Microbiological Risks 

Microbiological Risks

Microorganisms are too small to be seen. They can be found everywhere in the nature. Although they are mostly harmless, microorganisms that can make people sick constitute microbiological risks.

Microorganisms are classified as useful, destructive, and dangerous (pathogen). There are those that produce our foods such as yogurt, bread, pickles, etc., as well as those that taint our foods although they are not harmful to health, or those affect our health negatively although an organoleptic change is not seen on the food.

The microorganisms that can switch between animals and humans and the infections they cause are called "zoonosis". Zoonoses can pass directly through animals, through environmental conditions and through foods contaminated by microorganisms. Salmonella passing through poultry meat and Brucella passing through raw milk are common examples of food-borne zoonoses.

The most important cause of foodborne diseases worldwide is microorganisms. Examples include diseases caused by bacteria such as Salmonella, Listeria, Enterohemorrhagic Escherichia coli (EHEC), Campylobacter, and diseases caused by toxins produced by molds.

Microbiological food poisoning is caused mainly by bacterias and viruses, and less commonly by parasites. These organisms can be from faeces and soil. These microorganisms may be infected to foods through raw materials, waters, surfaces or people.

Foodborne microbiological diseases are addressed in two main groups:

Foodborne infections

Foodborne intoxications


Bacteria are microorganisms that can be seen with a microscope. Bacteria that cause food poisoning are mainly found in feces and soil. Food and water also come into direct or indirect contact with bacteria through feces, mouth, nose, ear and wounds of contaminated people and animals.

Food poisoning bacteria often do not change the food odor, taste and appearance. -Some of these bacteria only cause disease when they reach very high numbers, while others can cause disease even if they are very few. For this reason, we use many methods such as cooling, freezing, cooking, and drying to fight against these microorganisms. However, our main goal should be to prevent these microorganisms from being transmitted to food and food production environments.

Pathogenic microorganisms that frequently cause food poisoning in Turkey: Salmonella spp., Listeria monocytogenes, Thermotolerant Campylobacter spp., Escherichia coli O157, coagulase positive staphylococci, Bacillus cereus and sulfite-reducing anaerobic bacteria.

This web page will also provide general information about the most common bacteria and bacterial diseases in the world, including the above mentioned.

Bacillus cereus

There are two types of illnesses caused by toxins produced by Bacillus cereus: First, the disease is characterized by nausea, vomiting and abdominal cramps and a short incubation period of 1-6 hours and is called an "emetic form" or "short incubation form", this toxin is heat resistant.

Second, after 8 to 16 hours of incubation, it shows up with abdominal cramps and diarrhea and is known as "diarrheal form" or "long incubation form", it is not resistant to heat. In both types, the disease usually lasts less than 24 hours.

These bacteria can be found in food and can grow rapidly at room temperature.

Food sources: A wide variety of foods such as meat, milk, vegetables, have been related with diarrheal form. Foods with rice as an ingredient such as soup, sauces, and rice dish; starchy foods such as potato, pasta, and foods include vegetables such as gallimaufry, which are left at room temperature for a long time, have been associated with the emetic form.


Some Brucella species cause brucellosis, also known as Malta Fever, Mediterranean Fever, Bang Disease. The disease mainly affects mammals such as cattle, sheep, goats, pigs and therefore causes significant economic losses. The disease also affects humans either through contact with infected animals or through food obtained from these animals. Brucella melitensis is the most common species causing this disease.

In some developed countries disease has been disappeared with the control programs applied. In our country there is still a risk, but a significant decrease has been recorded in recent years. According to the Turkish National Public Health Agency, the number of cases of brucellosis in humans decreased from 10,810 in 2006 to 7.177 in 2011 and to 4173 in 2015.

The most common way of transmission Brucella to humans is to drink the milk the sick animal without heat treatment and consume the products made with this milk before it is pasteurized. Not only because of Brucella, raw milk and dairy products made from raw milk should not be consumed since they can be the source of many other diseases.

Symptoms: fever, excessive sweating, weakness-fatigue, anorexia, headache, pain in the muscles, joints and back. Afterwards, recurrent fever, arthritis, liver growth and / or spleen, testicles swelling, neurological manifestations, chronic fatigue and depression. The disease can last for a few weeks but also can last for months even for years.

Incubation period: Usually 2-4 weeks. However, the incubation period can range from 1 week to 2 months, and even the symptoms can be seen after 2 months.


Among Campylobacter species, those with thermotolerant are considered pathogenic in humans. Among the thermotolerant species, there are Campylobacter jejuni, C. upsaliensis, C. lari and C. coli. However, C. jejuni is responsible for approximately 80% of all Campylobacter infections.

Disease symptoms: diarrhea, abdominal pain and abdominal cramps, fever and sometimes bloody stool. It typically takes 7-10 days.

Incubation period: Usually 2-5 days.

Food sources: raw or poorly cooked poultry meat, red meat, raw milk and water not coming from a reliable source.

Clostridium botulinum

This bacteria produces a toxin that causes botulism and is dangerous enough to cause death by paralyzing the muscles that move the lungs to breathe.

Disease manifestations: neurotoxic symptoms such as double vision, difficulty to swallow, difficulty to speak, and respiratory system paralysis. Botulism can be fatal, so medical advice should be taken without delay.

Incubation period: Usually 4-36 hours.

Food sources: This bacteria only produces toxins in anaerobic (oxygen-free or low-oxygen) and low-acid environments; and this toxin causes food-borne botulism. Their spores are heat-resistant and they continue to live in food that is applied false or inadequate heat treatment and whose pH is above 4.5. Most cases of botulism are caused by canned food made in the house, and rarely by industrial canned food, which has production defect.

In addition, C. botulinum spores are found in the soil, in the dust and in the honey. Adults taking these spores by breathing or by eating honey do not cause any adverse effects. In children younger than one year old whose development has not yet been completed, germs can produce toxins by germinating in the digestive system. For this reason, even honey should not be given to babies before their age even to sweeten their pacifier.

Escherichia coli (E. coli)

E. coli is a large group of bacteria found naturally in the intestines of humans and animals. For this reason, the presence of feces is indicative of fecal contamination. Most of the strains are harmless, but there are also some very dangerous ones. Some strains of E. coli cause diarrhea, while others can lead to urinary tract infections, respiratory tract diseases such as pneumonitis, and other serious diseases.

Some species of E. coli cause disease due to the "shiga toxin" they produce and are therefore termed "shiga toxin producing E. coli (STEC)". However, this group is also known as Verotoxigenic E. coli (VTEC) or Enterohemorrhagic E. coli (EHEC). Within this group:
E. coli O157: H7 (often referred as E. coli O157 or simply "O157"): The news about the epidemia of E. coli infection is usually related to this strain. One of the most common STECs is E. coli O157, which can produce deadly toxins.
E. coli O104: H4: An important epidemic cause in Europe in 2011 and announced as EHEC in general.
Non-O157 STEC: serogrup STEC causing other types of diseases than O157. Information on this group is limited, since there are still few people's health screenings pertaining to the formation of this group all over the world.

Disease symptoms: Starts slightly and mildly with abdominal pain or non-bloody diarrhea and become more serious in a few days. Some types of STEC lead to serious illnesses such as hemolytic-uremic syndrome (HUS), a type of bloody diarrhea and renal failure. HUS may occur in about 7 days after the first symptoms and diarrhea is finished.

Food sources: especially uncooked hamburger is in the first place; beef, raw milk and unpasteurized fruit juice, raw consumed greens, vegetables, and fruit.

STEC lives in the intestines of mammals such as sheep, goats and cattle, and cattle is the main source for people's illness. Although STEC does not usually make animals sick, it causes the disease in humans.

Incubation period: usually 3-4 days, but sometimes as short as 1 day and as long as 10 days.

Listeria monocytogenes

This bacterium causes a serious disease called "listeriosis", mainly in pregnancies, newborns and adults with weakened immune systems. Rarely, people who are not in these risk groups can also have disease.

L. monocytogenes is more resistant to temperature, salt and acid than many microorganisms and can live and even grow in the fridge at low temperature.

Disease symptoms: fever, headache, nausea and vomiting. It can cause fetal problems during pregnancy related to embryo and child deaths.

The incubation period varies from 7 to 30 days, but most of the symptoms are seen 48 to 72 hours after consumption of contaminated food.

Food sources: unpasteurized dairy products, ice cream, cheese, meat products such as sliced ham, smoked fish, hot dog sandwiches and eggs, salads containing seafood and chicken.


In the world, it is the most common cause of diarrhea, the most common cause of bacterial and food-borne deaths. For example, Salmonella is responsible for 1.2 million food-borne illnesses and about 450 deaths per year in the United States.

The disease caused by Salmonella is also called salmonellosis.

There are many species of Salmonella, but the most common are S. typhimurium and S. enteritidis.

Risks of Salmonella infection:   Salmonella infections are more common in summer than in winter.
Children under 5 years old have the highest risk for Salmonella infections.
Elderly people over 65 years old and people with weak immune systems are other risk groups for Salmonella infection.
Some drug treatments (e.g., treatments that reduce gastric acidity) increase the risk of Salmonella infection.
Disease symptoms: diarrhea, fever, abdominal cramps, vomiting. It usually takes 4-7 days.

Incubation period: 12-72 hours.

Food sources: raw and poorly cooked eggs, undercooked chicken, red meat, fresh fruit and vegetables, unpasteurized milk and dairy products. And all the foodstuffs that include these food products.

Staphylococcus aureus

S. aureus is the second or third most frequent pathogen bacterial after Salmonella, which causes extensive food poisoning in our country and many countries.

S. aureus is a common bacterium in the nose and skin of nearly 25% of healthy people and animals and will not cause any health problems unless they contaminate food. For this reason, provision of personnel hygiene in food production is the most important step to prevent contamination of these bacteria. S. aureus produces a toxin (enterotoxin) that causes vomiting shortly after ingestion in the body and is responsible for a significant amount of food poisoning.

Disease symptoms: Diarrhea, nausea and vomiting, abdominal pain and cramping, weakness. Fever is rarely seen. The duration of acute symptoms is usually 24 to 48 hours and the mortality rate is very low.

Incubation time: Usually 30 minutes to 8 hours.

Food sources: High protein foods cooked but left at room temperature for a long time; Meat and meat products, poultry, egg products, dairy products, tuna fish, potatoes and pasta salad.


Shigella bacteria is the cause of the "shigellosis" disease known as bacillary dysentery. Less than 100 bacteria are able to infect the body after being taken in. This is one of the most common bacterial diarrheas. It is estimated that the cause of about 500,000 diarrhea cases in the US is Shigella per year. There are four types: S. sonnei, S. flexneri, S. boydii, S. dysenteriae. The last one can still lead to fatal epidemic diseases in developing countries.

Disease symptoms: diarrhea (mild or severe, bloody at 25-50% of cases), fever, abdominal pain, spasms in the intestines, rectal spasms. It usually takes 5-7 days in humans with a good immune system. Diarrhea usually passes completely through this period, but it can take several months to return to previous intestine habits from the disease. Shiga-toxin producing strains (most commonly produced by S.dysenteriae) can cause hemolytic uremic syndrome (HUS), a type of renal failure that destroys red blood cells.

Incubation period: 1-2 days.

Food sources: salads, milk and dairy products, poultry meats, any food produced with unsafe water or by someone infected with this bacterium.


Vibrio cholerae

Cholera, caused by V. cholerae, is a disease that causes death if left untreated, but can easily be prevented and treated. Cholera outbreaks are closely linked to inadequate environment and water management, and places such as tenement districts and immigrant villages that lack of clean water and sanitation infrastructure are the most risky areas.

Disease symptoms: Watery diarrhea, frequent vomiting and leg cramps. If left untreated, death may occur within a few hours due to rapid water loss and shock.

Incubation period: 1-5 days

Food sources: V. cholera spreads as a result of contamination of water resources and food by people's feces. These people may be the source of contamination even if there are no symptoms of infection in the infected person. The most common sources of cholera are sewage water used as drinking and potable water mixed with still water or well water, raw fruit and vegetable watered with these waters, raw or not enough cooked seafood.

Although cholera has declined substantially in the world at the beginning of the 2000s, it has increased since 2005 and is still seen as a major problem in Africa and some Asian countries, especially where hygienic conditions are inadequate. According to the WHO report, this disease has been zeroized in the Americas during the 2000s, after 2010 the number of cases has again reached considerable levels and it is estimated that 1.4-4.3 million cases and 28.000 - 142.000 deaths are caused each year. In 2014, 55% of the cases were reported in Africa, 30% in Asia and 15% in the Americas.

In our country recently, cholera outbreaks occurred in 1915 in the Balkans, in 1960 and in 1970 in Istanbul, leading to the death of many people. After an epidemic that killed 21 people in Ankara in 1994, there is no official record of the cholera epidemic in our country.


V. parahaemolyticus, V. vulnificus, and V. alginolyticus are the most common species causing "vibriosis" disease, together with the Vibrio species that cause about a dozen diseases. Vibrio is a salt-resistant bacterium and is naturally found in less salty and salt water. For this reason, people are caught in "vibriosis" because of raw or undercooked seafood or in sea water exposed to bacteria from any wound on their bodies. Most infections occur between May and October, when the temperature of the water is warm. In the United States, Vibrio causes approximately 80,000 people to become ill and 100 people to die every year.

Although everyone is likely to get vibriosis, those with a weak immune system, especially those with chronic liver disease, are at greater risk. Eating raw sea food, especially oysters, and exposing open wounds with low salty / salty water increase the possibility to get vibriosis.

Disease symptoms: watery diarrhea with abdominal cramps, nausea, vomiting, fever and chills.

Incubation period: Usually 24 hours - 3 days.

Food sources: raw or undercooked seafood, especially sea shells.


Viruses are smaller creatures than bacteria. When they infect food, even in very small quantities, they can make us sick. Hepatitis A and neuroviruses are viruses transmitted through food. Viruses and particularly noroviruses are found in the feces and in the vomit, of a person who is carrying the disease. So they can be transmitted to food through sick people working in food production or sick cooks. It is spread by leakage from sewage to the water we use for food.

Hepatitis A

Hepatitis A virus (HAV) causes liver infection and the disease is called hepatitis A. Hepatitis A spreads through fecal food and water consumption. In addition, infected people who are closely related are also important sources of transmission. The disease may last a few weeks with mild symptoms in some people, but may also cause serious illness in others which last couple of months. The disease is asymptomatic in the majority of children or cannot be diagnosed based on mild symptoms.

To kill HAV, It is enough to heat up to 85 °C for 1 min. The application of simple hygiene rules such as washing hands before leaving the toilet and before starting to prepare food and cleaning the surfaces with 1/100 diluted bleach is also important for hepatitis A prevention.

Disease symptoms: fever, jaundice, clay-colored feces, anorexia, nausea-vomiting, abdominal pain, dark urine, weakness, joint pain.

Incubation period: 15-50 days, average 28 days.

Food sources: Raw or undercooked seashells, drinking infected water, raw foods and, if cooked, the food and utensils contacted by a person carrying the disease.


Norovirus is a very contagious virus; it is possible to get sick by touching infected person, infected food and water, and even infected surfaces. It is very important that the infected person does not work in food preparation, food production, enter food preparation area. Noroviruses cause inflammation of the stomach or intestine, or both (acute gastroenteritis).

Disease Symptoms: The most common symptoms are stomachache, nausea, vomiting and diarrhea, rarely fever, headache and body pain. Symptoms pass within 1-3 days.

Incubation period: 12-48 hours

Food sources: Any food contaminated by a virus-infected person.



Rotavirus is an infectious virus that causes gastroenteritis and affects the stomach and intestines. It is most commonly seen in infants and young children, but it can also cause illness in young people and adults. According to the World Health Organization (WHO) estimates, rotavirus causes 215,000 children less than 5 years of old to die each year, especially in poor countries.

Incubation period: Approximately 2 days.

Disease symptoms: Vomiting with severe watery diarrhea, fever, and abdominal pain. By causing the body to lose water, it can have serious consequences, especially in infancy and childhood, leading to death. Adults pass the disease with milder symptoms.

Food sources: Any food contaminated by a virus-infected person.


Intestinal parasites such as tenia worms cause disease by locating in the intestines of mammals, which is called "infestation". It passes to people through raw and undercooked meats which are contaminated during cutting, fruits and vegetables growing on the fertilized soil that has parasites. Food-borne illness is seen as an effect in all countries, more often in countries where sanitation is not adequately addressed.

Some people may have abdominal pain, cramps, constipation, gas and diarrhea while some doesn’t have symptoms despite of carrying parasites. In more serious cases, weight loss, fever, nausea, vomiting, or bloody defecation may be detected. Some parasites can lead to cancer, asthma, nervosity, skin rashes, and some may migrate to other parts of the body.

Many parasites can pass to people from food. The most common food-borne parasites are: Single cells (protozoa) such as Cryptosporidium spp., Giardia intestinalis, Cyclospora cayetanensis, Toxoplasma gondii, roundworms such as Trichinella spp. and Anisakis spp. and tapeworms such as Diphyllobothrium spp. and Taenia spp (tenia saginata / tenia solium - cattle / pig tenia).

Most of these organisms can pass to anyone, through water, soil or direct contact from person to person, the most essential sources are raw vegetables, raw meat, fish, aquatic plants such as watercress, and raw vegetables contaminated with human or animal feces. Contamination of food with parasites also occurs when the person working in the kitchen or food production does not comply with the hygiene rules.

The disease symptoms vary greatly depending on the type of parasite. Protozoans such as Cryptosporidium spp., Giardia intestinalis, Cyclospora cayetanensis most commonly cause diarrhea and gastrointestinal disorders. Helminthic (round and tape worms) infections have many other symptoms depending on the abdomen, diarrhea, muscle aches, cough, skin lesions, malnutrition, weight loss, neurological disorders and organism. Most of food-borne parasitic diseases can be treated.

Toxoplasma gondii


Prions "Prions" are very small particles that are infectious (infectious), which can cause diseases, even though they are normal proteins of human and animal tissues. They are not cells or viruses, and they are 100 times smaller than viruses. The neurodegenerative (brain-damaging) diseases they cause are generally called "prion diseases or transmissible spongiform encephalopathies (TSEs)". It affects specific types of proteins that are abundant in brain cells, causing loss of brain cells, causing the brain to take a spongy structure, and the disease develops over a long incubation period, expressed in years. When the incubation period is complete, it progresses rapidly and is deadly. It is known as "mad-cow" disease in our country, which has been seen in Europe for a while and creates fear in the world.

Antimicrobial Resistance

Antimicrobial resistance (AMR) is one of the major threats to human health in recent years. AMR states the target bacterium gains resistance through mutation to drugs used to treat diseases caused by bacteria, so the drug previously effective for that bacterium becomes ineffective. Today, it has become a serious public health problem that is getting bigger in all over the world and our country. Every year thousands of deaths and very high medical costs occur due to drug resistent infections. Treatment of infections such as pneumonia, tuberculosis has become very difficult and even impossible.

Antibiotics are the most discussed topics regarding antimicrobial resistance. Infections caused by bacteria that are resistant to antibiotics can now more difficultly be treated or cannot be treated. The development of new medicines is also ineffective if people do not change their habits and behaviors. Struggling with AMD: Prevention of the use of antibiotics without prescription in the treatment of both humans and animals; prevention of spread of infections by vaccination; reduction of infection presence and frequency, and for this purpose hands hygiene in food production is remarkably important.