MICRO- UNIT 3 NOTES

Chapter 19.1-19.4- Microbial Ecology

Ecological Concepts• Ecosystem-- the sum total of all organisms and abiotic factors in a particular environment

– Anywhere that has plants and animals, there are also microbes there…even if there are no platns or animals, chances are there are still microbial organisms even in boiling hot springs—so still an ecosystem

• Population-- group of organisms of the same species in the same place (habitat) at the same time• Community-- two or more cell populations coexisting in a certain area (habitat) at a given time• Habitat--portion of an ecosystem where a community could reside• Guild-- metabolically related microbial population

– Make up a community • Niche--habitat shared by a guild

– For every organism, there is a prime/realized niche where they will be most successful and they will be the dominant organism in that niche

• symbiotic relationships– parasitism– mutualism– Commensalism (not harmed or hurt by relationship

Species Diversity• alpha diversity – diversity within a community (sample)• Metabolic diversity allows microbes to flourish in lots of environments

– Richnessthe total number of different species present (all are same richness, have 16)– abundancethe proportion of each species – evennesshow similar the abundances are (relative abundance of different species)

• beta diversity: comparison of samples (between community diversity) – Could be between regions or over time (applied)

• gamma diversity: the total species diversity for the different ecosystems within a region (landscape diversity)

Biogeochemistry• study of biologically mediated chemical transformations• many recycling activities carried out by microbes• biogeochemical cycles: carbon, nitrogen, sulfur, and iron

– Some steps in these cycles ONLY microbes can do, so they’re very important in recycling these nutrientsThe Nitrogen Cycle

What organisms can survive depends on what types of electron donors and acceptors are available in a certain environment. Ex. In anoxic sediment, have to use anaerobic respiration, fermentation or methanogens; energy yield getting smaller /worse the farther you go down

Metabolic byproducts and waste can affect environment too

• Nitrogen is necessary for ALL life• A lot of these involve giving nutrients in a form plants can use• Nitrification: the oxidation of ammonia to nitrate

o Plants can use ammonia to make glucose because it doesn’t leach easily from soil (nitrate does leach into soil easily, not used easily by plants, not good)

• Denitrification: the reduction of nitrate to nitrogen gas o Not good for agriculture, we want nitrogen is soilo Nitrogen in atmosphere can harm atmosphere

• nitrogen fixation: the reduction of nitrogen gas to ammoniao This is good--- good nitrogen source for plants

• Ammonification: the release of ammonia during the decomposition of organic nitrogen compounds (dead things)

• Anammox: the anaerobic oxidation of ammonia to nitrogen gaso Putting nitrogen back in the atmosphere

Redox Cycle for Nitrogen

Yellow arrows oxidationsRed arrows reductionsNitrogen fixation: take nitrogen from atmosphere and fix it into ammoniaAmmonification: decomposition of living organisms, can be made into ammoniaNitrification: ammonia nitrite then nitrate (two-step process)Denitrification: nitrate to nitrite to nitrogen gas; NOT good, lost to atmosphere, plants can’t use itDRNA: nitrate is used in anaerobic respiration as final electron acceptor (turns it to ammonia)

The Legume- Root Nodule Symbiosis• plant-bacterial mutualism• legumes: plants with seeds that grow in pods

– soybeans, clover, alfalfa, beans, peas, peanuts– grow well in nitrogen deficient soils because of bacterial relationships– Plants can assimilate nitrogen (from nitrogen gas) into ammonia because they have nitrogen fixing

bacteria in their roots– key role in crop rotation– Farmers don’t have to add nitrogen to fertilizers

• Bacterial infection of legume roots by nitrogen-fixing bacteria (rhizobia) leads to the formation of root nodules –

The Rumen and Ruminant Animals• ruminants

– herbivorous mammals that possess a rumen – Rumen: organ, before acidic stomach– cows , sheep, goats, etc.

• Cow eats grass, goes into reticulum• If particles are small enough go to omasum• If too big, go to rumen to be digested further by microbes• In rumen, it’s a “fermentation vessel” with lots of cellulose digesting bacteria to release sugar• Glucose from rumen goes directly into blood stream• Particles could stay in rumen for days

• Ruminiation--- cows keep chewing • Fermination vessel – fermination occurs in rumen• Rumen: digestive organ within which cellulose and other plant polysaccharides are digested by microbes

Microbes of the Rumen• 1010 to 1011 microbes/g rumen contents • cellulolytic microbes hydrolyze cellulose to free sugars • fermentation of sugars yields

– Volatile fatty acids • acetate, propionate, butyrate• pass through rumen wall into bloodstream• serve as ruminant’s main energy source

– CO2 and CH4

• released via eructation (burping)• constant temperature and pH (5.5-7)• free sugar from cellulose then fermented into fatty acid

– fatty acids pass through walls of rumen into the blood animals – MAIN source of energy

Biochemical Reactions in the Rumen

Digest cellulose into simple sugars pyruvatefermentation lactate acetate, proprionate & Butryate (main source of energy)

Microenvironments• microbial environments in nature

– only about 6 mm in diameter• up to 10 microenvironments in one soil particle

– oxygen levels• less oxygen in the middle of the envviroment

– are complex – constantly changing– conditions determined in part by metabolic activities of the community

• succession of microbes due to metabolic activities – resources and growth conditions are highly variable and often suboptimal

• not likely to have an extended period of exponential growth in nature due to variable conditions• grow in spurts linked closely to the availability and nature of resources

• “feast-or-famine” existence – competition for resource• The organisms that dominate the niche: it will be its prime niche—maybe if it has the

most numbers in that environment• inhibitory substances

– competition/cooperation• syntrophic- where organisms work together for a process because neither organism can

accomplish alone • Nitrification/nitric cycle

Biofilms• assemblages of bacterial cells attached to a surface• bacteria WANT to live in biofilms (offer each other protection in a community)

– heterogeneous community• a lot of different bacteria in ONE biofilm- a lot of different environments in one biofilm• metabolic differences

» oxygen is limited in the middle» few nutrients in the middle of the biofilms

• only those that can survive on fewer nutrients will live there • location

» do need a little moisture- interfaced with some water source• enclosed in adhesive matrix• trap nutrients for microbial growth and help prevent detachment of cells• provide protection

– phagocytes cant engulf biofilms; thus biofilms are resistant to phagocytosis– can’t be washed away because stick togethher

• microbial interactions—act differently in their biofilms than they would if they were alone – stick them together- mainly sugar that holds them together (negatively charged)– metabolic exchange- bacteria communicate with each other– DNA uptake– Quorum sensing

• Density dependent– communication doesn’t work until there are large numbers of bacteria present

• EX. Strep is an organism (pathogen with capsule, without capsule it is not pathogenic) has the ability to make biofilm if has a capsule. Always producing protein into its environment. A lot of

strep cells a lot of protein in environment– if it rises to a certain concentration the strep cells become competent (take naked DNA and then can produce bacteria SIMS- little antibiotics)

Biofilm Formation• Clean environments are BAD—any surface over time is going to start to attract some ambient molecules *make

it where bacteria will start to attach)•

Biofilm in Water Pipe

Problems Associated with Biofilms• Medical: form on medical devices (implants, heart valves

– Very difficult to treat with antibiotics usually just have to go in, clean it out and replace– cause disease: dental caries, pneumonia

• Industrial: interfere with fluids distribution– corrosion potential

Chapter 27.11-27.14, 27.17 – Antimicrobial DrugsAntimicrobial Drugs

• Compounds used to treat disease by destroying or inhibiting the growth of pathogenic microbes within a host (in vivo)

• Many times you don’t take a true antibiotic but take a synthetic or semisynthetic• Classification

– molecular structure– mechanism of action

o How are they inhibiting or killingo What are they going after

– spectrum of antimicrobial activity (group of organisms they affect)• Are they inhibiting growth of gm + and – • Antifungal or antiviral?

• Categories:– Synthetics- chemicals– Antibiotics- microbial products (purified product) – Semisynthetic- chemically modified antibiotic

General Characteristics of Antimicrobial Drugs• selective toxicity

– ability of drug to kill or inhibit pathogen while damaging the host as little as possible• Want to kill the pathogen but save the host• Penicillin is very selectively toxic it goes after peptidoglycan (only found in bacteria- eukaryotes

aren’t affected)• therapeutic (effective) dose

– drug level required for clinical treatment• toxic dose

– drug level at which drug becomes too toxic for patient (produces side effects)• therapeutic index

– ratio of toxic dose to therapeutic dose– TD 50– toxic dose for 50% of test subjects (or 50% of animals died at this level) divide by ED50 (effective

dose-50% of test subject survve)– the larger the therapeutic index, the better

• You want TD to be VERY HIGH – Morphine has a ratio of 70:1– Cocaine has a ratio of 10:1 just 10X concentration is toxic/deadly– Start with a drug with a larger therapeutic index, to avoid side effects

• Can use the lower therapeutic index if the others aren’t working• narrow-spectrum drugs

– attack only a few different pathogens– subjective

• broad-spectrum drugs – attack many different pathogens

• cidal agent – kills microbes

• static agent – inhibits growth of microbes (increasing concentration can go from static to lethal)

• side effects – undesirable effects of drugs on host cells

Spectrum of Activity

• Consider if you need to take broad or narrow spectrum microbial • Best to always take narrow spectrum if you can so the drug won’t have an effect on a lot of bacteria in body. • Broad spectrum has a lot of uses but can affect other bacteria in the body

Synthetic Antimicrobial Drugs• growth factor analogs

– structurally similar to an essential growth factor (vitamin)

Not responsible for molecular structureA lot of our drugs go after cell walls– selectively toxic since they are different based on cell type (peptidolgyca); Impair cell wall sythensisDNA gyrase- enzyme that packages DNARNA transcription50/30S in bacteria ribosomes (60/40S in eukaryotic ribosomes)--- selectively toxic but ribosomes in mitochondria could be affected by bacteria ribosomal antimicrobialsCan be inhibiting growth, kills organism or make it static--- works on actively growninig cells!

– disrupt cell metabolism– Static – broad spectrum– ex. sulfanilamide

• Folic acid important in DNA replication • quinolones

– interfere with bacterial DNA gyrase (packing DNA)– prevent DNA packaging– Cidal (defensive agasint gram positive and gram neg)– some narrow, some broad

• If parent is narrow (semisynthetic)– ex. Ciprofloxacin (commonly used for UTIs- gram negatives

Antibiotics: true/pure microbial products• antibiotics: naturally produced antimicrobial agents (microbial products)

– produced by Bacteria and fungi– released by the cell– made for cell-to-cell signaling and competition

• semisynthetics: chemically modified antibiotics – usually broaden spectrum

• β-Lactam antibiotics – include penicillins and cephalosporins– Produced by fungus– Bacteria resistant to these make enzyme that breaks down lactam– beta-lactamase

Penicillin• Discovered by Alexander Fleming• Effective primarily against gram-positive bacteria• Target cell wall synthesis

o Can’t get through to peptidoglycan of the gram negative because of the outer membrane • Narrow spectrum

Antibiotics from Bacteria• erythromycin (a macrolide)

– Found in soil– targets the 50S ribosomal subunit– static – broad spectrum– azithromycin (Z-pack) is a semisynthetic macrolide

• modified erythromycin; keeps the organisms from growing and increasing in number• tetracyclines

– target the 30S ribosomal subunit – static– broad spectrum – Skin issues/acne & used for animals

• Platensimycin– targets fatty acid– Don’t think bacteria can become resistant to this– biosynthesis

– broad spectrum• effective against MRSA (pussy boils) and VRE • Mulitdrug resistant staphaureous

Know Pencillin• Main problem with pencillin is allergy (serum of the blood contains antibodies binds to proteins and comes an

antigen) • Alone pencillin is not an antigen

Know tetracyclines • Problem= teeth discoloration

Know macrolides

The Serious Threat of Drug Resistance• antimicrobial drug resistance

– the acquired ability of a microorganism to resist the effects of a chemotherapeutic agent to which it is normally sensitive

• the Superbug = MRSA– methicillin resistant staphorous– isolated MRSA—foot ulcer of a diabetic

• The Problem– once resistance originates in a bacterial population, it can be transmitted to other bacteria– Usually if resistant to one, resistant to multiple drugs, a large class; if resistant to penicillin also resistant

to penicillin derivatives. – resistance mechanisms are not confined to a single class of drugs– erroneous practices select for the growth of resistant bacteria– it must have been sensitive to the drug before acquiring resistance (sometimes they are born with

resistance)

Mechanisms of Bacterial Resistance• Target modification (1)

• Target modification – target could be cell wall, ribosome, DNA gyrase: there is a mutation in the target so now the antimicrobial can’t find it (most spontaneous resistance, this is probably what happened)

• preventing entrance (2)– produce and expore an enzyme that breaks down antimicrobial before it can get it

• inactivation (3): drug gets in but an enzyme inside the cell inactivates them

• efflux pumps (4): revolving door, drug comes in but send it right back out: plasmid genes can make these pumps

• alternate pathway- cell compensates and uses a different pathway for a process

• impermeability—naturally the drug won’t be able to penetrate—impermeability of the bacteria surface and the drug can’t move in

Origin and Transmission of Drug ResistanceOrigin

• natural immunity genes (some make antibiotics, be resisitant to their own antibiotics)• spontaneous mutations• location of resistance genes

• chromosome • plasmids (R factors) resistance gens could have more than one mechansim• mobile genetic elements such as transposons- jumping genes, jump from

plasmid to DNA (more stable)Transmission

• horizontal gene transfer; types • Transformation- uptake of naked DNA from environment• Conjugation: transmission via sex pilus• Transduction– genes delivered via virus

Sources of Antibiotic Resistance

Preventing Emergence of Drug Resistance• give drug in high concentrations to destroy susceptible• give two or more drugs at same time• use antimicrobials only when necessary• take full course of antimicrobial • use narrow spectrum antimicrobials• possible future solutions

– continued development of new antimicrobials– use of bacteriophages to treat bacterial disease (viruses that go after bacteria)

Chapter 31.6- 31.14: the Microbiology of FoodFood Spoilage

• Food Spoilage– any change in appearance, smell, or taste of a food that makes it unpalatable to the consumer– Spoilage (if caused by bacteria) if its noticeably caused by bacteria that are now in the late exponential

phase– may be safe to eat; spoilage doesn’t mean it will make you sick– only true foodborne illness is caused by ingesting a pathogen or toxin– HOWEVER, if spoilage causing organisms are present, likely pathogens are present too

• Susceptibility to microbial spoilage– intrinsic factors

• food composition (chemical) and structure (physical)• Good supply of nutrients and water

– extrinsic factors• Environmental • What temperature being held at, what is oxygen availability, pH

• Categories:– Perishable: fresh food, meats, vegetables, some fruits, food you put in the fridge– semi-perishable: nuts, apples, bananas– Nonperishable: flour, sugar– USUALLY determined by water content of food; more water- more perishable

Food Composition and Spoilage• carbohydrates

– Mold/fungi predominates – degrades food by hydrolysis (also soft rots in fruits)– little odor– ergotism

• disease caused by Claviceps purpurea (fungus) toxins » Symptoms: hallucinogenic alkaloids, involuntary muscle contractions, sensation of bugs

crawling on you » Theory that Salem Witch trials; “witches” odd behavior likely caused by ergotism

• proteins or fats– bacterial growth predominates– Putrefication rotting

• anaerobic breakdown of proteins• foul-smelling amine compounds are released as proteins and are broken down

Intrinsic Factors• pH

– low pH favors yeast and mold– Ex. Pickles stored in vinegar, usually spoiled by mold

• presence and availability of water– in general, lower water activity inhibits microbial growth– Aw (scale from 0 to 1) where 1 is pure water

• oxidation-reduction potential– lower redox (less oxygen) – favors growth of anerobic bacteria– Cooked food, released oxygen, now there is less oxygen

• physical structure– grinding and mixing promotes microbial growth (ex. Ground beef)

• antimicrobial substances– Naturally found in food– coumarins, lysozyme, allicin, etc.

Extrinsic Factors• temperature

– lower temperatures retard microbial growth• relative humidity

– higher levels promote microbial growth– Dry foods can absorb water from air and become moist

• atmosphere– oxygen promotes growth– modified atmosphere packaging (MAP)

• use of shrink wrap and vacuum technologies to package food in controlled atmospheres• Can increase shelf life 2-5 times; wrapping is impermeable to oxygen

Food Preservation• Removal of microbes

– Filtration – Used for many foods that they don’t want to heat (beer and wine)

• Low temperature– refrigeration at ≤ 5°C

• Only retards growth– freezing at ≤ − 18°C

• STOPS growth, but doesn’t necessarily kill microbes• High temperature

– cooking and holding at high temperature– canning– Pasteurization

• The Danger Zone:– 5 - 60°C or 41 to 141 F where bacteria including pathogens

High Temperature: Canning • food heated to 115°C for 25 – 100 minutes (similar to autoclave)• Can sterilize, if endospores are killed• If you’re canning fruit, which is acidic, sterilization temps not necessary because acidity will prevent growth • kills spoilage microbes• Botulism (deadly disease, neurotoxin) will produce gas in can, causing it to buldge– sign of spoilage• spoilage of commercially canned foods is rare• Swollen cans indicates botulism (deadly) • One teaspoons of 1 botox toxin can kill 100,000 people • Dented can may be ok except if badly dented the seams may be punctured and open allowing bacteria to get in • Commercially canning food (like an autoclave) – not all canned food are sterilized because many of the time it

can destroy the quality of food. • Acidity is important when canning ( a lot of acidity- don’t need to take to high temperatures because endospores

and other bacteria cant grow in those conditions– • Don’t worry about botulism in canned fruit• Botulism a problem in home canning method

Pasteurization• kills pathogens and substantially reduces number of spoilage organisms

– does not sterilize- raising temperature of the foot to kill spoilage microbes and pathogens

• different pasteurization procedures heat for different lengths of time– shorter heating times result in improved flavor– shorter heating times means you need to increase temperature

• low temperature holding (LTH) – 63°C for 30 min

• high temperature short time (HTST) – 72°C for 15 seconds then rapid cooling

• ultrahigh-temperature (UHT) processing– 138°C for 2 seconds – 20 minutes– this process sterilizes , so technically not pasteurization– Amount of time depends on volume of product they are trying to sterilize– Used for coffee creamers, juice boxes, organic milk (shelf life of 75 days)

Reduction in Water Availability• Dehydration- reduces the amount of bacteria that can grow

o Less water decreases microbes• Adding solutes (sugar or salt)

o High solutes decreases amount of bacteria/microbesChemical-Based Preservation

• GRAS – chemical agents “generally recognized as safe”– Typically food additives– Can be carcinogenic precursors or potential mutagens

• radappertization– use of ionizing radiation (gamma radiation) to extend shelf life of foods

• does not make food radioactive– excellent penetrating power

• Cobalt 60 source– Not often used in the US– Ground beef– can be used to sterilize some foods

Foodborne Disease• about 48 million cases per year in U.S. (1/6 people will get a foodborne illness each year)

– 18% attributed to known pathogens– at least 3,000 deaths

• transmission– breakdown in hygiene (hand washing, processing of food– fecal-oral route – most are fecal contaminates of food– Fomites any inanimate object that can harbor pathogens and transmit pathogens (doorknob, food,

water, blanket)• The number one cause of foodborne illnesses are VIRUSES – usually fecal contaminates as well

– Noroviruses– Salmonella

• Get it fast and recover quickly

Food Intoxication/Poisoning vs. Food Infection• Food intoxication

– ingestion of preformed microbial toxins in foods (the pathogens don’t need to be in food anymore or can be dead- produce toxins that build up in food and you eat the food with toxins

– Toxins aka poisons – growth of the pathogen in host is not required – You get sick quickly– Majority are Gram-positive and produce exotoxins (secrete their toxins)

• Food infection– infection resulting from the ingestion of pathogens in food– Pathogens need be alive and grow/colonize in intestines– ingestion followed by colonization and growth in host– NOTE: Pathogens may produce toxins in host.– Need a little lead time- take longer to present symptoms– Generally Gram-negative, have endotoxins (Lipid A of LPS) they may produce exotoxins

Staphylococcus aureus• Gram + coccus, facultative aerobe• can thrive in high-salt (salt from sweat on skin)and low aw habitats (no need for a lot of water)• Usually carried on skin (opportunistic pathogen)• Sources: human nasal cavity, skin, skin sores

– Not considered a fecal contaminate• Puse forming bacteria • enterotoxin producer (gut- intestines)

– Toxins are heat stable (re-heating food may not be safe) and resistant to digestive proteases like stomach acid

• Foods: cream-filled baked goods, poultry, meat, gravies, egg and meat salads, puddings, vegetables– Basically can be in anything

Staphylococcal Food Intoxication• ≈ 185,000 cases/year in U.S.• foods usually contaminated during food preparation• contaminated foods are kept for several hours in the “danger zone”

– Only takes 2-4 hours in the danger zone to be contaminated– Can be dead already but able to make enough toxin

• Symptoms– Rapid onset (1-8 hours )– nausea, explosive vomiting, abdominal pain, diarrhea, headache, weakness, no fever (usually subnormal

body temperature- low body temperature)– NO FEVER—distinguishing characteristic of this

• Duration: 1-2 days

Clostridium Botulinum• Gram + bacillus, spore-former, strict anerobe• Sources: soil and water• Implicated in wound (similar to tetanis), infant and food-borne botulism• Produces a heat labile (cook it for a while and your good), proteinaceous neurotoxin goes after nerves

(exotoxin) • Toxin is produced best in high protein, low acid foods • Toxins are destroyed by high heat (80ºC for 10 minutes)• Foods: nonacid home-canned vegetables like corn and beans, smoked and fresh fish

– Food needs to be anoxic to support botulinum– Likes protein rich foods– pH lower than 4.6 will NOT grow

Botulism (Food Intoxication)• Endospores may contaminate raw foods before harvest or slaughter

– Normally in soil: accidental contamination• Most foodborne cases occur from eating foods that are not cooked after processing• Home-canned foods implicated in > 72% of foodborne outbreaks, < 10% from commercially processed (not

pressurized canner, not enough vinegar)• Infant botulism usually occurs in infants up to 2 months old (raw honey)

– Endospores get into gut of infant and giving them botulism • Symptoms

– Onset: 18 – 24 hours– blurred vision, dizziness, cramps, sometimes vomiting, no fever, nausea, constipation, heart paralysis,

difficulty in swallowing, speaking, and breathing– Duration: 1-10 days to life– Mortality: 3 – 5 %– Treatment: antitoxin

Clostridium perfringens- Food Infection• ≈ 1 million cases/year in U.S.• Needs to be presence in body to cause disease• In food:

– spores activated by cooking and germinate under anoxic conditions • In intestines:

– large numbers of cells (>108) must be ingested– sporulation of vegetative cells occurs in the intestine triggering the production of the enterotoxin– Vegetative cells killed by cooking, extended refrigeration, freezing

• Symptoms– Onset: 7-15 hours– Cramps, diarrhea, nausea (fever and vomiting are rare)

• Duration: 12 - 24 hours• Foods: meat, poultry, fish, dehydrated soups, sauces, foods cooked in bulk and then left at 20-40ºC for short

time periods

Salmonella enterica• Gram − bacillus, facultative aerobe• 2nd leading cause of foodborne illness (nuerovirus is #1) • Most strains are pathogenic• Sources: sewage (G.I. of birds and other animals)• Foods: poultry, beef, pork, fruits, vegetables, egg (custards, cakes, pies, eggnog), dairy products

Salmonellosis (Food Infection)• ≈ 1 million cases/year (US)• serovars Typhimurium and Enteritidis (common causes of gastrointeritis)• Cells multiply and colonize in the small and large intestine, then invade and grow in phagocytic cells• Infectious dose: usually 107-109 viable cells (less than that does not affect body)• Virulence factors

– Endotoxins (lipid A LPS)

» Absorbed into blood stream as cells die– enterotoxins– cytotoxins – kill cells of intestines

• Fecal contamination of food via food handler or livestock• Contaminated foods not heated before consumption

– Higher fat meal- more likely to become infected • Symptoms

– Onset: 8 - 48 hours– headache, chills, vomiting, diarrhea, fever, (enterocolitis)– Duration: usually 2 – 5 days– 10-20% of victims become carriers for 4-8 weeks

Pathogenic Escherichia coli • Live in our intestines, most are not pathogenic• Closely related to salmonella • Gram - , facultative aerobe, coccobacillus• Sources: fecal contaminates- sewage (G.I. tract of animals); food growing in contaminated wwater• Strains:

– Enterotoxigenic (ETEC): “traveler’s diarrhea” (Montezuma’s Revenge)– Enteropathogenic (EPEC): infantile diarrhea– Enteroinvasive (EIEC): watery diarrhea– Shiga Toxin-Producing/ enterohemorrhagic (STEC or EHEC): bloody diarrhea (O157:H7)

– Deadly– Leading cause of kidney failure in infants

• Foods: • ETEC- contaminated drinking water• STEC - undercooked ground beef, unpasteurized dairy products and fruit juices, spinach, water

• E.Coli in the flesh of the leaf- plant was growing in contaminated water—washing the plant will not decontaminate MUST COOK TO KILL

Enterohemmorrhagic E. Coli O157:H7 (Food Infection)• Leading cause of kidney failure in children

• Toxin causes bloody diarrhea and attaches to kidney epithelial cells – immune cell attack kidney tisue• Infectious dose: unknown (may be as little as 10 bacteria)• Produces verotoxin

– Hemorrhagic colitis– Hemolytic Uremic Syndrome

• Bacteria destroyed by proper heat treatment• Symptoms

• Onset: 3 – 5 days • bloody stools, intense abdominal pain, fever and vomiting rare, kidney failure, brain damage, death• Duration: 5- 10 days• ≈ 73,000 cases per year in the U.S. resulting in 60 deaths• Most susceptible – very old, very young and immunocompromised

• - Antibiotics not good- cells lyse and release more toxins– pushing over the edge in kidney failure

Campylobacter• Gram - , motile, microaerophilic (less than atmospheric oxygen), spiral shaped rods• Sources: G.I. of animals (chickens, turkeys, hogs, dogs)

– Transmisssion from touching your dog• Destroyed by pasteurization, sensitive to air, freezing, and gastric acid

– Problem for people who take antacids because it raises pH of stomach and bacteria can survive• Termed heat-tolerant campylobacters since they grow at 42ºC, not at 25ºC

– Cooking can be protective

Campylobacter jejuni and fetus Food Infection• > 2 million cases/year (US)• Foods involved: poultry, pork, raw clams, dairy

– Usually undercooked foods or unpasteurized dairy• Multiplies in the small intestine and invades the epithelium• Produces an enterotoxin and a cytotoxin• Infectious dose: 500-104 bacteria• Symptoms

– Onset: 2 – 10 days– severe diarrhea, malaise, headaches, abdominal cramps, high fever (over 104F/40C), vomiting

uncommon, occasionally ulceration of ileum (causing bloody diarrhea)• Duration: 1 – 10 days

Listeria monocytogenes• Causes food infection Gram +, facultative aerobe, coccobacillus

– Most of the time gram – causes food infection but this is an EXCEPTION• Psychrotolerant (grow in the refrigerator) , acid-tolerant, salt-tolerant• Sources: soil, water, fecal material, vegetation, silage (virtually everywhere)• Even though its everywhere, healthy people don’t get infected, but old, young and immunocompromised at

higher risk • Foods: uncooked meat and vegetables, fruits, processed foods, unpasteurized milk and milk products

– invasive pathogen (proliferation in phagocytes of the gastrointestinal tract)• Grow in phagocytes, takes over and reproduces in cell then lyses to release • Similar to salmonella

– Infectious dose: < 1000 in susceptible individual• LOW DOSE

Listeriosis (Food Infection)• Fewer than 100 cases/year, but cause an estimated 20% of all deaths from foodborne illness (high mortality)• Symptoms

– Onset: few days to 2 months (> 12 hours for gastrointestinal symptoms) – fever, muscle aches, nausea, diarrhea, headache, bacteremia (growing in blood), meningitis, confusion,

loss of balance, miscarriage • Flu like symptoms

– Duration: usually 5 – 10 days • pregnant women, young and old, and immunocompromised individuals most vulnerable• responsible for the largest meat recall in U.S. (2002)• cantaloupe (2011)• at-risk people should not eat soft cheeses, refrigerated smoked meats, deli meats, and undercooked hot dogs• Treatments with antibiotics if severe

Other Foodborne Infectious Diseases• Most foodborne infections are thought to be caused by viruses (70% of all cases are cause by viruses)

• Incubation of 24-48 hours• Symptoms: gastroenteritis characterized by diarrhea, nausea, and vomiting• Recovery is spontaneous and rapid (usually within 24-48 hours)

– Quick recovery– Responsible for the 24 hour bug

• Noro- viruses are responsible for most mild foodborne infections in the U.S. (9 million of the 13 million)– Outbreaks on cruise ships

• Rotavirus, astrovirus, and hepatitis A collectively cause 100,000 cases

Foodborne Protozoan Diseases• Giardia intestinalis and Cryptosporidium pa rvum can be spread via food (contaminated by fecal matter in

untreated water that is used to wash, irrigate, or spray crops), and via drinking water– Explosive diarrhea, extreme weight loss– Recurrence caused by stress– Stream water in the forest– Cryptosporidium: Milwaukee, cysts that are resistant to chlorine; animals can get it to

• Foods involved: fresh foods such as fruit, often imported from other countries• Toxoplasma gondii is a protozoan spread through cat feces or undercooked meat

– prenatal infection can cause blindness and stillbirth– Really bad if pregnant– Once infected it stays with you– Refers living in cats, if a rat is infected, protozoan will affect rat behavior and make them attracted to cat

(cat ladies)

Prion Disease• Prion- infectious agent made of proteins that cause disruption in neural tissue

– Misfolded protein that can affect other proteins and causing them to misfold• Symptoms: depression, loss of motor coordination, dementia, death

– Brain shrinkage and deterioration occurs rapidly – Spongiform pathology

• vCJD linked to consumption of meat products from cattle afflicted with BSE (“mad cow disease”)– No matter how you cook the meat the cow will have the disease

• No treatment – dead in 13 months• Incubation time of 10 years • Fed infected cows to other cows and that how it was spread • Ban on feeding cattle meat and bone meal have appeared to stop the development of new cases of BSE in

Europe

Food Safety • Clean - wash hands and surfaces often, wash raw fruits/vegetables• Separate - don’t cross-contaminate• Cook - cook to proper temperatures

– Most protective- kill most of the foodborne pathogens• Chill – refrigerate promptly• Always refrigerate perishable food within 2 hours (1 hour when temp. is > 90ºF)

• Use cooked leftovers within 4 days

Fermented Foods Supplement

Fermented Foods• dairy products• meat products• vegetables and vegetable products• yeast bread• Chocolate (sweat boxes)

– Yeast fermentation creates alcohol and CO2– Lactic acid increase pH and limiting bacteria– Acetic acid bacteria kill sprout in the cocoa seeds – Needs to go in a certain order- if sprout is killed to early the flavor of the chocolate is altered (bitter) if

too long there will be a lot of contamination in the sweat boxes • Glucose pyruvate fermentation products recycle NADH• “lacto” – lactic acid bacteria

Fermentation in Food• used for food preservation• may involve a succession of microbes• a self-limiting process • changes the flavor, texture, and odor of the food• starter cultures= inoculate milk with lactobacteria • natural rind = biofilm

Fermented Dairy Products• Lactic acid bacteria (LAB)

– gram-positives that tolerate acidic conditions (to a point), non-spore forming, aerotolerant (oxygen doesn’t have an effect on metabolism with a strictly fermentative metabolism (NOT aerobic or anerobic)

• Lactobacillus, Lactococcus, Leuconostoc, Streptococcus Probiotics vs. Prebiotics

• probiotics– live microorganisms, which when administered in adequate amounts, confer a health benefit to the host

• fermented food, dietary supplements (capsule form), non-oral supplements (lotion)– Help immune system by out competing bad pathogens in gut

• prebiotics– substances (such as food) that promote the growth of probiotics– Give probiotics nutrients– fibers

Probiotics • Pros (possible benefits)

– considered safe for healthy individuals• If you are really immunocompromised can lead to disease if

– improve general intestinal health and balance• improve lactose intolerance• control of diarrhea• anticancer effects (prevent colon cancer)• treatment of enteric disease• colonization resistance (help outcompete pathogens in the gut)

– may lower • blood pressure • serum cholesterol

– Immunomodulation: immune system is trained in the gut where you distinguish between good and bad pathogens

– improve oral health: biofilm flora in mouth, prevent cavities, periodontal and gum disease • Cons

– difficult to accurately assess effectiveness • each probiotic and each individual is different

– not regulated by FDA• misleading advertising• Not regulated• Seem to be more like a supplement • most yogurts have relatively low CFU counts- you need to consume a lot• Fat helps bacteria get through stomach acid (need to eat with probiotics)• voluntary “Live Active Culture” seal– 100 million live/active lactic acid bacteria• If capsule needs to be acidtolerant

– may cause • mild side effects• systemic infection in severely immunocompromised individuals

PRACTICE PROBLEMS

Legumes don’t need nitrogen fertilizers, because the rhizobia in their root nodules A. change ammonia into nitrate (nitrification) B. use ammonification to make ammonia from decaying organisms in the soilC. fix nitrogen gas into ammoniaD. change nitrate into nitrogen gas (denitrification)

Which of the following is not true of the rumen?A. It is where bacteria ferment the sugars that have been released from cellulose.B. It is anoxic, so anaerobic microbes predominateC. Volatile fatty acids are absorbed into the bloodstream of the ruminant animal and serve as its main source of

energyD. Most of the carbon dioxide and methane made in the rumen are released via flatulence

If an antimicrobial drug has a high selective toxicity, it means that it will…A. Cause noticeable side effects in the hostB. Be bacteriocidalC. Be more active against the pathogen, than the host tissuesD. Have a narrow spectrum of activity

Suppose you have been suffering from a terrible cold for 10 days and have decided to go to the doctor for help. Which one of the following doctor statements would assure you that you have found a competent doctor?

A. Let me prescribe you a Z packB. Take this antibiotic until you feel betterC. I will call you tomorrow after I have looked at the bacterial culture results D. Since you’ve had this cold for seven days, I am going to prescribe you a broad spectrum antimicrobial.

(Taking antimicrobials does NOT cause resistance, but they do select for growth of microbes that have resistance)

Suppose you are cleaning out your refrigerator and find a container of meat-loaf that you made last month. Upon opening the container, you smell a putrid odor and the meat appears to be slimy. Would you get sick if you eat the meat loaf?

A. Absolutely- pathogens are present, or have previously grown in the foodB. No- spoilage microorganisms are present, but will not cause diseaseC. Maybe- spoilage microorganisms are present which indicates that pathogens may be present (or have

previously grown in the food)D. No- regardless of the microorganisms present, I have an iron stomach

(Pathogens or toxins must be present in the food- we are not all super sick after thanksgiving- leaving food out for a long period of time)

Food infection results from the ingestion of ___________, while food intoxication results from the ingestion of ______________.

A. Bacteria, virusesB. Microbial toxin, foodborne pathogensC. Viruses, bacteriaD. Foodborne pathogens, microbial toxins

Which of the following foodborne pathogens is not considered a fecal contaminant?A. Escherichia coliB. Staphylococcus aureusC. Salmonella enterica serovar TyphimuriumD. All of the above are fecal contaminants

(Staph comes from skin bacterium; it would not be appropriate to treat toxin with antimicrobial or antibiotics)

Which one of the following statements does not describe microbial fermentation in food?A. may increase the shelf-life of the foodB. may enhance the flavor and/or texture of the foodC. may spoil the foodD. is a self-limiting processE. may involve a succession of microbesF. maintains a constant pH in the food