Food microbiology

# Overview
Food microbiology is the study of the microorganisms which inhabit, create or contaminate food. Of major importance is the study of microorganisms causing food spoilage. However "good" bacteria such as probiotics are becoming increasingly important in food science. In addition, microorganisms are essential for the production of foods such as cheese, yogurt, other fermented foods, bread, beer and wine.

# Food safety
Food safety is a major focus of food microbiology. Pathogenic bacteria, viruses and toxins produced by microorganisms are all possible contaminants of food. However, microorganisms and their products can also be used to combat these pathogenic microbes. Probiotic bacteria, including those which produce bacteriocins can kill and inhibit pathogens. Alternatively, purified bacteriocins such as nisin can be added directly to food products. Finally, bacteriophage, viruses which only infect bacteria, can be used to kill bacterial pathogens. Thorough preparation of food, including proper cooking will eliminate most bacteria and viruses. However, toxins produced by contaminants may not be heat-labile, and some will not be eliminated by cooking.

# Fermentation
Fermentation is one way microorganisms can change a food. Yeast, especially S. cerevisiae, is used to leaven bread, brew beer and make wine. Certain bacteria, including lactic acid bacteria, are used to make yogurt, cheese, hot sauce, pickles and dishes such as kimchi. A common effect of these fermentations is that the food product is less hospitable to other microorganisms, including pathogens and spoilage-causing microorganisms, thus extending the food's shelf-life.
Some cheese varieties also require mold microorganisms to ripen and develop their characteristic flavors.

# Foodborne pathogens
Foodborne pathogens are the leading causes of illness and death in less developed countries killing approximately 1.8 million people annually. In developed countries foodborne pathogens are responsible for millions of cases of infectious gastrointestinal diseases each year, costing billions of dollars in medical care and lost productivity. New foodborne pathogens and foodborne diseases are likely to emerge driven by factors such as pathogen evolution, changes in agricultural and food manufacturing practices, and changes to the human host status. There are growing concerns that terrorists could use pathogens to contaminate food and water supplies in attempts to incapacitate thousands of people and disrupt economic growth.

## Enteric Viruses
Food- and waterborne viruses contribute to a substantial number of illnesses throughout the world.  Among those most commonly known are hepatitis A virus, rotavirus, astrovirus, enteric adenovirus, hepatitis E virus, and the human caliciviruses consisting of the noroviruses and the Sapporo viruses.  This diverse group are transmitted by the fecal-oral route, often by ingestion of contaminated food and water.
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## Protozoan Parasites
Protozoan parasites associated with food and water can cause illness in humans. Although parasites are more commonly found in developing countries, developed countries have also experienced several foodborne outbreaks. Contaminants may be inadvertently introduced to the foods by inadequate handling practices, either on the farm or during processing of foods. Protozoan parasites can be found worldwide, either infecting wild animals or in water and contaminating crops grown for human consumption. The disease can be much more severe and prolonged in immunocompromissed individuals.

## Mycotoxins
Molds produce mycotoxins, which are secondary metabolites that can cause acute or chronic diseases in humans when ingested from contaminated foods.  Potential diseases include cancers and tumors in different organs (heart, liver, kidney, nerves), gastrointestinal disturbances, alteration of the immune system, and reproductive problems. Species of Aspergillus, Fusarium, Penicillium, and Claviceps grow in agricultural commodities or foods and produce the mycotoxins such as aflatoxins, deoxynivalenol, ochratoxin A, fumonisins, ergot alkaloids, T-2 toxin, and zearalenone and other minor mycotoxins such as cyclopiazonic acid and patulin. Mycotoxins occur mainly in cereal grains (barley, maize, rye, wheat), coffee, dairy products, fruits, nuts and spices. Control of mycotoxins in foods has focused on minimizing mycotoxin production in the field, during storage or destruction once produced. Monitoring foods for mycotoxins is important to manage strategies such as regulations and guidelines, which are used by 77 countries, and for developing exposure assessments essential for accurate risk characterization.

## Yersinia enterocolitica
Yersinia enterocolitica includes pathogens and environmental strains that are ubiquitous in terrestrial and fresh water ecosystems. Evidence from large outbreaks of yersiniosis and from epidemiological studies of sporadic cases has shown that Y. enterocolitica is a foodborne pathogen. Pork is often implicated as the source of infection. The pig is the only animal consumed by man that regularly harbours pathogenic Y. enterocolitica. An important property of the bacterium is its ability to multiply at temperatures near to 0C, and therefore in many chilled foods. The pathogenic serovars (mainly O:3, O:5,27, O:8 and O:9) show different geographical distribution. However, the appearance of strains of serovars O:3 and O:9 in Europe, Japan in the 1970s, and in North America by the end of the 1980s, is an example of a global pandemic. There is a possible risk of reactive arthritis following infection with Y. enterocolitica.

## Vibrio
Vibrio species are prevalent in estuarine and marine environments and seven species can cause foodborne infections associated with seafood. Vibrio cholerae O1 and O139 serovtypes produce cholera toxin and are agents of cholera.  However, fecal-oral route infections in the terrestrial environment are responsible for epidemic cholera.  V. cholerae non-O1/O139 strains may cause gastroenteritis through production of known toxins or unknown mechanism.  Vibrio parahaemolytitucs strains capable of producing thermostable direct hemolysin (TDH) and/or TDH-related hemolysin are most important cause of gastroenteritis associated with seafood consumption.  Vibrio vulnificus is responsible for seafoodborne primary septicemia and its infectivity depends primarily on the risk factors of the host. V. vulnificus infection has the highest case fatality rate (50%) of any foodborne pathogen.  Four other species (Vibrio mimicus, Vibrio hollisae, Vibrio fluvialis, and Vibrio furnissii) can cause gastroenteritis.  Some strains of these species produce known toxins but the pathogenic mechanism is largely not understood.  The ecology of and detection and control methods for all seafoodborne Vibrio pathogens are essentially similar.

## Staphylococcus aureus
Staphylococcus aureus is a common cause of bacterial foodborne disease worldwide. Symptoms include vomiting and diarrhea that occur shortly after ingestion of S. aureus-contaminated food. The symptoms arise from ingestion of preformed enterotoxin, which accounts for the short incubation time. Staphylococcal enterotoxins are superantigens and, as such, have adverse effects on the immune system. The enterotoxin genes are accessory genetic elements in S. aureus, meaning that not all strains of this organism are enterotoxin-producing. The enterotoxin genes are found on prophage, plasmids, and pathogenicity islands in different strains of S. aureus. Expression of the enterotoxin genes is often under the control of global virulence gene regulatory systems.

## Campylobacter
Campylobacter spp., primarily C. jejuni subsp. jejuni is one of the major causes of bacterial gastroenteritis in the U.S. and worldwide.  Campylobacter infection is primarily a foodborne illness, usually without complications; however, serious sequelae such as Guillain-Barre Syndrome occur in a small subset of infected patients.  Detection of C. jejuni in clinical samples is readily accomplished by culture and non-culture methods.

## Listeria monocytogenes
Listeria monocytogenes is Gram-positive foodborne bacterial pathogen and the causative agent of human listeriosis.  Listeriae are acquired primarily through the consumption of contaminated foods including soft cheese, raw milk, deli salads, and ready-to-eat foods such as luncheon meats and frankfurters.  Although L. monocytogenes infection is usually limited to individuals that are immunocompromised, the high mortality rate associated with human listeriosis makes L. monocytogenes the leading cause of death amongst foodborne bacterial pathogens.  As a result, tremendous effort has been made at developing methods for the isolation, detection and control of L. monocytogenes in foods.

## Salmonella
Salmonella serotypes continue to be a prominent threat to food safety worldwide. Infections are commonly acquired by animal to human transmission though consumption of undercooked food products derived from livestock or domestic fowl. The second half of the 20th century saw the emergence of Salmonella serotypes that became associated with new food sources (i.e. chicken eggs) and the emergence of Salmonella serotypes with resistance against multiple antibiotics.

## Shigella
Shigella species are members of the family Enterobacteriacae and are Gram negative, non-motile rods.  Four subgroups exist based on O-antigen structure and biochemical properties; S. dysenteriae (subgroup A), S. flexneri (subgroup B), S. boydii (subgroup C) and S. sonnei (subgroup D).  Symptoms include mild to severe diarrhea with or without blood, fever, tenesmus, and abdominal pain.  Further complications of the disease may be seizures, toxic megacolon, reactive arthritis and hemolytic uremic syndrome.  Transmission of the pathogen is by the fecal-oral route, commonly through food and water. The infectious dose ranges from 10-100 organisms.  Shigella spp. have a sophisticated pathogenic mechanism to invade colonic epithelial cells of the host, man and higher primates, and the ability to multiply intracellularly and spread from cell to adjacent cell via actin polymerization.  Shigellae are one of the leading causes of bacterial foodborne illnesses and can spread quickly within a population.

## Escherichia coli
More information is available concerning Escherichia coli than any other organism, thus making E. coli the most thoroughly studied species in the microbial world.  For many years, E. coli was considered a commensal of human and animal intestinal tracts with low virulence potential.  It is now known that many strains of E. coli act as pathogens inducing serious gastrointestinal diseases and even death in humans.  There are six major categories of E. coli strains that cause enteric diseases in humans including the (1) enterohemorrhagic E. coli, which cause hemorrhagic colitis and hemolytic uremic syndrome, (2) enterotoxigenic E. coli, which  induce traveler's diarrhea, (3) enteropathogenic E. coli, which cause a persistent diarrhea in children living in developing countries, (4) enteroaggregative E. coli, which provoke diarrhea in children, (5) enteroinvasive E. coli that are biochemically and genetically related to Shigella species and can induce diarrhea, and (6) diffusely adherent E. coli, which cause diarrhea and are distinguished by a characteristic type of adherence to mammalian cells.

## Clostridium botulinum and Clostridium perfringens
Clostridium botulinum produces extremely potent neurotoxins that result in the severe neuroparalytic disease, botulism. The enterotoxin produced by C. perfringens during sporulation of vegetative cells in the host intestine results in debilitating acute diarrhea and abdominal pain. Sales of refrigerated, processed foods of extended durability including sous-vide foods, chilled ready-to-eat meals, and cook-chill foods have increased over recent years. Anaerobic spore-formers have been identified as the primary microbiological concerns in these foods. Heightened awareness over intentional food source tampering with botulinum neurotoxin has arisen with respect to genes encoding the toxins that are capable of transfer to nontoxigenic clostridia.

## Bacillus cereus
The Bacillus cereus group comprises six members: B. anthracis, B. cereus, B. mycoides, B. pseudomycoides, B. thuringiensis and B. weihenstephanensis. These species are closely related and should be placed within one species, except for B. anthracis that possesses specific large virulence plasmids. B. cereus is a normal soil inhabitant and is frequently isolated from a variety of foods, including vegetables, dairy products and meat. It causes a vomiting or diarrhoea illness that is becoming increasingly important in the industrialized world.  Some patients may experience both types of illness simultaneously. The diarrhoeal type of illness is most prevalent in the western hemisphere, whereas the emetic type is most prevalent in Japan. Desserts, meat dishes, and dairy products are the foods most frequently associated with diarrhoeal illness, whereas rice and pasta are the most common vehicles of emetic illness.  The emetic toxin (cereulide) has been isolated and characterized; it is a small ring peptide synthesised non-ribosomally by a peptide synthetase. Three types of B. cereus enterotoxins involved in foodborne outbreaks have been identified. Two of these enterotoxins are three-component proteins and are related, while the last is a one-component protein (CytK). Deaths have been recorded both by strains that produce the emetic toxin and by a strain producing only CytK.  Some strains of the B. cereus group are able to grow at refrigeration temperatures. These variants raise concern about the safety of cooked, refrigerated foods with an extended shelf life. B. cereus spores adhere to many surfaces and survive normal washing and disinfection (except for hypochlorite and UVC) procedures. B. cereus foodborne illness is likely underreported because of its relatively mild symptoms, which are of short duration.