Chapter 6 Biochemistry The Chemistry of life Organic

Chapter 6 Biochemistry: The Chemistry of life

• Organic Chemistry: Is the study of compounds that contain carbon • Inorganic Chemistry: Involves all other chemical reactions • Biochemistry: Is the chemistry of living cells or it is the study of biology at the molecular level, or the chemistry of life, or the study of the biomolecules that are present within living organisms

Carbon bond (Covalent bond) • Single bond----- e. g methane • Double bond---- e. g ethylene • Triple bond----- e. g acetylene Hydrocarbon: is an organic molecule that contains only carbon and hydrogen atoms Cyclic Compound: when carbon atom link to other carbon atom to close the chain forming ring or cyclic compound

Carbohydrates: are biomolecules composed of carbon, hydrogen and oxygen in the ratio 1: 2: 1 e. g---- glucose, fructose, sucrose, lactose, maltose, starch, cellulose, glycogen • Monosaccharides: are sugars composed of only one ring e. g: glucose • Disaccharides( sucrose, lactose, maltose) – Are double-ringed sugars that result from the combination of two monosaccharides during this process a removal of water molecule occur by dehydration synthesis reaction

The bond holding the two monosaccharides together is glycosidic bond Hydrolysis reaction: Disaccharide + water=> two monosaccharides • Sucrose + water => glucose + fructose • Lactose + water => glucose + galactose • Maltose + water =>glucose + glucose Peptidoglycan: is composed of a repeating disaccharide attached by polypeptides (effect of antibiotic) • 3 monosaccharides =>Trisaccharide • 4 monosaccharides=>Tetrasaccharide • 5 monosaccharides=>Pentasaccharid Polysaccharides: are defined as carbohydrate polymers containing many monosaccharides

• Polymers: molecules consisting of many similar subunits • Glycogen: is the common storage molecule in animals and bacteria and found in the liver and in muscles • Starch : is the common storage molecule in plants and algae, it is found in potatoes, vegetables and seeds Hydrolysis of starch Starch(polysaccharide) maltose(disaccharide) α glucose(monosaccharide) glucose + Protein => glucoseamine

Lipids: • Constitute an important class of biomolecules • Most lipids are insoluble • But soluble in fat solvents such as ether, chloroform and benzene • Fatty acids: are the building blocks of lipids Lipids---- fatty acids • Glycolipids: glucose + lipid

Proteins • Is the most essential chemicals in all living cells • Proteins are polymers of amino acid • Proteins contain C, H, O, N and sometimes S Protein => amino acids • 2 amino acids----- dipeptide • 3 amino acids----- tripeptide • Polymer or chain------ polypeptide • Enzymes: are protein molecules produced by living cells and it is known the biological catalyst (endoenzymes & exoenzymes) • Catalyst: an agent that speeds up a chemical reaction without being consumed in the process Substrate=> Products

Nucleic acids • Are polymers, composed of nucleotides(building blocks of nucleic acids), nucleotides in a single strand are held together by covalent bond • The two categories of nucleic acids are deoxyribonucleic acid (DNA the hereditary molecule) and ribonucleic acid (RNA) • There are three types of RNA, messenger RNA (m. RNA), transfer RNA (t. RNA) and ribosomal RNA (r. RNA) • In a double-stranded DNA molecule, the nucleotides in one strand are connected to nucleotides in the other strand by hydrogen bond • DNA is the primary component of chromosomes. Genes are located along the DNA molecule • DNA molecules are used as templates to produce other DNA molecules by the process known as DNA replication

• The most important enzyme in DNA replication is DNA polymerase • The flow of genetic information within a cell follows the sequence DNA---m. RNA----protein. This is known as central dogma • The information (genetic code) in one gene of a DNA molecule is used to produce a m. RNA molecule, this process is known as transcription, the most important enzyme in transcription is RNA polymerase • Information in one m. RNA molecule is used to produce a protein, this process is translation (protein synthesis) and occurs at a ribosome

• Transfer RNA(t. RNA) molecules activate amino acids and transfer them to the growing protein chain. Specific amino acids are added at the correct locations because three-nucleotide sequences (anticodons) on t. RNA molecules recognize threenucleotide sequences(codons) on m. RNAmolecule.

Chapter 7 Microbial Physiology and Genetics

Nutritional Requirements: Categorizing microorganisms according to their energy and carbon sources: • Phototrophs…… organisms that use light as an energy source • Chemotrophs…. . organisms that use chemicals as an energy source • Autotrophs……. organisms use carbon dioxide as a carbon source • Heterotrophs…… organisms that use organic compounds other than carbon dioxide as a carbon source – Photoautotrophs…. . algae, plants, some photosynthetic bacteria (cyanobacteria) – Photoheterotrophs…. some photosynthetic bacteria – Chemoautotrophs…. . some bacteria – Chemoheterotrophs…protozoa, fungi, animals, most bacteria

Metabolism: • All the chemical reactions occurring within a cell Metabolites: • Is any molecule that is a nutrient, an intermediate product or an end product in a metabolic reaction Types of Metabolism • Catabolism: – The breaking down of larger molecules into smaller molecules, requiring the breaking of bonds, and then release energy • Anabolism: The assembly of smaller molecules into larger molecules, requiring the formation of bonds, and hence energy required for bond formation

• Nucleotide + nucleotide => nucleic acid • Monosaccharide+ monasaccharide => disaccharide • Amino acid +amino acid => polypeptide NB: Energy that is released during catabolic reactions is used to drive anabolic reactions. • Energy obtained from sun rays or by catabolic reaction is stored as ATP molecules (adenosine triphosphate) which are the major energy-storing in a cell ATP=> ADP=>AMP

Aerobic Respiration of Glucose • The complete catabolism of glucose by the process known as aerobic respiration occurs in three phases or chemical pathway: • Glycolysis=> anaerobic process • Krebs cycle=>aerobic • The electron transport chain=> aerobic

Fermentation of glucose: Fermentation usually take place in anaerobic environment • Glucose =>fermentationglycolysis=>pyruvic acid +2 ATP • Pyruvic acid=>yeast(saccharomyces)or Zymomonas=>ethyl alcohol+carbon dioxide • Pyruvic acid =>bacteria=>lactic acid (cheese, yogurt, pickles, cured sausages) • Pyruvic acid=>Lactic acid in muscles (bad) • Glucose =>oral bacteria streptococcus =>lactic acid (eat the enamel leads to tooth decay) • Lactose=>lactic acid bacteria=>curd and whey • Pyruvicacid=>propionibacterium=>propionic acid (swiss cheese) flavor + CO 2 holes

Biosynthesis of Organic Compounds • Photosynthesi(light and ATP) 2 CO 2 + 12 H 2 O => C 6 H 12 O 6 + 6 O 2 + 6 H 2 O +ADP + P • Chemosynthesis: 4 H 2 + CO 2 => CH 4 + 2 H 2 O

Bacterial Genetics • Genetics: The study of heredity: DNA, genes, the genetic code, chromosomes, DNA replication, transcription, translation • Genotype (genome): complete collection of genes or the genetic makeup of an organism • Phenotype: physical expression of the genotype In human (hair, eye, skin, color) In bacteria (presence or absence of enzyme, capsules, flagella, pili) Phenotype depend on genotype

A mutation A change in the characteristics of a cell caused by a change in the DNA molecules (genetic alteration) that is transmissible to the offspring. • Beneficial mutation: enables the organism to survive in an environment where organisms without mutation would die (resistant to antibiotic) • Harmful mutation: leads to the production of a nonfunctional enzyme which is unable to catalyze a chemical reaction essential to the life of the cells, (the cell will die…. Lethal mutation)

• Silent mutation: neutral mutation, which mean have no effect on the cell – Spontaneous mutation: mutation which occur randomly throughout a bacterial genome with no mutagen(x-rays, U. V. light, radioactive substance) – Induced mutation: are produced by agents called mutagens which increase the rate of mutation

Ways in which bacteria acquire new genetic information Gene transfer: movement of genetic information between organisms • Vertical gene transfer: passes genes from parent to offspring during cell division • Lateral gene transfer: passes genes to other cells. In bacteria it occurs by any of the following mechanisms:

• • • Transformation: release of DNA fragments and their uptake by other cells Transduction: transfer of genes (parts of DNA) by a prophage from a cell that was lysogenic to another cell that gets infected with this phage Conjugation: transfer of large quantity of DNA from one living cell to another by direct contact

Genetic Engineering An array of techniques to transfer eukaryotic genes, particularly human genes, into other easily cultured cells to facilitate the large scale production of important gene product (e. g Insulin) Genetic engineering can be achieved by one of the following techniques: 1. Genetic fusion 2. Protoplast fusion 3. Gene amplification 4. Recombinant DNA: is DNA from two different species of organisms

Steps: • Identification of the desired gene on the DNA of the donor organism • Culturing of the desired gene • Transfer of the desired gene to a vector (a virus or plasmid) • Insertion of the gene into the DNA of the recipient organism Some application Production of human insulin Some bacteria are engineered to control insects that destroy crops (not polluted)

Chapter 8 Controlling Microbial Growth in Vitro

Factors that affect microbial growth Microbial growth is affected by many different environmental factors including: • Availability of nutrients • Moisture • Temperature • p. H • Osmotic pressure • Barometric pressure

Terms related to optimum environmental factors: • Thermophiles: Microorganisms that prefer to live in hot temperature(minimum: 25 o. C, optimum: 50 o. C-60 o. C, maximum: 113 o. C) • Mesophiles: microorganisms prefer moderate temperature(minimum: 20 o. C, optimum: 20 o. C-40 o. C, maximum: 45 o. C) • Psychrophiles: microorganisms prefer cold temperature(minimum: -5 o. C, optimum 10 o. C-20 o. C, maximum: 30 o. C) NB: Psychrotrophs are a group of psychrophiles that prefer to live at refrigerator temperature 4 o. C

• Acidophiles: microorganisms live in acidic environment(p. H<7) • Alkaliphiles: microorganisms live in alkaline environment(p. H>7) (e. g Vibrio cholera) NB: neutral environment p. H= 7 • Halophiles: microorganisms that live in salty environment (e. g Vibrio cholera also are Capnophiles) • Haloduric : microorganisms that do not prefer to live in salty environments but are capable of surviving there • Barophiles: microorganisms that live where there is high baromatic pressure (atmospheric pressure)

Osmotic pressure: • Is the pressure that is affect on a cell membrane by solutions both inside and outside the cell. Osmosis: • Is defined as the movement of a solvent(water) through a permeable membrane, from a solution having a lower concentration of solute to a solution having a high concentration of solute

Hypertonic solution: When the concentration of solutes in the environment outside of a cell is greater than the concentration of solutes inside the cell • Human red blood cell=> loss of water=> cell shrink • Shrinkage=> crenation • Cell=> crenated • In plant cell=> cell wall not changed but cell membrane shrink (plasmolysis) Hypotonic solution: concentration of solutes outside a cell is less than the concentration of solutes inside the cell • Human red blood cells=> burst or lysis ( hemolysis) • Plant cell=> not burst but pressure increase but with time cell ruptures (plasmoptysis) Isotonic solution: The concentration of solutes inside and outside the cell is equal

Bacterial Population Growth Curve Lag phase: is the first phase of the growth curve, during which the bacteria absorb nutrients, synthesize enzymes, and prepare to cell division. No increase in number in this phase Log phase(exponential): is the second phase of the growth curve. In this phase the bacteria multiply so rapidly Stationary phase: when the nutrients in the liquid medium are used up and the concentration of toxic waste products of bacteria increase so the rate of divisions slows, and the number of bacteria that are dividing equals the number that are dying Death phase: As overcrowding occurs, the concentration of toxic waste products increase and the nutrient supply decreases the microorganisms then die at a rapid rate

Many industries use the chemostat microorganisms are cultured continuously in a controlled environment, which regulate the supply of nutrients and the removal of waste products • Yeast=>beer and wine • Bacteria- Fungi=> antibiotics

Inhibiting the growth of microbiology in vitro Definition of terms • Sterilization: is the complete destruction of all living organisms including spores and viruses – Dry heat – Autoclaving (steam under pressure) – Gas (ethylene oxide) – Chemicals (formaldehyde) – Radiation (U. V. and γrays) • Disinfection: is the destruction or removal of pathogens from nonliving objects by physical or chemical methods • Pasteurization: is a method of disinfecting liquids and it is used today to eliminate pathogens from milk and beverages, and it is not a sterilization because not all microbes are destroyed

• Disinfectants: chemical agents used to eliminate pathogens • Antiseptics: are solutions used to disinfect skin and other living tissue • Sanitization: is the reduction of microbial populations to levels considered safe by Public Health Standards (e. g Restaurants) • Lyphilization (freeze-drying): using liquid nitrogen, are microbistatic techniques that are used to preserve microbes for future use or study • Sepsis: refer to the presence of pathogens in blood or tissues • Asepsis: means the absence of pathogens • Aseptic techniques: are employed to eliminate pathogen (e. g hand washing- sterile gloves- masks- gowns) • Antisepsis: is the prevention of infection • Antiseptic technique: refers to the use of antiseptics. • Sterile technique: it is used to exclude all microorganisms from a particular area to be sterile

• Bactericidal agents (bactericides): are disinfectants that kill bacteria but not endospores (spore coat are thick and resistant) Sporicidal – Fungicidal - Algicidal- Viricidal. Pseudomonicidal – Tuberculocidal • Bacteriostatic: drug or chemical that inhibits growth and reproduction of bacteria

Using chemical agents to inhibit microbial growth Factors affect the efficiency of disinfectants • Prior cleaning of the object or surface to be disinfected • Presence of organic materials (feces-blood-vomits-pus) on the materials being treated • Bioburden: mean the type and level of microbial contamination • The concentration of the disinfectant • The contact time (the amount of time that the disinfectant must remain in contact with organisms in order to kill them) • The physical nature of the object being disinfected (smooth or rough surface) • Temperature and p. H

Characteristics of ideal chemical antimicrobial agent • It should have a wide or broad spectrum (should kill a wide variety of microorganisms) • Fast acting (the contact time should be short) • Should not be affected by the presence of organic matter • Must be nontoxic to human tissues, noncorrosive and nondestructive to materials • Should be soluble in water and easy to apply • Should be inexpensive and easy to prepare • Should leave residual antimicrobial film on the treated surface • Should be stable as concentrate and dilution • Should be odorless

Chapter 9 Using antimicrobial agents to control microbial growth in vivo

The father of chemotherapy is Paul Ehrlich, he use chemicals to affect bacterial cell not human cell Antimicrobial agent: • Antibacterial agents => kills bacteria • Antifungal agents => kills fungi • Antiprotozoal agents => kills protozoa • Antiviral agents => kills virus

The first who discover antibiotics is Alexander Fleming

Ideal qualities of an antimicrobial agents • • • Kill or inhibit the growth of pathogens Cause no damage to the host Cause no allergic reaction in the host Be stable when stored in solid or liquid form Remain in specific tissues in the body long enough to be effective • Kill the pathogens before they mutate and become resistant to it. NB: Narrow Spectrum & Broad Spectrum Antibiotics. Synergism: Some infectious diseases are treated by two drugs because one drug alone will not be effective.

How antimicrobial agents work • Inhibition of cell wall synthesis • Damage of cell membranes • Inhibition of nucleic acid synthesis (either DNA or RNA synthesis) • Inhibition of protein synthesis • Inhibition of enzyme activity

How bacteria become resistant to drugs: • Intrinsic resistance: bacteria are naturally resistant to a particular antimicrobial agent because they lack the specific target (Mycoplasmas no cell wall) or the drug is unable to cross the organisms cell wall or cell membrane and thus cannot reach its site of action • Acquired resistance: bacteria were once susceptible to a particular drug to become resistant to it by the following (Table 9 -5)

Chapter 10 Environmental Microbiology Microbial Ecology

Microbial Ecology: Is the study of the interrelationships among microorganism and the living and non-living world around them

Symbiotic Relationships involving Microorganisms • Symbiosis (Symbiotic relationships): is defined as the living together or close association of two different species and the organism in this relationships is known as symbionts

• Neutralism: a symbiotic relationship in which neither symbiont is affected by the relationship • Commensalism: a symbiotic relationship that is beneficial to one symbiont and is neither beneficial nor harmful to the other (indigenous microflora of humans) • Mutualism: is a symbiotic relationship that is beneficial to both symbionts – E. coli=> vitamin K (blood clotting factor) to the host (human) – Termite and protozoa • Parasitism: a symbiotic relationship that is beneficial to one symbiont (the parasite) and harmful to the other symbiont NB: A host can harbor a parasite without the parasite causing harm to the host • There are 2 kinds of parasites: Smart parasite=> do not cause disease but take only nutrients Dumb parasite=> kills their hosts then they must either find a new host or die

Synergism (synergistic infections): sometimes, two or more microorganisms may “team up” to produce a disease that neither could cause by itself Biofilms: In nature microorganisms are often organized in combination or close association to each other know as biofilm. The biofilms have some characteristics including: 1. Very resistant to antibiotics 2. Break down nutrients 3. Produce many different types of proteins

The Nitrogen Fixing Bacteria • • • Rhizobium Bacteria Occur in root nodules Leguminous plants Fix nitrogen N 2 Mutual symbiotic relationship

Chapter 11 Epidemiology and Public Health

• Communicable Disease: infectious disease is transmissible from one human to another(person to person) e. g Gonorrhea • Contagious disease: infectious disease is easily transmitted from one person to another e. g influenza (movie and theatre) • Zoonotic diseases: infectious diseases that humans acquire from animal sources • Incidence and Morbidity rate: is defined as the number of new cases of that disease in a defined population over a specific period

• Prevalence • Period prevalence of a particular disease is the number of cases of the disease existing in a given population during a specific period • Point prevalence of a particular disease: is the number of cases of the disease existing in a given population at a particular moment in time • Mortality rate (death rate): is the ratio of the number of people who died of a particular disease during a specified period per a specified population • Sporadic diseases: Is one that occurs only within the population of a particular geographic area

Endemic diseases: • Are diseases that are always present within the population of a particular geographic area. The number of cases of the disease may fluctuate over time, but the disease never dies out completely, e. g Tuberculosis, Staphylococcus, Streptococcus, Gonorrhea and Syphilis Epidemic diseases(or outbreak): • Is defined as a greater than usual number of cases of a disease in a particular region Pandemic disease: • Is a disease that is occurring in epidemic proportions in many countries simultaneously sometimes worldwide • HIV/AIDS- Tuberculosis- Malaria

Reservoirs of Infection Is any site where the pathogen can multiply or merely survive until it is transferred to a host Living Reservoirs 1. Human Carrier A carrier is a person who is colonized with a particular pathogen but the carrier not causing disease in that person – Passive carriers: carry the pathogen without ever having had the disease – Incubatory carrier: is a person who is capable of transmitting a pathogen during the incubation period of an infectious disease – Active carriers: have completely recovered from the disease but continue to harbor the pathogen (typhoid Mary the cook)

2. Animal Carriers: diseases that humans acquire it from animal sources are zoonotic diseases or zoonoses (rabies, toxoplasmosis from protozoa) 3. Arthropods Carriers (vector) (Insects--mosquitoes, biting flies, lice, fleas) (Arachnids---mites and ticks) A vector first take a blood meal from an infected person or animal and then transfers the pathogens to a healthy individual

Non-Living Reservoirs • Non- living or inanimate reservoirs of infection include air, soil, dust, food, milk, water, and fomites NB: Fomites are: patients gowns, bedding, towels, eating and drinking utensils and hospital equipment…etc Modes of Transmission See Figure 11 -4 and Table 11 -5 World Health Organization (WHO) See Table 11 -6

Bioterrorist and Biological Warfare: • Biological warfare: pathogenic microorganisms sometimes are used to cause harm to others • Biological warfare agents: microbes used in this process • Terrorist use pathogens to create fear, chaos, illness, and death and use bioterrorist agents (dead bodies in wells)

Water Supplies and Sewage Disposal • Water is the most essential resource necessary for the survival of humanity • Lakes, rivers, reservoirs and groundwater are the main sources of community water supplies There are two kinds of pollution: – Chemical pollution: industrial installation dump waste products into local waters without proper pretreatment or pesticides – Biological pollution: waste product of humans (fecal materials and garbage) the main cause of epidemics

Water Treatment • • • Filtration: water first filtered to remove large pieces of debris Sedimentation or settling: water remain in holding tanks to complete settles of debris to the bottom Coagulation: addition of Alum[aluminium potassium sulphate] to coagulate small pieces of debris, which settle to the bottom Filtration through sand filter to remove bacteria, protozoa cysts Chlorination: 0. 2 -1. 0 ppm to kill most bacteria, some use O 3 or U. V. light

Water considered Potable or Drinkable (safe to drink) or Suitable for human consumption when the water samples contain: less than 1 coliform per 100 ml of water contain < 1 coliform /100 ml

Sewage Treatment 1. Primary Sewage Treatment – Screening: large debris filtered out, remove floating grease and oil and debris is ground – Sedimentation – Coagulation: to complete settlement – Accumulation of primary sludge at the bottom 2. Secondary Sewage Treatment - The liquid undergo aeration or trickling filtration NB: aeration is to encourage the growth of aerobic microorganism which oxidize the dissolved organic matter to CO 2 and H 2 O -The activated sludge is transferred to a settling tank -The remaining liquid is filtered and disinfected by chlorination the effluent pass to rivers or oceans

3. Tertiary Sewage Treatment In some desert cities where water is in shortage the effluent water from sewage is further treated to be returned directly to drinking water system which is very expensive

Chapter 12 Healthcare Epidemiology Nosocomial Infections and Infection Control

• Nosocomial Infection (hospital-acquired infections): infectious diseases that are acquired within hospitals or other healthcare facilities • Community-Acquired Infections: infectious diseases are acquired outside of healthcare facilities • Iatrogenic Infections: diseases are results of medical or surgical treatment caused by surgeons

Pathogens most often involved in Nosocomial infections • Gram-positive cocci – Staphylococcus aureus – Coagulase-negative staphylococci – Enterococcus spp. • Gram-negative bacilli – E. coli – Pseudomonas aeruginosa – Enterobacter spp. – Klebsiella spp.

Most Common Types of Nosocomial Infections • Urinary tract infection (UTIs) • Surgical wound infections • Lower respiratory tract infections (pneumonia) • Bloodstream infections (septicemia)

Patients most likely to develop Nosocomial infections • Elderly patients • Women in labor and delivery • Premature infants and newborns • Surgical and burn patients • Diabetic and cancer patients • Patients receiving treatment with steroids, anticancer drugs, antilymphocyte serum, radiation • Immunosuppressed patients (patients whose immune systems are not function properly) • Patients who are paralyzed or are undergoing renal dialysis or catheterization (normal defense mechanisms are not functioning properly)

Major factors contributing to Nosocomial infections • An increasing number of the drug resistant pathogens • The failure of healthcare personnel to follow infection control guidelines • An increased number of immunocompromised patients • The bad use of antimicrobial agents • Over crowding of hospitals and healthcare facilities • Overuse and improper use of indwelling medical devices

What can be done to reduce the number of Nosocomial infections Hand washing is the single most important measure to reduce the risks of transmitting pathogens from one patient to another or from one anatomical site to another on the same patient Wash your hands before you: • Prepare or eat food • Treat a cut or wound to someone who is sick • Insert or remove contact lenses Wash your hands after: • Use the rest room • Handle the uncooked food (raw meat- poultry or fish) • Change a diaper • Cough- sneeze or blow your nose • Touch a pet • Handle garbage

Wash your hands in the following manner: • • Use warm or hot, running water Use soap (preferably an antibacterial soap) Wash all surfaces of your hands Rub hands together for at least 10 -15 seconds

Medical Asepsis • Medical asepsis: clean technique to reduce the numbers and transmission or pathogens • Medical aseptic techniques: hand washing, personal grooming, proper cleaning of techniques, disinfection, proper disposal of needles, contaminated materials. • Surgical asepsis: or sterile technique to keep objects and area sterile (free of microorganisms) Joseph Lister a British surgeon: contribution in the area of antisepsis

Source Isolation: patients with tuberculosis or other contagious diseases are placed into protective isolation to protect other people from becoming infected

Chapter 13 Diagnosing Infectious Diseases

Proper selection, collection, and transport clinical specimens: • The specimen must be of appropriate type for diagnosis of the suspected infectious disease • The specimen must be properly and carefully collected • Material should be collected from a site where the suspected pathogen is found and the least contamination occur • Specimens should be obtained before antimicrobial therapy has begun, or should the lab know what antimicrobial obtained • Acute stage is the appropriate time for specimen collection

• Specimen should be performed with care and no harm and instruction for sample collection in the case of urine and sputum • Sufficient quantity of the specimen must be obtained • Specimen should be placed or collected into a sterile container • Specimen should be protected from heat and cold • Sterile, disposable specimen containers should be used • Specimen container must be properly labeled • Specimen should be collected and delivered to the lab as early in the day as possible

Types of clinical specimens usually required to diagnose infectious disease: 1. 2. 3. 4. 5. 6. 7. 8. Blood Urine (clean-catch, mid-stream urine CCMS urine) Cerebrospinal fluid Sputum Throat swabs Wound specimens GC (gonococci) Fecal specimens.

• Bacterimia=> presence of bacteria in blood stream • Bacteuria=> presence of bacteria in urine • Septicemia=>bacterial toxins in blood stream(serious disease) chills, fever

The pathology department (the lab) • Pathology: is the study of the structural and functional manifestations of disease • Pathologist: A physician who has had extensive, specialized training in pathology Clinical Microbiology Laboratory See Figure 13 -4

Chapter 14 Pathogenesis of Infectious Disease

• Localized infections: Disease may remain localized to one site or it may spread e. g: boils, abscesses, pimples • Systemic infections or generalized infection: When infection has spread throughout the body by way of lymph, blood • Acute disease: has a rapid onset, followed by a rapid recovery e. g: measles, mumps, influenza • Chronic disease: has a slow onset and lasts a long time e. g: tuberculosis, leprosy, syphilis

• Symptomatic disease or clinical disease: a disease in which the patient is experiencing symptoms • Asymptomatic disease (subclinical): a disease that the patient is unaware of because he or she is not experiencing any symptoms • Sign of a disease: type of objective evidence of a disease abnormal heart or breath sounds, blood pressure, pulse rate, enlarged liver (hepatomegaly) or spleen (splenomegaly)

• Latent infections: disease may go from symptomatic to asymptomatic and some time later go back to being symptomatic • Primary infection: one infection disease may commonly follow another, the first disease is primary infection and the secondary infection

Steps in the pathogenesis of infectious diseases 1. Entry=> penetration of skin, or mucous membranes, inhalation, arthropods 2. Attachment of pathogen to some tissue 3. Multiplication of the pathogen (localized or systemic) 4. Invasion/spread of the pathogen 5. Evasion of host defenses 6. Damage the host tissue

• Virulent strains: are capable of causing disease • Avirulent strain: are not capable of causing disease Virulence factors (enable pathogens to attack, escape, destruction and cause disease

Chapter 15 Nonspecific Host Defense Mechanisms

Host defense mechanism: Ways in which the body protects itself from pathogens 1. Nonspecific host defense: • First line: skin, mucus membranes, dryness, p. H, temperature, digestive enzymes, acidity of stomach (p. H 1. 5), alkalinity of the intestines, microbial antagonism(competition for colonization site, for nutrients, production of substances to kill other bacteria)

2. Second line: – Transferin: prevent pathogen of essential nutrient – Fever: stimulation white blood cells to destroy invador – Interferon: antiviral(interfere with viral replication) – inflammation (redness, heat, swelling and pain, pus formation) • localize an infection • prevent the spread of microbial infection • neutralize any toxins being produced at the site • aid in the repair of damage tissue – Phagocytosis (white blood cells are phage cytes) surround and engulf foreign material

Chapter 16 Specific Host Defense Mechanisms: An Introduction to Immunology

• Immunology: is the scientific study of the immune system and immune responses • Immunity: is the condition of being immune or resistant to a particular infectious disease Acquired Immunity 1. Active acquired immunity a. Natural active acquired immunity (response of actual infection) b. Artificial active acquired immunity (vaccines) 2. Passive acquired immunity a. b. Natural passive acquired immunity (mother to fetus) Artificial passive acquired immunity (receiving antibodies

Vaccine: material that can artificially induce immunity to an infectious disease, following injection, or ingestion of the material

Types of Vaccines • Variety of materials are used in vaccines • Most vaccines are made from living or dead or attenuated pathogens • Or from certain toxins they produce See page 408 An ideal vaccine – Contains enough antigens – Contains antigens from all the strains of pathogens (polio 3 strains) – Has few side effects – Does not cause disease in the vaccinated person

• Antigens (immunogen): any foreign organic substance that is large enough to stimulate the production of antibodies • Antibodies: are glycoproteins produced by lymphocytes in response to the presence of antigen Antibodies found in=>tears, saliva, mucous membranes, colostrum, lymph, blood plasma • Ig. G------remote infection • Ig. M------recent infection • Autoimmune disease: when a person’s immune system no longer recognizes certain body tissues and attempt to destroy those tissues as foreign

• Immunocompetent person: a person’s immune system is functioning properly • Immunosuppressed person or immunocompromised or immunodepressed: a person’s immune system is not functioning properly Acquired immuno deficiencies caused by drugs (cancer chemotherapeutic agents, transplant patients) irradiation, HIV infection Immunodiagnostic Procedures Serologic procedures See Figure 16 -11