Foundations in Microbiology – Flashcards

- Hemolysis: Gamma (none), alpha (partial), and beta (full)

- Gram staining: G+ (purple) and G- (pink/red)

- Cell shape: Coccus (sphere), bacillus (rods), coccobacillus, spirochete (spiral), and vibrio (kidney bean)

- Arrangement: Chains, clusters, and pairs (diplococci)

- Mycobacteria: Too much lipid in cell wall --> Acid-fast stain

- Treponema pallidum: Too thin to see --> Dark-field microscopy or immunofluorescence

- Mycoplasm pneumoniae: No cell wall/very small --> No stain

- Legionella pneumoniae: Intracellular --> Silver stain/immunofluorescence

- Chlamydiae: Intracellular --> Giemsa stain or inclusions

- Rickettsiae: Intracellular --> Giemsa or immunofluoresence

- Determines if the strain is a obligate aerobe, facultative anaerobe, aerotolerant anaerobe, and obligate anaerobe

- Yellow discoloration in tubes means culture growth

- Coagulase: Stimulates coagulation

- S. aureus: +

- S. epidermidis: -

- Easy way to test for the difference between the two

- Kirby-Bauer and E-strip Tests

- Particularly important now because so many organisms are antibiotic resistant

- Depends on age group

- S. pneumoniae, N. meningitidis, enterovirus, and herpes simplex virus for 6-60 year olds

- N. meningitidis --> G- diplococci

- S. pneumoniae --> G+ diplococci

- Eukaryotes: Nuclear membrane, 23 pairs of chromosomes, divides via mitosis, 80S ribosomes, presence of organelles, no cell wall, and cell membrane with sterols

- Prokaryotes: No nucleus, 1 chromosome, divides via binary fission, no organelles, 70S ribosomes, cell wall and cell membrane but no sterols

- Gram-positive: Thick peptidoglycan layer, teichoic acid, no LPS, no periplasmic space, and no outer membrane

- Gram-negative: Thinner peptidoglycan layer within periplasm, no teichoic acid, and LPS and lipid A in outer membrane

- Repeating units of N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG) units

- Cross-linked by tetrapeptide

- Cross-linking is the site for B-lactams such as penicillin G

- Lysozyme cleaves NAM and NAG bonds --> Weakens cell wall so cell might burst when put in hypotonic medium

- Found both in gram-negative and gram-positive

- Outer portion: repeating O-antigen subunits

- Middle portion: Core polysaccharide --> Hydrophilic

- Inner portion: Lipid A --> Embeds structure into the outer membrane

- Potent endotoxin due to lipid A --> Important in sepsis responses

- Found only in gram-negative bacteria

- Found only in some gram-positive bacteria

- Polymers of ribitol or glycerol connected by phosphates

- Found in peptidoglycan layer

- Endotoxin but less potent than LPS

- Can mediate cell attachments and may contain antigenic determinants for vaccines, identification, and antibody formation

- Inner membrane

- Periplasm containing thin peptidoglycan layer

- LPS, mebrane proteins, and porins within outer layer

- Porins determine what moves in and out of the cell wall and membranes

- No sterols in either the inner or outer membranes

- Does not contain sterols

- Site of active transport of molecules, electron transport chain, synthesis of cell wall precursors, and signal transduction

- Contains nucleoid, 70S ribosomes, granules, plasmids, and transposons

- Polysaccharide layer surrounding outer membrane

- Found in some gram-postive and gram-negative strains

- Increases virulence

- Makes surface sticky --> Non-specific binding to surrounding

- Seen on staining through the Quellung reaction

- Inhibits phagocytosis

- Surface of capsule can be used to create vaccines that will opsonize the bacteria

- Collections of bacteria

- Bacteria stick together via capsules

- Develop on the surface of teeth, contact lenses, mechanical valves, and artificial joints

- Produce polysaccharides which form mushroom-like shapes that help surround and protect bacterial colonies from phagocytosis and opsonization

- Overwhelm immune response simply by being too large for one macrophage or phagocytic cell to engulf on it's own

- Found on some gram-positive and gram-negative bacteria

- Good target for antibodies

- Allows bacterium to move

- Structure is anchored into the inner plasma membrane and functions as a protein motor

- Movement can increase virulence

- E. coli have flagella --> Cause UTIs by traveling up the urethra

- Pili/fimbriae

- Shorter than flagella

- Allow specific adhesion and binding of bacterium to surfaces or specific host cells

- Can be used as targets for vaccines, etc

- Long pillus extended from one bacterium to another

- Pulls two cells close enough to eachother to transfer genetic material

- Conjugation: Process for genetic exchange

- Primarily present in G- bacteria

- Proteinaceous syringes that extend from the bacterium to the host cell

- Injects substances into host cell --> Genetic material, proteins, etc

- Makes the host cell do what the bacterium wants it to

- Only present in Clostridium and Bacillus (G+ rods)

- Mechanism for survival in response to adverse environmental stimuli

- Have a keratin-like coat --> Extremely resistant to heat and disinfectants

- Metabolically inactive so can survive for many years

- Can germinate when conditions are right --> One bacterial cell

- Dipicolinic acid in the coat is also a Ca++ chelator

- Interior contains basically just the nucleoid and no other cytoplasm

- Occurs through binary fission

- Can be alot faster than in eukaryotes

- Only need to replicate one chromosome

- Replication time will determine how fast species can be cultured --> S. pneumoniae needs 2 weeks

- Transcription and translation are coupled so DNA replication and protein synthesis can be very fast

- Can occur on solid media, broth culture, blood agar, or on biofilms

- Lag phase: Bacteria are acclamating to their new environment --> No growth

- Exponential phase: Exponential growth

- Stationary phase: Growth stops

- Decline: Cells begin to die

- Four phases represented on a standard growth curve

- Phases and cell number can be seen by performing a direct cell count

- Turbidity of broth culture is also proportional to cell mass

1. Cell wall extends to size of about 2 cells

2. Chromosome replicates

3. Septum forms and DNA binds at the mesosome

4. Cell splits into two separate daughter cells

- Primarily through catabolism to form ATP

- Cellular components are then synthesized through anabolism

- Minimal growth requirements: Carbon, nitrogen, and iron

- Anaerobes: Glucose --> Pyruvate via glycolysis --> Fermentation to get ATP + NADH (2 ATP)

- Aerobes: Glucose --> Pyruvate --> Kreb's --> Electron Transport Cahin (38 ATP)

- Specific can be classified by:

1. Carbon source

2. Obligate vs. facultative intracellular grwoth

3. Aerobes vs. anaerobes

4. Ability to ferment certain sugars

- Obligate aerobe --> +SOD/+catalase

- Facultative anaerobe --> +SOD/+catalase

- Aerotolerant anaerobe --> +SOD/-catalase

- Strict anaerobe --> -SOD/-catalase

- Microaerophile --> +SOD/(-/+catalase)

- SOD and catalase used to degrade free radicals such as superoxide and hydrogen peroxide that are normally produced through ETC

- Identification test

- Determines Staphylococcus from Streptococcus bacteria

- Staphylococcus + --> Facultative anaerobe

- Streptococcus - --> Strict anaerobe

- Determines the ability to ferment lactate

- If bacteria grows then bacteria is able to ferment, if not then no

- Many antibiotics target the assembly of cell wall proteins/structures

- Peptidoglycan units must be transported into periplasm to be assembled

- Bacitracin: Inhibits recycling of bactoprenol (NAM transporter)

- B-lactams: Inhibit tetrapeptide cross-linking

- Fosfomycin: Inhibits NAG-NAM binding

- Encodes a protein that is required for virulence

- Might allow for adhesion and allow the bacteria to establish infection

- Examples: Pili/adhesin or biofilm protein

1. Low free iron availability: Stimulates diptheria toxin production

2. 37C vs. 20C: Stimulates pilin protein production by E. coli that allows bacteria to adhere to bladder wall

3. Eukaryotic cell binding: Initiates type III secretion system formation --> Inserts genes that inhibit macrophage phagocytosis, cytokine secretion, and initiate apoptosis (Yersinia)

4. High cell density/Quorum sensing: Used by P. aeuruginosa in CF patients 

- Binds gene promoter and inhibits transcription

- Ex. Diptheria toxin promoter region bound when Fe concentrations are high

- Activator proteins bind DNA at promoter to activate transcription

- Also directly interact with RNA polymerase

- Two component system: Signal sensor in membrane and transducer that actually binds DNA + RNA polymerase

- Ex. Salmonella: Type III secretion system injects proteins to induce gut epithelial cells to engulf bacteria --> Sensor in bacterial membrane now realize that it's in phagosome --> Stimulates proteins that allow bacteria to live in that environment

- Anti-phagocytic capsule (H. influenzae, N. meningiditis, and S. pneumoniae)

- Intracellular growth

- Antigenic variation (N. gonorrhoeae): DNA rearrangement occurs within pilin protein genes

- N. gonorrhoeae: Has 18 pilin genes --> Only PilE gene can be transcribed because it has promoter, others are PilS genes

- Variation due to recombination of PilS genes into the PilE gene to create a new pilin gene formation

- Bacteria pickes up naked DNA from the environment

- DNA then inserts itself into the chromosome via homologous recombination

- Common in N. gonorrhoeae and S. pneumoniae

- Transformation can occur to change pilin protein and account for antigenic variation as well

- Process of mutations causing a gene to now encode a protein with different function --> Generally presents as a difference in phenotype

- Genotype: Linear DNA sequence

- Phenotype: Growth/appearance of bacterial cell

- Can result from a missense, nonsense or frame-shift mutation

- Most mutations are silent or very detrimental

- Slow and inefficent process but it does happen

- Due to the prevalence of prophylactic treatment with antibiotics

- Antibiotics are put into cattle feed --> Environmental tolerance

- Resistance found in chromosomal DNA that has entered via recombination

- Changes the structure of antibiotic targets such as ribosomes, membrane transporters, and RNA polymerase

- Renders the antibiotic ineffective at active site

- DNA can also now encode sequences for efflux pumps for antibiotics

- Ex. DNA might now encode for a methylase which methylates active site

- Small circular replicons --> Contain origin of replication (ori) site

- Carry non-essential genes for cell growth/replication

- Some carry transfer (Tra) genes --> Allows for transfer or conjugation between cells

- Other plasmids not containing Tra genes can be transferred but they must be recombined into a plasmid containing the Tra gene first (mobilization)

- Can transfer between bacteria and even yeast

1. One bacterial cell with a plasmid containing the F+ gene will extend sex pilus to another cell

2. Sex pilus then contracts to pull cells close together

3. Plasmid undergoes special type of DNA replication --> One parent strand goes to one cell while the other remains --> Complementary strands replicated during transfer

4. Plasmids can then recombine with other plasmids or incorporate into chromosome

1. Transposons: Carry genes needed for transposition (transposase) and generally carry the antibiotic resistance genes --> Must be taken up from environment by bacterial cells 

2. Conjugative Transposons: Also have tra genes --> Able to move between two bacterial cells

- Transposons can then insert themselves into plasmids within the cytoplasm

- Viruses that infect bacterial cells

- Consist of DNA/RNA molecule and surrounding proteins

- Most have a capsid and phage tail --> Attachment

- Need to infect a cell to replicate

- Converts the infected bacteria into a phage-producing factory

- Virulent phage: Phage that only grows lytically

- Can produce 100-10,000 new phage

- Proteins and DNA synthesized --> Phage particles assembled

- Bacterial cell wall degraded by enzymes --> Phages released

- Phage DNA becomes incorporated into bacterial chromosome at attachment (att) site

- Some phage have tRNA-like genes that simply integrate via homologous recombination with tRNA genes

- Repressor protein is transcribed --> Represses the lytic gene

- Prophage: Phage integrated into host DNA

- Lysogenic/Temperate Phage: Capable of both the lytic and lysogenic phases

- Enters into lytic phase once repressor protein is no longer produced and lytic gene is turned on --> Random event

- Phage carried bacterial chromosomal DNA within its capsule

- This DNA was acquired during lytic phase when bacterial DNA was packaged into phage instead of phage DNA

- These phage cannot duplicate because they do not contain phage DNA

- This DNA must be integrated into the host in order to replicate again

- Phage DNA contains extra genes that appeared due to imprecise excision from host DNA, integration of a transposon or another random recombination event

- These phages are always lysogenic

- DNA is then incorporated into new host DNA

- Lysogenic conversion occurs in the host

- Ex. Diptheria and cholera toxins

- Since bacteriophages infect bacteria, could potentially be used to treat infections

- Highly specific to bacterial species

- Non-toxic to animals and plants

- Side effects and allergic reactions have rarely been seen

- Contiguous blocks of virulence genes found in bacterial DNA --> Usually on plasmids

- Found in diverse bacterial species

- Genes generally code for proteins with the same functions and amino acid sequences

- Implies that these genes came from one common ancestor

- Acquired by genetic transfer between species --> Different GC content from rest of DNA

- Bacterial strains without island of DNA show little or no virulence --> Specific DNA sequences confer virulence

- Ratio determined by the LD50/ID50

- Can change depending on particular host --> Age, disease state, medications, etc

- Decreased LD50 --> Increased virulence

- Shigella: Extremely virulent (ID50~10-100)

- Salmonella: ID50= 10^6 normally, but much lower in patients on antacids

- Factors: Pili, capsules, LPS, peptidoglycan, and teichoic acid structure, flagella, outer membranes, and surface proteins

- B-cells: Bacterial infections (antibodies crucial)

- T-cells: Viral and fungal infections (Killer T-cells crucial)

- B+T-cells: Bacterial, viral, fungal, and protozoal infections

- Phagocytic deficiencies

- Complement deficiences: Recurrent Neisseria infections

- Factors for immunodeficiencies: AIDS, immunosuppressive drugs, diabetes, genetic disorders, old age, stress, poor nutrition, pregnancy, splenectomy, tobacco, drugs, alcohol, and medications

- Most infections are acute and assymptomic

- Symptoms short lived if present at all

- Chronic infections --> May begin as asymptomatic (carrier) but can transmit to others

- MRSA, gonorrhea, and chlamydia are common chronic infection bacteria

1. Incubation period: Time from acquisition to first specific symptom (days to months)

2. Prodrome: Period with general illness symptoms (fever, malaise, muscle cramps, etc)

3. Clinical Illness: Time from the first specific symptom to the resolution

4. Recovery: Time till you're back to normal

- Relates back to the structure of the bacteria itself

- G- are tough --> Can live in water/environment

- G+ are more delicate --> Transmitted by close contact (Neisseria)

- Points of entry: Nose, mouth, eyes, respiratory tract, genitourinary tract, and skin (cuts and sores)

- Must overcome normal flora for space, food, etc

- Normal flora also produce natural antibiotics

- IgA protease --> Break down mucosal IgA antibodies

- Factor A: Binds Fc region on IgG to inhibit complement activation

- Leukocidins: Destroy leukocytes and macrophages

- Coagulase: Helps surround pathogen with fibrin clot

- Capsules inhibit phagocytosis

- Biofilm formation also inhibits phagocytosis and opsonization

- Ability to escape phagosome after phagocytosis

- Ability to inhibit lysosome binding with phagosome after phagocytosis

- Pili, capsules, and teichoic acid structure

- Localized --> S. aureus abcess

- Minimal spread --> Erysipelas due to Strep.

- Disemination systemically --> N. gonorrhoeae

- Intracellular growth: Invade using special surface proteins or type III secretion systems

- Can also grow in biofilms 

- One way to cause disease

- Produce enzymes to help spread and break down barriers --> hyaluronidase, collagenase, phospholipase, and streptokinase

- Anti-phagocytic factors --> Factor A and capsule

- Pyogenic inflammation --> Pus-producing --> Neutrophils (acute)

- Granulomatous inflammation --> Chronic with macrophages and T-cells

- Secreted by pathogens

- Encoded by genes on phages or plasmids

- Very toxic in small doses

- Good antigens --> Can produce toxoids

- Some have A-B subunit --> A is active (toxic) and B is the binding portion for cell receptors

- Superantigens: Simultaneously bind T-cell receptor and MHC class II molecule on APC --> Cytokine storm!!!

- Integral part of cell wall of G- rods and cocci --> Primarily LPS

- Also possible with peptidoglycan, teichoic acid on G+ bacteria (S. aureus) --> Not as potent

- Encoded by genes in bacterial chromosome

- Less toxic than exotoxins

- Not good antigens --> No toxoids

- Released upon lysis or blebbing of bacteria

- Most common cause of sepsis and disseminated intravascular coagulation (DIC)

- Induce high concentrations of IL-1, TNF, NO, and complement

- By-products: Acids and gas production leading to tissue damage

- Immunopathogenesis: Molecular mimicry --> Cross-reactivity between pathogen and host tissue

- Ex. Rheumatic heart disease

- Neoplasia: Can be caused by persistent infections

1. Stain with crystal violet

2. Stain with Grams iodine

3. Wash with alcohol

4. Stain with safranin