Micro study guide

The upper respiratory tract

Mouth, nose, nasal cavity, sinuses, pharynx, epiglottis, larynx, Eustachian tubes

The lower respiratory tract

Trachea, bronchi, bronchioles, alveoli

Respiratory defenses

-Mucus, nose hairs, ciliated epithelium of trachea and bronchi which move mucus out, sneezing, swallowing, coughing
-Complement proteins in the lungs to poke holes in pathogens, alveolar macrophages, IgA, increased levels of cytokines and antimicrobial pe

Normal Biota of Respiratory Tract

-Respiratory tract has a lot of commensal organisms due to constant contact with environment
-The normal biota includes Streptococcus progenies, Neisseria meningitidis, Staphylococcus aureus, streptococcus pneumonia, and Haemophilus influenza all of which

The Common Cold

-67 million colds per year in U.S. causing $40 billion in medical costs and 22 million missed days of work
-Sneezing, scratchy throat, runny nose
-Not usually accompanied by a fever
-can predispose patients to secondary infections
-Caused by 200


-Inflam of sinuses
-Caused by allergy or infection
-patients with cold often develop sinusitis
-Sinus pain, nasal congestion, pressure, headache, or toothache, discharge is opaque yellow or green
-If caused by bacteria, it will usually be recurrent due to

Whooping cough

-Caused by Bortella pertussis
-Makes pertussis toxin and other that damage the ciliated epithelium cells in the upper respiratory tract, so it impairs the ability to get mucus up and out of the respiratory tract.
-Causes massive coughing fits because we a

Bordetella pertussis

-Gram negative rod
-Strictly aerobic and fastidious
-Has a filamentous hemagglutin for attachment and stops cilia from moving
-Pertussis toxin causes massive mucus production
-Tracheal cytotoxin causes direct destruction of ciliated cells
-Vaccine does no


-Pneumonia is an anatomical diagnosis, but can be caused by many different things
-Fluid fills the alveoli
-Pathogens must be able to avoid or survive phagocytosis
-Viral is usually milder than bacterial
-Fungi can cause but is usually only in the immunoc

Streptococcus pneumonia

-Gram positive coccus
-Can be asymptomatic part of normal biota but can get in the deep parts of the lungs and cause pneumonia
-Polysaccharide capsule prevents phagocytosis and blocks complement
-There is a vaccine that stimulates antibodies against the c

Mycoplasma pneumoniae

-Causes walking pneumonia
-Lacks a cell wall
-transmitted by aerosol droplets

Legionella pneumophilia

-Gram negative
-Discovered after legion convention from a cooling tower
-lives in freshwater
-Opportunistic disease
-Pathogen that normally targets amoebas, but mistakes our macrophages as amoebas

Histoplasma capsulatum

-Affects both lungs
-Dimorphic Fungus
-Targets immunocompromised
-Found in chicken workers and spelunkers
-Common in Ohio and Mississippi River valleys

Pneumocystis jiroveci

-Another fungus
-Very common in AIDS patients and chemotherapy patients

Health-care associated pneumonia

-Associated with mechanical ventilation
-30-50% mortality rate
-Polymicrobial in origin
-E. coli can get in from GI tract through aspiration
-300,000 cases per year in US

GI tract

-Eight main segments include mouth, pharynx, esophagus, stomach, small intestine, large intestine, rectum, anus
-Accessory organs are salivary glands, liver, gallbladder, pancreas

GI Defenses

-Covered in thick mucus membrane to protect us from pathogens and digestive enzymes
-Peristalsis keeps microbes moving
-Secretory IgA
-Saliva contains lysozyme and lactoferrin
-Stomach has low pH
-Bile is antimicrobial
-GALT is gut associated lymphoid tis

Normal Biota

-Oral cavity has over 600 species of bacteria
-Esophagus and stomach has 200 species
-Large intestine has 10e11 of microbes per gram of contents
-Accessory organs are free of resident microbiota
-Normal biota can help digest food and outcompete with bad p

Gastritis and Gastric Ulcers

-Gastritis is a sharp burning pain in abdomen
-Gastric or peptic ulcers are lesions in the mucosa of stomach or SI
-Caused by Helicobacter pylori
-Treated with tetracycline + metronidazole

Acute Vomiting and Diarrhea

-Pain, nausea, diarrhea, vomiting
-Caused by exotoxin from pathogen or directly by pathogen
-Short duration
-Staphylococcus aureus produces exotoxin causing acute, it thrives because of high salt tolerance, likes to live in creamy foods, enterotoxin is he

Chronic Diarrhea

-Lasts longer than 14 days
-Can have infectious or noninfectious cause (IBS, AIDS)
-Enteroaggregative E. coli causes it a lot in children, has virulence factors that allow it to adhere to cells and aggregate, stimulates a lot of mucus

Enterobius vermicularis

-Life cycle A
-Pronounced anal itching
-Common in children

Trichuris trichuria

-Life cycle A
-Humans are sole host, so transferred person to person
-Can cause rectal prolapse, dysentery

Diphyllobothrium latum

-Life cycle C
-humans are main host but intermediate host is fish
-Sushi :(
-Common in the Great Lakes

Ascaris lumbricoides

-Giant intestinal worm
-Life cycle A, but once it gets in it becomes complex
-Larva penetrates intestinal wall, works it's way up the respiratory tract and we swallow it back into intestines

Taenia solium

-Life cycle C
-Found in pork
-Causes cysticercosis when we eat eggs instead of cysts and tapeworm gets into CNS and places it should not be

Opsithorcis sinensis and Clonorchis sinensis

-Chinese liver flukes
-Life cycle D
-larvae hatch and crawl into bile duct, shed eggs into intestinal tract
-Can block bile duct
-Causes enlarged liver and distention

Fasicola hepatica

-Liver fluke
-Common in cattle
-Get it from eating watercress
-Life cycle D


-Life cycle C
-Eating pork
-Gets into muscle tissue, lungs, brain, heart and can cause serious problems


-Primary habitat in the natural world for a pathogen
-Can be human, animal, water, soil, plant


-Source is actually where you get infected from


Reservoir without symptoms or signs


-Transmits disease
-Biological vector is infected
-Mechanical just transports


-Where the disease is for animals, but can get humans too


Current number of cases in a population


Number of new cases in a certain amount of time

Mortality rate

How many people die from a disease

Point source epidemic

-disease is spread from a single source in a short period of time
-Ex/contamination of cheese at a pizza place

Common source epidemic

-Disease spreads from one constant source
-Legionella causing pneumonia

Propagated epidemic

Person to person


Is a disease that is always present to a certain extent

Sporadic disease

Pops up every once in a while
Haunt virus is present when there is heavy rain


The degree to which the test does not test positively for people who do not have the pathogen
Avoids false positives


Ability to test for very small amounts of a pathogen
Avoids false negative


-Looking to see if the patient has antibodies to a pathogen
-Cons are it takes a while to make antibodies, so if someone has only been sick for two days these tests won't work, and antibodies can stick around even after recovery
-If it is in the right tim

Western blot test

-blood test to detect various antibodies in bloodstream such as HIV antibodies; considered more precise than ELISA
-Takes patient sample containing proteins and run it across gel, transfer to paper and add specific antibodies. If the antibodies stick we w


-method of tagging antibodies with a luminating dye to detect antigen-antibody complexes
-dye on antibodies allows us to see pathogen
-In direct, the antibody is tagged and known and added to identify unknown antigen
-In indirect a known antigen is added


Measures the concentration of antibodies in a sample
Used to check effectiveness of vaccines


Uses radioactive tag
-Not used much
-Radioactive antigen and antibody would be added and if they attach it sinks to the bottom
-Check precipitate for radioactivity to indicate presence of antibodies


-Direct antigen testing is similar to direct fluorescence because we are using known antibodies to identify antigens, reactions can be see with the naked eye
-dipstick tests for the presence of antigen specific antibody with a paper containing antigens an

ELISA test

Basically we make an antibody sandwich
-If bacteria is present, it sticks to the antibody
-Second antibody contains enzyme that will turn sample yellow
-Screens for HIV and helicobacter

In vivo testing

-Antigens are introduced into person
-If inflammation occurs it indicates presence of antibodies
-TB test

Genetic Testing

-Looks for DNA or RNA from pathogen
-Very specific
-Very sensitive
-Con is we have to know the sequence of the pathogen before testing
-Hybridization is taking a piece of DNA/RNA and adding a fluorescent tag to it allowing us to find the complement strand


Using a small chip that contains the gene sequences for thousands of pathogens
great because tests for a lot fo stuff at once

Next generation sequencing

Takes a sample and sequences every piece of DNA present
A lot of junk
Less expensive
Be used on 16s so bacteria
Viruses can be sequenced by examining all DNA or RNA

Urinary tract

-Removes substance from the blood
-Regulates certain body processes
-Forms urine and transports it out of the body
-Kidneys, ureters, bladder, urethra

Defenses of urinary tract

-flushing action of urine
-Acidic pH of urine
Lysozyme and lactoferrin
-Secretory IgA

Defenses of female reproductive tract

-Vary over the lifetime of a woman
-Protective covering of secreted mucus
-Low pH of vagina beginning in adolescence
-Biota of women in childbearing years prevents establishment and invasion of microbes

Normal biota

-Female urethra is shorter which acts as pipeline for microbes from anus
-Males who are circumscised have different normal biota, and are less susceptible to infection
-Urethra has same residents as penis in males, includes lactobacillus and streptococcus


-Infection of the bladder
-pain in pubic area, frequent urge to urinate, pain during urination, cloudy or bloody urine


-Infection of the kidneys
-Symptoms of cystitis but also back pain and high fever
-can result in permanent damage to kidney
-comes from blood, not from urinary tract


Infection of urethra

UTIs causative agents

-Most UTIs are caused my E. coli (80%). their adhesion allows for attachment to urinary epithelial. Is transmitted from GI tract
-Staph and enterococcus can cause UTIs but are more opportunistic and common with catheters
-Leptospira interrogans has adhesi


-Inflam of vagina, vaginal itching, burning and discharge
-Candida albicans is a dimorphic fungus that is opportunistic when the normal biota gets out of whack
-Trichomonas vaginalis is a parasite that is normally asymptomatic in men but causes a white to


-Inflam of prostate gland
-Acute is almost always caused by bacteria, normally fro GI tract
-chronic is caused by bacteria but is unresponsive to antibiotics due to biofilm


-caused by Neisseria gonorrhoeae which is a gram negative diplococcus that uses timbre to attach to epithelial cells
-Usually asymptomatic in men
-Causes salpingitis in females, along with bloody discharge and painful urination. also can cause infertility


-HSV-1 causes oral herpes
-HSV-2 causes genital herpes
-Causes single or multiple vesicles that are painful to the touch
-Can cause encephalitis
-recurrent episodes due to latency
-Goes dormant in lumbosacral nerves
-Can be transmitted to baby during birt

Strep B

-Colonizes 10-40% of women
-Beta hemolytic and group B
-Can cause life threatening infections in infants like meningitis or pneumonia if passed during birth


-Inflam of meninges
-Caused by a lot of different things
-Photophobia, headache, stiff neck, fever, increased WBC in CSF
-Diagnosed with gram satins or culture of CSF
_treated with broad spectrum antibiotics

Neisseria meningitidis

-Gram negative diplococci
-Associated with epidemics of meningitis
-responsible for 25% of cases
-Polysaccharide capsule protects against phagocytosis and helps it get through blood brain barrier
-Meningococcemia is when it gets into the blood stream, the

Streptococcus agalactiae

-Group B
-beta hemolytic
-Colonizes 10-30% of female genital tracts
-Most frequent cause of neonatal meningitis
-treated with penicillin

Viral meningitis

-Also called aseptic meningitis because it is not culturable
-Majority of cases are in children
-90% are caused by enteroviruses
-HIV and HSV can cause it
-Milder than bacterial or fungal


-inflammation of the brain
-Naegleria fowler is a small amoeba that is in warm bodies of freshwater and it forces its way up the nasal passages through the olfactory nerve to the brain and causes PAM. Rapid massive destruction of the brain tissues. Cases

Encephalitis from arboviruses

-Transmitted from arthropod vectors
-no satisfactory treatments
-West nile encephalitis emerged in US in 1999 and CDC reported in 2008 that 1% of population has infection. Zoonosis
-La crosse, Jamestown canyon and powassan viruses

Encephalitis from Toxoplasma gondii

-Flagellated parasite
-Primary reservoir is cats
-More likely to seek thrills
-Causes still birth, or severe deformities in fetus if pregnant

African Sleeping Sickness

-Trypanosoma brucei
-Transmitted by tsetse fly
-Causes extreme sleep disturbances
-Eventually causes coma and death