Micro
Taxonomic classification of bacterial species is best assisted through analysis of genome.
Past classification techniques based on biochemical capabilities of species, morphology of a species, or other phenotype-related data of a species has led to misclassification.
R plasmids are plasmids that include genes conferring resistance to antimicrobial agents
Neubauer chamber (or hemocytometer) is a specialized, thick glass microscope slide used to manually count the concentration of cells or microorganisms in a liquid sample
volume of the smallest RBC counting chamber is 0.002 nL at 0.1 mm depth
100 nL is the volume of WBC counting grid.
Nitrogen fixation: N2 to NH3
Denitrification: NO3– to N2
Ammonification: Organic N to NH4+
Nitrification: NH4+ to NO2– then NO2– to NO3–
Structural flexibility of enzyme and double-stranded DNA are responsible for the incorporation of mispaired bases, known as "wobble."
The effect of this flexibility (wobble) allows for mispaired bases to remain.
DNA inversion within bacterial populations can cause Generation of variation - create successful combinations that promote fitness
Transient bacteremia is responsible for migration of S. viridans from the oral cavity (during dental work) to damaged heart valves and causes bacterial endocarditis
In medicine, a clinical picture is the complete collection of signs, symptoms, test results, and causative factors a healthcare provider uses to diagnose and treat a disease
flagella:
amphitrichous arrangement has flagella on both polar ends of the organism.
A lophotrichous arrangement has multiple flagella grouped on one polar end of the organism.
A monotrichous arrangement has one flagellum on one polar end of the organism.
A peritrichous arrangement has flagella all around the organism.
Hosts:
Primary host (definitive host): harbors a virus or parasite that is matured and is ready for reproduction
A secondary host (intermediate host): harbors a virus or parasite for a short period of time, just until the developmental phases are completed.
A reservoir host is a type of host that harbors a virus or parasite; however, it poses no health threat to the host.
Drugs:
acyclovir: damages nucleic acid to prevent DNA synthesis
metronidiazole: treats bacterial vaginosis
symptoms of bacterial vaginosis: grey-white discharge and fishy oder
fluconazole: treats yeast infections
doxycyline: treats cervicitis caused by clamydia
cefriaxone: treats cervicitis caused by gonorrhea
vancomycin (Vancocin): has retained activity against Gram-positive organisms, including MRSA.
amantidaine: treats influenza A and also useful for parkisons
prevents uncoating of the virus that would normally release of viral RNA into host
azetronam = carbapenem with antipseudomonal activity
last resort for multi-drug resistant bacterial infections
gentamicin = aminoglycoside (binds with ribosome to stop protein synthesis)
azetronam and gentamicin are used together to treat psudomonal skin infections with biofilm
Reguation
An operon is a group of genes that participate in the same metabolic activity
Two tryptophan molecules bind to a repressor, which binds to the operator to prevent the transcription of the trp operon.
This blocks RNA polymerase, which is bound to the promotor region
Bacteria:
Gram Positive Bacteria:
have Pentaglycine cross-bridges are a feature only found in Gram-positive bacteria.
Teichoic acid carbohydrate chains are only found in Gram-positive bacteria.
They may help stabilize the peptidoglycan and help the bacteria bind to host cells.
Gram Negative Bacteria Identification:
periplasmic space of the Gram-negative cell is where a small amount of peptidoglycan can be found.
O antigen within the lipopolysaccharide of Gram-negative cell walls is used to identify different bacterial species and strains.
In Gram-negative bacteria, there is a direct cross-link between tetrapeptide chains extending off of NAM molecules.
Lipopolysaccharide molecules are found in Gram-negative bacteria.
They are composed of a lipid and a polysaccharide chain and act as an endotoxin—a toxin released when the bacterial cell wall becomes damaged.
The outer membrane is found in Gram-negative bacteria external to the peptidoglycan cell wall.
Porin channels are protein channels found in Gram-negative bacteria that allow passive diffusion of molecules into the periplasmic space between the outer membrane and inner membrane.
Bacteria:
Staphylococcus aureus is a catalase- and coagulase-positive species that produces golden-yellow colonies on media.
They are a Gram-positive coccus occurring in clusters.
Clostridioides difficile: associated with heavy and frequent use of antibiotics.
causes loss of appetite, nausea, and persistent mucoidal liquid stools
Streptococcus spp is a normal host flora commonly found in the stomach.
streptococcus pyogenes: causes strep throat
clostridium botulinum: used for botox
causes botulinum toxin
source of transmission is inadequately cooked canned veggies
Bacteroides spp, Enterobacter spp, and Klebsiella spp are all commonly found in the colon.
Francisella tularensis: the causative organism of tularemia, is a zoonotic disease that can infect people through contact with ticks or deer flies commonly on rabbits and other animals.
People can also be exposed to tularemia from contaminated water, aerosols, and bioterrorism.
Mycobacterium tuberculosis has an unusually thick (waxy) lipid cell wall made up of mycolic acids, causing waxy
It surrounds the entire bacterial cell and hides it from the immune system/ preventing the bacteria from being attacked.
This cell wall also makes infection very difficult to treat with antibiotics, which cannot get through the dense lipid matrix.
Streptococcus pneumoniae is encapsulated, making it hard to phagocytose
gram positive dicocci
causes pneumonia in the lungs and meningitis in the meninges
Treponema pallidum is classified as a spirochete.
causes syphillis
Other spirochetes include Borrelia and Leptospira
Escherichia coli is associated with ileal tissue in patients with Crohn's disease
shingella and entero-invasive e.coli have common characteristics
Bacillus anthracis
infect livestock, so transmission to humans can occur through skin inoculation of spores derived from livestock or contact with contaminated bone meal fertilizer, wools, or hides
Clostridium tetani
causative agent for tetanus, a serious disease characterized by muscle stiffness and spasms
enters the body through abrasions, punctures, and other instances of broken skin
pseudomonas aeruginosa and burkholderia have similar pathology
cause less severe infections to burns, wounds, and lungs
nesseria gonorrhoeae: gram negative diplococci
causes dysuria and urethral discharge
chlamydia trachomatis: obligate intracellular aerobe
conjunctivitis, urethritis, and pelvic inflammation diseases
Fungi
candida: orgal and esophageal thrush in immunocompromised patients
aspergillus fumigatus: septate hyphae that branches at 45 degree angle
causes invasive aspergillosis in immunocompromised people with chronic granulomatous disease
causes aspergillomas in immunocompromised people with pre-existing lung diseases
Microsporidia are obligate intracellular unicellular fungi that lack centrioles, peroxisomes, and mitochondria
Agaricus are a group of mushrooms; some are poisonous, and some are edible. Basidiomycota are fungi that have fruiting bodies called basidiocarps; they include mushrooms, rusts, and stinkhorns.
Cryptococcus fungi are found as yeast; they infect people with weak immune systems.
Glomeromycota: consists of species of fungus that live in a close highly evolved symbiotic association with the roots of plants.
zygomycota: rapid growing saprobe (feeds on dead) fungi
lives off of decaying organic material (bread, fruit, veggies)
example: rhizopus stolonifer
Blastomyces dermatitidis: causes Acute pulmonary blastomycosis
Transmission of blastomycosis is usually via inhalation.
symptoms: non-specific symptoms of fever, cough, night sweats, loss of appetite, fatigue, chest pain, myalgias, and arthralgias, leading to potential confusion with many other pathogens.
Infection risk factors include travel to endemic areas in the US, such as midwestern, south-central, and southeastern states, particularly the Ohio and Mississippi River valleys and the Great Lakes.
Cryptococcus neoformans: round organism on microscopy, typically seen as an encapsulated yeast by India ink preparation.
Infection is rare without immunodeficient risk factors such as HIV or immunosuppressive therapies.
histoplasma capsulatum: transmitted by bat droppings
endemic to mississippi river valleys, ohio, and missouri
Parasites
trichinella spiralis = nematode parasite
round worm in pigs, bears, horses and humans
found in undercooked meat (pork)
causes trichinosis
symptoms: nausea, vommitting, diarrhea and sweating within 1st 24 hours
pseudomonas aeruginosa
ciphyllobothrium latum: tapeworm in undercooked fish
taenia saginata: tapeworm in undercooked beef
Viruses
Herpes simplex virus 1 (HSV-1) most commonly causes oral cold cores, which present as grouped or singular vesicular lesions that become pustular and then ulcerate.
HSV-1 is a common cause of sporadic encephalitis, which can present as altered mental status, seizures, and vesicular lesions in exposed newborns.
latent herpes simplex 1 virus resides in the trigeminal nerve ganglion
enveloped double-stranded DNA viruses.
Herpes simplex virus 2 (HSV-2) causes genital herpes and is transmitted through sexual contact and perinatally. HSV-2 can be transmitted perinatally.
Herpes simplex virus 3 (varicella-zoster virus, VZV) causes chickenpox and shingles.
Primary varicella-zoster virus infection (varicella, chickenpox) is usually mild and manifests as crops of lesions appearing first on the trunk and spreading to face and extremities.
reactivation of varicella-zoster viral latent infection (herpes zoster, zoster). The lesions reflect the particular dermatome fed by the infected ganglion.
Varicella infection tends to be more severe in immunocompromised patients, such as patients receiving chemotherapy.
Varicella infection tends to be more severe in older patients rather than in young children,
Herpes simplex virus 4 (Epstein-Barr virus, EBV) causes mononucleosis, which presents as fever, hepatosplenomegaly, pharyngitis, and lymphadenopathy. EBV remains latent in B cells.
Rotavirus is a virus that causes gastroenteritis.
influenza is an enveloped negative-sense single-stranded RNA virus.
It causes disease by first merging with the membrane of a host cell, then releasing its contents into the host cell cytoplasm.
Host ribosomes then begin translating the viral RNA into proteins and enzymes that will form viral progeny that infect more host cells.
Human herpesvirus 6 (HHV-6) is the cause of body rash of roseola and high fever
ALL VIRUSES ARE DOUBLE SRANDED DNA (EXCEPT PARVOVIRUS)
Parvoviruses have single-stranded DNA as their nucleic acid structure
severe respiratory syncytial virus (RSV) infection
risk factors:
Exposure to cigarette smoking
Breastfeeding for at least 6 months
male sex
Orthomyxovirus is an enveloped single-stranded RNA virus.
contains the neuraminidase proteins targeted by Neuraminidase inhibitors (oseltamivir and zanamivir).
Neuraminidase inhibitors prevent the release of progeny influenza virus.
Diseases:
HIV:
acute phase: viral replication
spreads to the lymphoid tissue
after acute phase: depletion of CD4 cells, manifestation of opportunistic infections, development of neoplasms (tumors)
When untreated, the progression of HIV to AIDS is expedient.
With treatment, the progression of HIV to AIDS is highly variable with some patients experiencing moderate rates of progression to others experiencing prolonged progression.
Unprotected intercourse among males remains the highest route of transmission of HIV.
Intravenous drug use, receiving a blood transfusion, and unprotected vaginal intercourse represent lesser risk
Antiretroviral therapy is the treatment of HIV
hepatitis B: infects hepatocytes
chronic hepatitis. B: inflammation, scarring and cancer of the liver
severe hepatitis B: liver failure and death
Cholestasis (reduction of bile flow) is associated with hepatitis B infection
Most cases of hepatitis B are transmitted through the action of an asymptomatic carrier
H. influenzae is predominately isolated within the respiratory tract
syphillus
congenital syphillus: present at birth with deformities to the bone
Primary syphillus: painless ulcers and rash that dissolves
secondary syphillus: maculopapular rash on palms and soles
tertiary syphillus: present 15-20 years after initial exposure
includes neurological, cardiovascular, or granulomatous changes
scurvy: disease caused by deficiency in vitamin C
Leprosy
tuberculosis leprosy: skin and nerve involvement on face, trunk, and limbs with raised edges and dry, hairless centers
lepromatous leprosy: characterized by widespread skin lesions and systemic involvement that often leads to significant disability if left untreated.
large, more severe
Immune System
chemokines: molecules that influence movement of cells and are effectors of leukocyte migration
Lipid A is part of the lipopolysaccharide component of the Gram-negative cell wall.
It is released during systemic Gram-negative reactions and can cause production of cytokines and toxicity.
Th1 cells: play role in intracellular mediated immunity
Th2 cells: activated forms of helper T cells that produce multiple interleukins and promote destruction of parasites through eosinophils and mast cells
Th17 cells: crucial for defending mucosal barriers against extracellular bacteria and fungi.
complement system: uses C6, C7, C8, C9 to form membrane attack complexes
Antigens: activate B cells
Exogenous antigens enter the body from the outside (e.g., injection, vaccines, ingestion, inhalation) and include bacteria, viruses, and fungi.
alloantigen: only in some people (example: ABO blood type)
Endogenous antigens are within the body, including the body's own cells, such as blood-group antigens.
An autoantigen is a normal protein or protein complex that the immune system identifies as abnormal, triggering an immune response as in an autoimmune disease like rheumatic heart disease.
Neoantigens are newly formed antigens derived from tumor-specific mutations or viral proteins.
Immunoglobulins:
Structure:
Fv: Fragment variable region, which is responsible for antigen binding and determined by both heavy and light chains.
F(ab): arms of the Y
Fc: leg of the Y
protein A: can specifically bind to the Fc region, prevents phagocytosis
produced by staphylococcus aureus
IgE is not a common antibody, but it is mainly involved in the allergic response and anti-parasitic response to parasitic infections
IgM is always the first antibody to be produced in a humoral response because IgM can be expressed without isotype switching.
IgM circulates in the blood as a pentamer and is present on the surface of mature B cells.
Tests:
mannitol salt agar: selective differential media for staphylococcus species
staphylococcus aureus grows and produces color change
staphylococcus epidermis grows but doesn’t change color