W1 Flashcards
The most abundant organisms on Earth comprise of:
- Acellular organisms (viruses)
- Unicellular organisms without a nucleus (prokaryotes/bacteria)
- Unicellular organisms with a nucleus (eukaryotes/fungi and some parasites)
- Multicellular organisms all have nuclei (eukaryotes/parasites)
Viruses: alive or dead?
dead. they are an obligate parasite, they use our hosts to survive
Prokaryote Morphology
Coccus (pl. cocci)
- Spherical shape
Bacillus (pl. bacilli)
- Rod shape
Sphirochete (pl. spirocheta/ spirochetes [eng])
- Cork-screw shape
Vibrio (pl. vibriae)
- Comma shape
Difference between
a. Coccus
b. Diplococci
c. Streptococci
d. Staphylococci
Coccus: single ball shape
Diplococci: two ball shapes
Streptococci: balls in a line
Staphylococci: like a bundle of grapes
staphyl: means grapes
Escherichia coli
- morphology
aka e.coli, lives in your gut
common cause of UTI’s in many people
bacilli shaped
Syphilis Bacteria’s name
- type
Treponema Pallidum
spirochete/cork screw
Helicobacter Pylori
common cause of gastritis, peptic ulcers
Eukaryote
- some examples
Single or multi-cell organisms
- With a nucleus, mitochondria, and membrane-bound organelles
Fungi, Plants, Parasites, Animals, Us
Plasmodium Falciparum
ONe agent of malaria
Candida Albicans is what type of eukaryote?
YeasT
Which eukaryote makes up mould?
commonly it is: Aspergillus Fumigatus
black you’d see in shower tubs or kitchen
What is the smallest microbe organism
VIRUSES are the smallest
Reproduction in Prokaryotes
Binary fission
- No mitosis
- asexual
Clonal expansion
if they mutate with resistance, all the clones following that will have that resistance
Reproduction of Viruses
Fission
- Asexual
- Use host apparatus to reproduce
Clonal expansion
more infectious than variant forming
Reproduction in Eukaryotes
Binary fission
- Yeasts and some protozoa
- Clonal expansion
Sexual reproduction
- Not clonal expansion
- Mitosis occurs
Reproduction in Bacteria
Bacterial conjugation
Occurs commonly, through the use of pili
There is no production of “daughter cells” per se
Transfer of genetic material
Eg. Plasmids
Eg. Transmission of antimicrobial resistance
Plasmids live outside of the nucleus just floating in the cell, they contain antibiotic resistance genes that are passed through the pilus into another bacteria.
Nomenclature of Microbes
Genus is umbrella, the under it there are types of Species
i.e.
Staphylococcus = Genus
Aureus and epidermis = different species
Slamonella, Bacillus, Streptococcus, Plasmodium, Candida = different GENUS
Key divisions of Bacteriology
GRAM STAIN
there’s also
- pathogens vs non pathogens vs opportunistic pathogens
- aerobes vs anaerobes vs facultative anaerobes
Gram’s stain
Concept is:
What colour are the individual bacteria under a microscope?
The use of 2 dyes:
- Crystal violet (BLUE – PURPLE)
- Iodine fixator
- Acid alcohol or acetone decolorization - Safranin (RED – PINK)
Cell wall of bacteria
- how is it created
- What is it made up of
called Peptidoglycan
created using penicillin binding protein
Made up of: NAG, NAM, and oligopeptides
Named penicillin binding protein because this is the target of penicillin used to create a whole in the bacteria and weaken the wall
Gram + means
It binds to the blue/purple dye because it has a THICK cell wall, and you can’t decolourize it (the step before putting the red dye)
it has a SINGLE cell membrane
the cell wall is thick and above the cell membrane
Gram - means
- What are the layers of the wall in order
That the cell wall is thin so the blue dye got removed with the de-colouring agent and allowed for the red dye to bind
it has a DOUBLE cell membrane, space between = periplasm
layers from outer to inner:
a. outer membrane
b. cell wall with peptidoglycans
c. periplasms
d. inner membrane
Most POSITIVE gram (blue staining) have masculine sounding names EXCEPT for the following three
Listeria spp
Nocardia spp
Gemella spp
typical gram negative bacteria:
Staphylococcus spp
mycobacterium spp
streptomyces spp
Most gram NEG (pink staining) have feminine names EXCEPT for those with the following suffix
- monas
- PHilus
- bacter
these all sound masculine but they are
Negative/PINK/FEMININE
examples of typical gram negative names (most end with an -a or other vowel)
Pasteurella spp,
Moraxella spp,
Escherichia
Providencia
What are examples of Bacteria without cell walls
- What colour do they stain?
They don’t stain because they don’t have a wall for the stain to attach too*
Examples:
Mycoplasma spp
- Mycoplasma pneumoniae
- Mycoplasma hominis
Chlamydia spp
- Chlamydia trachomatis
Chlamydophila spp
- Chlamydophila pneumonia
- Chlamydophila psittaci
Bacterial physical defence barriers and adherence
Capsule
- fatty coat
eg. Streptococcus pneumoniae
Biofilms
- where they live, hang out in possies, barf on each other, forming a sticky matrix that antiboitics don’t penetrate well
i. e. catheters, deep central lines. The plastic ends form a biofilm that can cause an infection - Walking on river and slipping on the gooey rock = biofilms
eg. Staphylococcus epidermidis
Fimbriae
- little hairs that make it stick on to a surface- nOT a pilus, a pilus is longer
eg. Escherichia coli
Lipopolysaccharide
another bacterial virulence factors
Lipopolysaccharide: Outer cell wall of Gram negative bacteria Endotoxin Leads to immune response - Cytokine release - Fever - Shock
Toxins
Bacterial virulence factor
They can work systemically or locally (G, CNS, resp)
Toxin induced systemic effects
Superantigens
- Activate about 10% of lymphocyte pool
- Directly bind MHCII presenting cells and T cells
Toxic shock syndrome
TSST-1
- S. aureus
- S. pyogenes
Toxins that induce GI distress
Shigatoxin
- Shigella dysenteriae
- E. coli O157:H7
Shiga-like (vero)toxin
- E. coli O157:H7
Toxins A and B
- C. difficile
Cholera toxin
- V. cholerae
Food poisoning:
- Staphylococcal enterotoxin
S. aureus
- CPE enterotoxin
Clostridium perfringens
Neurotoxin Examples
Botulinum toxin (Botox) -Paralysis “Sausage toxin” C. botulinum Tetanospasmin Tetanus C. tetani Shigatoxin seizures
Neurotoxin Examples
Botulinum toxin (Botox)
-Paralysis
- “Sausage toxin”
C. botulinum
Tetanospasmin
- Tetanus
C. tetani
Shigatoxin
- seizures
Toxins that induce respiratory distress
Diphtheria toxin
- Upper respiratory tract illness
- Respiratory obstruction
C. diphtheriae
Pertussis toxin
- Insulin-induced hypoglycemia
- Whooping cough(?)
B. pertussis
Botulinum toxin
- Through paralytic effect
Necrotizing pneumonia
- Panton Valentine Leukocidin
- S. aureus
Toxins that induce Tissue changes
Tissue changes
Alphatoxin
- Gas gangrene
- C. perfrigens
Anthrax toxin
- Edema factor
- B. anthracis
Exfoliatin
- Staphylococcal scalded skin -syndrome
- S. aureus
Panton Valentine Leukocidin
- Leukocyte and epithelial cell lysis
Community-acquired MRSA
Pyogenic exotoxin
- Superantigen
-Necrotizing fasciitis
S. pyogenes
Toxins that induce Renal Failure
- Shiga-like toxin
- Verotoxin
- Hemolytic Uremic Syndrome
Hemolysis
Bloody diarrhea
Thrombocytopenia
Renal failure
- E. coli O157:H7
Enterohemorrhagic E. coli
Listeriolysin O
gram positive bacterial toxin
Causes lysis of phagosomes
Allows the bacterium to replicate intracellularly
Allows the bacterium to evade the immune system
- L. monocytogenes
Antimicrobial Resistance
Resistance to antibiotics in the bacterial world all has to do with the concentration of the antibiotic that you can get into a specific tissue in order to overcome the minimum inhibitory concentration of that antibiotic for that particular bacterium
Minimum Inhibitory Concentration (MIC)
The lowest concentration of an antibiotic needed to prevent or inhibit the growth of a microorganism in the laboratory
Must be able to correlate this clinically
- Can we safely achieve such a concentration in a specific tissue?
What 2 factors limit ability to overcome antibacterial resistance
a. Antibiotic Bioavailability
b. Antibiotic Toxicity
Where do bacteria contain resistance genes?
In their:
Chromosomes AND on their plasmids
These genes can be transferred from bacteria to baceries
e.g. plasmids during bacterial conjugation
resistance genes give rise to proteins which:
- Are secreted and cleave antibiotics
- Beta-lactamases, cephalosporinases
- S. aureus, N. gonorrheae, Enterobacteriaceae (beta-lactamases, ESBL) - Form mutated binding sites for antibiotics
Decrease antibiotic binding where they are supposed to act
a. Mutated penicillin-binding proteins
- S. pneumoniae and beta lactams
- MRSA and all beta-lactams/cephalosporins/carbapenems
b. Mutated cell wall
- Vancomycin resistant enterococci
c. Mutated gyrase enzyme
- Ciprofloxacin resistance
d. Mutated ribosomes
- Aminoglycoside (eg. Gentamicin) resistance
- Don’t allow antibiotics (that act on ribsosomes or DNA) to enter the bacterium
a. Mutates Porin proteins
- Fluoroquinolone resistance
b. Efflux pumps
- Erythromycin resistance
Two Major Divisions of Fungi
They are either Yeast OR Mould
Yeasts (examples include):
Candida spp
Moulds (examples include):
Aspergillus spp
Rhizopus spp
Some fungi are dimorphic
Yeast at 37oC AND mould at 25oC
Histoplasma spp.
Coccidioides spp
How is fungal cell wall different from bacterial wall?
Contains CHITIN
Polymer of N-acetylglucosamine
Insects,crustaceans, mollusks, squid, and octopi also contain chitin
Plants have cellulose instead- completely different
Thus, Antibiotics would NOT work, because they target peptidoglycans specifically. you need anti-fungals
Viruses
- relative size
- How do they survive?
What are the two major divisons
Not free living organisms Smallest of the micro-organisms Need a living host to replicate Use the host’s cellular machinery to replicate Host’s enzymes Host’s ribosomes etc
there are two major divisions
DNA vs RNA viruses
What are examples of DNA Viruses
Herpes virus group HSV 1 and 2 EBV, CMV. VZV HHV-6, 7, 8 Adenovirus Hepatitis B virus Human papilloma virus Parvovirus Poxvirus
What are examples of RNA viruses
Hepatitis A virus Hepatitis C virus Rhinovirus Measles virus Mumps virus Rubella virus Influenza virus Human Immunodeficiency Virus Enteroviruses Poliovirus Coronaviruses
Among many others
How long do Viruses last in our bodies?
Many viruses cause chronic infections
HIV, Hepatitis B, Hepatitis C, Human papilloma virus, HSV 1 and 2
Some viruses are never cleared from the human host
Herpes group (HSV 1 and 2, EBV, VZV, HHV-6 etc)
Adenovirus
HIV
Most of the viruses that remain in humans are DNA viruses
Please note: HIV while an RNA virus initially, becomes a DNA virus once inside cells
DNA viruses NEVER leave our bodies. They integrate into our own DNA
i.e. chicken pox as a kid can become shingles later on
Herpes comes back every time you’re stressed or immune system goes down.
HPV: cervical cancer, anal warts/cancer
RNA viruses are usually transient visitors EXCEPT HIV because it is a RETROVIRUS
Retrovirus
RNA viruses are usually transient visitors EXCEPT HIV because it is a RETROVIRUS, that translates RNA into DNA and acts as a DNA virus that never leaves us.
This is possible because it has an enzyme: reverse transcriptase
Viruses and Cancer
Some viruses cause cancer By integrating into our DNA By disrupting oncogenes - Hepatitis C - HIV - EBV - HPV - HHV-8 (Kaposi’s sarcoma virus)
Among others
SAR-2 Coronavirus
Coronavirus group of viruses
- Family of animal RNA viruses discovered in the 1930s (named in 1968)
- Human coronaviruses discovered in the 1960s
Name derives from the protein spikes it has on surface
- Attachment to ACE receptors
- Looks like a crown
Latin: corona (“crown, “wreath”)
Transmission of COVID
Like most respiratory viruses Large droplets (2 m or 6 feet away)
BUT:
Aerosols (potential for airborne spread) Aerosol generating procedures (AGP) CPAP Intubation/extubation Deep tracheal suctioning Open circuit suctioning (ventilated patients) Drilling Endoscopy with biopsy Flushing a high efficiency toilet Singing? Talking? Laughing? Shouting? Stool
Know you COVID-19 Tests: RATs
Rapid Ag Tests (RATs)
50% sensitive when asymptomatic
70-80% sensitive when symptoms for more than 24 hours
Repeat testing (12-48 hours later) needed if negative and you’ve tested “early”
Close to 100% specific
Isolation time for COVID
- what is the area first infected by COVID
10 days* to reduce your transmissibility
- throat is the first area that gets infected
Know your COVID-19 Tests: PCR
NP (and throat) PCR is gold standard
Almost 95% sensitive ( depends on a Cycle threshold)
100% specific
- COVID infects throat area first so best to swab the throat, not nasal
What’s different about Omicron
significantly more infectious
Multiple mutations in the spike protein
Seems to have originated in parallel to other mutants
Huge replication in throat and trachea
Massive viral load in upper respiratory tract (main symptoms are sore throat and headache)
Less predilection for lung tissue (not too much cough)
Ro (R not) which was 2-3 for original wuhan virus has come up to 30!!! for omicron
How to calculate the percentage of population that needs to be vaccinated
It’s a mathematical equation:
1 – (1/R0) X 100% = “Herd immunity” calculation
Then divide by vaccine efficacy (%) = TOTAL (not just eligible) population needed to be vaccinated in order to achieve said “herd immunity”.
Wuhan ancestral strain (R0 2.5) = 63% (remember that number?) Aα, Bβ variants (R0 4) = 79% Δδ variant (R0 8) = 97% Oo variant (R0 32) = 100%
This means young children (about 12% of Quebec population) need to be vaccinated, irrespective of whether the virus is “deadly” for them.
Treatment for viral infection/COVID
there is no cure or treatment however STEROIDS (anti-inflammatory) helps to suppress CYTOKINE STORM
Multisystem Inflammatory Syndrome in Children/Adults aka Paediatric/Adult Inflammatory Multisystem Syndrome
Rare but serious syndrome <2% of children infected with COVID-19 (risk about 1 in 3,500)
Mortality: <1%
It occurs 4-6 weeks after (even from an asymptomatic) infection.
Decreased by 90% after vaccinations
What are the two types of parasites
There are two types:
Protozoa vs Multi-Celled Organisms
Atabrine
anti-malaria drug
don’t take it = become a skull
Protozoa
- give examples
Single celled organisms Examples include: Plasmodium spp Entamoeba spp Dientamoeba spp Cyclospora spp Isospora spp Toxoplasma spp
Multi-celled organisms
Worms (examples include): - Nematodes/Roundworms Ascaris spp - Platyhelminths/Flatworms and Flukes Tinea spp Schistosoma spp Echinococcus spp
pregnancy and vaccination
Increased risk of miscarriages, pre-term births, and maternal morbidity/mortality with COVID-19.
Anti-COVID-19 vaccines have been approved and recommended for use in pregnancy (all trimesters) and for breastfeeding women. They are safe and effective and provide transfer of antibodies to the newborn.
Vaccines and menstruation changes? Study showed ½ day change only Other vaccines (and viral illnesses) can do this too.
Vaccines and infertility?
