Microbiology Lectures PDF

Epidemiology - the science that evaluates the occurrence, determinants, distribution, and control of health and disease in a defined human population. Epidemiologist - one who practices epidemiology Health - organism and all its parts functioning normally; a state of physical and mental well-being...

Epidemiology - the science that evaluates the occurrence, determinants, distribution, and control of health and disease in a defined human population. Epidemiologist - one who practices epidemiology Health - organism and all its parts functioning normally; a state of physical and mental well-being, not merely the absence of disease Disease - an impairment of the normal state of an organism or any of its components, which hinders the performance of vital functions Epidemiological Terminology 1. Sporadic Disease ​ occurs occasionally at irregular intervals in a human population. 2. Endemic Disease ​ maintains a relatively low-level frequency at a moderately regular interval ​ flue, dengue, malaria, sore eyes, tigdas, 3. Hyper Endemic ​ gradual increase in frequency above the endemic level, but not to the epidemic level. 4. Epidemic ​ sudden increase in frequency above endemic level. 5. Index Case ​ the first case in an epidemic (first person that have been infected) 6. Outbreak ​ epidemic-like increase in frequency, but in a very limited (focal) segment of the population. 7. Pandemic ​ long-term increase in frequency in a large (usually world-wide) population ​ COVID 19, monkeypox, HIV 8. Enzootic ​ moderate prevalence in animals 9. Epizootic ​ sudden outbreak of disease in animals 10. Zoonosis  ​ diseases of animals that can be transmitted to humans ​ Ex. rabies Frequency Rates 1. Morbidity Rate ​ number of new cases in a specific time per unit of population ​ newly infected 2. Prevalence Rate ​ number of individuals infected at any one time per unit of population ​ all infected are included 3. Mortality Rate ​ number of individuals infected at any one time per unit of population ​ all individuals that died Disease Surveillance 1. Signs ​ objective changes in the body (e.g. fever, rash, etc.) that can be directly observed. 2. Symptoms ​ subjective changes (e.g pain, appetite, etc.) experienced by the patient. 3. Syndrome ​ set of signs and symptoms that is characteristics of a disease Patterns of Disease 1. Incubation Period ​ period after pathogen enters the body ​ there are no signs and symptoms 2. Prodromal Period ​ onset of signs and symptoms, but not yet clear enough for diagnosis 3. Period of Illness ​ disease is most severe ​ there are sign and symptoms 4. Period of Decline (Convalescence) ​ sign and symptoms begin to disappear Epidemic Recognition 1. Common-source Epidemic ​ there's a sharp rise to a peak and then rapid but not as pronounced decline in the number of cases ​ results from exposure of all infected individuals to a single common, contaminated source, such as food or water. 2. Propagated Epidemic ​ gradual increase and gradual decline in the number of cases. ​ results from the introduction of one infected individual into a population, who then infect others; until an unusually large number of individuals within the population are infected. 3. Herd Immunity ​ resistance of a population to infection and to the spread of an infectious organism due to the immunity of a large percentage to the population ​ achieved by vaccination, quarantine, avoid contaminated water or food ​ limits the effective contact between infective and susceptible individuals 4. Antigenic Shift ​ changes in the antigenic character of a pathogen so that it is no longer recognized by the host's immune system (e.g. new flu strains) ​ antigenic drift - smaller changes ​ can lead to increase in disease frequency because the population of susceptible host increases Infectious Disease Cycle 1. Disease Cause ​ the clinical microbiology laboratory plays an important role in the isolation and identification of the pathogen 2. Disease source or Reservoir ​ Source - location from which organisms are immediately transmitted to the host ​ Reservoir - site or natural environmental location where organisms is normally found 3. Disease Carrier ​ Carrier - infected individual who is a potential source of a pathogen Types of Carrier a.​ Active Carrier - has overt clinical case of the disease  b.​ Convalescent Carrier - individual who has recovered but continues to harbor large numbers of the pathogen c.​ Healthy Carrier - individual who harbors pathogen but doesn't have ill d.​ Incubatory Carrier - has pathogen but is not yet ill. e.​ Casual Carrier (acute, transient carriers) - Carrier who carries pathogen for a short period of time (hours, days, weeks) f.​ Chronic Carrier - carriers who carries pathogen for a long period of time (months, years, or life) 4. Disease Transmission ✓1.Airborne Transmission - suspended in air; travels a meter or more ✓A. Droplet Nuclei - may come from sneezing, coughing, or vocalization ✓B. Dust Particles - microorganisms adhere readily to the dust ✓2. Contact Transmission - touching between host and the source ✓A. Direct - person to person; physical interaction between infected person an host ✓B. Indirect - involves an intermediate ✓3. Vehicle Transmission - inanimate materials or objects are involved in transmission ✓A. Common Vehicle Transmission - single vehicle serves to spread the pathogen to multiple hosts, but does not reproduce (ex. towel, needle, etc.) ✓B. Fomites - surgical instruments, bedding, eating utensils ✓C. Food and Water - common vehicle ✓4. Vector-borne Transmission - living transmitters, such as arthropods or vertebrates ✓A.External (mechanical) Transmission - passive carriage of the pathogen on the body of a vector with no growth of the pathogen during transmission (ex. flies, ticks, etc.) ✓B. Internal Transmission - carried within the vector ✓B1. Harborage Internal Transmission - (ex. dengue, malaria) the pathogen is inside the animal, but the animal doesn't have illness/disease. ✓B2. Biologic Internal Transmission - the pathogen is inside the animal and the animal is infected (ex. rabies) 5. Disease Susceptibility ✓depends in the defense mechanism of the host and the pathogenicity of the pathogen 6. Pathogen Escape ✓Active Escape - movement of the pathogen to the portal of exit (ex. many helminths) ✓Passive Escape - excretion in feces, urine, droplets, saliva, or desquamated cells Signs Vs. Symptoms Signs ✓a health issue that can be observed ✓can be identified by anyone ✓should be professionally diagnosed by a doctor, who have training and experience to identify their possible cause ✓ex. Skin rash, rasping on coughs, red rings around eyes, etc. Vital Sign ✓most important medical sign ✓ex. Heart rate, breathing rate (oximeter) blood pressure, and temperature (thermometer) Symptoms ✓subjective experience of potential health issue, which cannot be observed by a doctor ✓the doctor cannot see, hear, feel, or smell any of these issues ✓can only be described by patient ✓ex. stomach cramps, throbbing headache, fatigue Types of Signs 1. Diagnostic ✓one that helps a doctor to diagnose a medical problem. ✓ex. secretion, rashes, etc. 2. Pathognomonic ✓same as diagnostic but with much greater certainty. ✓exact ✓ex. red rashes = allergy 3. Prognostic ✓predicted health outcome for a patient. ✓used to predict what will happen to patient. 4. Anamnestic ✓indicator of a past medical condition of a patient. Types of Symptoms 1. Chronic Symptoms ✓tend to recur over a long period of time ✓ex. migraine, fever 2. Relapsing Symptoms ✓symptoms that have occured previously, were considered to be resolved, but have returned. 3. Remitting Symptoms ✓symptoms that improve or disappear Common Infectious Diseases 1. Worm Infection ✓hookworm infection, tapeworm infection, ascaris infection, and fluke infection ✓hookworm - found in blood vessel ✓tapeworm and ascaris - found in intestine ✓fluke - found in liver ✓Sporadic - minsanan lang ✓can turn into common source endemic ✓vehicular transmission 2. Diarrheal Diseases ✓Salmonellosis (from poultry such as chicken, eggs, etc.), Shigellosis (seafoods such as talaba, hipon), Typhoid fever (food in contact with flies), Botulism (from can goods), Cholera (from water), Viral and Bacterial Gastroenteritis (from spoiled food) ✓Sporadic ✓can turn into common source endemic ✓vehicular transmission 3. Schistosomiasis ✓caused by Schistosoma sp (from snail) ✓Sporadic ✓can turn into common source endemic ✓vehicular transmission 4. Spongiform Encephalopathy ✓from prions ✓foot and mouth disease, mad cow disease ✓Sporadic ✓can turn into common source endemic ✓vehicular transmission ✓Zoonotic - comes from animals 5. Hepatitis Infection ✓Hepatitis A,B,C,D, and E virus ✓Hepa A - from contaminated food ✓Hepa B - from blood (contaminated syringe) ✓Hepa C - from mother to infant ✓Hepa D - you must have Hepa B before Hepa D; there's a presence of cirrhosis (pagsusugat ng atay) ✓Hepa E - from water; like in Cholera ✓Sporadic ✓can turn into common source endemic ✓vehicular transmission 6. Tetanus ✓Clostridium tetani ✓sporadic ✓vehicular transmission ✓symptoms: paralysis, lack of jaws 7. Gas Gangrene ✓Clostridium perfringens ✓sporadic ✓vehicular transmission ✓can cause decomposition of the flesh 8. Leprosy (Ketong) ✓Mycobacterium leprae ✓parang trangkaso tapos magkakaroon ka ng butlig (boils) ✓sporadic ✓common source endemic/propagated epidemic ✓vehicular transmission/contact transmission 9. Poliomyelitis ✓polio virus ✓parang trangkaso tapos liliit yung leg muscles (kinakain sya ng virus) ✓sporadic ✓common source endemic/propagated epidemic ✓vehicular transmission/airborne transmission 10. AIDS ✓caused by HIV ✓sporadic ✓propagated epidemic ✓sexual contact transmission ✓Zoonotic (because aids comes from monkey) 11. STD's (Sexual Transmitted Diseases) ✓Gonorrhea (tulo), Syphilis (nabubulok yung sexual organ), Vaginal infections (itching or secretion) ✓sporadic ✓can turn into propagated epidemic ✓sexual contact transmission 12. Chickenpox ✓Varicella virus ✓endemic ✓can turn into propagated epidemic ✓airborne transmission ✓symptoms - butlig na may tubig 13. Influenza ✓caused by flu virus ✓symptoms - may lagnat, masakit katawan, sipon, headache ✓endemic ✓can turn into propagated epidemic ✓airborne transmission 14. Measles (Tigdas) ✓caused by Rubeola virus ✓symptoms - rashes na sobrang kati ✓endemic ✓can turn into propagated epidemic ✓airborne transmission 15. Mumps (Beke) ✓caused by Rubula virus ✓swelling of salivary glands ✓endemic ✓can turn into propagated epidemic ✓airborne transmission 16. Diphtheria ✓Corynebacterium diphtheriae ✓symptoms - gray membrane in the throat ✓endemic ✓can turn into propagated epidemic ✓airborne transmission 17. Pertussis ✓caused by Bordetella pertussis ✓also known as "wheezing cough" ✓endemic ✓can turn into propagated epidemic ✓airborne transmission 18. Colds (Sipon) ✓caused by Rhinovirus ✓endemic ✓can turn into common source epidemic/propagated epidemic ✓airborne/ vehicular/ contact transmission 19. Pneumonia ✓can be caused by bacteria, virus, or fungi ✓symptoms - nagkakaroon ng tubig sa baga ✓endemic ✓can turn into common source epidemic/propagated epidemic ✓airborne/ vehicular/ contact transmission 20. Tuberculosis ✓Mycobacterium tuberculosis ✓symptoms - blood in the phlegm, nocturnal fever ✓endemic ✓can turn into common source epidemic/propagated epidemic ✓airborne/ vehicular/ contact transmission 21. Leptospirosis ✓Leptospira interrogans ✓comes from urine of rodents ✓symptoms - liver or kidney failure ✓endemic ✓zoonotic ✓contact transmission 22. Rabies ✓rabies virus ✓comes from bite or scratch of an animal ✓symptoms - aerophobia or hydrophobia; psychosis (nababaliw) ✓endemic ✓zoonotic ✓contact transmission 23. Sore Eyes/ Conjunctivitis ✓caused by virus ✓endemic ✓can turn into propagated epidemic ✓contact transmission 24. Skin Infections ✓Cellulitis (intense itching), Impetigo (crusting of skin), Erysipelas (galis-aso), Acne (pimple, white heads, black heads), Furuncles (pigsa), Carbuncles (pigsa na marami) ✓same sa sore eyes 25. Mosquito Borne Infections ✓caused by mosquitoes ✓Dengue fever (hemoragic; magkakaroon ng pag durugo), Zika fever (nagkakaroon ng microcephali; lumiliit ang ulo), Yellow fever (nagkakaroon ng jaundice), Filariasis (elephantiasis, pamamga ng isang body part), Malaria (convulsion) ✓endemic ✓can turn into outbreak or epidemic ✓vector transmission 26. Flea and Tick-Borne Infections ✓Plague, Tick bite, and Flea Bite Fevers ✓same sa mosquito 27. Ebola ✓Ebola virus ✓symptoms - nagkakaroon ng intense bleeding ✓epidemic to pandemic ✓vector/ contact transmission ✓zoonotic 28. AH1N1 (Swine Flu) and Covid 19 ✓corona virus ✓symptoms - respiratory infections then magiging pneumonia ✓common source epidemic / propagated epidemic to pandemic ✓all kinds of transmission ✓zoonotic 29. Bird flu ✓bird flu virus ✓symptoms - respiratory infections then magiging pneumonia ✓common source epidemic / propagated epidemic to pandemic ✓all kinds of transmission ✓zoonotic - sa bird 30. Anthrax ✓bacillus anthracis ✓can be respiratory infections or skin infections ✓common source epidemic / propagated epidemic to pandemic ✓all kinds of transmission ✓zoonotic - nanggaling ang unang anthrax sa infected na sheep 31. Meningococcemia ✓Meningococcus sp ✓symptoms - parang flue then eventually magkakaroon ng damage sa brain ✓propagated epidemic to pandemic ✓airborne transmission 32. SARS (Severe Acute Respiratory Syndrome) Cov, and MERS (Middle Eastern Respiratory Syndrome) CoV ✓propagted to epidemic to pandemic ✓airborne transmission Communicable VS. Non Communicable Diseases 1. Duration ✓Com - Acute (mabilisan; appear quickly) ✓NonCom - Chronic (longer period) 2. Seasonality ✓Com - Yes, seasonal ✓NonCom - Not seasonal 3. Cause ✓Com - pathogenic microbes ✓NonCom - nutrition deficiency, hormonal deficiency, abnormal cells 4. Inheritance ✓Com - can't be inherited ✓NonCom - can be inherited 5. Spread ✓Com - air, direct or indirect, contaminated things, or vector ✓NonCom - do not spread (diabetes, cancer, mental disorder) 6. Sign and Symptoms ✓Com - can be observed quickly ✓NonCom - can't be observed quickly 7. Observed ✓Com - less severe; short term threat ✓NonCom - more severe, long term threat 8. Diagnosis ✓Com - acurate diagnosis ✓NonCom - acurate diagnosis are not available 9. Treatment ✓Com - short treatment ✓NonCom - long treatment 10. Curability ✓Com - can be cured except for AIDS/HIV ✓NonCom - don't have specific cure 11. Prevention ✓Com - prevent by conventional methods (paghuhugas ng kamay, pag lilinis, pag aayos ng pagkain) ✓NonCom - need special operations Normal Microbiota Types of Microbiota A. Endosymbiosis - inside the body B. Ectosymbiosis - outside the body Parts of the Body and Microbiota 1. Skin ✓skin bacteria are found on superficial cells, dead cells, or closely associated with oil and sweat glands. ✓generally is a hostile environment ✓skin surface undergoes periodic drying, slightly acidic, salty, has antibacterial substance (lysozyme). A. Skin Microbes 1. Staphylococcus epidermis and Corynebacterium (dry areas and sweat glands) 2. Gram-negative bacteria (moist areas) 3. Yeast (scalp) 4. Dermatophytic fungi (e.g., those causing ringworm and athletes foot) 5. Propionibacterium acnes is prevalent in the skin glands and is associated with acne vulgaris 2. Nose A. Nose Microbes 1. Staphylococcus epidermidis 3. Nasopharynx Nasopharynx Microbes ✓contains non encapsulated strains of some of the same species that9r may cause clinical infection (e.g., streptococci and Neisseria); other species also are found. 4. Oropharynx (Throat) Oropharynx Microbes ✓staphylococci and streptococci 5. Respiratory Tract ✓no normal microbiota due to the enzyme lysozyme in mucus and the phagocytic action of alveolar macrophages ✓Tuberculosis, Pneumonia 6. Mouth ✓normal microbiota includes streptococci, lactobacilli, and actinomycetes; some contribute to the formation of dental plaque, dental caries, gingivitis, and periodontal disease. ✓dental plaque (naninilaw) ✓dental caries (cavities) ✓gingivitis (swelling of gums) ✓periodontal disease (nabubulok ang bibg) 7. Eye ✓Eyes Microbes - aerobic commensals are found on the conjunctiva. ✓sore eyes 8. Ears ✓resemblance the microbiota of the skin; has fungi ✓otitis (luga) 9. Stomach ✓most microbes are killed due to acidity ✓no. of microbes increased after eating, but decreases quickly ✓ulcer (mangyayari pag di masyadong kumakain) 10. Small Intestine ✓duodenum microbes - gram positive rods and cocci ✓few microbes due to acidity, bile, and pancreatic secretions ✓Jejunum Microbes - enterococcus fecalis, diphtheroids, lactobacilli, and Candida albicans ✓ileum microbes - microbiota resembles that of a colon (gram negative rods and enterobacteriaceae) 11. Large intestine/ colon ✓colon microbes - largest microbial population of the body ✓microbes are excreted by peristalsis, segmentation, desquamation, and movement of mucus, but are replaced rapidly because of high reproductive rate. ✓microbial community is self- regulating and can be disturbed by stress, attitude, starvation, diet, parasite infection, diarrhea, and use of antibiotics or probiotics. ✓peristalsis - paggalaw ng tyan ✓segmentation - putol na paglabas ng poop ✓desquamation - gagawin compact yung poop ✓movement of mucus - pampadulas ng poop 12. Genitourinary tract ✓urinary tract - microbes can cause (UTI) ✓urinary tract - Kidneys, ureter, and bladder are normally free of microorganisms; though in both males and females a few microorganisms are found in distal portions of the urethra. ✓genital tract - lactobacillus acidophilus ✓genital tract - Female genital tract hosts a complex microbiota in a state of flux due to menstrual cycle; Lactobacillus acidophilus predominates; it forms lactic acid and thereby maintains an acidic pH in the vagina and cervix. Relationship of Microbiota to the Host ✓mutual (2 benefit) ✓commensal (only 1 benefit) ✓Normal microbiota compete with pathogenic microbes and release inhibitory secretions ✓Under some conditions, normal microbiota can become pathogenic, such microorganisms are referred to as opportunistic Compromised host ✓host that Is seriously debilitated and has lowered resistance; Is often targets of opportunistic microorganisms Parasitology and Infectious Disease Parasitism ✓relationship of host and parasite Host and Parasite Interaction Ectoparasite ✓lives on the surface of the host Endoparasite ✓lives within the host Final Host ✓host on (or in) which the parasite elther gains sexual maturity or reproduces Intermediate Host ✓host that serves as a temporary but essential environment for parasite development Transfer Host ✓host that Is not necessary for development but that serves as a vehicle for reaching the final host Reservoir Host ✓organism that is infected with parasite that can also infect humans Infection, Pathogenicity, and Virulence Infectious Disease ✓change from a state of health because of an infection by a parasitic organism Pathogenicity ✓ability of a parasitic organism to cause a disease Virulence ✓the degree or intensity of pathogenicity of an organism Pathogen ✓parasitic organism that produces an infectious disease Primary / Frank Pathogen ✓organism that causes disease in the host by direct interactions with the host Opportunistic Pathogen ✓organism that is normally free-living or part of the host's normal microbiota, but which adopts a pathogenic role under certain circumstances Invasiveness ✓the ability of the organism to spread to adjacent tissues Infectivity ✓the ability of the organism to establish a focal point of infection Pathogenic Potential / Toxigenicity ✓degree to which the pathogen can cause morbid symptoms Pathogenesis of Viral Diseases To cause a disease, a virus must: 1. Enter a host 2. Contact and enter susceptible cells 3. Replicate within the cells 4. Spread to adjacent cells 5. Cause cellular injury 6. Activate a host immune response 7. Be either cleared from the body of the host, establish a persistent infection, or kill the host 8. Be shed back into the environment Pathogenesis of Bacterial Diseases To cause a disease, a bacteria must: 1. Maintain a reservoir 2. Initially be transported to the host 3. Adhere to, colonize, or invade the host 4. Multiply or complete its life cycle on or in the host 5. Initiate mechanisms and evade host defenses 6. Possess ability to damage the host 7. Leave the host and return to the reservoir or enter new host Viremia ✓presence of virus in the blood Bacteraemia ✓Presence of bacteria in the bloodstream Septicaemia ✓Release of toxins by bactería into blond stream Tropism ✓Specificity of a virus to a type of cell, tissue, or organ Patterns of Viral Infections Lytic ✓cell virus multiplies, kills host immediately, and releases new virions Persistent ✓virus lives in host cell and releases small number of viruses over a long time; little damage to host Latent ✓virus resides in host cell but produces no virions; at later time, virus is activated, and lytic infection occurs Transformative ✓virus transformed host cell into cancer