Microbiology Exam 3 Flashcards

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Symbiosis

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Greek sym, together; bios, life
Symbiosis is usually restricted to mutualism, but may be extended to include parasitism and commensalisms.

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Symbiosis may be divided into two groups:

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endosymbiosis and ectosymbiosis

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endosymbiosis

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microorganisms grow within the host cells

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ectosymbiosis

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microorganisms attach but remain outside of host cell

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Mutualism

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both organisms benefit from the associations.

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Examples of mutualism

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nitrogen fixation, lichen, mycorrhizae, flashlight fishes, symbionts of protozoa, symbionts of insects, and symbiosis in ruminants.

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Rhizobia (nitrogen fixation)

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Some gram-negative heterotrophic soil bacteria (Rhizobia) form symbiotic association with plants of the legume family.

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actinomycetes (Frankia)

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Some actinomycetes (Frankia) also form symbiotic associations with non-leguminous actinorhizal plants such as alder (alnus), the california lilac (Ceanothus), and the Australian pine (Casuarina)

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Nitrogen fixation

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In the fixation process, N2 is reduced to ammonium (N≡N → NH3) by the enzyme complex nitrogenase.

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Nitrogenase consists of two separate proteins

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dinitrogenase and dinitrogenase reductase

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Both components contain

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iron (Fe) and dinitrogenase contains molybdenum (Mo).

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The Fe and Mo are contained in a cofactor known as

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FeMo-co

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Nitrogenase is irreversibly destroyed when exposed to

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oxygen

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In rhizobia-legume symbiosis...

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leghemoglobin binds and removes oxygen from the vicinity of nitrogenase

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The genes for dinitrogenase and dinitrogenase reductase were well studied in

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Klebsiella pneumoniae

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How many genes were identified and grouped into how many operons

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The 20 identified genes of the nif cluster are grouped into 7 nif operons

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How are nitrogenase and nitrogenase reducase formed

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Nitrogenase (Component I) and nitrogenase reductase (Component II) are formed independently to make up the nitrogenase complex.

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Nitrogenase also reduces

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Cyanide (CN-), acetylene (HC≡CH), and several other triply bounded compounds.

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What is used for assaying the activity of nitrogenase?

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The reduction of acetylene (C2H2) to ethylene (C2H4)

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Lichen

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Symbiosis between a fungus and an alga or a cyanobacterium

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The fungi in lichen are most commonly

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Ascomycota

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Lichen are found in...

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Lichen are found in such diverse places as deserts and the Arctic and Antarctic.

Lichen can grow in very inhospitable environments-- on rocks, sides and branches of trees, gravestones, therefore function as primary colonizers of stressful habitats.

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Lichens are also food of animals such as

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reindeer and caribou

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Lichens are sensitive to...

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air pollution, especially sulfur and nitrogen, and so they are natural indicators of air quality

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Lichens grow...

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extremely slow, usually 1-2 mm per year

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Mycorrhizae

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Symbiosis between fungi and plants

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What do plants obtain from fungi, and what do fungi obtain from plants?

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Plants obtain mineral nutrients from fungi, and fungi obtain carbohydrate for their corresponding growth in the association

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Two major types of mycorrhizae found in nature;

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ectomycorrhiza and endomycorrhiza

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What types of plants form ectomycorrhizae with fungi

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Many woody plants, such as pine, oak and birch

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Explain the characteristics of the ectomyrrhizal relationship

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The mycelium of ectomycorrhizal fungi forms a sheath, or mantle around the roots of the symbiont plant. From the mantle, a hyphal network called the Hartig net (named after Robert Hartig) extends into the root, between the cells, but not penetrate into the cortical cells

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Hartig net

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a hyphal network that extends into the root, between the cells, but does not penetrate into the cortical cells

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Aprixomately ___ of ______ plants form edomycorrhizae

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Approximately 80% of vascular plants for endomycorrhizae.

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In Endomycorrhizae, fungi ____ into root cortical cells and form special structures within cortical cells

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penetrate.

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Example of special structures formed in endomycorrhize

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arbuscular

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Endomycorrhize are further divided into:

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arbuscular, orchid and ericoid mycorrhizae based on their morphology and host plants

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Flashlight fishes are symbiotic relationships that involve...

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luminescent bacteria and fishes of the family Anomalopidae

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The light emitted by Flashlight fishes is used to:

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communicate, lure prey and confuse predators

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Bacteria can be endosymbionts of:

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Paramedium aurelia and amoebas

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T/F. The bacteria are highly host specific

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True

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Infections of a Protozoa by a Bacteria appears to depend on:

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one or two specific genes in the protozoa

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Endosymbiotic bacteria produce___________ and assist protozoa in ________ _________

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Endosymbiotic bacteria produce cellulose and assist protozoa in cellulose digestion.

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Some bacteria are _________ to different types of insects

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Some bacteria are endosymbionts to different types of insects.

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In some insects, such as wood-eating cockroaches and termites, the bacterial endosymbionts probably play an important role in:

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the degradation of wood cellulose

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Certain microorganisms form mutualistic relationships with ruminants, which are

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plant-eating animals such as cows, goats, giraffes, camels, and sheep.

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What does the microbial symbiont do?

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It decomposes cellulose and other plant materials and are also a source of vitamin and proteins for ruminants

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What does the rumen do for the microbial symbiont?

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The rumen provides favorable environments for microbial growth

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Parasitism

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Symbiotic relationships between two organisms in which one species (parasite) benefits for growth and reproduction to the harm of the other species (host)

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What plant disease is one of the most devastating plant disease?

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Potato late blight is one of the most devastating plant disease. The epidemics that destroyed potato crops in Europe in the 1840s led to mass starvation ("The Great Irish Famine")

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How many people died in the three years from 1846 to 1849 due to the great Irish famine?

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One million people died in the three years form 1846 to 1849, about 12% of the population. Another one million are estimated fled as refugees to Great Britain, the U.S., Canada, and Australia

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Malaria is caused by

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Protozoan parasites of the genus Plasmodium. It causes disease in approximately 400 million people and kills between one and three million, most of them young children in Sub-Saharan Africa

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Chlamydiae

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a bacterial phylum whose members are obligate intracellular pathogens, cause disease in birds and in humans and other mammals

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Chlamydiae are unable to synthesize...

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their own high-energy compounds, but benefit from their parasitism of the host's metabolic energy

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Bdellovibrio

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a curved gram-negative bacterium that preys on gram-negative bacteria by boring through the other membrane and cell wall of the host bacterium and dividing in the periplasm.

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What happens after Bdellovibrio does cell division

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The progeny of bdellovibrios are released as the host cell lysis

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Commensalisms

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Symbiotic relationship in which one organism is benefited and the other organism is unaffected

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Mutualism, commensalism, and parasitism are _________ relationships that can change depending on environmental conditions.

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dynamic relationships

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The line between mutualism or commensalism and parasitism can be altered in hosts when they....

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have other infections, are administered broad spectrum antibiotics, or immune system has been impaired by disease or treatment.

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Microbes that populate the human body in mutualistic or commensalistically become the:

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normal flora of the human body

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The human body has ___ cells and is comprised of ___ microbes

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The human body has 10^13 cells and is comprised of 10^14 microbes.

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Normal flora consists of

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Resident flora and transient flora

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Resident flora

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more or less constant

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Transient flora

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inhabit a specific spot for a short period of time

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Antagonism

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This is how bacteria that are part of the "normal flora," provide the host with protection against potentially pathogenic bacteria

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Examples of antagonism

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Lactobacilli inhabit the vagina and help to keep the population of the yeast Candida low.

Low number of Clostridium difficile in the colon will increase when antibiotics are given and the result is PMC, fever, cramps, and diarrhea.

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What is PMC?

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Pseudomembranous colitis. This disease has been increasing since the 1970s.

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Synergism

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Some bacteria grow better in combination than alone

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Examples of Synergism

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Enterococcus fecalis requires folic acid for growth and gets it from Lactobacillus arabinosus. The enterococci produces phenyalanine which the lactobacilli needs.

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Infection

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growth of micribes in tissues of the host

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infectious disease

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infecting microbe causes damage to the host

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communicable diseases

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transmitted from one host to the next

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Reservoirs

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Where infectious microbes can be found

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Inanimate reservoirs

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Soil, food, and water.

Soil: anthrax spores
Water: fecal coliforms
Food: ground beef, E.coli

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Animate reservoirs

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human beings: carriers

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Different types of human carriers

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1) healthy; no visible signs of disease
2) incubatory; before the clinical symptoms appear
3) convalescent; recovered from disease no symptoms, but still shed the agent

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Direct disease transmission

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Pathogens transmitted directly to the host. Person to person contact. Example: syphilis, gonorrhea Also, direct contact with infected animals, anthrax

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Indirect disease transmission

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pathogens transmitted via objects, "fomites," dishes, clothing, needles and dust.

"vectors," living organisms that transfer infectious agents, lice, fleas, ticks. Sometimes, dogs, cats, rodents are agents

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A fomes (formite)

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is any object or substance capable of carrying infectious organisms, such as germs or parasites, and hence transferring them from one individual to another

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Ports of entry into the host

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nose, mouth, eyes, ears, genitourinary tract, cuts. Usually the pathogen establishes itself and spreads

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Sequence of infectious disease

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-Incubation period
-Clinical illness
*Prodromal period
*Acute period
*Decline period
*Convalescent period

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Incubation period:

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Initially begins with a subclinical situation, the microbe will grow and multiply and establish a focus of infection in the host. Often no clinical signs of disease. Begins with exposure to the etiological agent

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Clinical illness

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visible symptoms

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Prodromal period (during clinical illness)

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symptoms first appear

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Acute period (during clinical illness)

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symptoms reach their peak

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Decline period (during clinical illness)

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disease resolves

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Convalescent period (during clinical illness)

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Patient recovers

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Latent infections

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These diseases do not immediately produce detectable signs or symptoms.

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Example of Latent infections

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Herpes simplex virus, remains latent until stress causes it to grow, remains dormant in host cells, not totally eliminated by body’s host defense mechanisms

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Most pathogens invade...

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a specific tissue or organ

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Shigella dysenteriae colonizes...

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the GI tract

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Brucella...

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grows in the placenta of infected animals,, needs erythritol, 4 carbon ROH(alcohol) for growth

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N. gonorhoeae possess...

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pili to attach to urogenital mucosal epithelial cells

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Microbial enzymes....

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aid in pathogenesis

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Hemolysins

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made by Streptococcus pyogenes, destroy RBC’s.

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Streptococcus pyogenes makes 2 hemolysins:

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streptolysin O and streptolysin S

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Streptolysin O

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is inactivated by oxygen, impacts Red Blood Cells and White Blood Cells. With White Blood Cells, it causes release of cytoplasmic granules.

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Streptolysin S

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is oxygen stable

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Streptokinase

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a protease that converts plasminogen in human serum to plasmin.

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The plasmin....

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The plasmin dissolves blood clots and thus promotes disease spread.

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Capsules protect the microbe from _________. They are important in the virulence of which bacteria?

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Protect the microbe from phagocytosis. Important in the virulence of Streptococcus pneumoniae, Klebsiella pneumoniae, Neisseria meningitidis, and Bacillus anthracis.

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Microbes produce 2 types of toxins:

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exotoxins and endotoxins

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exotoxin

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a soluble protein released into the surrounding environment by the microbe during growth and metabolism

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Endotoxin

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the lipopolysaccharide portion of the outer membrane of a gram-negative bacterium.

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Lipid A is...

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the toxic portion of the lipopolysaccharide molecule

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Endotoxin is released only upon:

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death and lysis of the Gram negative cell

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Different types of exotoxins:

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Enterotoxins: impact the small intestine.
Neurotoxins: affect nerve tissues
Cytotoxins: impact all cells

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Diphtheria

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is an example of a cytotoxin since it disrupts protein synthesis

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Botulium toxin

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is an example of a neurotoxin; it blocks the release of acetylcholine

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Enterotoxins produced by S. Areus

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impacts the small intestine

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Exotoxins converted to toxoids via formaldehyde treatment

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toxoids

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Toxoids

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They have lost their toxic activity but are still immunogenic, will cause the production of an immune response in humans

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Endotoxins bacterial source

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gram negative bacteria

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Endotoxins location

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lipolysaccharide

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Endotoxins toxic moiety

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Lipid A

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Endotoxins Heat stability

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1 hr @ 121 C

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Endotoxins toxicity

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low

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Endotoxins toxoid form produced?

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no

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Endotoxins symptoms

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fever, inflammation, increased phagocytosis, rash, septic shock

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Endotoxins detection

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Limulus amoebocyte lysate assay (LAL) assay. Detects 10^-12 (picogram) quantities of LPS

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Endotoxins induce fever by causing....

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the release of endogenous pyrogens (temperature elevating substances) from leukocytes. These pyrogens act at the hypothalamus.

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Septic shock:

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is caused by an increase in capillary permeability, resulting in reduced blood pressure

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Innate (nonspecific) resistance:

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Does not depend on prior exposure of the host to the invading organism

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Acquired (specific) resistance of immunity

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This involves specific proteins, antibodies and white blood cells (T cells)

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Factors that influence the condition of the host:

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sex, race, nutrition, stress and occupation

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Physical barriers (nonspecific host resistance)

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protection afforded by the skin and mucous membranes. Skin, tightly packed epithelial cells. Mucous membranes line portals of entry, respiratory tract.

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Lisozyme (nonspecific host resistance) - antimicrobial protection

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produced in tears, saliva and nasal secretions. It hydrolizes cell wall peptidoglycan, resulting in cell lysis.

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Interferon -

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antiviral agent. Interferons are proteins made and released by host cells in response to the presence of pathogens such as viruses, bacteria, parasites or tumor cells

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sebaceous gland

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produces an oily substance , to form a film on the skin’s surface, sebum

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Nonspecific host resistance

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Protective factors in the blood

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The average human has __ to ___ liters of blood that cost of _____

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Average human has 5 to 6 liters of blood, consists of a fluid portion, plasma, and a cellular portion.

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If the plasma is allowed to clot, the remaining fluid portion is called...

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serum

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The serum contains:

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different proteins, antibodies and complement. Antibodies interact with antigens. Three major cellular components include: erythrocytes, platelets, and leukocytes.

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Blood

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Erythrocytes, RBC’s, contain hemoglobin and transport oxygen and CO2 in the circulatory system.

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Platelets, thrombocytes, are involved in

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coagulation and the transport of serotonin.

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Leukocytes, lack pigment, differentiated into 5 types

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basophils, eosinophils, neutrophils, lymphocytes, and monocytes

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Granulocytes

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Basophils, eosinophils, and neutrophils. Short life span , 2 weeks

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Basophils

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contain vasodilator histamine, released during hypersensitive reactions, causes increased capillary permeability

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Eosinophils

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have an affinity for Ag-Ab complexes, which they phagocytize.

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Neutrophils

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commonly called PMN’s, play a large role in phagocytosis, normally present in low numbers except during infections.

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Agranulocytes

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Lymphocytes and monocytes. They do not contain cytoplasmic granules and are long living.

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Lymphocytes

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T and B cells, cell mediated immunity and antibody production

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Monocytes

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active in phagocytosis, macrophages are a differentiated form of monocytes.

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Primary Defenses of the Body

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Reticuloendothelial system and the lymphatic system.

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Reticuloendothelial system

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consists of wandering macrophages and stationary macrophages.

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Lymphatic system

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interconnecting network of vessels, collects excess fluid called lymph from the body’s tissues. This fluid flows through small structures called lymph nodes, which contain lymphocytes and macrophages to help clear the lymph of pathogens.

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Inflammation

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is the body’s nonspecific response to injury, irritation or infection. What is usually observed, dilation and increased permeability of blood vessels, producing edema, erythema, pain and heat.

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Phagocytosis

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The process of ingestion and digestion by cells of a substance that is foreign. This a part of the nonspecific defense in a host.

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Phagocytosis begins with

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recognition and adherence to the infectious agent. Chemotatic factors released by pathogenic bacteria attract phagocytes.

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Phagocytosis is reduced by the presence of

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bacterial capsules,

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Phagocytosis is enhanced by

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the presence of opsonins. Opsonins are proteins that form a bridge between surfaces of phagocytes and thus promote the process.

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After attachment, the phagocyte ingests the particle by extending

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pseudopods around the object. Inside the cytoplasm it fuses with lysosomes to form a larger structure a phagolysosome.

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Lysosomal enzymes, proteases, nucleases, lipases (phagocytosis)

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help to destroy the particle.

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Major components of the immune system

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Humoral, associated with proteins, antibodies.

Cellular, involves the interaction of antigens with host cells, T lymphocytes.

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Humoral immunity

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This develops from the formation of specific antibodies (immunoglobulins) to specific antigens.

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Lymphoid tissue represents about __% of total body weight

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2%

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Lymphocytes arise from_____ _______ ___ ___ ________ ________. These cells differentiate in _____ _______ _______ ______.

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Lymphocytes arise from stem cells in the bone marrow. These cells differentiate in the central lymphoid organs, B cells in the bone marrow, T cells in the thymus.

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These cells migrate from the tissues through the bloodstream to:

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secondary lymphoid organs, lymph nodes, spleen, tonsils, mucosa, Peyer’s patches, and appendix.

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Peyer's patches

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They are aggregations of lymphoid tissue that are usually found in the lowest portion of the small intestine, the ileum, in humans

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B and T lymphocytes

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Both cells originate in the bone marrow, B cell lymphocytes mature there, T cell lymphocytes mature in the thymus.

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B cells or B lymphocytes when they are activated differentiate into

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plasma cells that produce antibodies

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T lymphocytes or T cells. How many classes and what do they differentiate into?

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There are 2 main classes. One class which differentiates on activation into cytotoxic T cells, which kill cells infected with viruses.

The second class of T cells differentiates into cells that activate other cells such as B cells and macrophages.

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naive lymphocytes

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Small T and B lymphocytes that have matured in the thymus and bone marrow that have not encountered antigens are called naive lymphocytes.

These cells circulate from the blood into the peripheral lymphoid tissues. They are returned to the blood via lymphatic vessels

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In the event of an infection, the lymphocytes that recognize the infectious agent...

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are arrested in the lymphoid tissue where they proliferate and differentiate into effector cells, capable of combating infection.

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Antigens

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The definition of this molecule is: induces production of an antibody, is able to react with antibody, is a macro molecule with high MW, > 10,000 daltons, usually foreign to the host.

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Antigens must have immunogenicity, which is:

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the ability to elicit antibody formation. Bacteria, fungi, protozoa, viruses, bacterial toxins, proteins, and carbohydrates.

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Antibody reacts to the epitope, which is

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antigenic determinant.

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A single antigen may have one or more determinative sites, sometimes called

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valence

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Haptens

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are antigenic determinants that are incapable of stimulating an antibody response, they become immunogenic by covalent linkage to an immunogenic molecule.

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The antibody molecule has 2 separate functions:

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one, to bind specifically to molecules from the pathogen that elicited the immune response; the other is to recruit other cells and molecules to destroy the pathogen once the antibody is bound to it. Both functions are found on the antibody molecule, V or C regions

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Antibody Variable region, V region

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Variable region, V region, this is the antigen binding region of the antibody molecule, it varies extensively between molecules. Individuals make a vast number of antibodies because of this region.

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Antibody Constant region, C region

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this portion of the molecule engages the effector functions of the immune system.

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5 major classes of immunoglobulins

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IgG, IgM, IgA, IgE, and IgD.

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Describe the shape of Immunoglobulins

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Immunoglobulins are roughly Y-shaped molecules consisting of 3 equal portions, connected by a flexible tether.

The 2 arms of the Y vary between different antibody molecules- V region, which are involved with antigen binding. The stem of the Y, or the C region is less variable and is the part that interacts with the effector cells and molecules.

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IgG

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The only immunoglobulin to cross the placenta, provides immunity to the neonate. The predominating circulating immunoglobulin, it constitutes 80% of all the antibodies found in the human body.

MW 146 to 165 kDa, half life in our serum 21 days.

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IgC binds to...

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Binds to microbes to enhance their phagocytosis and lysis, reacts with surface Ag (Antigen?) to activate complement.

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IgM

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Generally the first antibody to be produced during an antibody response. It is able to bind bacterial surface antigens and activate complement. The largest of the immunoglobulins, MW 970 kDa, has 10 Ag binding sites.

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Five monomeric units of IgM are held together by

Back 176

disulfide bonds and a polypeptide J chain. Half life in serum 10 days.

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IgA

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Found in serum and body secretions. Serum IgA is a monomer, secretory IgA is a dimer consisting of 2 monomers joined by a J chain, a secretory component polypeptide is probably wrapped around the dimer.

MW 160 kDa monomer, or 320 kDa dimer, half life in serum 6 days.

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IgA is the principal antibody in:

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mother’s milk, saliva, tears, and GI and respiratory secretions. This is the first existing antibody to contact invading microbes.

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IgM is the first to be produced

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in response to invading microbes.

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IgE

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Found in low concentrations throughout the body and i s involved with Type I hypersensitivity reactions. These immunoglobulins attach to tissue mast cells and basophiles

MW 188kDa, half life 2 days in serum.

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When the IgE on the surface of these molecules bind antigen

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they stimulate the cells to release histamine and serotonin. The chemicals of hypersensitive reactions

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IgD

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Function unknown, present on the surface of certain B cells, therefore possibly involved with Ag reception, regulation of the synthesis of other immunoglobulins. MW 184 kDa, half life 3 days in the serum.

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Structure of Immunoglobulins

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They have a basic structure made up of 4 polypeptide chains, two light (L) chains and two heavy (H) chains. The light chains are attached to the heavy chains by a disulfide linkage. The heavy and light chains are arranged as a Y-shaped molecule with a flexible hinge.

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Enzymatic digestion of Igs

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Digestion of IgG with papain, (proteolytic enzyme), cleaves the Ig into 3 fragments, 2 Fab, and 1 Fc.

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The 2 Fab fragments

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are identical, and the amino end of the fragment is where the antigen binding portion of the molecule.`

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The Fc region

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The Fc region does not combine with antigen but does bind to complement. There are Fc receptors on the surface of macrophages, neutrophils and other cells, this enhances phagocytosis.

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Structure of Igs

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The H and L chains of the immunoglobulins have amino acid sequences that are constant and variable. The antigen binding region of both the L and H chains are variable, in the Fab portion of the molecule. This variable region is called the idiotype. This gives diversity to the Ig molecule. The constant region of the H chains have a constant amino acid sequence within a class of molecules, IgG vs IgM, however subclasses due exist, IgG1, IgG2, IgG3 etc.

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idiotype

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The antigen binding region of both the L and H chains are variable, in the Fab portion of the molecule. This variable region is called the idiotype.

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How do we make specific antibodies to millions of different antigens?

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1976, it was discovered that different parts of the human chromosome encode for the constant and variable portions of the Ig molecule, and are rearranged in B cells during their development to give an infinite diversity of Igs.

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Combinatorial joining

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which occurs during B cell development, when the DNA sequences for the H and L chains are randomly assembled from various gene segments for the variable, joining, diverse segment for the variable region, and the constant region.

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This chance rearrangement of gene sequences provide up to

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17,280,000 different varieties of antibody gene combinations

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The different varieties of antibody gene combinations is achieved in several ways:

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The V regions are encoded by separate gene segments that are brought together by somatic recombination to make a complete V-region gene. Many different V-region gene segments are present in the genome of an individual, and provide a heritable source of diversity. Certain lymphocyte factors (proteins), catalyze this rearrangement process. The evolution of these proteins enables this strategy of combinatorial diversity to appear.

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Antibodies generated in a normal immune response are

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very heterogeneous

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Therefore to obtain a homogeneous preparation of antibody, researchers turned to

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patients with multiple myeloma, a common tumor of plasma cells. This disease is associated with large amounts of homogeneous gamma globulin being produced.

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Kohler and Milstein, Monoclonal Antibodies

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Kohler and Milstein, devised a technique for producing a homogeneous population of antibodies of known antigenic specificity. They fused spleen cells from an immunized mouse to the cells of a mouse myeloma to produce hybrid cells (called hybridomas) that secreted a specific antibody to a specific antigen. The result is a limitless supply of antibody of a single specificity, useful for diagnostic probes.

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Tumor specific Ab

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antibodies bind to tumor cell and destroy it

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Tumor specific Ab conjugated to a toxin

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this conjugate binds to the tumor cell and destroys it

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Tumor specific Ab conjugated with radioisotope

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binds to a tumor cell and kills the cell and neighboring cell.

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T cell subpopulations

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T lymphocytes maturation in the thymus, involved with cell mediated immunity, half life years, widely distributed,

function: delayed hypersensitivity

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T helper cells (TH)

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activate B cells, produce cytokines, are involved in cell-mediated immunity

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cytotoxic T (TC)

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cells destroy cells with antigen on their surface.

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T lymphocytes have various..

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Have various cell surface receptors, (TCR), they show antigen specificity. When activated through their surface receptors form clones from a common ancestor.

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TC cells

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interact with and destroy cells containing antigen on their surface`

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TH cells

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produce various cytokines, stimulate B cells to produce Ab’s, and are involved in cell mediated immunity.

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Cytokines

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Low MW proteins that regulate important biological processes such as, cell growth, cell activation, tissue repair, immunity, inflammation. For example, interferons, interleukins, colony stimulating factors, tumor necrosis factors.

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Interferons

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These are antiviral proteins produced by cells in response to viral infections. The interferons, α,ß have 3 major functions, induce resistance to viral replication in uninfected cells by activating genes that cause the destruction of mRNA and inhibit the translation of viral and some host proteins. Increase the synthesis of molecules that make infected cells more susceptible to TC cells. Activate cells that kill virus infected cells selectively.

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Interleukins

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Are cytokines produced by T cells. IL 1, stimulates macrophages and activates lymphocytes. IL 2, stimulates J chain synthesis. IL 4, for the growth and survival of T cells, inhibits macrophage activation. IL 5, involved with IgA synthesis.

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Tumor necrosis factor. Also, explain what TNF α and TNF ß do

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TNF α, is a cytokine produced by macrophages and T cells that have multiple functions, cell associated proteins or secreted proteins that interact with TNF receptors which communicate with the interior of the cell. It activates and induces NO (nitric oxide) production in macrophages.

TNF ß, inhibits B cells, kills T cells, activates induces NO production.

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Major Histocompatibility Complex (MHC)

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The ability of cytotoxic T cells to recognize and react with antigens on target cell surfaces depends on a set of cell surface histocompatibility antigens, HLA’s. Cells in the human body have HLA’s on their surfaces. Prior to birth, the body recognizes , removes or inactivates T lymphocytes specific for these antigens. This allows for differentiation between self and non self. Immunologic tolerance is important, otherwise we would attack self. The MHC complex of genes codes for “self”.

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MHC. Where is it encoded and details

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In humans encoded on chromosome 6. Fifty different genes encode HLA’s. Low chance of 2 people having identical MHC molecules is low except for identical twins.

These genes encode for 3 types of proteins: Class I, II and III.

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Class I

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these proteins are found on surfaces of all nucleated cells in the body, serve to identify self from non self. Basis of HLA typing in organ transplants.

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Class II

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on the surface of antigen presenting cells, B cells, macrophages, are involved with presenting antigen to TH cells

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Class III

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encode for the C4 protein of the complement pathway.

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Activated B lymphocytes Clonal selection theory, by Macfarlane

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The explanation for the development of genetically diverse B cells develop into antibody secreting plasma cells. B cells have a receptor, (IgM, IgD). There is a separate cell for each antigenic determinant. As a specific antigen is bound to these receptors , the B cell is activated. In theory, some of these activated cells multiply and mature into clones of antibody secreting plasma cells. Other B cells that do not differentiate into plasma cells become, memory cells. Longer living memory cells are activated when the host is reexposed to the antigenic determinant.

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g’s bind antigenic determinants very closely, by

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van der Waals forces, H bonds, hydrophobic interactions, electrostatic forces.

Primary goal of the immunologic response is host defense.

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The immunologic response is measured by

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antibody level or titer (a way of expressing concentration) in the serum.

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Upon initial exposure, it takes a few days for the B cells to

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differentiate into antibody producing plasma cells

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Primary response

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is a slow gradual rise in antibody production followed by a decline

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Secondary response

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is the anamnestic response, when the host is exposed a second time and there is a rapid increase in antibody titer. This response is the basis for immunization, initial dose of antigen sensitizes the body for antibody production.

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Naturally acquired active immunity

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seen in a person through natural infection. This immunity is long lasting.

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Naturally acquired passive immunity

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this is seen with the transfer of antibodies from one person to another person by natural means. Example the transfer of maternal antibodies from the mother to the fetus via the placenta. This lasts for the first few months of life.

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Artificially acquired passive immunity

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this is seen with the use of gamma globulins formed in one host and injected into another host. Example hepatitis A virus, provides temporary protection against exposure to an antigen, lasts only a few weeks.

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Vaccines

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Produce artificially acquired active immunity. Three types of vaccines

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Live attenuated vaccine

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live organisms that have been rendered avirulent or with reduced virulence. Injected microbe is still alive and multiplies in the host. These are good at producing immunity, however concern over back mutation to become virulent. Examples, polio, mumps, rubeola vaccines.

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Killed vaccines

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the virulent infectious agent is killed by chemicals or radiation. Safer than non killed vaccines, immunity produced generally not long term. Examples, cholera, typhoid, influenza.

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Toxoids, cellular components

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toxoids are exotoxins that have been chemically modified to non toxic forms, treated with formalin. Examples diphtheria and tetanus. Cellular components are sometimes subunit vaccines, made via rDNA technologies.

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Goal of immunization ?

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To provide herd immunity so that a large proportion of susceptible community is unable to spread an infectious agent. For most diseases this is 70%, for highly infectious you need 95%.

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Diseases that impact immunity: Agammaglobulinemia

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a genetic disease characterized by a total lack or partial ability to produce gamma globulins. These patients are highly susceptible to infectious diseases.

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Hypersensitive Reactions

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A body’s response to antigenic stimulation that results in injury to the host. This results from an abnormally sensitive host response to an antigen. The is first sensitized to an antigen, the hypersensitive reaction occurs after the second exposure.

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Types of Hypersensitive reactions: Type I

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Type I: Anaphylactic reactions, antibody mediated, involve IgE, antigen combines with IgE associated with Mast cells and basophils, this results in the release of histamines, prostaglandins, leukotrienes. Examples, insect stings, bronchial asthma, hay fever, food allergies, drug reactions.

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Types of Hypersensitive reactions: Type II

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Type II: cytotoxic reactions, antibody mediated, IgG, IgM, circulating antibodies react with tissue cells or particles, resulting in complement mediated cytolysis or increased phagocytosis. Blood transfusion reactions, Rh incompatiability.

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Types of Hypersensitive reactions: Type III

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Type III, antibody mediated hypersensitive reactions that are characterized by immune complexes. IgG and IgM are associated with these, the antibody combines with large amounts of antigen to Ab-Ag complexes that trigger the release of histamines and other chemical substances, resulting in tissue necrosis and inflammation. Arthus reaction, and serum sickness

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Types of Hypersensitive reactions: Delayed hypersensitive response

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Delayed that are cell mediated. Delayed hypersensitive response, no antibody, antigen sensitizes T lymphocytes that results in the release of cytokines and other substances from sensitized T lymphocytes. Ex, tuberculin reaction

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Types of Hypersensitive reactions: Transplant rejection

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Transplant rejection, cell mediated, no antibody. Foreign antigen in donor tissue causes recipients T lymphocytes to release cytokines and other chemical substances, results in rejection of donor tissue. Graft rejection.

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Autoimmune disorders

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Occurs when the immune system loses the ability to distinguish between self and non self antigens. These disorders sometimes involve autoantibodies.

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Complement

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The complement system is a set of plasma proteins that act together to attack extracellular pathogens. This is a group of about 20 serum proteins that mediate the action of specific antibodies in their destruction of bacteria and other particles. These proteins are present in the host serum independent of host immunologic response.

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Complement Further information

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Certain of these components are heat labile and inactivated after 30 min @ 56 C.

These proteins are in the serum as inactive molecules and are activated through a series of cascading reactions, that follow one of these pathways: classical or alternative.

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Classical complement pathway

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This is triggered by the binding of an immunoglobulin molecule to an antigen. Only immunoglobulins IgG or IgM classes can activate complement. The mechanism, has distinct stages,
(1) recognition (C1),
(2) enzymatic activation (C4, C2 and C3),
(3) membrane attack (C5 through C9). The fully assembled C5-C9 structure is the membrane attack complex.

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Alternative complement pathway

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Also called the properdin pathway, it occurs in the absence of Ag-Ab (antigen-antibody) complexes. It is activated by bacterial, fungal and plant polysaccharides, LPS and other molecules. This pathway bypasses the initial sequence C1 to C2 and instead involves the serum protein properdin. The complement protein C3 is activated, tick over activation. After several different steps the classical pathway occurs.

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Infectious diseases: They can be acquired by different routes:

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Respiratory tract
Oral cavity and digestive system
Skin and genitourinary tract

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Respiratory tract microflora Lower RT

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Lower RT, is free of microbes due to the constant removal of foreign particles due to cilia.

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Respiratory tract microflora Upper RT

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Upper RT, is inhabited by: streptococci, staphylococci, neisseriae, diphtheroids and yeasts. Some of these are potentially pathogenic but are normally controlled by the presence of other microbes and host antibodies.

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Respiratory Tract Pathogens S.pyogenes

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Upper RT: More than 90% of these infections are caused by viruses. Strep throat caused by, Streptococcus pyogenes is the most common bacterial infection. These Group A strep are called pyogenic cocci, “associated with pus formation”. Symptoms include, fever, inflammation of the mucous membrane of the throat, glandular swelling. Usually self limiting however if all three symptoms are seen treatment is recommended. Infections can lead to scarlet fever, rheumatic fever and acute glomerulonephritis.

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Scarlet Fever (S. pyogenes)

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Scarlet fever, is caused by lysogenic strains of S. pyogenes that synthesize an exotoxin called, erythrogenic toxin,which causes a red rash throughout the body. Strawberry tongue is also a characteristic of this illness. This toxin is under the control of a temperate bacteriophage. Penicillin is the treatment.

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Rheumatic fever and acute glomerulonephritis (S. pyogenes)

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Rheumatic fever and acute glomerulonephritis are nonsuppurative (non pus forming) sequelae of strep throat. Rheumatic fever is characterized by lesions that appear in the heart, joints and skin that appear 2-3 wks post strep throat. These people have a high anti-streptolysin O titer. Streptolysin O is a hemolysin produced by these bacteria. Acute glomerulonephritis, is often seen in children following strep throat or a cutaneous strep infection; edema, hypotension blood in urine are symptoms.

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Necrotizing fasciitis (S. pyogenes)

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Necrotizing fasciitis, rapid destruction of fibrous tissue that encloses and separates muscle, caused by S. pyogenes, aka “flesh eating bacteria”.

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Identification of streptococci

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Gram positive cocci in chains, catalase negative. On blood agar three different types of hemolysis are observed, S. pyogenes, Group A produces β hemolysis, or complete lysis of sheep’s blood. This strain is also bacitracin sensitive. Confirmatory test coagglutination.

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Streptococcus pneumoniae

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This bacterium is also known as pneumococcus. Bacterial pneumonia is often a secondary infection that follows viral infections of the upper respiratory tract. Bacteria ends up in the lung, fluid accumulates in lungs to produce edema. Complications of this illness lead to meningitis, pleurisy (inflammation of the pleura), abscess formation, septicemia.

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Streptococcus pneumoniae (more in depth characteristics)

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Gram positive, encapsulated , lancet shaped diplococci that are seen in the patient’s sputum. These species are α hemolytic, optochin sensitive and bile soluble. Optochin is ethylhydrocupreine hydrocholoride, it inhibits the growth of S. pneumoniae. This strain also produces an autolytic enzyme, N-acetyl-muramyl-L-alanine amidase, that solubilizes the cell wall peptidoglycan and results in cell lysis. This is the basis of bile solubility, pneumococcal cells are incubated in sodium deoxycholate and lysis is observed. Quellung reation, capsular swelling in the presence of antisera directed against capsular antigens.

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Legionnaires’ Disease

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Form of pneumonia caused by Legionella pneumophila, aerobic, Gram negative rod, first isolated in 1976. This microbe has an incubation period of 2-10 days, headache, fever 104-105 F, chills, muscle aches, dry cough, chest pain, abdominal pain, diarrhea. This is usually describes as a bronchopneumonia. Grows on medium containing L-cysteine and iron salts, charcoal yeast extract and Mueller Hinton agar base with L-cysteine and iron. Colonies visible after 4-5 days, incubation 35 C under CO2 tension.

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How to confirm identity of Legionella pneumophila (responsible for Legionnaire's Disease)

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Several ways to confirm identity, immunofluorescence, DNA probe, ELISA. Mortality in untreated cases 15 to 25 %, high with immunocompromised patients. 1,000 cases / yr in US, a milder form of the disease is called Pontiac F

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Whooping Cough

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Bordetella pertussis, Gram negative, coccobacillus bacterium that causes an acute respiratory disease. Bacterium is transmitted through infected droplets in the air, highly contagious. Severe coughing, gasps for air between coughing aka “whoops”. A heat sensitive exotoxin as well as an extracytoplasmic adenylate cyclase that increases cAMP levels contribute to the pathogenesis. Isolated on Bordet Gengou agar. Mild cases no treatment necessary, serious require Er, children immunized with DPT vaccine.

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Diphtheria

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Corynebacterium diphtheriae is the causative agent. Gram positive, pleomorphic rod shaped bacterium, obligate aerobe. It produces Babes-Ernst bodies, polyphosphate intracellular granules. Strains with the lysogenic bearing prophage produce the diphtheria exotoxin, which when cleaved into components fragment A & B. Fragment A inhibits eukaryotic protein synthesis by modifying EF2, inhibiting protein synthesis. In the throat a grayish pseudomembrane forms, necrosis, inflammation result is suffocation. Identification /isolation on the basis of tellurite containing agar, colonies appear black-grey. Exotoxin assayed using Guinea pigs or Elek gel diffusion test.

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Tuberculosis

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TB is caused by Mycobacterium tuberculosis an acid fast organism, cell wall has a high lipid content, mycolic acids. The cell wall is thus impermeable to stains and nutrients thus accounting for its slow growth. This causes a lung disease and is transmitted by droplets from coughs, causes a characteristic lesion in the lung “tubercule”, Grows slowly on Lowenstein-Jensen medium. 2 to 6 weeks in 5 to 10 % CO2.

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Screening and Treatment for Tuberculosis

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Screen for exposure using the tuberculin skin test. Injected into the forearm, examined at 48 hrs, look for zone of induration. Treatment, Sm, Rif, isoniazid. In Europe a vaccine bacile-Calmette-Guerin (BCG) is used. It contains live, attenuated M. bovis, gives immunity to TB.

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Infections of the Meninges, Meningitis

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An infection of the membranes that surround the brain and spinal cord, can be caused by a variety of bacteria. Hib vaccine, prevents H.influenzae type b. Before this vaccine 20,000 cases/ yr in the US.

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Oral Cavity/Digestive Tract

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Disease of the digestive tract second most frequent cause of illness in the US after respiratory tract.
Oral cavity, colonized during and after birth.

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Oral Cavity Pathogens - Dental Plaque

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Dental Plaque: sticky film of bacteria, embedded in a polysaccharide-glycoprotein matrix on the surface of teeth. 60-70% of plaque is comprised of bacteria.

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Oral Cavity Pathogens - Dental Caries

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Dental caries: the destruction of the tooth enamel by acid forming bacteria. Streptococcus mutans principal bacterium responsible for caries. Makes dextrans from sucrose which gives it adherence to teeth.

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Oral Cavity Pathogens - Periodontal disease

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Periodontal disease: major cause of tooth loss in people over 30. Gingivitis most common form, trench mouth involves necrosis of the gums.

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Digestive system microflora

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This system consists of the esophagus, stomach, small intestine and large intestine. Few bacteria reside in the stomach, some acid tolerant bacteria and Helicobacter pylori, the leading cause of peptic ulcers. The pH becomes less acidic in the lower portion of the small intestine, numbers and diversity of the flora increase. The large intestine has numbers as high as 1012 bacteria/ g of fecal matter, facultative anaerobes and anaerobes are found.

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Helicobacter pylori

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the leading cause of peptic ulcers.

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Food infection

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Food infection: occurs when the infectious agent establishes an active infection in the small intestine. Disease occurs after the infection has multiplied.

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Food intoxication:

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Food intoxication: symptoms are the result of consumption of food or water contaminated by bacteria such as: Clostridium botulinum, Clostridium perfringes, Staphylococcus aureus.

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Food borne botulism

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Botulism, is a food intoxication caused by Clostridium botulinum, an anaerobic Gram positive spore former. First observed in the 18th century in the consumption of blood sausage. The preparing of these sausages made them susceptible to infection with these spore formers. Fairly uncommon in the US, 50 cases/yr. The toxin is a potent neurotoxin, that is observed in 8 different types. Symptoms include weakness, dizziness, dryness of the mouth, blurred vision, usually observed 18-36 hrs post ingestion.

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Infant botulism

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first described in 1976, acquired through the ingestion of spores, “soils”. Different symptoms, weakness, weak neck muscles, paralysis, respiratory problems, impaired sucking ability.

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Botulinum toxin

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1 microgram of pure toxin can kill a human being. The toxin binds irreversibly to neuromuscular junctions and blocks the release of acetylcholine.
Detected using lab mice.
Treatment antitoxin, immediately.

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Staphylococcal food poisoning

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This food intoxication is caused by enterotoxin producing, Staphylcoccus aureus. Six different enterotoxins have produced and implicated by S. aureus. Usually due to improperly refrigerated foods, pastries, salad dressings, sliced meats. The bacteria grow in the food and produce the toxin. Nausea, cramps, vomiting, diarrhea are the usual symptoms. Symptoms appear in 1-6 hrs post exposure, resolved in 1 or few days. These are heat stable enterotoxins.

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Cholera

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Seen in developing countries when fecal matter contaminates water supplies. Vibrio cholerae, is the causative agent of this disease, Gram negative, curved rod, motile, oxidase+, grows at pH 9.0-9.6. 2-5 day incubation period, abdominal cramps, appetite loss, vomiting, watery diarrhea, “rice water stools”. Loss of 10-15 liters per day. Non tissue invasive, but disrupts normal intraintestinal exchanges of water and electrolytes. The toxin consists of 2 subunits. The cholera toxin activates adenylate cyclase to convert ATP to cAMP. Treatment replace water and electrolytes, antibiotics do not shorten duration of illness. The infection requires as many as 106 bacteria/ml.

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Typhoid fever

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A systemic infection caused by the Gram negative rod, Salmonella typhi. The disease is transmitted via contaminated food and water. The disease begins with fever, abdominal pain and headache. In untreated patients the disease starts in the gut and multiplies and disseminates via the blood to other areas. Complications include intestinal hemorrhages or perforation of the abdominal wall. Rose colored spots, appear on the abdomen. Approximately 37% of patients are asymptomatic carriers and shed large numbers in their feces because the bacterium lives in their gall bladder, Typhoid Mary.

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Salmonellosis

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Salmonella enteritidis, causes this milder and common form of this gastrointestinal disease. Each year in the US 40,000 cases are reported. May be as high as 4 million cases /yr. Due to improper food handling, symptoms include: moderate fever, nausea, abdominal cramps and diarrhea. Raw eggs also infected, via cracks in the shell and ovarian infections.

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Shigellosis

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Aka, “bacillary dysentery”, a Gram negative non motile rod bacterium. Usually obtained from fecal contamination of food and water. Shigella sonnei (73%), Shigella flexneri (25%) cause shigellosis. Disease characterized by fever, abdominal cramps, diarrhea, blood and mucous in the feces. These bacteria do not penetrate the the intestinal mucosa. This genera does not ferment lactose or produce H2S. Patients usually recover without therapy.

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Campylobacter

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A Gram negative bacterium that causes abortion and infertility in cattle. Two species important to man, C. fetus, C. jejuni, cause disease in man from the animal reservoir. May be as common as salmonellosis. Isolated from feces in medium containing antibiotics to inhibit the other flora.

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Escherichia coli

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Four groups are associated with human intestinal disease. EHEC , hemolytic-uremic syndrome is associated with E.coli 0157:H7. The recent outbreaks in the lettuce fields in California.

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Helicobacter pylori

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Associated with peptic ulcers in humans. Two Australian physicians figured it out in the 1980’s. This bacterium is believed to be involved in 75-90% of all the cases of peptic ulcers.

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Viral hepatitis

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A viral disease that is caused by 6 different types of this virus, A,B,C,D,E and G. This is an RNA enterovirus, infects the intestine and spreads by the blood to liver, kidneys and spleen. Symptoms include: loss of appetite, nausea, diarrhea, fever, discomfort and jaundice.

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Diseases of the skin

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with injury, cuts, wounds or damage from burns or penetration by bites, a portal of entry is established. The skin consists of 2 layers an outer epidermis and thicker underlying dermis. Skin has a low pH and low moisture content. Principal skin inhabitants are the diphtheroids. Propionibacterium acnes, formerly Corynebacterium acnes, is the principal skin inhabitant. It is thought to be involved in acne. Human body odor is the bacterial metabolism of lipids by Corynebacterium xerosis. Deodorants formulated to inhibit Gram positive bacteria. Second largest skin group staphylococci.

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Staphylococcus epidermidis

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is a salt-tolerant gram-positive bacterium commonly found on the surface of the skin. S. epidermidis is a frequent contaminant or the nose , throat, urogenital and rectal cultures. Generally not pathogenic, but can lead to postoperative endocardiatis.

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Pityrosporum ovale

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yeast found in the skin

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Pyodermas

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Inflammatory skin infections caused by pus forming bacteria such as: Staphylococcus aureus, Streptococcus pyogenes. Theses infections range from a simple pimple to a large lesion with rapid tissue destruction. Major forms: furunculosis, erysipelas, impetigo, and scalded skin syndrome.

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Furunculosis

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Staphylococcal disease that originates by infection in a hair follicle. The infection spreads and a boil or furuncle forms. If the infection is deep seated and involves several abscessed hair follicles it could form a carbuncle. Carbuncles usually form on the upper back and neck. Cure surgical drainage.

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Erysipelas

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Skin disease caused by S. pyogenes. Aka, St. Anthony’s Fire, because of bright red patches appear on the skin.

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Impetigo

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Secondary skin infection caused by S. pyogenes, and S. aureus. This disease begins as a small vesicle containing clear fluid that becomes a small pustule. These rupture and then become encrusted, they are highly infectious. The infection than can spread to other body parts.

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Scalded skin syndrome

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This is caused by S. aureus, the skins lesions look like scalding by boiling water. The layers of the epidermis are peeled off as a consequence of necrosis. This disease occurs in infants and children under the age of 4. A staphylococcal exotoxin, exofoliatin, is responsible for the pathogenesis of this disease.

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Leprosy

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Hansen’s disease, after the person who first described the agent in 1874. Mycobacterium leprae is the acid fast rod shaped microbe that causes the disease. It is believed that the disease is spread through a cut or direct skin to skin contact. These bacteria multiply very slowly in the body, the incubation period is 3 to 5 years, but may be as long as 20 to 40 years.

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Indeterminate leprosy,

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early lesion, consists of hypopigmented macules with a small number of bacteria. In 75% of these cases the disease is self healing with no further progression.

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Lepromatous phase (leprosy)

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disfiguring lesions inside lepra cells (macrophages with large amounts of mycobacteria and foamy cytoplasm).

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Borderline phase:

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intermediate phase between lepromatous and tuberculoid phases.
Loss of sensation in affected areas during tuberculoid leprosy.

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Culturing and therapy for Leprosy

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This microbe can not be cultured on lab media, grown in cell culture and n animals as the armadillo and mouse.
Therapy, rifampin, disease is most prevalent in the tropics, 15-20 million cases in the world today. First case reported in the US in the 1700’s in Florida.

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Pseudomonas aeruginosa

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Opportunistic pathogen associated with burn victims. Common in the environment. Produces a number of extracellular factors and has antimicrobial resistance. Gram negative rod with a polar flagellum, oxidase positive.

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Rickettsia

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Obligate intracellular parasites transmitted by arthropods ( lice, fleas, ticks and mites). Following direct inoculation of the skin the rickettsiae proliferate in endothelial cells and cause widespread lesions.

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Lyme Disease

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Borrelia burgdorferi, disease was first described in 1975, in Old Lyme, Connecticut. Disease demonstrates a disease skin rash that looks like a “bull’s eye”. Fever, fatigue, headache, and arthritis are the symptoms. The disease is spread via the deer tick, up to 80% of these ticks in the US are infected.

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Genitourinary system

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In humans it has 2 functions, collecting, concentrating and excreting wastes while regulating the concentrations of body fluids and electrolytes. Producing gametes for propagation in the male, and supporting the embryo in the female.

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Genitourinary system pathogens

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The male urethra is normally free of bacteria. The female urethra short and near the anal and vaginal openings has extensive normal flora. This plays a role in UTI’s in females.

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Escherichia coli

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Most common cause of UTI’s. Several categories of UTI’s: Cystitis, bladder infection. Pyelonephritis, kidney infection. Bacteriuria, presence of bacteria in the urine and may reflect the above diseases.

Urines obtained from a clean catch with greater than 100,000 bacteria/ml are considered a bacteriuria.

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STD’s

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STD’s are not confined to the genital tract may appear elsewhere, oral cavity, anus, conjunctiva, and skin.

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Gonorrhea

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History, goes back in time, Napoleon etc, agent first described by Neisser in 1879, Neisseria gonorrhea. Disease first described clinically 130 A.D., “flow of seed”, purulent discharge. This is a Gram negative, aerobic, diplococcus. Transmission is through sexual contact. The bacteria attach to mucosal epithelium via pili, where it causes inflammation.

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Neisseria gonorrhea produces...

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an IgA protease which helps with pathogenesis. Symptoms, males, purulent discharge, pain on urination. In females they are usually asymptomatic because of the short urethra, if untreated may lead to PID (Pelvic Inflammatory Disease.) Gonorrhea is treated with penicillin, there penicillinase producing strains, PPNGs appeared in 1976 from SE Asia.

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Syphillis

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Less frequent than gonorrhea, but is more serious and potentially fatal. Caused by Treponema pallidum, a spirochete. Epidemic in Europe in the later 15 th century.

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Stages of Syphilis

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Primary stage, appearance of a chancre, at the site of inoculation, usually 2-3 weeks post exposure.

Secondary stage, a general skin rash, low grade fever, lesions in body organs. Both of these stages are contagious.

Tertiary stage, several yrs after initial appearance of the disease, patient might observe serious dermal lesions, gummas, and neurological syphillis, tabes dorsalis, invasion of the central nervous system.

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Tabes dorsalis

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is a slow degeneration (specifically, demyelination) of the nerves primarily in the dorsal columns (posterior columns) of the spinal cord

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Gummas

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is a soft, non-cancerous growth resulting from the tertiary stage of syphilis.

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Nongonococcal urethritis (NGU)

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Inflammation of the urethra not caused by N. gonorrhoeae. These are caused by, Chlamydia trachomatis, Ureaplasma urealyticum. These strains are sometimes difficult to isolate and cultivate in the lab.

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Toxic Shock Syndrome

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Disease first described in 1978, caused by S. aureus. In 1980, 941 cases, 73 deaths. Superabsorbent tampons seemed to be involved.

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Acquired Immune deficiency syndrome (AIDS)

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First cases described in 1981. Two human immunodeficiency viruses involved, HIV-1, HIV-2. HIV-1, is an enveloped retrovirus, ssRNA genome. This virus lives inside of CD4 containing T lymphocytes, T helper cells. Inside the host cell it becomes an integrated provirus. Antibodies to HIV do not stop the progression of the disease. Drugs used to treat HIV include AZT, an reverse transcriptase inhibitor.

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AZT

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Used to treat HIV. A reverse transcriptase inhibitor

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Epidemiology

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A field in which health professionals trace diseases and recommend control.
Diseases studied include infectious and non infectious

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John Snow, 1854

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John Snow was conducting a series of investigations in London that warrant his being considered the “father of field epidemiology.”

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Epidemics

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An epidemic is a markedly increased occurrence of a disease in a particular population during a specific period.

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Common source epidemic

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a group of people is exposed at one time to a particular disease agent from a common source of contamination. Ex: An outbreak of botulism from people eating at a single restaurant.

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Propagated epidemics

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an infectious agent is transmitted from one host to another via direct contact or a vector. Measles outbreak from one student to many others

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Pandemics

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these are epidemics that affect several countries or major portions of the world. Plague in Europe, killed 25 M people.

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Endemic

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this describes a disease that is constantly present in a population. Measles, gonorrhea are examples of these disease endemic in the US

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Mortality

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this refers to the number of deaths in a population.

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Mortality rate

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per 1,000, see formula

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Morbidity. Also describe prevalence rate and incidence rate

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this describes the number of cases of disease in a population

Prevalence rate, describes the occurrence of existing cases of disease in a population during a specified period of time.

Incidence rate, is the number of new cases of disease in a population from a previously nondiseased persons in a given time period.

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Disease rates and time

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changes in morbidity and mortality rates with time suggest that contributing factors for the disease have changed. Ex, influenza, highs and lows versus the season. Arthropod transmitted diseases occur during times of the year that favor these vectors

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Disease rates and place

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some disease are more common in certain geographical places. Ex, STD’s occur more frequently in the Southeastern US.

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Disease rates and people:

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Morbidity and mortality rates higher with infants and the elderly.
Morbidity and mortality rates differ with sex of the individual
Morbidity and mortality rates differ among races.

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New Orleans

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has the highest rates of STD’s in the U.S.

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n the 1960s and 1970s...

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Gonorrhea rates increased because of the occurrence of birth control pills.

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Nosocomial Infections

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Hospital acquired infections, 10% of people admitted to a hospital acquire an infection during their stay. Today with MRSA infections hospital are pre screening patients for the microbe prior to admission.

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There are two types of MRSA:

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community-acquired and hospital-acquired. The community-acquired numbers are dropping.

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Collection of Epidemiological Data

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interviews and diagnostic test screening. Biases: interview surveys are easy but validity and accuracy in question due to reluctance of patient to be truthful.

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Diagnostic Test should be:

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Accurate, sensitive and specific, it must be able to differentiate people with the disease and those that do not have the disease. Tests in series, skin test followed by a chest x ray. Tests in parallel, person is considered positive if any test demonstrates positive. Breast cancer, physical lump detection, mammography, MRI.

Test, should be reliable, reproducible or both. Sometimes cancer cell slide examination is read be experts in several labs to verify the results

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Screening test should be performed on....

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a population with a high frequency of the disease.

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Experimental studies

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the investigator controls the influence of factors that cause a disease. Ex, study of the influence of fluoride added to water supplies to control dental carries.

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Observational studies

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when the conditions are uncontrolled. This may lead to (Retrospective studies), comparisons are made between a group of persons who have the disease and those that do not. (Prospective studies), involves following a group of people free of a given disease, but who vary in exposure to the suspected disease associated characteristic.

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Retrospective studies

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comparisons are made between a group of persons who have the disease and those that do not

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Prospective studies

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Involves following a group of people free of a given disease, but who vary in exposure to the suspected disease associated characteristic.

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Example of Prospective studies

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180,000 white males (50-60 yrs old), annual smoking history and deaths from lung cancer, correlation with lung cancer and number of cigarettes smoked per day.

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1995, Japanese cult....

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releases nerve agent sarin into a Tokyo subway system, 5,500 injuries, 12 deaths.

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USSR stockpiled...

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anthrax, small pox, botulinum toxin and other weapons, 1980’s.

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1991, Iraq, had....

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380,000 l of botulinum toxin, deployed 160 aerial bombs each with 90 l of the material.

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During the French and Indian war,

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British supplied Indians with smallpox contaminated blankets

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Why biological agents for bioterrorism?

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Biological agents are inexpensive, nuclear is very expensive.

Microorganisms are readily available.

Scientific knowledge to produce these is available, many unemployed from the USSR.

Biological weapons easy to transport, without detection, Airport security does not pick them up.

Effect of the attack not known for days.

Small attacks generate fear.

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Weaponizing

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The development of biological agents into effective agents of mass destruction.
Modify virulence
Vaccine resistant
Antibiotic resistance
Small particle size, hang time in the air increased, therefore more regional infectivity.

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Epidemiological clues of the attack

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Unusual appearance of disease

Multiple disease entities in the patient, ie anthrax, plague, smallpox.

Large number of casualties, point source outbreak.

Apparent transmission by aerosol, over a large region.

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Classifying Bioterrorism Agents

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CDC list of agents, Category A,B or C.

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Category A Bioterrorism agents

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High priority agents that pose a risk to national security because of easy dissemination or transmission person to person. High degree of mortality, cause social panic, require special health preparedness.

Anthrax
Botulism
Plague
Smallpox
Tularemia
Viral hemorrhagic fevers, Ebola

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Category B Bioterrorism Agents

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moderate dissemination, moderate mortality.

Brucellosis
Glanders
Q fever
Staph enterotoxin B
Epsilon toxin Clostridium perfringens
Ricin toxin, from the Castor Bean

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Category C Bioterrorism Agents

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emerging pathogens that could be engineered for high mortality.

Hantavirus
Multiple drug resistant TB
Tickborne, encephalitis, hemorrhagic fever viruses
Yellow fever

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Biochemical cycles

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The movement of chemical elements through the biological and geological world.

Bacteria play a big role in recycling. Break down chemical substances into simpler compounds or elements.

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Mineralization

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conversion of organic matter to minerals and other inorganic materials.

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Elements of bacteria

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Six major elements, C,N,S,P,O,and H.
Minor elements, Mg, K, Na.
Trace elements, Al, Cu, Zn.

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The Carbon cycle

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Single most important element in the biosphere. Most of the earth’s carbon stored as fossil fuels, coal, peat, oil and natural gas.

Ultimate carbon source is carbon dioxide , from photosynthesis and waste product of respiration.

Carbon transformation occurs via the carbon cycle. Primary producers fix carbon dioxide, including plants, algae, cyanobacteria, phototropic bacteria.

Fixed carbon is returned to the atmosphere as CO2, in one of 3 ways, respiration, food for herbivores and carnivores, decomposition of dead tissues.

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Primary Producers

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Photoautotrophic bacteria fix CO2 via the Calvin cycle and by a reversal of the TCA cycle. This reversal of the TCA cycle occurs in the Green sulfur bacteria.

Chemoautotrophic bacteria, derive their energy from the oxidation of chemical compounds, NH3, CH4, H2S. Small % of CO2 fixation.

Heterotrophic CO2 fixation, synthesis of the intermediates of the TCA cycle.

Methanogens, reduce CO2 to CH4. This occurs via several steps.

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Herbivores

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Herbivores consume organic material formed from CO2 fixation, and then become food sources for carnivores. The ultimate herbivore is the cow

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Microbes as decomposers of cellulose

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Cellulose is hydrolyzed to glucose. Plant cell wall cellulose degraded by many different types of bacteria. Breakdown of the beta 1,4 linkages, Rumen stomach.

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Microbes as decomposers of chitin

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Chitin, poly N-acetlyglucosamine, found in insect exoskeleton, hydrolyzed by chitanases mainly Streptomyces.

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Microbes as decomposers of Synthetic carbon compounds

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Syntheic carbon compounds degraded by specialized bacteria, ie Pseudomonads.

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Nitrogen cycle

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Most abundant gas in the earth’s atmosphere. Each yr 1 billion tons of nitrogen is transformed by the N cycle. The biogeochemical recycling of nitrogen requires microbial activities and consists of 4 stages: nitrogen fixation, ammonification, nitrification and denitrification.

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Nitrogen Fixation

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N2 has triple bonds, hard to break. Done symbiotically via certain bacteria, ie, Rhizobium, Bradyrhizobium. Non symbiotically the bacteria involved include, Klebsiella, Chromatium. Needs a lot of ATP to accomplish the reaction.

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Ammonification

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Nitrogen taken up by bacteria is converted into proteins, nucleic acids, therefore it must be decomposed into ammonia, example urea into ammonia.

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Nitrification

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ammonia is oxidized into nitrate. 2 steps involved, ammonia into nitrite, nitrosofying bacteria. Then nitrite converted into nitrate, nitrifying bacteria.

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Denitrification

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is the formation of N2, as well as NO and N2O from nitrite or nitrate. Pseudomonads most common denitrifier, nitrate reductase.

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The phosphate cycle

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Important in living cells, ie ATP, high E bonds. Microbes solubilize phosphate salts as part of this cycle.

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The sulfur cycle

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Sulfur is widely distributed in nature. Fossil fuels, rocks and sulfur deposits. It occurs in 3 states, S0, S-2, and SO4-2.

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1) Beggiatoa, Thiothrix

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convert sulfide into elemental sulfur.

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2) Thiobacillus

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converts elemental sulfur and sulfides into sulfate.

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Sulfates form...

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Sulfates also form from the anaerobic oxidation of sulfides and thiosulfates by green and purple phototropic bacteria.

Sulfates formed can be assimilated into cellular proteins or reduced to hydrogen sulfides . Desulfovibrio, is able to demonstrate dissimilatory sulfate reduction to sulfide.

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Desulfovibrio

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is able to demonstrate dissimilatory sulfate reduction to sulfide.

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Microbes and the soil

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Microbes found in high #’s in the soil. Their presence depends on the substrates present for their cultivation. The most prolific organisms in the soil are atenomycyns and streptomycins.

As you go down that soil column, it becomes more anaerobic.

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Leaching

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is used to extract copper, lead, zinc and uranium from sulfide containing ores. Bacteria are involved, Thiobacillus ferrooxidans, T. thiooxidans. T. ferrooxidans obtains its carbon from carbon dioxide and its E from the oxidation of either iron or sulfur, elemental sulfur, sulfides, and thiosulfate.

Commercial scale operations crushed low grade copper, containing T. ferrooxidans, sprayed with dilute sulfuric acid and oxidizes CuS in the ore

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Pseudomonas

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Used to clean up soil that has been contaminated with toxic hydrocarbons, ie petroleum based.

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Microbes and water

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In the sea, pH is 8.3 to 8.5, salinity is 0.5 to 2.5%. In the coastal region, pseudomonads, vibrio and flavobacterium are important. Vibrio parahaemolyticus and V. vulnificus are very important.

In the fresh water environment, many heterotrophic bacteria, pollution and sewage runoff can influence water quality dramatically. Seasonal changes influence microbial flora.

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vibrio vulnificus

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can cause rare flesh-eating diseases

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vibrio parahaemolyticus

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is constantly being monitored for in shellfish

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Water quality and sewage

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Less than 2% of the world’s water is potable, suitable for drinking

Sewage is measured by COD and BOD.

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BOD

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biochemical oxygen demand, is defined as the quantity of oxygen required to meet the metabolic demands of microbes oxidizing the organic matter in the water. Done as a lab test over 5 days at 20 C, in a sealed container. Water if the initial BOD is 300ppm after treatment it should be reduced to <30ppm in sewage treatment.

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Primary sewage treatment

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Primary sewage treatment, involves the removal of suspended solids and floating materials.

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Secondary sewage treatment

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Secondary sewage treatment, biological agents are used to purify the sewage.

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Tertiary sewage treatment

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Tertiary sewage treatment, additional purification, filtration , chlorination.

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Indicator bacteria

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Pathogens are usually in low numbers, therefore coliforms are used to monitor water quality. MPN and MF tests are ways to monitor water for coliforms.

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Raw Milk

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Normally sterile before it is drawn from the cow.
Raw milk has bacteria introduced via the equipment, these bacteria include: Lactococci, Pseudomonas, Alcaligenes, Flavobacterium

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Souring of milk caused by

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Lactococcus lactis. A homofermentative bacterium.

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homofermentative bacterium

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makes lactic acid from lactose.

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Raw milk can also be contaminated by....

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by workers carriers of: Salmonella, Corynebacterium, Shigella.

Or the milk could be infected by an infected animal: Brucella abortus, undulant fever; Coxiella burnetii, Q fever.

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Pasteurization

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LTH: low temperature holding, 62.8 C for 30 min. HTST: high temperature short time,71.7 C for 15 sec. These methods destroy all non spore forming pathogenic bacteria and many non pathogenic bacteria in raw milk.

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UHT

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ultra high temperature, 137.8 C for a few seconds, then placed in sterile container, milk can be stored without refrigeration for months

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Phosphatase Test

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Phosphatase is an enzyme in Raw milk that is destroyed by pasteurization. Therefore the absence of this enzyme in raw milk means the raw milk was pasteurized properly. The enzyme phosphatase degrades disodium phenylphosphate to phenol and sodium phosphate.

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For fermented Milks and Milk Products, a variety of lactic acid bacteria are used as....

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Starter Cultures

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Yogurt production

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Made from whole milk. Supplemented with skim milk powder. This gives protein –gel structure of the product. Raw materials are heated and cooled. Inoculation with Streptococcus thermophilus, Lactobacillus delbrueckii ssp. bulgaricus. In a ratio 1:1. The strep produces the acid, the lactobacilli produces the flavor. Possible to add probiotics to the mixture.

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Butter

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Two main types: sweet cream and cultured butter. Cultured butter, pasteurized cream ripened with bacteria 24-48 hrs prior to churning. Lactococcus lactis ssp. diacetylactis, Leuconostoc citrovorum, are used. This produces diacetyl the butter note, in butter.

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Cheese production

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No standard method:

Pretreatment of raw milk (pasteurization, culturing)

Formation of solid curd (rennet enzyme addition)

Removal of the liquid whey from the curd

Curd processing ( cooking, washing, milling, salting)

Ripening and aging

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Differences in cheeses depend on:

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Type of milk used.

Diet of milk producer

Particular strain of starter culture used

Processing methods used

Environmental conditions used during ripening,
temperature, humidity.

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Soft cheeses (unripened)

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Soft (unripened)
Cottage, Lactococcus lactis, Leuconostoc citrovorum.

Cream, Lactococcus cremoris

Mozzarella, Lactobacillus bulgaricus, Streptococcus thermophilus.

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Soft cheeses (ripened 1-5 months)

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Brie, Lactococcus lactis, Leuconostoc cremoris

Semi soft, Roquefort (ripened 1-12 months)
Lactococcus lactis, L. cremoris, Penicillium roqueforti

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Hard cheese (ripened 1-12 months)

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Cheddar Lactococcus lactis, Lactobacillus casei, Lactococcus cremoris.

Very Hard (ripened 12-18 months), Parmesan, Lactococcus lactis, Lactobacillus bulgaricus, Lactococcus cremoris, Streptococcus thermophilus.

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Fermented meats process

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Process: Cut meat, add spices, add starter culture: Pediococcus acidilactici, Staphylococcus carnosus. Fermentation occurs, pH drops below 5.0, Add nitrites to control Clostridium botulinum.

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Preservation of meats

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Raw meat stored at 5 C for 3-10 days, or at 0 C for 30 days. Growth of psychrophiles is not prevented, Pseudomonas sp.

Also dehydration and curing

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Dehydration and curing

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Dehydration, jerky, reduces moisture, prevents growth of bacteria.

Dehydration and curing, these agents include sodium nitrate, sodium nitrite, lowers water activity of the meat, nitrite inhibits Clostridium botulinum. Nitrate gives meat a red color.

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Fermented fish

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Fermented fish, sauces and pastes, seen in SE Asia, whole, chopped, mashed fish and shrimp. Salted and sealed in vessels. Flavourings added, natural microflora, natural fermentation. Normally strains of S. carnosus. Mam-tom of China, mam-rouc of Cambodia. Ratio 1:3 salt to fish.

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Spoilage in Poultry

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Spoilage in chicken, processing, usually Pseudomonas. In chicken houses Salmonella. Chicken egg is infected via, cracks in the shell, and ovarian infection, both have Salmonella involved.

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Canned foods

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Commercial canning involves heating canned goods at a high temperature long enough to destroy spores of Clostridium botulinum. 100 C for foods with pH below 4.0, 121 C for foods with a pH above 4.5. A heat resistant spore, Bacillus stearothermophilus is a QC indicator test organism.

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Sauerkraut

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Wilted shredded cabbage mixed with 2-3% salt. Natural fementation in large tanks, Lactobacillus plantarum, Lactobacillus brevis, Leuconostoc mesenteroides, are observed in the growth until acid level reaches 1.0%, lasts 20-30 days at room temperature, acid reaches 1.5%.

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Probiotics

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Are bacteria that promote development and maintenance of balanced intestinal flora. Lactic acid bacteria: Lactobacillus acidophilus, L. casei and Bifidobacterium bifidum. Effects include stimulating the immune response, often see a stimulation in the production of IgA

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Bread

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Involves the use of yeast to leaven cereal products to generate CO2 which makes the dough rise. Saccharomyces cerevisiae, ferments the sugars make carbon dioxide.

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Beer Production

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Beer is a term associated with non-distilled alcoholic beverages made from partially germinated cereal grains, referred to as malt. These include ales, lagers and stouts, which normally contain 3-8% ethanol. The main ingredients are hops (giving beer the characteristic flavor and aroma), water and yeast.

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Beer Brewing Stage 1: Malting

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the partial germination of cereal grain to form malt (6-9 days). This is the primary beer ingredient, it contains mainly starch. Malted barley , or malted wheat, or malted oats.

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Beer Brewing Stage 2: Mashing and wort preparation

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the production of an aqueous fermentation medium, “wort”. It contains fermentable sugars, amino acids and nutrients. This is sterilized by boiling, and hops are added for flavor.

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Beer Brewing Stage 3: Yeast fermentation

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selected strain of Sacchromyces cerevisiae, the wort undergoes an alcoholic fermentation, to produce ethanol, CO2, 2-7 days, depending on the beer produced.

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Beer Brewing Stage 4: Post fermentation

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the fresh beer is subjected to various treatments to make it acceptable for the shelf.

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Wine production

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Wine can be made from any plant extract or fruit juice that contains sufficient levels of fermentable sugars . However, most wine is made from grapes, Vitis vinifera, which can be grown all over the world.

Natural acidity, pH 2.8-3.8 prevents spoilage from occurring. Most table wines are 14% ethanol

Some regions fortify the wine with ethanol, sherry, port may be as high as 22% ethanol

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Winter fermentation

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Done in a controlled cool setting, for every 10g/l of sugar fermented the temperature of the vat rises 1.3 C, therefore temperature control a must. White wine fermentation is maintained at 10-20 C, red wine maintained at 24-29 C.

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Whiskies

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made from malts except the wort is not boiled, no hops are added. “Sour mash” whiskies also have a primary fermentation with Lactobacillus delbrueckii, the lactic acid produced is 1.5% before being killed. The yeast used for fermentation is S. cerevisiae, distillation follows to increase the ethanol level.

usually 40% ethanol at bottling.

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Industrial process of fermentation

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Stainless steel vessels; These vessels are temperature controlled with jackets and controllers, pH controllers, aeration if necessary, nutrients are added at the beginning (batch), or throughout (continuous). Culture medium contains, carbohydrate, hydrolyzed protein, trace elements, and buffers.

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Biomass yield coefficient (Y)

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Y carbon(g/g)= biomass produced(g) /
carbon substrate utilized (g)

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Carbon sources

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Used in the fermentation process, is required for all biosynthesis leading to reproduction, it also serves as an energy source.

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Culture Methods

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Batch vs. Continuous
Liquid vs. solid
Immobilized microbial cells

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Industrial enzyme production

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Total industrial enzyme market is > $1 billion/yr.

Typical enzyme yield/bacillus fermentation is 20 g/liter. Therefore per 1000 l fermentation, 20,000 g of enzyme. Genetically engineered strains have improved the yields.

Historically, B. licheniformis, B. amyloliquefaciens, are the choices for these fermentations.

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tarch degrading enzymes, amylases

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this enzyme is used to convert starch into high fructose corn syrup, used in the beverage soft drink industry.

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Cellulases

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bacterial cellulases differ from fungal cellulases, bacterial cellulases function best at neutral or alkaline pH values. Used in fruit juice and olive oil extractions, also used in stone washed denim products.

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Lipases

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fastest growing applications include detergent applications. Also for the removal of fat in leather processing. Important in cheese and meat applications.

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Proteases

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most important enzymes produced by Bacillus sp. Have of the enzyme market are these enzymes. Subtilisin, for use in laundry detergents, baking, brewing, cheese making, meat tenderizers, leather processing.

Seven different extracellular proteases are produced by B. subtilis.

Two of these proteases present in the highest concentrations are neutral and serine protease (subtilisin).

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Bacteria produce amino acids

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glutamate; Corynebacterium glutamicum, yield up to 60g/liter of broth.

This species has an incomplete TCA cycle and therefore produces glutamte, lacks α-ketoglutarate dehydrogenase. Lysine is also produced by a mutant of this species.

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Organic acids

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Aspergillus niger, makes citric acid. Lactobacillus delbrueckii, makes lactic acid, used for the food industry.

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Polysaccharides

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dextrans, homopolysaccharides, α linked polymers of glucose, Leuconostoc dextranicum. Xanthan gum, a heteropolysaccharide made by Xanthomonas campestris.

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Vitamins

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vitamin B12 made by Propionibacterium freundenenreichii, P shermanii.

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Penicillin

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produced by Penicillium chrysogenum, grown in glucose, corn steep liquor and phenylacetic acid. The fermentation takes 200 hrs, extracted on a rotary vacuum filter drum, chemical extraction 99.5% pure.

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Cephalosporins

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made by Cephalosporium

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Tetracyclines

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made by Streptomyces aureofaciens, in production broth it will inhibit the producing strain, therefore it is precipitated from the medium during growth with calcium ions.

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Streptomycin

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is produced by Streptomyces griseus.

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Single cell protein

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Microbial cells, contain as much as 60-70% protein. Therefore it represents a food or animal feed supply. Cost of production can limit its use.