What are the Pathogens of Gastroenteritis? How to Use the Gastroenteritis RT-qPCR Panel Test? - Vitrosens Biotechnology - Human and Animal Health Rapid Test Kits

What are the Pathogens of Gastroenteritis? How to Use the Gastroenteritis RT-qPCR Panel Test?


Pathogens of Gastroenteritis

Gastroenteritis is defined as inflammation of the stomach and intestines that may result in a wide range of symptoms, from asymptomatic infections through mild complaints to life-threatening conditions that lead to death. [1]

Most cases are infectious, although gastroenteritis may occur after ingesting drugs, medications, and chemical toxins – e.g., metals, plant substances –. Transmission can be through foodborne, waterborne, person-to-person, or sometimes zoonotic spread. [2]

Symptoms include anorexia, nausea, vomiting, diarrhea, and abdominal discomfort. Three main categories can cause Gastroenteritis, such as bacterial pathogens, viral pathogens, and parasitic pathogens.

Symptoms include

What are Bacterial Pathogens?

Bacterial pathogens are one of the significant causes of gastroenteritis. Here are some common bacterial pathogens associated with gastroenteritis:

Salmonella: Salmonella is a group of bacteria that can cause salmonellosis. It is commonly transmitted through contaminated food, particularly poultry, eggs, and unpasteurized milk. Symptoms include diarrhea, abdominal cramps, fever, and sometimes vomiting.

Campylobacter jejuni: Campylobacter is a bacterial species that can cause campylobacteriosis. It is often contracted by consuming undercooked poultry, contaminated water, or unpasteurized milk. Symptoms include diarrhea – often bloody –, abdominal pain, fever, and sometimes nausea and vomiting.

Escherichia coli (E. coli): While most strains of E. coli are harmless, certain pathogenic strains can cause gastroenteritis. The most well-known pathogenic strain is E. coli O157:H7, which produces toxins that can lead to severe symptoms, including bloody diarrhea, abdominal cramps, and sometimes kidney complications. [3]

Shigella: Shigella is a group of bacteria that causes shigellosis. It is highly contagious and spreads through the fecal-oral route, often due to poor hygiene practices. Symptoms include diarrhea – sometimes it may be bloody –, abdominal cramps, fever, and vomiting.

Vibrio cholerae: Vibrio cholerae is the bacterium responsible for cholera, a severe diarrheal disease. Cholera is typically transmitted through contaminated water or food, particularly seafood. Symptoms include profuse watery diarrhea, vomiting, leg cramps, and dehydration.

Yersinia enterocolitica: Yersinia enterocolitica is a bacterium that causes yersiniosis. It is commonly found in raw or undercooked pork and contaminated water. Symptoms include diarrhea (sometimes bloody), abdominal pain, fever, and occasionally joint pain.

These are just a few examples of bacterial pathogens that can cause gastroenteritis. It is worth noting that each bacterial pathogen may have distinct characteristics, routes of transmission, and associated symptoms. Proper hygiene, safe food handling, and clean water sources are crucial in preventing bacterial gastroenteritis.

What are Bacterial Pathogens

What are Viral Pathogens?

Viral pathogens commonly cause gastroenteritis, often called viral gastroenteritis or stomach flu. Here are some of the primary viral pathogens associated with gastroenteritis:

Norovirus:  Norovirus (NoV) is the most common single cause of foodborne gastroenteritis worldwide. Transmission of Norovirus can be through the fecal-oral route, either directly from person to person or indirectly via food or surfaces. Severe vomiting and diarrhea are the most common symptoms caused by Norovirus infection. The small nonenveloped Norovirus particles are highly infectious and resistant to common disinfectants. They can persist outside the host for long periods on surfaces, water, and food.  [4]

Rotavirus: Rotavirus primarily affects infants and young children. It spreads through the fecal-oral route and can be contracted from contaminated hands, objects, or surfaces. Rotavirus infections cause severe diarrhea, vomiting, fever, and abdominal pain.

Adenovirus: Certain strains of adenovirus can cause gastroenteritis. Adenovirus infections are more common in children but can affect people of all ages. In addition to gastrointestinal symptoms like diarrhea and vomiting, adenovirus can cause respiratory symptoms and conjunctivitis (pink eye).

Astrovirus: Astrovirus is another viral pathogen associated with gastroenteritis, particularly in young children. It spreads through the fecal-oral route and can cause diarrhea, vomiting, abdominal pain, and low-grade fever.

Sapovirus: Sapovirus infections are less common than norovirus and rotavirus but can still cause gastroenteritis. Sapovirus is often transmitted through contaminated food or water. Symptoms of Sapovirus infection include diarrhea, vomiting, abdominal pain, and fever.

It’s important to note that viral gastroenteritis is highly contagious, and the viruses responsible for it can spread rapidly in close communities, such as schools, nursing homes, or cruise ships. Proper hand hygiene and sanitation practices are crucial in preventing the transmission of viral gastroenteritis.

What are Viral Pathogens

What are Parasitic Pathogens?

Parasitic pathogens can also cause gastroenteritis. Here are some common parasitic pathogens associated with this condition:

Giardia lamblia: Giardia is a tiny parasite or germ causing the diarrheal disease giardiasis. Giardia can be present on surfaces or in soil, food, or water that has been contaminated with feces from infected people or animals. Giardiasis can be triggered by swallowing Giardia germs. Giardia has two modes of spreading: from person to person or through contaminated water, food, surfaces, or objects. [5]

Cryptosporidium parvum: Cryptosporidium parvum is a crucial gastrointestinal parasite of humans and other animals that can be transmitted via contamination of food and water [6]. Symptoms may be long-lasting, including diarrhea, loose or watery stools, stomach cramps, upset stomach, and a slight fever.

Entamoeba histolytica: Entamoeba histolytica is a parasite that causes amoebiasis. It is typically transmitted through ingesting food or water contaminated with fecal matter containing the parasite’s cysts. Amoebiasis can result in diarrhea, abdominal pain, bloody stools, and, in severe cases, liver abscesses.

Cyclospora cayetanensis: Cyclospora is a parasite that causes cyclosporiasis. It is often associated with contaminated fresh produce and water. Symptoms include watery diarrhea, loss of appetite, weight loss, abdominal cramps, and fatigue.

These parasitic pathogens are typically acquired through ingesting contaminated food or water. Good hygiene practices, including washing hands thoroughly and consuming properly cooked or treated food and safe drinking water, can help prevent parasitic gastroenteritis. If you suspect you have a parasitic infection, seeking medical attention for proper diagnosis and treatment is essential.

How to Diagnose Gastroenteritis?

Gastroenteritis is typically diagnosed based on a combination of clinical symptoms, medical history, and sometimes laboratory tests. Here are the common methods used to diagnose gastroenteritis:

Medical History and Physical Examination: Your symptoms, particularly the onset, persistence, and intensity of any abdominal discomfort, diarrhea, or vomiting, will be the first thing the doctor will inquire about. Inquiries will also be made concerning recent travel, eating habits, and potential contact with contagious people. A physical examination could be performed to check for symptoms, including fever, stomach pain, or dehydration.

Stool Sample Analysis: A stool sample may frequently be taken and sent to a lab for examination. Pathogens like bacteria, viruses, or parasites can all be detected in the laboratory. They might use tests like a stool culture, enzyme immunoassays (EIAs), polymerase chain reactions (PCR), or microscopic examination to find particular pathogens or signs of infection.

Blood Tests: White blood cell count (which indicates inflammation or infection), electrolyte levels (to check for dehydration), and markers of organ function are just a few of the characteristics that can be assessed by blood testing. Blood tests are beneficial when a doctor has a strong suspicion of a severe infection or other problems.

Imaging and Endoscopy (in some instances): In some cases, imaging tests such as abdominal X-rays, ultrasounds, or computed tomography (CT) scans may be prescribed if the symptoms are severe or persistent or if the doctor detects an underlying illness. The gastrointestinal tract may be examined via endoscopy, which uses a flexible tube with a camera to take samples for a biopsy if required.

It’s important to note that the specific diagnostic approach may vary depending on the suspected cause of gastroenteritis, the severity of symptoms, and individual circumstances. Proper diagnosis is essential to identify the underlying pathogen or cause and guide appropriate treatment and management strategies. Therefore, it is recommended to consult a healthcare professional for an accurate diagnosis and proper care.

How to Use the Gastroenteritis RT-qPCR Panel Test?

The Gastroenteritis RT-qPCR (Reverse Transcription-quantitative Polymerase Chain Reaction) Panel Test is a laboratory test used to detect and identify various viral and bacterial pathogens associated with gastroenteritis. Here’s an overview of how the test is typically performed:

Sample Collection: The test requires a stool sample to be collected. Your healthcare provider will provide you with a sterile container or a collection kit designed explicitly for stool sample collection. Follow the instructions provided by your healthcare provider for proper sample collection.

Laboratory Analysis: Once the stool sample arrives at the laboratory, it will undergo analysis using the Gastroenteritis RT-qPCR Panel Test. This test uses the technique of reverse transcription followed by quantitative polymerase chain reaction (RT-qPCR) to detect the presence of specific viral and bacterial genetic material (RNA or DNA) associated with gastroenteritis pathogens.

Pathogen Detection: The RT-qPCR technique amplifies and detects the genetic material of the target pathogens. The test can screen for multiple viral and bacterial pathogens simultaneously, allowing for a comprehensive evaluation. Depending on the specific panel used, common targets may include norovirus, rotavirus, adenovirus, Salmonella, Campylobacter, and other relevant pathogens.

Reporting of Results: The laboratory will analyze the RT-qPCR results and provide a report to your healthcare provider. The results will help guide further diagnosis, treatment decisions, and appropriate management of gastroenteritis.

It’s important to note that the specific instructions and procedures for the Gastroenteritis RT-qPCR Panel Test may vary depending on the laboratory and the specific panel used.


[1] Nicola Anne Page, Sandrama Nadan, Janet Mans, Chapter 11 – Viral Gastroenteritis, Editor(s): Guy D. Eslick, Gastrointestinal Diseases and their Associated Infections, Elsevier, 2019, Pages 135-149, ISBN 9780323548434, https://doi.org/10.1016/B978-0-323-54843-4.00011-8.

[2] Diarrhoeal Disease Collaborators: Estimates of the global, regional, and national morbidity, mortality, and aetiologies of diarrhoea in 195 countries: A systematic analysis for the Global Burden of Disease Study 2016. Lancet Infect Dis 18(11):1211–1228, 2018. doi: 10.1016/S1473-3099(18)30362-1.

[3] Gutema, F. D., Rasschaert, G., Agga, G. E., Jufare, A., Duguma, A. B., Abdi, R. D., … & De Zutter, L. (2021). Occurrence, molecular characteristics, and antimicrobial resistance of Escherichia coli O157 in cattle, beef, and humans in Bishoftu Town, Central Ethiopia. Foodborne Pathogens and Disease, 18(1), 1-7.

[4] Michael J. Arvin, Norovirus, Reference Module in Food Science, Elsevier, 2023,ISBN 9780081005965, https://doi.org/10.1016/B978-0-12-822521-9.00058-7.

[5] Conners EE, Miller AD, Balachandran N, Robinson BM, Benedict KM. Giardiasis Outbreaks — United States, 2012–2017. MMWR Morb Mortal Wkly Rep 2021;70:304–307. DOI: http://dx.doi.org/10.15585/mmwr.mm7009a2.

[6] Mac Kenzie at Al. (1994). A massive outbreak in Milwaukee of cryptosporidium infection transmitted through the public water supply. The New England journal of medicine, 331(3), 161–167. https://doi.org/10.1056/NEJM1994072133103.


Vitrosens Biotechnology is a high-tech company in Turkey founded for the development, manufacture, and delivery of in vitro diagnostic devices (IVD) to the world.
Follow USVITROSENS on Social Media
For our updated news and products follow us on social media.

vitrosens logo new

Vitrosens Biotechnology is a high-tech company in Turkey founded for the development, manufacture, and delivery of in vitro diagnostic devices (IVD) to the world.
Human Health
Animal Health
Follow USVITROSENS on Social Media
For our updated news and products follow us on social media.