Microbiology Week of March 21 Notes
Microbiology Week of March 21 Notes MICR 3050
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This 12 page Class Notes was uploaded by Toni Franken on Sunday March 27, 2016. The Class Notes belongs to MICR 3050 at Clemson University taught by Dr. Whitehead in Spring 2016. Since its upload, it has received 34 views. For similar materials see General Microbiology in Microbiology at Clemson University.
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Date Created: 03/27/16
MICR 3050 – Notes Set from 03/27/2016 Dr. Whitehead, Clemson University Chapter 41 Continued – Microbiology of Food Food Borne Disease: There are about 80 million cases of food borne illness per year in the US. Most are unknown pathogens due to affected people not going to the Doctor. Most cases are self resolving. There are at least 5000 deaths per year in the US due to foodborne pathogens. These are trasmitted usually through breakdown in hygiene protocols, by fecaloral contamination, through fomites (objects that can be used as transmission for infectious agents) such as tables, doorknobs, cutting boards, money, etc. Most common food borne agents include the norovirus, which causes: o “Explosive” vomiting and diarrhea. o High amounts of shedding (billions of doses of norovirus spread through shedding of the virus). o Salmonella, and Campylobacter jejuni are also possible pathogenic organisms that travel in food items. o Food infection vs. Intoxication: Food infection: Pathogenic organism is present in the contaminated food when ingested. o Process: Food is infected with a pathogen, you ingest the food, and the pathogen manages to grow inside your body. o The Problem: Any number of things can happen while it is growing, such as toxin production, tissue invasion, etc. The key to the infection definition is that the pathogen must actively grow inside your body. Typically takes 12 hours or so to appear – relatively long incubation time – Incubation time: time from when you’re exposed to time when symptoms appear. It takes time for the pathogen to grow to amounts that cause the symptoms. Many types of food infection can be treated with antibiotics because it is based on the presence of actively growing bacteria. There are some exceptions where antibiotics make the infection worse, but those are few and far between. Food intoxication: Pathogens were present in the food at some point, but they aren’t the causative agent of illness. The residual toxins from their presence are. o Process: At one point in time, there was a pathogen in the food. While it was in the food, it produced large amounts off the toxin, which do not deteriorate. o The Problem: You ingest the food that contains the toxins, and as soon as those toxins cause their damage, you’re going to be exhibiting symptoms. Usually takes less than 12 hours, sometimes even as short as 3 or 4 hours. Because there are no actively growing bacteria, antibiotics won’t work. Toxins cause the damage. o Common treatment is antitoxin – where you actually give person a substance that will bind to the toxin and prevent it from having its action. NOTE: Toxins can be involved in both cases! Big difference is the presence or absence of actively growing organisms. Common FoodBorne Pathogenic Agents: Toxoplasma gondii: Most people in the US get toxo from undercooked pork. Fungi don’t tend to cause illness in people. Staph aureus – incubation time is about 8 hours. Usually intoxication. E. coli – longer incubation period – Always causes food infection (3 – 5 days). Many of these organisms have overlapping symptoms, FOCUS ON THE UNIQUE CHARACTERISTICS. Listeria monocytog Food Infection o Gram positive o Facultative aerobe grows in any oxygen conditions, but prefers oxygen heavy environments. o Coccobacillus very short rod. o Psychrotolerant – tolerant of cold temperatures, so refrigeration doesn’t help. o Characteristics: It is also acid tolerant and salttolerant. Can grow at refrigerator temperatures, and does so effectively. This is not the optimum temperature, but it can still thrive. Contaminated food, if left directly on the shelves of the refrigerator, can transfer organisms there, which can subsequently contaminate the next item placed there. Can be found in fecal material of warmblooded animals, as well as soil, water, vegetation, or silage (fermented grain fed to livestock). Produce is open for contamination by listeria. o Largest Problem: It can grow almost anywhere in the body it wants to go, ranging from the GI system, where it can then leave from to cause infections of the blood stream, causing meningitis (which has high rates of mortality), and is one of the few organisms that can cross the placental barrier where it can cause miscarriage or stillbirth. This is why pregnant women are told to not eat deli meat, unpasteurized dairy products, etc. High rates of hospitalization. Infectious dose is about 1000 bacteria. Listeria was involved in the largest meat recall we’ve ever had (deli meats and hot dogs) in 2002. It was the recall of almost 30 million pounds of meat. There was also a cantaloupe outbreak in 2011, which was the deadliest foodborne outbreak that the US had seen in the over 100 years. 147 people got sick, 142 hospitalized, about 20% mortality rate. o Almost always causes food infection. Classic GI symptoms will probably occur within the first 24 hours. Onset is a few days to 2 months, however, for other symptoms, such as fever, muscle aches, nausea, diarrhea, meningitis, confusion, loss of balance, and miscarriage. The duration of illness is usually about 5 – 10 days WITHOUT further complications. People at most risk (for severe complications) are pregnant women, children less than a year old, and individuals over 65 years old (considered elderly) due to low immune efficiency. Tends to be fatal through comorbidity (more than one illness involved in elderly patients). People that are immunocompromised due to illness or medications are also heavily at risk. o Foods it commonly passes in are uncooked meat and vegetables, fruits, processed foods, unpasteurized milk, and milk products. Atrisk people should not eat soft cheeses, refrigerated smoked meats, deli meats, and undercooked hot dogs. PSYCHROTOLERANT AND VERY INVASIVE (LEAVES THE GI TRACT). These are the characteristics that make Listeria very dangerous. Salmonella: Food Infection o Gram negative o Rod bacillus o Facultative aerobe o Major sources: Fecal contamination Big problem with Salmonella getting inside of eggs due to infected ovaries of birds. Small reptiles commonly carry salmonella. Foods that are commonly infected include beef, pork, fruits, veggies, eggs (custards, cakes, pies, eggnog), and dairy, products. o Salmonella cases stay relatively steady throughout the year, except for the occasional large outbreak. Caused by food infection, but commonly expressed as gastroenteritis (salmonellosis). Gastroenteritis: Infection of GI tract where cells multiply and colonize in the GI tract. Cellassociated endotoxins are responsible for symptoms. Infectious dose – at least 1000 viable cells (generally), but this is up for debate due to variety of salmonella and host factors. Highly survivable – most people don’t need medical intervention. Endotoxins: Wide range of toxins may be produced by microbes. Exotoxins are toxins that organisms secrete into the environment. These toxins are typically proteinaceous, and secreted by the organism that makes them. LPS (lipopolysaccharides) is a typical toxin. The immune system will respond to it. Escherichia coli: Pathogenic E. coli (many strains of E. coli exist some are used as probiotics, and some are commensal and don’t cause us harm, others are pathogenic and cause illness). Food Infection. o Gram negative o Facultative aerobe o Typically rod shaped, but there are certain strains and conditions that result in a coccobacillus shape. o Source: Almost all contamination results from fecal contamination from a variety of animals. Different strains of E. coli cause different kinds of disease. Example Categories: ETEC – Enterotoxigenic – traveler’s diarrhea. Comes from contamination drinking water. It is a Nonshigatoxin producing organism. Tends to be selflimiting and doesn’t need medical attention. EHEC or ESTEC – Enterohemorrhagic – bloody diarrhea. Comes from undercooked ground beef, unpasteurized dairy products and fruit juices, spinach, and water. It is shiga toxin producing. Medical attention requirement depends on if complications arise or not. o E. coli O157:H7 (food infection) – most common type of EHEC. Leading cause of kidney failure in children. Has an incredibly low infectious dose (10 cells or less). Produces toxins – Shiga toxin for sure, which causes hemorrhagic colitis (severe inflammation of the colon that often leads to bleeding) and hemolytic uremic syndrome (HUS). HUS is the complication that kills people, where shiga toxin destroys and damages blood cells, which leads to clots. In the kidneys, there are very small, numerous blood vessels. If clots get into these vessels, it causes kidney damage, and eventually kidney failure. May often hear of dialyses to help with kidney damage. Bacteria will be destroyed by proper heat treatment of food. Symptoms appear in 3 – 5 days, and will result in bloody stools, intense abdominal pain, fever and vomiting are rare, kidney failure, brain damage, and death. Duration is about 5 – 10 days. Lower mortality rate than Listeria. MICR 3050 – Notes Set from 03/27/2016 Dr. Whitehead, Clemson University Chapter 41 Continued – Microbiology of Food Common FoodBorne Pathogenic Agents Continued: Staphylococcus aureus: Food Intoxication o Gram Positive o Coccus o Facultative Aerobe o Tolerant to high salt content o While it is capable of being a foodborne problem, it is also capable of causing a number of other infections. Most common type are skin infections, but this discussion involves foodborne staph. Unlike things like salmonella and listeria, the main place staph comes from is from people. Anytime you have staphborne illness, there has typically a breakdown in hygiene protocol. 25% of the population of humans are a carrier of staph, meaning they are unaffected by the infection. A lower percentage of individuals carry staph on their skin, most carriers have it in their nose. The biggest problem with staph carriers is that they shed staph routinely. o Enterotoxin producer – type of exotoxin. Something secreted by the organism. Staph produces a number of toxins – only a number cause issues in foodborne disease. The toxin is very heat stable and resistant to digestive proteases in saliva or stomach fluids. o The foods it is found in it vary widely – often seen in creamfilled baked goods, poultry, meat, gravies, egg and meat salads, puddings, veggies. Tends to be starch heavy foods that have issues. In food problems, staph is an intoxication. o Common scenario of contamination – food gets contaminated while being prepared, and then sits out for a period of time (room temp, potluck, picnic, etc.). The staph organisms grow, and the toxin builds up. o Symptoms: Rapid onset (1 – 8 hours) – nausea, explosive vomiting, abdominal pain, diarrhea, headache, weakness, no fever (usually subnormal body temperature). Duration is about 1 – 2 days. Clostridium botulinum: Food Intoxication o Gram positive o Rodshaped bacteria o Spore formation o Strict anaerobe. CANNOT grow in the presence of oxygen. Oxygen may trigger spore formation. o Sources: Naturally found in soil and water. Honey is a common source. o Different types of diseases can be caused by clostridium botulinum – some are intoxications, some are infections. Wound botulism: Someone gets wounded, and botulism got into it. This is an infection. See a few cases in the US, and commonly associated with IV use. Infant botulism: An active infection, and usually results from a baby eating something that contains botulism spores. The spores germinate in the baby’s GI tract, and cause an infection. Adults are not as susceptible to these spores. Microbes in the GI tract have colonization resistance, which keeps you from getting sick from pathogenic microbes ingested from food. Endospores are not destroyed by baking, so baked goods with honey in them are also possible carriers. Foodborne botulism: An intoxication – someone consumes food that contains a large amount of botulinum toxin in it. Single most toxic product that we know of, and it is an exotoxin. It is very sensitive to heat, though, and in theory you can destroy the toxin by boiling for 10 minutes. Intoxication usually occurs from improper cooking. We usually see this intoxication in nonacid homecanned vegetables like corn/beans/smoked and fresh fish. Usually occurs from eating food that are not cooked. 10% of contamination issues in canned goods comes from industrial canned, and 75% comes from homecanned. o Adults should not be susceptible to botulism infection in most cases o Symptoms: Onset is in 12 – 72 hours, blurred vision, dizziness, cramps, vomiting, no fever, nausea, constipation, heart paralysis, difficulty in swallowing, speaking and breathing. Most severe and fatal issue is the inability to breathe properly. In babies, it presents differently, and is usually seen as severe constipation. Duration of the intoxication is heavily dependent on how quickly you get treated with an antitoxin. This antitoxin is made of preformed antibodies that can bind to the toxin and prevent it from having its effects. The mortality rate for botulism before the antitoxin was about 50%, and now it is somewhere around 5%. If you have an outbreak of botulinum intoxication, the first person has a much higher mortality rate. Other foodborne infectious diseases: Most foodborne infections are thought to be caused by viruses. Typically have to treat with rehydration more than anything. Symptoms for most viral infections are gastroenteritis (swelling/inflammation of GI tract), which is accompanied by diarrhea, nausea, and vomiting. Recovery is spontaneous and rapid (usually within 24 – 48 hours). Usually selflimiting. Primary agents are noroviruses: Also have rotavirus (number of cases has declined substantially since the introduction of rotovirus vaccines – every child is vaccinated against it), astrovirus, and hepatitis A. Food borne Protozoan diseases: o Giardia lamblia, Cryptosporidium parvum, and Cyclospora cayetanensis can be spread via food. Typically due to contamination by fecal matter in untreated water that is used to wash, irrigate, or spray crops, and via drinking water. Foods usually involved are fresh foods (fruit, veggies). o Toxoplasma gondii is a protozoan spread through cat feces or undercooked meat (often pork) – prenatal infection can cause blindness and stillbirth. The most common cause, however, is pork that is undercooked. Toxo tends to reside in the brain, but many people that have it don’t exhibit symptoms. In rodents, this brain infection causes “zombie” rodents. Toxo can only fully complete its life cycle in cats. Main thing that cats eat – rodents and birds – so we often see toxoplasmosis infection in rodents. Rodents infected with toxo lose their fear of cats, which allows the transfer of the protozoa. It was found that the parasite alters the response of rats to cat urine – instead of being fearful of the smell of cat urine, cat urine lights up the part of the brain that lights up a positive response to a potential mate. T. gondii has also been studied for other effects on the brain. They suggest that infected individuals are more extroverted, more likely to get into car accidents (shown by numerous studies). There is a lot of controversy about whether there is any relationship between schitzophrenia and T. gondii infecitons. Yet, this has not been really shown. Prion based diseases: Incredibly stressresistant and infectious proteins. They are infectious agents made of proteins that cause disruption in neural tissue. We have nothing that can treat prionbased diseases. Nothing has shown any level of slowing down disease progression, or treatment. Symptoms are usually neurological – depression, loss of motor coordination, dementia, death. o Spongiform encephalopathy. o Main type of prion disease is vCJD linked to consumption of meat products from cattle afflicted with BSE (mad cow disease). Beef contaminated with a prion is not safe to consume – nothing can be done to make it safe for consumption. Appeared to stop the development of new cases of BSE. No longer using cow brains as animal byproduct. Food safety: o There are many protocols now in place to help prevent foodborne illness. o Keep things clean (wash hands, and surfaces, wash raw fruits and veggies). o Separate – don’t crosscontaminate (meat on different cutting board). o Cook to proper temperatures. o Chill – refrigerate promptly. Always refrigerate food that is perishable within 2 hours. (1 hour when temp is over 90 degrees outside). o Use cooked leftovers within 4 days. o CDC says that water is usually fine alone to use to clean foods. Look at the surface of the fruit – rough needs more scrubbing, smooth doesn’t take much. MICR 3050 – Notes Set from 03/27/2016 Dr. Whitehead, Clemson University Chapter 41 Continued – Microbiology of Food Monday will be diseases and any review questions. Wednesday guest speaker = exam material. Fermented Foods: Some food that undergo fermentation: Dairy products, meat products, vegetables and vegetable products, yeast bread, chocolate. Wine and beer production. Humans have been utilizing fermentation for food for centuries, if not thousands of years. Evidence as early as 6000 B.C. Many dairy products undergo fermentation such as yogurt and cheese, as do veggies like pickles and kimchee. The primary organisms in dairy food fermentation are Lactococcus and Lactobacillus, as well as Streptococcus thermophiles. In soy sauce, aspergillus (a fungus) might be used. Most common organisms are lactic acid fermenters. Fermented milk products include buttermilk, yogurt, cheeses, etc. Most of these are created using lactic acid bacteria (Lactobacillus, Lactococcus, Leuconostoc, and Streptococcus). o The main characteristic of lactic acid fermenters is the production of lactic acid. Can divide into two groups: Homofermenters (only produce lactic acid) Heterofermenters (mainly produce lactic acid, but also produce carbon dioxide and ethanol). There are several unifying characteristics of lactic acid producing organisms: All are gram positive. They are acid tolerant, nonspore forming, aerotolerant, and fermenting. Most of the organisms, especially the Lactobacillus and Lactococcus, are considered beneficial organisms. So, rather than causing illness, have beneficial sideeffects to the host. Only time they cause issues is if they get into the blood stream. Largely where the idea of probiotics comes from. Probiotics: May be able to intentionally inoculate yourself with certain types of bacteria that are beneficial. Can take a pill or eat a particular food that contains beneficial microbes. Live microorganisms are contained in these items, and in adequate amounts, confer a health benefit to the host (Lactobacillus and Bifidobacterium). o The problem with probiotics is that they are not regulated by the FDA. If they tell you certain numbers of bacteria, or certain types of bacteria, are contained in an item, they might not actually be true. Probiotics MUST be a live microbe. It can be any number of bacteria, and there are some yeast species that classify as probiotics. Take that microbe, and give it in an adequate amount, there will be a health benefit. This is a poor definition – don’t know adequate amounts. Most probiotics don’t actually come out and tell you what good they will do. Activia was getting in trouble for specific health benefits since it is not actually a medication. When organisms are put onto products, they tend to be given funny names. L rhamnosus GG is often abbreviated LGG. L reuteri (ATCC 5S730) used to be included in Stonyfield Farms products – L reuteri protectis was the name on the label. Same company had probiotic gum, and had a straw that had added dehydrated lactobacillus inside the straw and the drink would rehydrate the bacteria. Neither did very well. There is a lot of literature to suggest that there is something to the idea of probiotics (improving GI health, improve the normal microbiota population, etc.). There is some suggestion that taking probiotics and antibiotics at the same time might help reduce antibioticassociated diarrhea. There are strains of microbes that might help stimulate immune responses. A number will improve lactose intolerance due to the use of the lactose to make lactic acid – lactose intolerant people generally have an easier time eating yogurt than drinking milk. Control of diarrhea – some research to suggest anticancer effects. Some argument to lower serum cholesterol (but mainly in animals, not in humans). Most of the work done with probiotics was done in mice, which makes it hard to compare for human use. Production of alcoholic beverages: Alcohol is typically produced as a product of fermentation (primarily ethanol). There are certain types of alcoholic products that are also carbonated, which might come directly from the heterofermentation (production of lactic acid, ethanol, and carbon dioxide). We often start with easily fermentable carbohydrates, such as sugars in fruit. Wine production (called Enology – the science of wine): o The first process is preparation of the Must – the idea is to get the carbohydrates available for the microbes to use so that fermentation can progress in a reasonable fashion. First thing in wine is to crush the grapes to yield must. You’ll get a grape juice separated from the skins and everything. For white wines, the skins are removed early in the process. Red wines keep the skins longer. The must is the actual juice remaining. You can make some beers out of wild yeasts – just let any yeast ferment it. You can also do this with wine – plenty of wild yeasts, but it is very unpredictable, and some will produce unsavory fermentation end products that will give it a skunky flavor. The classic way to prevent this is to add an antibiotic to kill off unusual microbes – a sulfur dioxide fumigant. Then, go in and add a desirable yeast strain (typically Saccharomyces cerevisia or S. elliposideus). o Fermentation will happen in two steps. Primary fermentation is done by the yeast, where much of the alcohol production occurs. You’ll let the fermentation itself kill the yeast – more alcohol can be produced by acidtolerant yeasts. The level of alcohol content of the wine is directly associated with how acid tolerant the yeast is. Also get the idea of dry versus sweet wines. Sweet wines will have sugar added to the must, creating rapid fermentation, quickly building high ethanol levels, killing your yeast more rapidly before all of the sugar is used up, so there is sugar left over to add sweetness to the wine. Dry wines have less sugar added, meaning slow fermentation, and by the time the yeast die from ethanol build up, most or all of the sugar has been used up. This fermentation step takes 3 – 5 days at 20 – 28 degrees C. Problem with yeasts (purpose of secondary Fermentation)– most often produce both ethanol and acids. Most common is malic acid, which doesn’t taste that great. So, we usually do a second fermentation to try to get rid of the malic acid. There are bacteria that can convert malic acid to lactic acid, which is much more desirable. This is called malolactic fermentation, and lasts 1 – 3 weeks at about 20 degrees C. (usually use lactic acid producing bacteria). o Aging – can let it rest – depth of flavor development. o Racking step – microbial growth produces a lot of sediment, which might collect at the bottom of the liquid. In wind, you have to get rid of this – you let the sediment settle out so it is not in the final product. o Red versus white – has to do with when skins are removed. That directly impacts the color of the wine. All grapes actually have white juice regardless of the color of the grape. Without letting the skins sit in the must, there would be no red color. Dry versus sweet has to do with sugar addition, and rapidity of fermentation. Sparkling wines occur when fermentation is allowed in the bottles to produce CO 2nd you capture it to add carbonation. In many cases, they just vent the CO 2produced in fermentation, and add it back to the bottle. In natural carbonated alcohols, you would add microbes and sugar to allow fermentation to occur in the bottle. Beers and Ales: o First step, you start with grains instead of grape juice. There are microbes that can use any and all carbohydrates. The microbes that can use complex carbs are rare, and are not often used in the food industry. So, in order for microbes to have access to these carbs in grains, we have to make them available by creating mash. o Mash – mashing is a process used to release fermentable sugars from grains. The first step is that you have to let the grains germinate (barley, wheat, rice) and activation of enzymes to yield malt. Take the malt, and mix it with water, and transfer to mash tun (container where fermentation occurs) to yield actual mash. o Wort – mash gets heated with hops in a brew kettle. Purpose to heating is to deactivate the enzymes that were activated earlier. Hops. Hops are a dried flower – adds flavor. Originally used due to antimicrobial capabilities, and will help to kill of natural microbes. The types of hops will affect the flavor. The hops will get removed, and the wort should be a clear liquid containing fermentable carbohydrates. Now, you’re ready for fermentation. o Next you’ll do pitching the wort, which just means inoculation with yeasts. Type of beer are determined by types of yeast. Bottom yeasts are used in production of lager beers, they will tend to settle to the bottom. Fermentation takes about 7 – 12 days at 6 – 12 degrees C for lager beers Top yeasts used in ales, which tend to float to the top. Fermentation takes about 5 – 7 days at 14 – 23 degrees C for ales. o Lagering: Then, you’ll perform storage, called lagering to allow for sedimentation and flavor development. Then bottling can occur. o Beer is carbonated, CO i2 usually added at bottling after pasteurization of the beer. Artificially carbonated. In other countries, and some small craft breweries, will perform bottle conditioning where they would not kill off all microbes, or add more yeast, then add some sugar to allow natural carbon dioxide production. Distilled spirits – whiskey and bourbon begin with sour mash (mash inoculated with homolactic bacterium) – liquid fermented grain that may have, and probably has, been used in previous fermentation. After flavor development, you get rid of the water, and distill the fluid to concentrate the alcohol. This is clear fluid, so the coloration will come from the aging in the barrel.
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