Gastrointestinal Pathogen Profile by PCR (Self-collect)

What is a Gastrointestinal Pathogen?

The gastrointestinal tract (often referred to as the GI tract or ‘gut’) is the body’s food tube that extends from the mouth to the anus. The GI tract is home to a variety of pathogens or disease-producing microorganisms, such as bacteria (e.g., Escherichia coli O157:H7, Salmonella, and Campylobacter), viruses (e.g., Norovirus and Rotavirus), and parasites (e.g., Giardia, Cryptosporidium, and Entamoeba).

GI pathogens can cause infection and illness. They usually enter the body via the mouth and pass out of the body in the stools (faeces or poo). In the intestines, they multiply, produce toxins, and damage the gut lining, causing GI signs and symptoms such as diarrhoea. If the pathogens invade the gut lining cells, they may cause greater cell damage, and enter the bloodstream, resulting in illness throughout the body, such as fever. GI signs and symptoms depend on the pathogen but often include watery or bloody diarrhoea, severe abdominal pain, nausea and vomiting, inflammation of the gut lining, fever, and dehydration. The term gastroenteritis is given to the inflammation of the stomach and intestines that causes these symptoms.

What is a Gastrointestinal Pathogen Profile by PCR?

A GI Pathogen Profile is a diagnostic test that analyses a sample of stool and detects the presence of one or more specific microorganisms that cause GI infections. Each GI Pathogen Profile can detect either one or many different microorganisms. The GI Pathogen Profile considered here detects at least 14 bacteria and bacterial toxins, six viruses, and four parasites.

A polymerase chain reaction (PCR) is a molecular technique that identifies the cause of the infection by detecting the genetic material (the DNA and RNA) of the pathogen in the stools. This GI Pathogen Profile test is known as a multiplex test because it looks for many different pathogens at the same time using molecular testing. It is also referred to as "real time" PCR, as information about the pathogen DNA is collected throughout the PCR process.

Why is a Gastrointestinal Pathogen Profile by PCR important?

The signs and symptoms of GI infections caused by many bacteria, viruses, and parasites can be very similar. It is therefore necessary to carry out tests to determine which microorganism is causing the infection. For example, signs symptoms that are typically overlap between infections include diarrhoea (that may be bloody with a bacterial infection, and watery with a parasitic infection), nausea and vomiting, stomach cramps/abdominal pain, and fever. Some GI infections are persistent, becoming serious and life threatening.

The PCR technique is highly sensitive and specific, and very quickly identifies the cause of infection, enabling the infected person to be treated promptly. The technique overcomes very small amounts of the microorganism’s DNA by making copies of the DNA, so that the pathogen is more easily identifiable the technique also provides results much faster than other laboratory methods.

Who should have a Gastrointestinal Pathogen Profile by PCR?

A GI Pathogen Profile may be requested if you have signs and symptoms (e.g., bloody diarrhoea) of an infection in your GI tract that have continued for several days. A test may also be carried out if you have recently travelled abroad, especially to least developed areas with high numbers of GI infections; been exposed to untreated water (e.g., consumed water from a stream); or eaten food that was undercooked (e.g., seafood or meat) or exposed to flies. Additionally, you may be tested if there has been close contact with another infected person or animal.

Testing may be particularly important in vulnerable people, such those who are very young or are elderly, or who have a gut condition such as inflammatory bowel disease or a compromised immune system. Men who have sex with other men may also be at high risk for infection.

How to test for the Gastrointestinal Pathogen Profile?

A stool sample is collected by you at any time during a 24-hour day. Your doctor at The Online Clinic will provide you with all that you need to collect the sample along with complete instructions. Before collection, fill in all labels and the request form with the date and time of the sample. To collect a stool sample, place toilet paper in the toilet bowl and poo onto the toilet paper (do not allow the stool to touch the water in the toilet). Wash your hands. Scrape the sampling stick (attached to the collection tube lid) over the stool until it is evenly coated, and put the sampling stick into the collection tube. Close the collection tube and wash your hands. Place the collection tube into the sample container and close the container; put the sample container and the completed request form into the test-kit box; and put the test kit box into the blue postal envelope. Post immediately as the stool sample must be tested as soon as possible for accurate analysis.

What do Gastrointestinal Pathogen Profile by PCR results indicate?

A GI Pathogen Profile by PCR result will determine if you have a bacterial, viral or parasitic infection caused by any of the pathogens that the test screens for.

Results are positive (or state “detected”) if the test found the microorganism’s DNA or RNA, and there is a bacterial, viral or parasitic GI infection. Results will also indicate which pathogen is present. Multiplex PCR can detect if you have a single pathogen infection or multiple pathogen infections.

A negative PCR test (“not detected”) means that the test did not find the microorganism’s DNA or RNA. It most likely means that none of the screened pathogens are present and your GI infection is caused by something else. However, a negative result may also mean that there was too little DNA or RNA to be detectable.

What are the risk factors for a Gastrointestinal bacterial, viral or parasitic infection?

Pathogens entering the body through the mouth (orally) and causing GI infections can originate from many sources. Risk factors for GI infection focus on contamination and poor hygiene. Infections are often acquired during travel to countries or areas where hygiene and sanitation is poor.

Common sources of contamination include:

water that is untreated or poorly-treated, such as water for drinking/ice, or water from a natural source (e.g., stream, lake, well or swimming pool);
food that is raw, under-cooked, exposed to flies, or prepared by an infected person;
self-contamination from transfer of stools on your hands in your mouth.
caring for an infected person; and
touching an infected surface or animal.

How to avoid a Gastrointestinal bacterial, viral or parasitic infection

As the name suggests, GI pathogens live in the intestines of infected people and animals; they are passed out of the body in the stools. Infection is transmitted when pathogens are swallowed by other people or by animals. Therefore, to prevent infection, the pathogens must not be swallowed.

Practices minimising the risk of infection include:

Before travelling, seek information on the risks of contaminated food and water in the destination country;
Drink only clean treated water by using bottled, boiled or filtered water, and avoid ice in drinks in areas where there are untreated or poorly-treated water sources;
Ensure food is cooked thoroughly, only drink pasteurised milk, and peel (and wash in clean water) fruit and vegetables before eating in areas where there is risk of infection;
Wash hands with soap after using the toilet, contact with infected people and animals, or before and after food preparation;
In households where someone is infected, disinfect surfaces, wear gloves when caring for infected people and pets, and avoid sharing personal items (e.g., towels);
If infected, stay at home and have minimal contact with other family members; and
Avoid sex with an infected person.