Chapter 1 - Microbiology: Then and Now

Leeuwenhoek observes living bacteria and other microbes (animalcules). Experimentation puts an end to the idea of spontaneous generation. Semmelweis and Snow pioneer investigations into the source, cause, and transmission of disease (epidemiology) Jenner demonstrates that vaccination can generate disease resistance. Pasteur proposes the germ theory; Koch proves the theory through his postulates.

Chapter 2 - The Chemical Building Blocks of Life

Matter is composed of elements, about 25 of which are essential to life; carbon, hydrogen, oxygen, and nitrogen being most abundant. An atom is the smallest unit of an

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element having the properties of that element. The atomic nucleus consists of protons (+) and neutrons (no charge) surrounded by a cloud of electrons (). Different numbers of neutrons form isotopes while changes in electron number generate ions. Atoms with unfilled electron shells tend to gain, lose, or share electrons with other atoms and form chemical bonds. Ionic bonds are electrical attractions between oppositely-charged ions; covalent bonds share electrons between atoms; hydrogen bonds are weak electrical attractions between oppositely-charged regions of molecules. Chemic al

Water is a polar molecule and the solvent for all chemical reactions. pH is a measure of the acidity of a solution and fluctuations are prevented by buffers. Organic molecules contain functional groups that determine molecular behavior. Carbohydrates consists of monosaccharides that are used for energy and as building blocks; disaccharides that have industrial uses and are part of microbial wall structure; and polysaccharides that store energy or have structural roles. Lipids are hydrophobic compounds used for energy, membrane structure, or wall structure. Nucleic acids are used to build DNA, which is the genetic material in all living organisms and RNA, which is an intermediate in the expression and control of genetic information but is also the genetic material of many viruses. Proteins are the workhorses of all cells whose three-dimensional structure determines function.

Chapter 3 - Concepts and Tools for Studying Microorganisms

Two types of cellular organization (prokaryotic and eukaryotic) are established. Ehrlich, Fleming, Domagk, & Waksman discover antibiotics as disease-curing chemical agents. Today, antibiotic resistance, emerging diseases, and bioterrorism are challenges facing microbiology. Microbial ecology and evolution are driving a new golden age of microbiology.

reactions change bonding partners as reactants are converted into products.

All living microbes must maintain homeostasis. Most bacterial species live a communal life in biofilms; and, as such, can exhibit a multicellular way of life. Prokaryotic and eukaryotic cells share several organizational patterns (genetic, compartmental, and metabolic) and have several structural distinctions (organelles). Microorganisms have been classified by shared characteristics and have a binomial name. Today, all organisms are assigned to one of three domains, which are primarily based on physical, biochemical, serological, and especially nucleotide sequencing. Microbes and viruses are very small and measured in micrometers and nanometers, respectively. The light (compound) microscope magnifies and resolves specimens using visible light; staining specimens or other optical configurations provide contrast.

The electron microscope provides detailed images of cell structure using the transmission or scanning scope.

Chapter 4 - Prokaryotic Cell Structure and Function

The domain Bacteria contains many common but diverse groups of bacterial species; the domain Archaea has some of the most unusual organisms (extremophiles) in terms of growth environments. Bacterial and archaeal species vary in cell shape and cell arrangements; most exhibit a rod, spherical, or spiral shape. Bacterial and archaeal species contain a variety of cell structures.

dependent on temperature, pH, noncompetitive, and competitive inhibition. Energy coupling through ATP is used to drive endergonic reactions. In microbes, cellular respiration can be aerobic (+O2) or anaerobic (O2) process. Cellular respiration has three stages; glycolysis splits glucose into pyruvate, netting two ATPs; Krebs cycle converts acetyl CoA CO2, producing two additional ATPs; and electron transport and chemiosmosis in the prokaryotic cell membrane generate an additional 34 ATPs from the electrons donated from glycolysis and Krebs.

Pili are proteins fibers allowing cells to attach to surfaces. Flagella are protein appendages used for motility. The glycocalyx (capsule or slime layer) is a carbohydrate-rich layer to prevent desiccation, allow attachment, or evade immune system defenses. The cell envelope consists of the cell wall, which maintains cell shape and prevents cell rupture; and the cell membrane, a typical phospholipid bilayer that separate environment from cell interior and regulates transport of materials into or out of the cell. The nucleoid is a subcompartment in the cytoplasm that contains the genetic information in the form of a circular bacterial chromosome. Plasmids are small cytoplasmic loops of DNA that carry nonessential genetic information. The cytoplasm also contains ribosomes for protein synthesis and inclusion bodies that store nutrients; gas vacuoles and magnetosomes may be present in some species. The prokaryotic cytoskeleton consists of cytoplasmic proteins that regulate cell division and help determine cell shape. Processes such as transcription and translation can be spatially separated in bacterial and archaeal cells.

A bacterial growth curve goes through four phases (lag, log, stationary, and decline). A few bacterial species can produce endospores in response to nutrient limitation. Physical factors controlling cell growth include temperature, oxygen, pH, and osmotic pressure. Chemical factors are based on the nutrients found in culture media (solid agar and nutrient broth), which can consist of a complex medium or synthetic medium. Selective, differential, and enriched media can be used, respectively, to select for or differentiate between species, or to grow fastidious microbes. Some 99 percent of all microbes cannot be grown in a known culture medium; they represent viable but not culturable (VBNC) species. Pure cultures can be prepared by a pour-plate or streak-plate isolation method. Population growth can be measured directly (direct microscopic count) or indirectly (most probable number or standard plate count).

Chapter 6 Metabolism of Prokaryotic Cells

Metabolism consists of two biochemical processes (anabolism and catabolism), many of which require or release energy (endergonic and exergonic). Enzymes are protein catalysts that speed up chemical reactions by lowering the activation energy of the reactions. The active site of an enzyme forms an enzyme-substrate complex that weakens or stretches chemical bonds, weakening the substrate(s). Metabolic pathways often are

Microbes can use other organic molecules for energy production including lipids and proteins. Many microbes employ anaerobic respiration, which uses the same stages as aerobic respiration, except an inorganic final electron acceptor other than O2 is used and a different final end product than water is formed. Some microbes can carry out fermentation if no inorganic final end product is present. The process allows glycolysis to continue to produce two ATPs per glucose consumed. Microbial fermentation pathways vary depending on the enzyme system they possess. Some microbes can carry out photosynthesis through a process similar to green plants. Microbes demonstrate four metabolic patterns (autotrophy and heterotrophy) depending on the energy source (light or chemical) and carbon source (CO2 or organic compounds) required.

Chapter 7 Prokaryotic Genetics

Chapter 5 - Prokaryotic Growth and Nutrition

Most bacterial and archaeal cells reproduce asexually by binary fission; the actual generation (doubling) time depends on physical and chemical factors in the environment.

regulated by enzyme function, which is

Bacterial and archaeal chromosomes are located within the nucleoid where the DNA is supercoiled in a looped domain structure. Circular plasmids may be present in the cytoplasm where they replicate independently of the chromosome. DNA replication consists of three stages: initiation at the origin of replication; elongation of the replication forks bidirectionally with the synthesis of

complementary polynucleotides by a DNA polymerase; and termination, which results in two identical DNA molecules. The central dogma summarizes the flow of genetic information; transcription involves the copying of a DNA template into RNA (tRNA, rRNA, or mRNA) by an RNA polymerase; translation is the synthesis of a polypeptide from an mRNA by ribosomes.

Transduction involves a bacterial virus transferring a donor DNA segment from dead donor to live recipient. Genetic engineering involves an alteration to the genetic material in a microbe using a recombinant plasmid so the genes expressed produce a novel product or trait.

Pneumonia can take several forms depending on the infecting bacterial species: Pneumococcal pneumonia is community acquired by infection with Streptococcus pneumoniae. Atypical pneumonia is caused primarily by Mycoplasma pneumoniae (walking pneumonia) or Legionella pneumophila (Legionnaires disease). Q fever is caused by Coxiella burnetii.

Psittacosis and chlamydial pneumonia result from infections by Chlamydia psittaci and C. pneumoniae, respectively.

Chapter 10 - Foodborne and Waterborne Bacterial Diseases

A bacterial operon consists of regulatory segments (promoter and operator) and functionally-related structural genes. A separate regulatory gene may produce a repressor protein that can exert negative control over an operon. Mutations are permanent changes in the DNA sequence caused by unrepaired replication errors, physical or chemical mutagens, or transposable genetic elements (transposons). Auxotrophs result from a nutritional mutation in a prototroph (wild-type) cell. Mutations can be detected by negative or positive selection plating techniques. The Ames test uses auxotrophic bacteria to identify a chemical that can act as a mutagen and carcinogen in humans.

Foodborne and waterborne infections can be the result of intoxications or infections. Water and food become contaminated through animal slaughter, exposure to animal mature, human sewage, or fecal matter. They can occur in many locations.

Chapter 8 - Gene Transfer, Genetic Engineering, and Genomics

Genes are passed between generations through vertical gene transfer or transferred to the same generation by horizontal gene transfer.

Biotechnology represents the process of producing commercial or industrial applications using genetic engineering. Microbial genomics includes sequencing microbial genomes to understand an organisms genetic organization and function (functional genomics) with the intent to use the information for scientific, medical, or industrial purposes. Comparative genomics compares genomes of similar or dissimilar species to study evolutionary relationships of the tree of life.

Chapter 9 - Airborne Bacterial Diseases

Transformation transfers a DNA segment from a dead donor cell to a competent live recipient. Conjugation through physical contact transfers an F plasmid or part of a chromosome (Hfr) from live donor to live recipient.

Several bacterial diseases affect the upper respiratory tract: Strep throat, scarlet fever, and rheumatic fever are caused by Group A streptococci. Diphtheria and pertussis involve bacterial toxins produced by Corynebacterium diphtheriae and Bordetella pertussis that inhibit protein synthesis and destroy the ciliated epithelium, respectively. Bacterial meningitis is caused by several bacterial species, including Neisseria meningitidis, which infect the nasopharynx and rapidly spread to the meninges. Several bacterial diseases affect the lower respiratory tract: Tuberculosis, caused by Mycobacterium tuberculosis, can result in a latent infection that can turn deadly in the lungs or spread to other parts of the body (miliary TB).

Intoxications include botulism (Clostridium botulinum) and food poisoning (Staphylococcus aureus or Clostridium perfringens). Foodborne and waterborne infections produce several diseases, including gastroenteritis. The major ones are: Typhoid fever (Salmonella enterica serotype Typhi). Salmonellosis (S. enterica serotype Enteritidis and Typhimurium). Shigellosis (Shigella sonnei).

Cholera (Vibrio cholerae). E. coli diarrheas (ETEC, EPEC, EHEC). Gastric ulcer disease (Helicobacter pylori) Campylobacteriosis (Campylobacter jejuni) Listeriosis (Listeria monocytogenes)

Peritonitis caused by Bacteroides fragilis;

Pseudomembranous colitis caused by Clostridium difficile; Actinomycosis and Nocardiosis is caused by Actinomyces israelii and Nocardia asteroides, respectively. Pasteurellosis, cat-scratch disease, and ratbite fever are diseases caused by bites from infected cats, dogs, and some wild rodents. Diseases of the oral cavity include dental

Chapter 11 - Soilborne and Arthropodborne Bacterial Diseases

Anthrax, tetanus, and gas gangrene are intoxications from the soilborne bacteria Bacillus anthracis, Clostridium tetani, and C. perfringens, respectively. Leptospirosis is spread from other animals to humans, often through water contaminated with Leptospira interrogans. Several bacterial diseases are arthropodborne: Plague is spread by rodents and their fleas infected with Yersinia pestis. Tularemia is caused by Francisella tularensis. Lyme disease and relapsing fever are tickborne diseases involving Borrelia species.

cytoplasm; and retroviruses reverse transcribe RNA into DNA. Some DNA viruses and retroviruses integrate their DNA into the host cell chromosome (provirus) and remain in a state of latency. Antiviral drugs can treat a few human viral diseases, such as cold sores and HIV infections. Interferon is a naturally-made human protein that puts cells in an antiviral state. Cytological investigations and cytopathic effects can be used to detect specific viruses. Many human viruses can be cultivated in cell cultures and enumerated by plaque formation. About 20 percent of human tumors have a viral association and can contain oncogenes that trigger uncontrolled cell growth. Several emerging viruses have appeared in human populations as the result of viral recombination and mutation. Three hypotheses (regressive, cellular, and independent) have been suggested to explain the origins of viruses Viroids are infectious RNA particles that affect some plant species; prions are infectious proteins that can cause neurologic degenerative diseases in many animals, including humans.

caries and periodontal disease. Urinary tract infections usually develop into urethritis, although bladder (cystitis) and kidney infections (pyelonephritis) can also occur due to a range of bacterial infections. Nosocomial infections or hospital-acquired infections are a major health care issue. Many opportunistic bacteria can cause infections

especially in immunocompromised patients. Other arthropodborne diseases include Rocky Mountain spotted fever, epidemic and endemic typhus that are caused by rickettsial bacteria; ehrlichiosis is transmitted by ticks infected with Ehrlichia species.

Chapter 14 - Viral Infections of the Respiratory Tract and Skin

Chapter 13 - Viruses and Virus-Like Agents

Chapter 12 - Sexually Transmitted, Contact, and Miscellaneous Bacterial Diseases

Syphilis, gonorrhea, and chlamydial urethritis are sexually transmitted diseases (STDs) caused, respectively, by Treponema pallidum, Neisseria gonorrhoeae, and Chlamydia trachomatis. Chancroid, Ureaplasma urethritis, lymphogranuloma venereum, and bacterial vaginosis are additional STDs. Contact infections include:

Leprosy (Hansen disease), which is a chronic and systemic infection caused by Mycobacterium leprae. Abscesses, boils, impetigo, and toxic shock syndrome resulting from infection with Staphylococcus aureus. Trachoma, caused by Chlamydia trachomatis, is the worlds leading cause of preventable blindness; bacterial conjunctivitis (pinkeye) caused by Haemophilus aegyptius (influenzae type III). Endogenous bacterial diseases include:

In the early part of the 20th century viruses were identified as the source of some infectious diseases in humans. Viruses consist of a genome packaged in a protein coat (capsid); some viruses have an envelope surrounding the nucleocapsid and spikes extending from the surface. Viruses are placed into one of three shapes (helical, icosahedral, or complex). Viruses exhibit a host range and, for animal viruses, a tissue tropism. Viruses can be classified into families based on nucleic acid type [DNA viruses (double or single stranded) and RNA viruses (double or single stranded); RNA viruses also be can be separated by being + or stranded. All viruses go through 5 phases of replication (attachment, penetration, biosynthesis, maturation, and release). Bacteriophages replicate within the host cell cytoplasm; new virulent phage burst out of the cell (lytic cycle) while temperate phage may integrate their DNA into the host chromosome as a prophage (lysogenic cycle). In animals, herpesviruses replicate within both the nucleus and cytoplasm of the host cell; RNA viruses replicate in the

Several viruses affect the human upper respiratory tract. The diseases include: Influenza, caused by influenza viruses A and B that change genetically every year as a result of antigenic drift and antigenic shift. Common colds, often caused by rhinoviruses and adenoviruses. Many viruses affect the human lower respiratory tract, responsible for disease that include: Viral pneumonia (respiratory syncytial virus), acute respiratory infections (parainfluenza viruses), and severe acute respiratory syndrome (SARS coronaviruses). Herpesviruses cause several infections and disease of the skin, including: Cold sores and genital herpes (HSV-1 and -2), chickenpox and shingles (varicella-zoster virus), roseola (HHV-6), and Kaposi sarcoma (HHV-8). Other skin diseases include measles and mumps (paramyxoviruses), rubella (togavirus), fifth disease (parvovirus), and common and genital warts (papillomaviruses). The poxviruses are most noted for causing smallpox, a viral disease that has been eradicated through vaccination from the world.

Chapter 15 - Viral Infections of the Blood, Lymphatic, Gastrointestinal, and Nervous Systems

AIDS are caused by the human immunodeficiency virus type 1 (HIV-1). HIV replication is dependent on a reverse transcriptase within its primary target cells, CD4+ T lymphocytes. HIV disease is the early stages (I and II)

Several types of encephalitis are caused by infections from arthropods infected with togaviruses, bunyaviruses, or flaviviruses (West Nile fever/encephalitis).

Coccidioidomycosis can be a disseminated

and life-threatening disease following infection by Coccidioides immitis spores.

Chapter 16 - Eukaryotic Microorganisms: The Fungi

Fungi, including the molds and yeasts, compose the kingdom Fungi within the domain Eukarya. Molds grow as filaments called hyphae that may be septate or nonseptate and form thick masses called a mycelium.

Pneumocystis pneumonia, caused by

Pneumocystis jiroveci, is an opportunistic infection often found in AIDS patients. Other fungal mycoses include aspergillosis and a mycotoxin intoxication called ergotism.

Chapter 17 - Eukaryotic Microorganisms: The Parasites

leading to AIDS (stage III). AIDS patients usually die from an opportunistic infection. HIV is usually transmitted through some form of blood transfer or sexual intercourse with an infected individual. Highly active antiretroviral therapy (HAART) is one antiviral drug combination used to slow down the infection process. Infectious mononucleosis and cytomegalovirus disease are blood-borne diseases caused by herpesviruses. Hepatitis B, C, D, and G are bloodborne viral diseases affecting the liver. Yellow fever and Dengue fever represent two viral hemorrhagic fevers caused by flaviviruses. Hantavirus disease, sandfly fever, and Rift Valley fever are bunyavirus-caused hemorrhagic fevers. Ebola and Marburg hemorrhagic fevers are caused by filoviruses that produce hemorrhagic lesions. Lassa fever is a hemorrhagic fever transmitted by rodents infected with this arenavirus. Hepatitis A and E are liver infections caused hepatitis viruses transmitted via the gastrointestinal tract. Viral gastroenteritis represents a common illness often due to viral gastrointestinal infections caused by rotaviruses, noroviruses, or enteroviruses. Rabies is a nervous system disease caused by infection of the rabies virus; once symptoms appear the disease is almost always fatal. Polio (poliomyelitis) is a potentially severe paralytic disease of the nervous system caused by infection with the polio virus.

Fungi are heterotrophic, most representing saprobes (decomposers). Like most organisms, fungal growth is influenced by oxygen, temperature, and pH. Symbiotic (mutualistic) relationships occur with plants, as mycorrhizae or endophytes. Reproduction involves formation of asexual and sexual spores that are often carried in the air. Sexual reproduction involves opposite mating types that forma fusion cell called a heterokaryon. The fungal taxonomic groups are usually assigned according to the form of sexual reproduction observed; the Zygomycota, Ascomycota, and Basidiomycota have unique sexual reproductive structures, while the mitosporic fungi (not a taxonomic group) are reassigned if a sexual stage is discovered. The yeasts reproduce by budding and play important roles in industry and research. Several fungi can cause diseases of the skin: Dermatophytosis (e.g., ringworm and athletes foot) is a relatively common infection caused by a variety of fungi. Candidiasis, caused by Candida albicans, is more commonly called vaginitis or thrush. Sporotrichosis forms lesions under the skin after an infection with Sporothrix schenkii. Fungal spores can infect the lower respiratory tract and cause several diseases: Cryptococcosis, caused by Cryptococcus neoformans, affects the lungs and meninges. Histoplasmosis and Blastomycosis are potentially systemic diseases caused, respectively, by Histoplasma capsulatum and Blastomyces dermatitidis.

The protists are a very heterogeneous group in the domain Eukarya, which includes the green algae and the protozoa. The protozoa include the parabasalids, diplomonads, and kinetoplastids that possess flagella; the amoebozoans that exhibit amoeboid motion; the ciliates that possess cilia; and the apicomplexans that are mot motile in the adult form. Many protozoan parasites have trophozoite and cyst stages and infection involves definitive and intermediate hosts. Some protozoal diseases affect the skin, or the digestive or urinary tracts: Leishmaniasis is a vector-borne (sandfly) disease causing a cutaneous (Leishmania major) or visceral disease (L. donovani). Amoebiasis (Entamoeba histolytica), giardiasis (Giardia intestinalis), cryptosporidiosis (Cryptosporidium parvum and C. hominis), and cyclosporiasis (Cyclospora cayetanensis) are diseases of the digestive tract. Trichomoniasis is a relatively common protozoal parasitic disease of the urinary tract caused by Trichomonas vaginalis. Malaria is caused by four species of Plasmodium. The malarial parasite requires both definitve (mosquito) and intermediate (human) hosts.

Trypanosomiasis can be transmitted Trypanosoma brucei-infected tsetse flies (human African sleeping sickness) or American trypanosomiasis (Chagas disease) involving T. cruzi-infected reduvid bugs. Babesiosis and Toxoplasmosis are additional bloodborne protozoal parastic diseases caused by Babesia macroti and Toxoplasma gondii, respectively. Primary amoebic meningoencephalitis is a rare nervoius system disease caused by Naegleria fowleri. The helminthic parasites are multicellular animals and include the flatworms and roundworms. Flatworm-caused diseases require definitive and intermediate hosts and include: schistosomiasis (Schistosoma species); lung and liver fluke diseases; and tapeworm diseases.

microbiota represent symbiotic relationships that are examples of mutualism or commensalism. Pathogenicity and virulence are important factors in the establishment of a disease, whether resulting from an endogenous or exogenous infection. Many opportunistic infections are secondary infections resulting from a primary infection. Microbes or viruses can be disseminated through the blood. A disease progresses through a series of five stages characterized by specific signs and symptoms. To become ill, the host must receive a certain infectious dose (characteristic of the pathogen) through some portal of entry.

Phagocytosis by phagocytes, which engulf

and clear microbes from the body.

Inflammation that heightens the immune

defenses and fever that can slow down pathogens while speeding up immune defenses. Natural killer (NK) cells can eliminate virus-infected cells and cancer cells. Complement, which enhances the processes of phagocytosis and inflammation while eliminating some pathogens. Pathogen-associated molecular patterns (PAMPS) can be recognized toll-like receptors present on macrophages, dendritic cells, and endothelial cells.

Infection and disease is the result of a pathogen overcoming host barriers, which may require the possession of virulence factors. Virulence factors include structural factors, enzymes, and toxins. Bacterial toxins include the exotoxins and endotoxins. Disease can be communicable or noncommunicable and transmitted by direct or indirect methods. Those areas where a microbe lives and multiplies are called reservoirs. Disease spread can have endemic, epidemic, or pandemic consequences. Nosocomial infections often results from a chain of transmission that can be broken using universal precautions. The emergence or resurgence of disease can be the result of several factors.

Chapter - 20 Resistance and the Immune System: Acquired Immunity

Chapter 19 - Resistance and the Immune System: Innate Immunity

Roundworm diseases do not require two hosts and include; pinworm disease (Enterobius vermicularis) and trichinellosis (Trichinella spiralis); soilborne diseases (ascariasis, and hookworm disease). Helminthic parasitic disease of the lymphatic system (filariasis) is caused by the roundworm Wuchereria bancrofti.

Chapter - 18 Infection and Disease

Infection, the competition between host and microbe or virus, precedes disease, which refers to a change from the healthy state. The human microbiota helps protect the host from pathogen colonization, as most

Leukocytes, especially neutrophils, macrophages, dendritic cells, and lymphocytes are blood cells important to innate and acquired immunity. The lymphatic system contains primary and secondary tissues important toward fighting infection and disease. Individuals are born with innate immunity while acquired immunity is a form of specific resistance gained during an individuals life. The innate first lines of defense include mechanical, chemical, and microbiological barriers. The innate second lines of defense include:

Acquired immunity requires the attributes of specificity, tolerance of self, minimal self damage, and immunological memory. Acquired immunity has two responses: a humoral response to pathogens in fluids and a cell mediated response to pathogens infecting cells. Lymphocyte activation involves only those B and T cells recognizing an epitope or antigen peptide, respectively; the result is activated effector cells (B and T cells). All immune defensive cells arise from hematopoietic stem cells in the bone marrow. The humoral response is mediated by activated B cells that mature into memory B cells and plasma cells. Antibodies are immunoglobulins; proteins consisting of four polypeptide chains, two identical heavy (H) chains and two identical light (L) chains in the monomer state.

Epitopes bind at the H-L antigen binding

sites and phagocytes may be able to bind to the Fc fragment.

There are five classes of immunoglobulins;

IgG, IgM, and IgA are the disease fighters while IgE plays a role in allergies and IgD is a receptor on B cells. A primary antibody response occurs to the first exposure to a pathogen (antigen) while a secondary antibody response is a much faster response mediated by memory cells to an ensuing exposure to the same antigen. The diversity in antibody populations is based on a somatic recombination process. Pathogen (antigen) clearance is dependent on phagocytosis by macrophages. The cell mediated response is controlled by activated T cells. T-cell receptors and coreceptors recognize and bind to major histocompatibility complex (MHC) proteins on antigenpresenting cells (APC; MHC-II) or infected target cells (MHC-I). Naive T cells recognize peptide fragments presented on antigen-presenting cells (macrophages or dendritic cells). Interleukin secretion generates a clone of immature T cells and T memory cells. Immature T cells mature into T helper (TH) cells; TH1 target infected macrophages while TH2 help activate epitope-bound B cells. Cytotoxic T cells, activated by dendritic cells or through an interaction of CD8 T cells with an APC, target and destroy infected cells.

Agglutination involves the clumping of cells

or objects (antigens) by antibodies.

Complement fixation involves the hemolysis

of red blood cells. Labeling methods detect antigen-antibody binding by: Fluorescent antibody, radioactive antibody (radioimmunoassay), or enzyme-linked antibody (ELISA). Monoclonal antibodies are laboratorydeveloped immunoglobulins that recognize only one epitope on a cell or other antigen. Gene probes are single-stranded DNA segments that recognize pathogen DNA.

Type IV cellular hypersensitivity is an exaggerated delayed cellmediated immune response by T cells. Autoimmune disorders can occur when acquired immunity loses selftolerance. Acquired immunity is responsible for tissue or organ transplant rejection. Immunodeficiency disorders occur when acquired or humoral immunity loses the ability to respond to non-self antigens.

Chapter 23 - Physical and Chemical Control of Microorganisms

Chapter 22 - Immune Disorders

A hypersensitivity results from an immediate or delayed exposure to an antigen or allergen.

Chapter 21 - Immunity and Serology

Active immunity involves the production of T and B cells, and antibodies, as a result of exposure to a pathogen or receiving a vaccine. Passive immunity involves receiving antibodies from another source. A vaccine is composed of a pathogen that has been treated in some way: Whole agent vaccines represent attenuated, inactivated, or toxoid vaccines. Other vaccines include subunit, conjugate, DNA, or recombinant vector vaccines. Passive immunity can be acquired through IgG passage to fetus (naturally acquired) or injection of antibody-rich sera (artificially acquired). Herd immunity protects a population by maintaining high vaccination levels within the population (herd). Although very rare, some vaccines can have dangerous side effects. Serological reactions involve antigenantibody interactions. Neutralization involves the inactivation of an exotoxin or virus. Precipitation forms visible aggregates often involving immunodiffusion or immunoelectrophoresis.

Sterilization involves the removal of all living microbes, spores, and viruses from an object or area while sanitization reduces the numbers to a level deemed safe. There are several physical methods of control: Dry heat (including incineration) can kill microbes while moist heat (such as pasteurization) can kill pathogens; other methods can control microbial levels and be measured through the thermal death time or thermal death point. Filtration is a mechanical method to removed microbes from air or water. Ultraviolet light is bactericidal while ionizing radiations are microbicidal and can be used to preserve foods. Salting and low temperatures are additional control methods. Chemical methods of control involve the use of antiseptics on living surfaces and disinfectants on inanimate objects.

Type I hypersensitivity involves IgE antibodies and degranulation of cell mediators from basophils and mast cells. Systemic anaphylaxis can cause a lifethreatening system-wide release of mediators while atopic disorders are localized and typical of common allergies. Asthma can be a dangerous hypersensitivity that constricts the airways. Allergy therapies include desensitization, blocking antibodies, and the use of antihistamines or other drugs. Type II cytotoxic hypersensitivity results from IgG interactions with cell surfaces. Type III immune complex hypersensitivity occurs when antibodies combine with antigens and form aggregates in blood vessels.

The effectiveness of chemical control can be measured by the phenol coefficient or the in-use test. Chemical control methods include:

Halogens, such as chlorine and iodine,

oxidize proteins.

Phenolic derivatives denature proteins. Heavy metals, such as mercury and silver,
interfere with microbial metabolism. Alcohols denature proteins and disrupt membranes.

Detergents, such as the quats, react with cell

membranes. Hydrogen peroxide can damage cellular components. Aldehydes, and ethylene oxide and chlorine dioxide gases, can sterilize.

(inhibits glucose uptake); and the avermectins (affect the nervous system). The effectiveness of antibiotics can be tested with susceptibility assays, including the tube dilution method and the agar disk diffusion method.

Chapter 24 - Antimicrobial Drugs

Antimicrobial drugs are a group of chemotherapeutic agents. The age of chemotherapy started with Ehrlich and Domagk, but the use of naturally produced chemicals (antibiotics) was most advanced by Fleming, Waksman, Florey, and Chain. The effectiveness of antibiotics depends on their selective toxicity and antimicrobial drug spectrum. The synthetic antibacterial agents include the sulfonamides, isoniazid, ethambutol, and the quinolones. Antibiotics with a beta-lactam nucleus inhibit cell wall synthesis and include the penicillins, cephalosporins, monobactams, and carbapenems. Other bacterially-produced antibiotics included: Vancomycin (cell wall inhibitor).

Resistance to antibiotics can be the result of mutations or lateral gene transfer conferring an altered metabolic pathway, antibiotic inhibition, reduced permeability/active export, or target alteration.

Chapter 25 - Microbiology of Foods

Food spoilage can be the result when foods are altered from their expected form.

Preservation of foods can involve freeze-drying (lyophilization) or the use of osmotic pressure to dehydrate foods. Chemical preservatives can inhibit the growth of microorganisms in food. Irradiated foods (UV and gamma rays) can reduce microbial surface contamination. Foodborne diseases involve food infections (ingestion of living microbes) or food intoxications (ingestion of microbial toxin). The Hazard Analysis and Critical Control Point (HACCP) is a food safety system designed to identify potential points of microbial contamination. Many foods (e.g., sauerkraut, pickles, vinegar, and soy sauce) are the result of a microbial fermentation process. Milk products (e.g., buttermilk, yogurt, and cheeses) are the result of a fermentation process.

Chapter 26 - Environmental Microbiology

Bacitracin and polymyxins (affect cell membranes). Aminoglycosides, chloramphenicol, tetracyclines, macrolides, clindamycin, the streptogramins, and oxazolidinones (translation inhibitors). Rifampin (transcription inhibitor) and the quinolones (DNA replication).

Surface water, unlike groundwater, is likely to become contaminated. The microbial population in unpolluted and polluted water differs, the later being potentially subject to coliform bacteria and algal blooms. Of the three types of water pollution, only biological pollution is the result of human waste introducing enteric microorganisms. The measurement of polluted water is

Antifungal drugs are fewer in number and include: polyenes and imidazoles (disrupt cell membranes); echinocandins (inhibit cell wall synthesis); flucytosine (inhibits nucleic acid synthesis); and griseofulvin (mitosis inhibitor). Antiprotozoal and antihelminthic drugs attempt to eradicate the parasite. Antiprotozoal agents: Aminoquinolines (antimalarial); sulfonamides and heavy metals (metabolic inhibition); and nitroimidazoles (inhibit DNA synthesis). Antihelminthic agents: Praziquantel (interferes with membrane permeability); mebendazole

The chemical and physical properties of food (water, pH, oxygen, temperature, physical structure, and chemical composition) determine what pathogen may grow on it. Spoilage can result from microbial metabolism, which often produces foul-smelling products. Meats and fish can become contaminated through the handling and processing procedures. Poultry and eggs can be contaminated from human contamination or by penetration of bacterial species. Breads and bakery products can spoil from bacterial or fungal growth. Grains can be contaminated by aflatoxin and ergot produced specific groups of fungi. Milk and diary products can spoil or curdle due to the presence of contaminating microbes that produce acids or enzymes. Foods can be preserved with heat (through chemical sterilization or pasteurization) or low temperatures (refrigeration and freezing).

determined by the biological oxygen demand. Many human intestinal and skin diseases (bacterial, protozoal, viral) can be transmitted through water. Water purification is a three step process involving sedimentation of large particulate matter, filtration to trap microorganisms, and chlorination to kill remaining microorganisms. In sewage treatment, the primary treatment removes grit and large insoluble waste; secondary treatment degrades the biological content of the sewage; and the tertiary treatment purifies any water remaining after solid sludge separation.

Industrial fermentation can involve aerobic or anaerobic organisms in a bioreactor. Useful organic compounds can be produced by microorganisms from primary and secondary metabolites. Microbial enzymes are another product of biotechnology. Alcoholic beverages (Beer, wine, and distilled spirits) are the result of controlled fermentation processes. Other microbial products of biotechnology include antibiotics and insecticides. The biotechnological industrialization of yeast growth and mushroom farming has generated food or food supplement sources. Bioremediation uses natural or engineered bacterial species to break down toxic waste, toxic plastics, and radioactive materials. Industrial genetic engineering using plasmid technology will provide limitless possibilities for startling future developments in medicine, agriculture, pharmaceutical, and chemical industries.

Biofilms are complex organizations of microorganisms in soil, water, inanimate objects, or the human body. The biological analysis of water involves techniques (membrane filter technique, standard plate count, or most probable number) to detect organisms indicating fecal contamination. The carbon cycle involves the exchange of carbon between living organisms, including microorganisms as decomposers, and the environment. The sulfur cycle is dependent on anaerobic organisms to convert sulfate to hydrogen sulfide and vice-versa. The nitrogen cycle involves a series of microbial processes by which nitrogen is converted from a gas in the atmosphere to nitrogen-containing substances in soil and then reconverting nitrates to nitrogen gas.

Chapter 27 - Industrial Microbiology and Biotechnology