is the solid or semi-solid waste material that is eliminated from the digestive system through the anus. Stool contains various substances, such as undigested food, water, mucus, bile, and bacteria. Bacteria are microscopic organisms that are present in almost every environment, including the human body. Bacteria can be classified into different groups based on their shape, structure, metabolism, and staining properties. One of the common ways to classify bacteria is by their reaction to a dye called Gram stain. Bacteria that retain the purple color of the dye are called Gram-positive, while those that lose the color and appear pink are called Gram-negative.

The bacteria found in stool are representative of the bacteria that are present in the digestive system (gastrointestinal tract). Certain bacteria and fungi called normal flora inhabit everyone’s gastrointestinal tract. They play an important role in the digestion of food and their presence keeps a check on the growth of disease-causing bacteria. The normal flora of the gastrointestinal tract varies depending on the location, diet, age, and health status of the individual. Some of the common genera of bacteria that are part of the normal flora include Bacteroides, Bifidobacterium, Lactobacillus, Escherichia, Enterococcus, and Clostridium.

However, not all bacteria found in stool are harmless or beneficial. Some bacteria can cause infections and diseases in the gastrointestinal tract or other parts of the body. These bacteria are called pathogenic bacteria. Pathogenic bacteria can enter the gastrointestinal tract through contaminated food, water, or contact with infected animals or people. Some of the common pathogenic bacteria that can be found in stool include Salmonella, Shigella, Campylobacter, Vibrio, Helicobacter, Yersinia, Proteus, Staphylococcus, Listeria, Fusobacterium, and Bacillus . These bacteria can cause various symptoms and complications, such as diarrhea, vomiting, abdominal pain, fever, dehydration, inflammation, ulcers, bleeding, sepsis, and cancer.

A stool culture is a laboratory test that can identify the type and number of bacteria present in a stool sample. The test helps to determine if pathogenic bacteria are the cause of a person’s gastrointestinal symptoms (gastroenteritis). The test involves placing a small amount of stool on a special medium that allows the growth of bacteria. The medium is then incubated for a certain period of time and observed for any bacterial colonies. The colonies are then further tested for their characteristics and susceptibility to antibiotics.

In this article, we will discuss some of the common Gram-negative and Gram-positive bacteria that can be found in stool and their role in causing gastrointestinal diseases.

Gram-negative bacteria are a group of bacteria that have a thin layer of peptidoglycan in their cell wall and stain pink or red with the Gram stain. They are usually more resistant to antibiotics than Gram-positive bacteria. Gram-negative bacteria can be found in the stool of healthy people as well as those with gastrointestinal infections. Some of the common Gram-negative bacteria in stool are:

• E. coli: E. coli is a normal inhabitant of the human gut, but some strains can cause diarrhea, urinary tract infections, sepsis, and other diseases. E. coli can be classified into different pathotypes based on their virulence factors and clinical manifestations. Some of the pathotypes are enteropathogenic E. coli (EPEC), enterotoxigenic E. coli (ETEC), enterohemorrhagic E. coli (EHEC), enteroinvasive E. coli (EIEC), enteroaggregative E. coli (EAEC), and diffusely adherent E. coli (DAEC). EHEC is one of the most dangerous strains, as it produces Shiga toxin that can cause bloody diarrhea, hemolytic uremic syndrome (HUS), and kidney failure.
• Klebsiella spp.: Klebsiella spp. are opportunistic pathogens that can cause pneumonia, urinary tract infections, wound infections, and septicemia. They can also cause gastroenteritis in immunocompromised patients or those with damaged intestinal mucosa. Klebsiella pneumoniae is the most common species isolated from stool samples of patients with inflammatory bowel disease, ulcerative colitis, and colorectal cancer. Klebsiella oxytoca is another species that can cause hemorrhagic colitis and necrotizing enterocolitis.
• Salmonella spp.: Salmonella spp. are one of the leading causes of foodborne illnesses worldwide. They can cause gastroenteritis, enteric fever, and systemic infections. Salmonella spp. can be divided into typhoidal and non-typhoidal serotypes based on their clinical presentation and host range. Typhoidal serotypes include Salmonella Typhi and Salmonella Paratyphi, which cause enteric fever or typhoid fever, a serious systemic infection characterized by fever, headache, abdominal pain, and rose spots on the skin. Non-typhoidal serotypes include Salmonella Typhimurium and Salmonella Enteritidis, which cause gastroenteritis or salmonellosis, a self-limiting infection characterized by diarrhea, vomiting, fever, and abdominal cramps.
• Shigella spp.: Shigella spp. are the causative agents of shigellosis or bacillary dysentery, a severe form of diarrhea that can lead to dehydration, electrolyte imbalance, and complications such as seizures and HUS. Shigella spp. can be classified into four species: Shigella dysenteriae, Shigella flexneri, Shigella boydii, and Shigella sonnei. Shigella dysenteriae is the most virulent species, as it produces Shiga toxin that can damage the intestinal epithelium and the kidneys. Shigella flexneri is the most prevalent species in developing countries, while Shigella sonnei is the most common species in developed countries.
• Vibrio spp.: Vibrio spp. are waterborne bacteria that can cause gastroenteritis, cholera, wound infections, and septicemia. Vibrio cholerae is the most important species that causes cholera, a life-threatening infection characterized by profuse watery diarrhea, vomiting, dehydration, and shock. Vibrio cholerae can be classified into two biotypes: classical and El Tor, based on their biochemical and genetic characteristics. Vibrio cholerae O1 and O139 are the serotypes that cause epidemic cholera outbreaks. Vibrio parahaemolyticus and Vibrio vulnificus are other species that can cause gastroenteritis and wound infections.

E. coli (Escherichia coli) is a Gram-negative, rod-shaped, lactose fermenting, facultatively anaerobic bacterium that belongs to the family Enterobacteriaceae. E. coli is normally present in the intestines of healthy people and animals, and most strains are harmless or cause relatively mild diarrhea. However, some strains of E. coli can produce toxins that damage the lining of the small intestine and cause severe symptoms such as abdominal cramps, bloody diarrhea, vomiting, fever, and dehydration . These strains are called pathogenic E. coli and are responsible for various gastrointestinal infections.

Some of the common pathogenic strains of E. coli are :

• Enteropathogenic E. coli (EPEC): These strains cause watery diarrhea and vomiting in infants and young children, especially in developing countries. They attach to the intestinal cells and disrupt their normal function.
• Enteroaggregative E. coli (EAEC): These strains cause persistent diarrhea in children and adults, especially in developing countries. They form aggregates on the intestinal cells and produce toxins that damage the mucosa.
• Enterohemorrhagic E. coli (EHEC): These strains cause bloody diarrhea and hemolytic uremic syndrome (HUS), a serious complication that can lead to kidney failure and death. They produce Shiga toxins that destroy the red blood cells and damage the kidneys. E. coli O157:H7 is the most common serotype of EHEC and is often associated with outbreaks linked to contaminated food or water.
• Enterotoxigenic E. coli (ETEC): These strains cause traveler`s diarrhea, a mild to moderate form of diarrhea that affects travelers to developing countries. They produce heat-labile and heat-stable toxins that stimulate fluid secretion in the intestine.
• Enteroinvasive E. coli (EIEC): These strains cause dysentery, a severe form of diarrhea with blood and mucus in the stool. They invade and destroy the intestinal cells and cause inflammation.
• Diffusely adherent E. coli (DAEC): These strains cause diarrhea in children and adults, especially in developing countries. They adhere diffusely to the intestinal cells and interfere with their function.

The diagnosis of E. coli infection is based on the symptoms and the stool culture test, which can detect the presence of E. coli bacteria and toxins produced by specific strains . The treatment of E. coli infection depends on the severity of the symptoms and the type of strain involved. In most cases, the infection resolves on its own within a few days without any specific treatment. However, some cases may require intravenous fluids and electrolytes to prevent dehydration, especially in children and elderly people. Antibiotics are generally avoided as they may increase the risk of complications such as HUS. In case of HUS, supportive care such as dialysis and blood transfusion may be needed.

The prevention of E. coli infection involves avoiding exposure to contaminated food or water, practicing good hygiene, washing fruits and vegetables thoroughly before eating, cooking meat properly, drinking pasteurized milk or juice, avoiding street food, washing hands before cooking or eating, especially after using the bathroom or changing diapers, and avoiding swallowing water while swimming or playing in lakes, ponds, or pools .

Klebsiella is a genus of Gram-negative, rod-shaped, and facultative anaerobic and capsule-forming coliform bacteria in the family Enterobacteriaceae. Klebsiella spp. are common in the GI tract of vertebrates. They are however responsible for gastroenteritis in case of weakened immune condition or case of any physical damage to the GI tract.

K. pneumoniae is common species isolated in the stool of patients with gastrointestinal diseases such as Crohn’s disease, ulcerative colitis, and colorectal cancer. K. pneumoniae can also cause pneumonia, bloodstream infections, wound infections, and meningitis. K. pneumoniae is often resistant to multiple antibiotics, making it difficult to treat.

K. oxytoca is another species reported for hemorrhagic enteritis. Toxin-producing K. oxytoca is reported in necrotizing enterocolitis, bloody diarrhea, and other gastroenteritis. K. oxytoca can also cause urinary tract infections, septicemia, and neonatal meningitis.

K. quasipneumoniae is another species responsible for opportunistic gastroenteritis. It is mainly reported in patients whose natural gut microflora is disturbed due to long-term administration of antibiotics. K. quasipneumoniae can also cause respiratory infections, endocarditis, and osteomyelitis.

Klebsiella infections can be diagnosed by culturing stool samples or other specimens on selective media and identifying the bacteria by biochemical tests or molecular methods . Treatment options depend on the type and severity of the infection, the susceptibility of the bacteria to antibiotics, and the patient`s condition . Prevention measures include good hygiene practices, proper disinfection of medical equipment, and prudent use of antibiotics .

Salmonella is a genus of Gram-negative, rod-shaped, flagellated, facultative anaerobic Gammaproteobacteria in the family Enterobacteriaceae. It is commonly found in the human GI tract and fecal contaminated environmental aspects. Salmonella spp. is responsible for food poisoning, diarrhea, and enteric fever (Typhoidal fever) .

S. enterica serovars

S. enterica serovars are responsible for several forms of gastroenteritis in humans. S. enterica subspecies enterica serovar Typhi and Paratyphi are responsible for enteric fever (Typhoid and Paratyphoid). They can be isolated in the stool of patients with enteric fever before the administration of antibiotics .

Non-typhoidal Salmonella (NTS) is the major cause of gastroenteritis worldwide. They usually cause self-limiting gastroenteritis, but in infants and immunosuppressed patients, the case may be fatal .

S. enterica serovar Typhimurium, S. enterica serovar Enteritidis are most common serovars associated with Salmonella gastroenteritis .

Diagnosis and treatment

Salmonella infection is diagnosed when a laboratory test detects Salmonella bacteria in a person’s stool, body tissue, or fluids . A stool culture can confirm the presence of Salmonella bacteria .

Most people recover without specific treatment. Antibiotics are typically used only to treat people with severe illness or those who are at risk of complications . Patients should drink extra fluids as long as diarrhea lasts . In some cases, diarrhea may be so severe that the person needs to be hospitalized . In rare cases, infection may spread from the intestines to the bloodstream, and then to other parts of the body. In these people, Salmonella can cause death unless the person is treated promptly with antibiotics .

Prevention

The best way to prevent Salmonella infection is to avoid eating or drinking contaminated food or water. Some tips to prevent Salmonella infection include:

• Wash your hands before and after handling food, especially raw meat, poultry, eggs, and seafood
• Cook food thoroughly and use a food thermometer to ensure that meat, poultry, and eggs are cooked to a safe temperature
• Refrigerate or freeze perishable food within two hours of cooking or buying
• Avoid cross-contamination by using separate cutting boards, utensils, and plates for raw and cooked foods
• Do not drink unpasteurized milk or juice or eat raw or undercooked eggs
• Wash fruits and vegetables before eating them
• Avoid contact with animals that may carry Salmonella, such as reptiles, birds, rodents, and pets
• Wash your hands after touching animals or their feces
• Do not prepare food for others if you have diarrhea or vomiting

Shigella is a genus of Gram-negative, rod-shaped, non-motile, facultative anaerobic bacteria in the family Enterobacteriaceae genetically related to E. coli. It is responsible for a gastrointestinal infection called shigellosis in humans and is the leading cause of diarrhea (bacillary dysentery) worldwide.

S. dysenteriae is the main species causing shigellosis. S. dysenteriae subtype 1 (SD1) produces the Shiga toxin. It is responsible for the most severe form of shigellosis like severe dysentery with systemic complications such as electrolyte imbalance, seizures, and hemolytic uremic syndrome (HUS) and has the highest mortality .

S. flexneri is another common species causing shigellosis. It is responsible for most of the shigellosis in South East Asia. It mostly causes a milder form of diarrhea but in some cases, they are reported for severe forms including HUS and seizures .

S. sonnei and S. boydii are responsible for a milder form of shigellosis .

The main sign of shigella infection is diarrhea, which often is bloody. Other symptoms include abdominal cramping, nausea, vomiting, and fever . Symptoms usually begin within 1–2 days of coming in contact with shigella.

Shigella infection is diagnosed when a laboratory identifies shigella bacteria in the stool of an ill person. The test could be a culture that isolates the bacteria or a rapid diagnostic test that detects the genetic material of the bacteria.

Shigella infection is treated with fluids to prevent dehydration and antibiotics to shorten the duration and severity of symptoms. However, some strains of shigella have become resistant to common antibiotics such as ciprofloxacin and azithromycin, making treatment more difficult. Therefore, it is important to prevent shigella infection by practicing good hygiene, washing hands with soap and water before eating and after using the toilet, avoiding contact with people who have diarrhea, and cooking food thoroughly .

Vibrio is a genus of Gram-negative, rod-shaped (comma-shaped), motile, non-sporing, facultative anaerobic Gammaproteobacteria in the family Vibrionaceae with characteristic 2 chromosomes. It is responsible for waterborne gastroenteritis.

V. cholerae is the most important pathogenic species responsible for a cholera outbreak. It is responsible for endemic, epidemic, and pandemic cholera, resulting in large volumes of rice-water stools due to the production of an enterotoxin . Severe dehydration is of concern in patients without access to adequate medical care. In the United States, Vibrio parahemolyticus is the most common cause of Vibrio disease.

V. parahaemolyticus is the second most common Vibrio species causing bacterial gastroenteritis, mostly in the Asian region. However, the severity is very less than V. cholerae infection.

V. vulnificus is another species responsible for a milder form of gastroenteritis with diarrhea, vomiting, and fever.

Infection is diagnosed when Vibrio bacteria are found in the stool, wound, or blood of a patient who has symptoms of vibriosis. Treatment is not necessary in mild cases, but patients should drink plenty of liquids to replace fluids lost through diarrhea. Although there is no evidence that antibiotics decrease the severity or duration of illness, they are sometimes used in severe or prolonged illnesses.

Helicobacter pylori (H. pylori) is a type of bacteria that infects the stomach and the first part of the small intestine (duodenum). It can cause inflammation, ulcers, and even cancer in the gastrointestinal tract. H. pylori infection is very common and affects about half of the world`s population.

H. pylori bacteria can be detected in stool samples using different methods. A stool antigen test can detect proteins associated with H. pylori infection in the feces. This test can be used to diagnose the infection and confirm that it has been cured after treatment. A stool PCR test can detect H. pylori DNA in stool samples and also identify mutations that may be resistant to antibiotics used to treat H. pylori. However, this test is more expensive and less available than a stool antigen test.

A stool test for H. pylori is noninvasive, easy to perform, and does not require fasting or stopping medications. It is also suitable for children and adults who can cooperate with the test. However, a stool test may not be accurate if the person has taken antibiotics or proton pump inhibitors (PPIs) within two weeks before the test. These medications can reduce the amount of H. pylori bacteria in the stool and cause false-negative results.

A stool test for H. pylori is one of the options for diagnosing and monitoring H. pylori infection. Other tests include a breath test, a blood test, and an endoscopy with biopsy. The choice of test depends on the availability, cost, accuracy, and preference of the patient and the health care provider.

Yersinia is a genus of Gram-negative, rod-shaped, facultatively anaerobic bacteria in the family Yersiniaceae. Yersinia spp. are associated with about 2% of gastroenteritis cases worldwide. Most of the cases are self-limiting, but some can be severe or fatal, especially in children and immunocompromised individuals.

The most common species causing gastroenteritis is Y. enterocolitica, which can be transmitted by contaminated food, water, or animals. Y. enterocolitica infection can cause fever, abdominal pain, and diarrhea, which may be bloody or mucoid. The symptoms usually appear 4 to 7 days after exposure and last 1 to 3 weeks or longer. In some cases, Y. enterocolitica can also cause complications such as reactive arthritis, erythema nodosum, iritis, or septicemia.

Another species that can cause gastroenteritis is Y. pseudotuberculosis, which is mainly transmitted by wild animals or their feces. Y. pseudotuberculosis infection can cause similar symptoms as Y. enterocolitica, but also mesenteric lymphadenitis, which can mimic appendicitis. Y. pseudotuberculosis can also cause complications such as reactive arthritis, erythema nodosum, or septicemia.

A third species that can cause gastroenteritis is Y. pestis, which is the causative agent of plague. Plague is a rare but serious disease that can be transmitted by rodents or their fleas. Plague can manifest as bubonic plague (swollen lymph nodes), septicemic plague (blood infection), or pneumonic plague (lung infection). Plague can cause high fever, chills, headache, weakness, and sometimes diarrhea or vomiting. Plague is a medical emergency that requires immediate treatment with antibiotics.

Yersiniosis is usually diagnosed by detecting the bacteria in the stool of an infected person . However, many laboratories do not routinely test for Yersinia, so it is important to notify the laboratory personnel when yersiniosis is suspected so that special tests can be done. The bacteria can also be detected in specimens from other body sites, such as blood, urine, throat, or joint fluid.

Yersiniosis usually goes away on its own without antibiotic treatment. However, antibiotics may be used to treat more severe or complicated infections. Treatment of yersiniosis usually involves treating the symptoms only, such as rehydration and pain relief.

Proteus is a genus of Gram-negative, rod-shaped, aerobic, and facultative anaerobic motile bacteria in the family Enterobacteriaceae best known for their swarming colonies . Proteus spp. are common commensals of the gastrointestinal microbiota, but they can also act as opportunistic pathogens and cause various infections.

Proteus spp. are responsible for gastroenteritis, appendicitis, Crohn’s disease, colitis, and colonization of nasogastric tubes . They can invade the intestinal mucosa and trigger inflammation, ulceration, and bleeding. They can also produce urease, which increases the pH of the intestinal environment and facilitates the growth of other pathogens.

P. mirabilis is the most prevalent Proteus species in gastroenteritis . It can cause acute or chronic diarrhea, abdominal pain, fever, and nausea. It can also induce key pro-inflammatory pathways, such as NOD-like receptor signaling, Jak-STAT signaling, and MAPK signaling, and activate inflammation-related genes in epithelial cells and animal models.

P. vulgaris and P. penneri are rarely involved in gastrointestinal infections, but they can cause severe complications in immunocompromised patients or those with underlying conditions. They can also produce hemolysins, which can damage red blood cells and cause hemolytic anemia.

Proteus spp. can be detected in stool samples by culture or molecular methods . The treatment of Proteus infections depends on the severity of the symptoms and the susceptibility of the bacteria to antibiotics . However, Proteus spp. are often resistant to multiple antibiotics due to their ability to produce beta-lactamases and efflux pumps. Therefore, alternative strategies, such as probiotics, prebiotics, or phage therapy, may be needed to restore the gut microbiome balance and prevent recurrent infections.

Clostridium is a genus of Gram-positive, rod-shaped, strictly anaerobic, spore-forming bacteria in the family Clostridiaceae. Some species of Clostridium are part of the normal intestinal flora and do not cause any harm. However, some species are pathogenic and can cause serious gastrointestinal infections, especially after antibiotic use or exposure to contaminated food or water.

C. difficile is one of the most important causes of nosocomial diarrhea. Toxin-producing strains are responsible for several forms of gastroenteritis, mostly diarrhea and colitis. C. difficile infection can range from mild to severe and can lead to complications such as dehydration, electrolyte imbalance, toxic megacolon, bowel perforation, sepsis, and death. C. difficile infection is diagnosed by detecting the toxins or the bacteria in stool samples. Treatment usually involves discontinuing the causative antibiotic and administering specific antibiotics such as vancomycin, fidaxomicin, or metronidazole.

C. perfringens is another species associated with acute gastrointestinal infections. It is responsible for food poisoning cases caused by ingestion of contaminated meat or poultry products. It results in mild diarrhea to severe necrotizing enterocolitis. C. perfringens produces Type A and Type C toxins that are responsible for diarrheal diseases. C. perfringens infection is diagnosed by detecting the toxins or the bacteria in stool samples or food specimens. Treatment usually involves supportive care such as fluid and electrolyte replacement.

Other species of Clostridium that can cause gastrointestinal infections include C. septicum, C. botulinum, C. tetani, and C. sordellii. These species produce potent neurotoxins that can cause life-threatening conditions such as gas gangrene, botulism, tetanus, and toxic shock syndrome. These infections are rare and require prompt diagnosis and treatment with antitoxins and antibiotics.

Clostridium spp. are also being explored as potential probiotics for various gastrointestinal disorders such as inflammatory bowel disease, irritable bowel syndrome, constipation, and colorectal cancer. Some studies have shown beneficial effects of Clostridium spp. on intestinal barrier function, immune modulation, anti-inflammatory activity, and production of short-chain fatty acids. However, more research is needed to establish the safety and efficacy of Clostridium spp. as probiotics and to overcome the challenges of their anaerobic cultivation and delivery.

Gram-positive bacteria are bacteria with thick cell walls that stain purple-blue in a Gram stain test. They are usually distinguished from gram-negative bacteria, which have thinner cell walls and stain pink-red in the same test. Gram-positive and gram-negative bacteria have different structures and require different treatments.

Some of the gram-positive bacteria that can be found in stool are:

• Staphylococcus spp. These are spherical (cocci) bacteria that form grape-like clusters. They are normal flora of the skin, but can cause food poisoning when they produce toxins that affect the gastrointestinal tract. Staphylococcal food poisoning is characterized by nausea, vomiting, abdominal cramps, and diarrhea that usually resolve within 24 hours. The most common species involved is S. aureus.
• Enterococcus spp. These are spherical (cocci) bacteria that form pairs or chains. They are commensal to the gastrointestinal tract and rarely cause gastrointestinal infections. However, they can cause intra-abdominal infections and gastritis in some cases. The most common species involved are E. faecalis and E. faecium. Some strains of enterococci are resistant to vancomycin, a common antibiotic used to treat gram-positive infections.
• Campylobacter spp. These are rod-shaped (bacilli) bacteria that have a curved or comma shape. They are microaerophilic, meaning they require low levels of oxygen to grow. They are responsible for a bacterial gastrointestinal infection called campylobacteriosis, which is one of the most common causes of diarrhea worldwide. Campylobacteriosis is characterized by fever, abdominal pain, bloody diarrhea, and sometimes complications such as reactive arthritis and Guillain-Barré syndrome. The most common species involved is C. jejuni.
• Listeria spp. These are rod-shaped (bacilli) bacteria that can grow at low temperatures and high salt concentrations. They are responsible for a disease called listeriosis, which can cause acute, self-limiting, febrile gastroenteritis or invasive gastroenteritis that affects the bloodstream, brain, or placenta. Listeriosis has a high mortality rate and is especially dangerous for pregnant women, newborns, elderly people, and immunocompromised individuals. The most common species involved is L. monocytogenes.
• Bacillus spp. These are rod-shaped (bacilli) bacteria that form endospores, which are resistant structures that allow them to survive harsh conditions. They are responsible for food poisoning when they produce toxins that affect the gastrointestinal tract. Bacillus food poisoning can result in emetic syndrome (vomiting) or diarrheal syndrome (diarrhea). The most common species involved is B. cereus.

These are some of the common gram-positive bacteria found in stool. However, there may be other species that can cause gastrointestinal infections or diseases. Therefore, it is important to consult a doctor if you experience any symptoms of gastrointestinal illness and get tested for the type and sensitivity of the bacteria involved.

Staphylococcus is a genus of Gram-positive, catalase-positive, cocci bacteria belonging to the family Staphylococcaceae, typically known for producing grape-like clusters under a microscope. They are normal flora of the skin and mucous membranes, but some species can cause infections in various parts of the body.

S. aureus is the most pathogenic species of Staphylococcus and is responsible for a variety of diseases, including skin infections, pneumonia, endocarditis, osteomyelitis, septicemia, and toxic shock syndrome. S. aureus can also cause food poisoning by producing enterotoxins that are heat-stable and resistant to gastric acid and enzymes.

Staphylococcal food poisoning is one of the most common causes of foodborne illness worldwide. It is usually caused by ingestion of contaminated food that has been improperly stored or handled. The symptoms include nausea, vomiting, abdominal cramps, and diarrhea that usually appear within 1 to 6 hours after eating and last for 24 to 48 hours.

Staphylococcal enterotoxins (SEs) are classified into several types (A to U) based on their antigenic properties and biological activities. SEs act as superantigens that stimulate a massive release of inflammatory cytokines from T cells and macrophages, leading to systemic effects such as fever, hypotension, and shock.

S. aureus can also produce other toxins that can affect the gastrointestinal tract, such as exfoliative toxins (ETs) that cause staphylococcal scalded skin syndrome (SSSS), leukocidins that cause necrotizing pneumonia and empyema, and Panton-Valentine leukocidin (PVL) that causes necrotizing fasciitis and community-acquired methicillin-resistant S. aureus (CA-MRSA) infections.

S. aureus can be detected in stool samples by culture or molecular methods. Culture methods involve enrichment in selective media such as mannitol salt agar or Baird-Parker agar, followed by identification based on biochemical tests or coagulase activity. Molecular methods include polymerase chain reaction (PCR), multiplex PCR, or real-time PCR that target specific genes such as nuc (thermonuclease), mecA (methicillin resistance), or sea to seeu (enterotoxin types).

The treatment of staphylococcal food poisoning is mainly supportive and symptomatic, such as oral rehydration therapy, antiemetics, and antidiarrheals. Antibiotics are not usually indicated unless there is evidence of invasive infection or complications. The prevention of staphylococcal food poisoning involves proper hygiene, sanitation, and refrigeration of food items.

Enterococcus is a genus of Gram-positive, facultatively anaerobic, lactose fermenting cocci (diplococci) bacteria in the family Enterococcaceae that can tolerate bile salt concentrations up to 40%. They are commensal to the GI tract and are rarely associated with gastrointestinal infections. However, they are a common cause of urinary tract infections (UTIs), bacteremia, and infective endocarditis. They also have intrinsic resistance to some antibiotics and can acquire and transfer resistance to other bacteria via mobile genetic elements.

Enterococcus spp. is not a cause of diarrhea, so when it is isolated from a stool specimen from a patient who was cultured because of diarrhea, it should be considered colonization. However, some species of Enterococcus spp. have been reported to cause gastritis and intra-abdominal infections in some cases .

E. hirae and E. durans are detected as the cause of gastritis in some patients. They can induce inflammation and damage to the gastric mucosa by producing cytotoxins and biofilms. They can also interfere with the normal flora of the stomach and increase the risk of Helicobacter pylori infection.

Vancomycin-resistant E. faecalis is another species responsible for some cases of gastroenteritis. It can cause acute or chronic inflammation of the small intestine by producing enterotoxins and adhesins that disrupt the intestinal barrier and activate the immune system. It can also cause opportunistic infections in immunocompromised patients or those with underlying GI disorders.

The diagnosis of Enterococcus spp. infection in stool can be aided by conventional Gram stain and cultures and newer techniques like MALDI-TOF, NAAT, and PCR. Antibiotic sensitivities should be obtained early on to help physicians formulate treatment plans. The treatment of Enterococcus spp. infection depends on the site and severity of infection, the antibiotic susceptibility profile, and the patient`s clinical condition. Some common antibiotics used for Enterococcus spp. infection include ampicillin, vancomycin, linezolid, daptomycin, and tigecycline.

To prevent the hospital-related spread of enterococci, especially VRE, it is important to follow strict infection control measures, such as hand hygiene, contact precautions, environmental cleaning, and antibiotic stewardship.

Campylobacter is a genus of Gram-negative, rod-shaped (comma-shaped), microaerophilic motile bacteria in the family Campylobacteraceae. It is responsible for a bacterial gastrointestinal infection called Campylobacteriosis.

Campylobacteriosis is one of the most common causes of acute bacterial gastroenteritis in children and adults worldwide. It causes diarrhea, vomiting, and abdominal pain. The symptoms usually last for 3 to 6 days and resolve without antibiotic treatment. However, some people with severe illness or at risk for complications might need antibiotic therapy.

Campylobacter infection is diagnosed when a laboratory test detects Campylobacter bacteria in stool (poop), body tissue, or fluids. The test could be a culture that isolates the bacteria or a rapid diagnostic test that detects genetic material of the bacteria. Campylobacter antigen can also be detected by enzyme immunoassay (EIA) that uses antibodies to capture Campylobacter-specific antigens in stool samples.

Campylobacter infection is usually transmitted by eating raw or undercooked poultry or eating something that touched it. It can also be spread by contact with animals, especially dogs, cats, and farm animals. Drinking untreated water or unpasteurized milk can also be a source of infection.

The most common species of Campylobacter that cause human illness are C. jejuni and C. coli. Other species such as C. fetus, C. upsaliensis, C. lari, and C. hyointestinalis can also cause infections in humans, but less frequently.

Campylobacter infection can sometimes lead to serious complications such as Guillain-Barré syndrome (GBS), a rare disorder that affects the nerves and can cause paralysis. Campylobacter infection is the most commonly identified cause of GBS. Other complications include reactive arthritis, irritable bowel syndrome, and inflammatory bowel disease.

To prevent Campylobacter infection, people should practice good food safety habits such as washing hands before and after handling food, cooking poultry thoroughly, avoiding cross-contamination of raw and cooked foods, and drinking only treated water or pasteurized milk. People should also avoid contact with sick animals or their feces and wash their hands after touching animals or their environments.

Listeria is a genus of Gram-positive, rod-shaped, non-sporing, facultatively anaerobic bacteria in the family Listeriaceae. It is responsible for a disease called listeriosis.

L. monocytogenes can cause acute, self-limiting, febrile gastroenteritis and invasive gastroenteritis. Listeria gastroenteritis has a very high mortality rate making it the food-borne illness with the third highest mortality rate.

L. monocytogenes can be isolated from stool samples of patients with listeriosis. The bacteria can invade the intestinal epithelium and spread to the bloodstream and other organs. Listeriosis can cause severe complications such as meningitis, septicemia, endocarditis, and abortion.

The main source of Listeria infection is contaminated food, especially unpasteurized dairy products, ready-to-eat meats, and raw vegetables. Listeria can survive and grow at refrigeration temperatures, making it difficult to control.

The diagnosis of listeriosis is based on the isolation and identification of L. monocytogenes from stool samples or other clinical specimens. The treatment of listeriosis is usually with antibiotics such as ampicillin or gentamicin.

The prevention of listeriosis involves proper food handling and hygiene practices, such as washing hands, utensils, and surfaces; cooking food thoroughly; avoiding cross-contamination; and storing food at safe temperatures. People who are at high risk of listeriosis, such as pregnant women, older adults, and immunocompromised individuals, should avoid eating foods that are likely to be contaminated with Listeria.

Bacteroides is a genus of Gram-negative, rod-shaped, bile resistant, non-sporing, motile or non-motile, obligate anaerobic bacteria in the family Bacteroidaceae. They are part of human gastrointestinal microflora and play a role in digestion, immunity, and protection against pathogens. However, they can also cause infections and diseases when they escape the gut or overgrow due to dysbiosis.

B. fragilis is the most prevalent and clinically significant species of Bacteroides. It is the only species reported to form abscesses in the intestine. It has a capsule and produces a toxin that can cause tissue destruction. If left untreated, it can disrupt the intestinal wall and cause intra-abdominal sepsis and appendicitis. It has a mortality rate of 19%, and when untreated it raises to 60%.

B. fragilis is also associated with other diseases, such as inflammatory bowel disease (IBD), colorectal cancer, obesity, diabetes, and arthritis. It can modulate the host immune system by inducing pro-inflammatory or anti-inflammatory responses depending on the context. It can also transfer antibiotic resistance genes to other bacteria by horizontal gene transfer.

Other species of Bacteroides that can cause infections include B. ovatus, B. thetaiotaomicron, B. vulgatus, B. distasonis, and B. uniformis. They can cause bacteremia, peritonitis, pelvic inflammatory disease, brain abscesses, skin and soft tissue infections, and osteomyelitis. They are often resistant to multiple antibiotics and require appropriate treatment based on susceptibility testing.

Bacteroides spp. can be detected in stool samples by culture or molecular methods. The GI Map Stool Analysis uses quantitative PCR to measure the levels of Bacteroides spp. in stool samples. The normal range for Bacteroides spp. is 10⁸ to 10¹¹ CFU/g of stool. Levels below or above this range may indicate dysbiosis or infection.

Fusobacterium nucleatum is a Gram-negative, rod-shaped, anaerobic bacterium that is normally found in the oral cavity. It is associated with periodontal disease and dental plaque formation. However, F. nucleatum can also translocate to the gastrointestinal tract and colonize the colorectal mucosa .

F. nucleatum has been implicated as a risk factor for colorectal cancer (CRC), as it is enriched in both stools and tumor tissues of patients with CRC . F. nucleatum can adhere to and invade colorectal epithelial cells, induce inflammation, modulate immune responses, and promote tumor growth and progression. F. nucleatum also interacts with other bacteria in the gut microbiota and influences their abundance and activity.

Several studies have reported that the detection of F. nucleatum in stool samples is associated with increased odds of CRC . The presence of F. nucleatum in stool samples may reflect its colonization of the colorectal mucosa and its involvement in colorectal carcinogenesis. Therefore, F. nucleatum may serve as a potential fecal microbial marker for CRC detection and prevention .

However, there are some limitations and challenges in using F. nucleatum as a fecal microbial marker for CRC. For example, the methods of detection, quantification, and identification of F. nucleatum vary among studies and may affect the accuracy and comparability of the results. Moreover, the prevalence and abundance of F. nucleatum in stool samples may depend on various factors such as diet, lifestyle, ethnicity, geography, and medication use . Therefore, more standardized and comprehensive studies are needed to validate the role of F. nucleatum in stool samples as a fecal microbial marker for CRC.

Bacillus is a genus of Gram-positive, rod-shaped, endospore-forming, aerobic or facultative anaerobic bacteria in the family Bacillaceae. They are widely distributed in the environment and can be found in soil, dust, water, and some foods. Some Bacillus species are part of the normal flora of the human gastrointestinal tract and are usually harmless.

However, some Bacillus species can cause food poisoning and gastroenteritis when ingested in large numbers or when the normal gut microflora is disturbed. The most common pathogenic species is B. cereus, which produces two types of toxins: an emetic toxin that causes vomiting and nausea, and a diarrheal toxin that causes watery diarrhea and abdominal cramps . The symptoms usually appear within 6 to 24 hours after ingestion and last for 24 to 48 hours. B. cereus food poisoning is often associated with foods that are cooked and then kept at room temperature for a long time, such as rice, pasta, meat, and dairy products.

Other Bacillus species that have been reported to cause gastroenteritis include B. subtilis, B. licheniformis, B. pumilus, B. megaterium, and B. thuringiensis . These species are less virulent than B. cereus and usually cause mild and self-limiting symptoms. However, they may also produce enterotoxins that can cause diarrhea, vomiting, and abdominal pain.

Bacillus spp. can be detected in stool samples by culture or molecular methods . The carriage rate of Bacillus spp. in stools of healthy asymptomatic individuals ranges between 0 to 43%. However, high levels of Bacillus spp. in stool may indicate reduced digestive function, small intestinal bacterial overgrowth (SIBO), or constipation. Treatment of Bacillus spp. gastroenteritis is usually supportive and involves fluid and electrolyte replacement. Antibiotics are rarely needed unless there are signs of systemic infection or immunocompromise.

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