Test 1 Flashcards
DNA sequence analysis of this structure is widely used in bacterial phylogenetic analysis.
Ribosome
Which one of the following is a cell wall component unique to bacteria?
Peptidoglycan
Bacteria
Prokaryotes (No nucleus) • Complex cell wall • No sterol • Membrane bound organelles are absent • A single circular chromosome (exceptions ?) and no histones • Ribosomes (smaller) 70s • No cytoskeleton • Asexual reproduction (binary fission)
Gram Postive Bacteria
Thick peptidoglycan
Gram negative bacteria
outer membrane, which contains lipopolysacciride - has a Lipid A(endotoxin) component
Mycobacteria
has mycolic acid in the membrane, which is why it stains positive in the acid-fast stain
Gram Staining
-based on peptioglycan thickness • Crystal violet- Primary stain • Gram’s Iodine- Mordant • Decoloriser-Acid Alcohol • Safranin-Counter stain • Gram Positive stain violet/blue( retains Crystal violet) • Gram negative stains Pink(safranin)
What is the cause of many clincial signs of Gram negative bacteria?
Lipid A or endotoxin( a component of the cell wall) Endotoxin binds to macrophage receptors and stimulates an inflammotory cascade
Test for Endotoxin
Limulus Amebocyte Lysate(LAL); everything has to be checked for endotoxin
Which are the bacteria that does not contain peptidoglycan
Mycoplasmia and Chlomydia
Flagella
Locomotion / Motility Number and arrangement can be used for identification
Endoflagella
Flagella inside the cell Endoflagella /axial filaments in the periplasmic space eg. spirochetes
Pili/ fimbriae
• Pili/ fimbriae: Small thread like structures • Facilitate adherence to the host tissue • Contribute to antigenicity Eg: Bordetella bronchiseptica, E.coli
K88
Neonatal piglets-Fimbrial antigens in E.coli
K99
Neonatal calves-Fimbrial antigens in E.coli
Capsule
Polysaccharide outer coating of the bacteria - Helps organisms to evade phagocytosis
Which bacterial species has a non-polysaccharide capsule?
Bacillus anthracis, thus staining for this capsule is how we ID this bacteria
Endospores
Produced when essential nutrients are depleted in a bacteria - or under BAD conditions as the spores are very virulent to poor conditions Organic acid called Dipicolinic acid protects the endospore from damage Eg: Clostridium, Bacillus THESE AID IN BACTERIAL SURVIVAL
aerobic, microaerophilic, capnophilic
Oxygen required for growth
obligate anaerobe, aerotolerant anaerobe
Oxygen not required or utilized for growth
facultative anaerobe
Oxygen not required but can be utilized for growth
Bacterial Virulence Factors
properties or traits found in isolates that cause disease but which are not found in isolates of the same species that lack ability to cause disease
Damage caused by bacteria
Damage caused by bacteria Using the host’s nutrients Direct damage to the host cell (Toxins) Hypersensitivity reactions (Type IV Hypersensitivity- Tuberculosis)
Pathogenicity
Pathogenicity is the ability of a pathogen to produce a disease by overcoming the defense mechanisms of the host.
Virulence
the degree of pathogenicity
Exotoxins
released from the cell; made in the cell
3 types of Endotoxins
- A-B toxins 2. Membrane disrupting toxins (Leukocidins kill white blood cells (phagocytes), Hemolysins destroy erythrocytes) 3. Superantigens
A-B Toxins
Most exotoxins(i.e. tetanus) are A-B toxin • A-B toxins consist of two polypeptides. • The A polypeptide is the active enzyme and the B polypeptide is a binding component • B binds to the cell, the complete toxin is taken into the cell, the two subunits separate, and the A subunit enzymatically kills the cell.
What are superantigens?
Cause non-specific activation of T-cells • result in polyclonal T cell activation and massive cytokine release. • Produced by pathogenic microbes (including viruses, mycoplasma, and bacteria) • Indiscriminate binding to MHC class II molecule on the antigen presenting cell and and T helper cell receptor • 1/1000(Superantigens) vs. 1/5 cells by an antigen • Nausea, vomiting, fever> shock
Example of a superantigen
Toxic shock syndrome in humans is caused by a superantigen
Main source of virulence factors in bacteria
Plasmids are smaller circular DNA present in Bacteria Bacteriophages are virus particles which attack Plasmids and bacteriophages may carry genes for antibiotic resistance, toxins, capsules and fimbriae and can mediate transfer. Plasmid genes; Tetanus neurotoxin Staphylococcus enterotoxin(superantigens) Bacteriophage genes; Corynebacterium diphtheria (Diphtheria toxin), Clostridium botulinum (Botulinum toxin), E. coli O157 H7( Shiga toxin)
Conjugation
is the process by which one bacterium( Bacterium with a fertility factor) transfers genetic material to another through direct contact.
Transformation
is the genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material from its surroundings and taken up through the cell membrane(s)
Transduction
is the process by which DNA is transferred from one bacterium to another by a virus
Biofilm
virulence factor Microbes come together in masses cling to surfaces, produce extracellular substances and take in nutrients and forms a biofilm Eg. Dental Plaque Pseudomonas aeruginosa biofilms in cystic fibrosis patients
Quorum sensing
- the bacteria appear relatively innocuous as they quietly grow in number 2. When their population reaches a certain level, instant changes occur in their behavior, appearance, and metabolism. 3. These changes culminate in an infection that can ambush and overwhelm our immune system defenses.
Opportunistic pathogens
organisms those do not cause disease in a healthy host, with a healthy immune system
True pathogens
equipped with virulence genes for adherence, invasion, evasion from the immune system and toxins
Nosocomial Infections
Hospital acquired infections Eg. Methicillin resistant Staphylococcus aureus Clostridium difficile
Generally bacteria are
extracellular pathogens
Obligate intracellular pathogen
Eg. Rickettsia, Chlamydia
Facultative intracellular pathogen
(can survive extracellular or intracellular) Eg. Mycobacterium
Cell wall component unique to gram negative bacteria
lipopolysaccharide
Gram positive staining in some bacteria is due to the presence of a:
Thick Peptiodoglycan
Acid fast staining in Mycobacteria is due to the presence of:
Mycolic Acid
Gram positive bacteria retains the color of the primary stain and Gram negative bacteria picks up the color of the counterstain. T/F
TRUE
Which one of the following process is a least likely virulence mechanism in a bacteria? a. bacterial movement using flagella b.bacterial attachment using fimbriae c. biofilm production and attachement to surfaces d. bacterial protein production by ribosomes
Bacterial protein production by ribosomes
Translation
Production of protein
DNA sequence coding. Which of these organelles is used for bacterial phylogentic analystis?
Ribosomes
Is mitochondria present in bacteria?
NOPE
What are antimicrobials?
Drugs that destroy microbes, prevent their multiplication or growth or prevent their pathogenic effect • Differ in their physical, chemical and pharmacological properties • Differ in their antibacterial spectrum of activity • Differ in their mechanism THESE DO HAVE TO KILL THE MICROBE, THEY CAN JUST PREVENT ITS GROWTH
• When do you use antimicrobials?
When the patient have a treatable microbial infection
Antimicrobial vs antibotic
Antibotics- produced by living organism, Antimicobrial is a broader term
What should you know to proceed with treatment with antimicrobials?
location of the infections, likely pathogens involved, which antimicrobials are likely effective against a particular pathogen at a particular site
What are the other factors to consider in antimicrobial therapy?
Cost, (type, dose and duration), safety, ease of use, and possible emergence of resistance
Antibiotic
chemical substance produced by a microorganism that inhibits the growth of or kills other microorganisms.
Antimicrobial agent
a chemical substance derived from a biological source or produced by chemical synthesis that kills or inhibits the growth of microorganisms.
Natural (true antibiotics)
produced by bacteria or fungus (Streptomycin, penicillin, tetracycline)
Semi-synthetic
chemically-altered natural compound (ampicillin, amikacin)
Synthetic
chemically designed in the lab (sulfonamide, enrofloxacin, marbofloxacin)
Classification of Antimicrobial agents
A. Chemicalfamilystructure B. Mode of action C. Type of antimicrobial activity D. Spectrum of antibacterial activity
What do you need to know to treat with antimicrobial agents?
•Know the drugs •Know the microbiology •Know the patient
Mode of action of antimicrobial
inhibitors of cell wall synthesis inhibitors of protein synthesis inhibitors of membrane function inhibitors of nucleic acid synthesis (anti-metabolites)
Antibacterial Susceptibility Testing
Done to figure out which antimicrbioals are the best to treat certain infections
2 types of Antibacterial Suscpetibility Testing
- Dilution (broth/agar) 2. Diffusion (disk)- aka Kirby Bauer Test
What is a Susceptibility break point?
A drug concentration above which an organism is considered resistant and at or below this value organism is susceptible to that drug. Three Break point values are set at Susceptible, Intermediate, or Resistant IMPORTANT FOR LABS DOING THIS TEST
What is Minimum inhibitory concentration (MIC)?
Minimum amount of drug required to inhibit bacterial growth Drugs with lower MIC values are better choices
Disk Diffusion
Disk Diffusion (‘Kirby Bauer’)
- Must use a bacterial isolate in pure culture
- Standardized bacterial inoculum spread on an agar plate
- Single-concentration antimicrobial disks are used
- Growth inhibition zone diameter measured
- Published reference breakpoints (zone size) to interpret results
- Different drugs will have different zone sizes based on the published data
Broth Dilution
• multiple dilutions of antimicrobial agents (usually 2-fold serial dilutions)
Use published reference breakpoints to interpret
• Measure AND report growth inhibition
endpoint (MIC) (MIC reported in micrograms per milliliter)
You always want to keep a dose (below or above) the MIC in the body?
above MIC in the body
Gradient diffusion test - E-Test
Measures MIC
Bactericidal
kills
Bacteriostatic
inhibits
Broad spectrum antibiotic
active against a wide variety of bacteria Eg. Tetracycline
Narrow spectrum antibiotic
affect only a narrow range of bacteria Eg. Penicillin
When do you use antimicrobial combinations?
- Mixed infections
- Prevention of antimicrobial resistance
- To increase effectiveness in treating some infections
Synergistic ( sequential action at different sites, enhanced uptake- beta lactam and aminoglycosides, interference with resistance mechanism,
Drugs metabolized to active metabolites (Enrofloxcin to Ciprofloxacin)
Innate resistance
preexisting genomic property
i.e. Mycoplasa does not have a cell wall, Therefore, you can’t use beta lactones
Acquired resistance
new genetically encoded trait not representative of the species
(acquired by mutation or horizontal gene transfer)
Processes that bacteria can aquire virulence factors:
-conjugation
Mechanisms of Resistance
- Enzymatic destruction or inactivation of drug
- Prevention of penetration to target sites within microbe
- Alteration of drugs target site
- Rapid efflux of antibiotics
Strategies to Reduce Antimicrobial Resistance
• Prudent drug use
- maximize efficacy of therapeutic regimens
- restrict extra-label use to high risk patients
- observe withdrawal period
- use antimicrobials of limited human health concern - use alternative therapies
• Pathogen control
- animal waste management
- reduce contamination in slaughter and processing - maintain herd health and infection control
• Policy
- control of drug use in food animals
- national antimicrobial resistance monitoring system
- educational efforts
What antimicrobial should you NOT use?
Vancomycin
Vancomycin resistant Enterococcus (VRE)
Antimicrobials are used in agriculture for?
Growth Promotion
What is one of the main problems with use of antimicrobials in vet med?
Extra Label Use
Which will be the least likely scientific factor to be considered regarding antimicrobial therapy?
A. know the drugs
B. know the microbes
C. Know the pt
D. Know the Client
D. Know the Client
T/F In general drugs with lower MIC values are better choices for treatment.
TRUE; because you can use a lower dose, but remember that MIC is not the only factor(microbe, site of infection etc)
Pure Culture of a bacteria is critical for obtaining accurate antimicrobial susceptibility pattern T/F
True- you MUST have a pure culture
Which of the following statements is incorrect?
A. MIC is the lowest concentration of antimicrobial agent which can inhibit the growth of bacteria
B. Published break points are required for interpretation of AST results
C. MIC can be measured in E-test
D. MIC can be accurately measured in Disk Diffusion test(Kirby Bauer test)
D. Kirby Bauer DOES NOT measured MIC accurately
Methods for IDing the agent
- Direct detection of the agent (simple/ differential staining, antibody staining)
- Isolation and identification
- Direct detection of antigens, toxins
(Immunology techniques such as ELISA0 4. Nucleic acid detection(PCR)
- Identification of the host immune response
Antibodies(Eg,Brucella infection),
Cell mediated immune response(eg.TB)—- very rare and only available for certain conditions
Ideal test has
Ideal test has high sensitivity and high specificity
Sensitivity
percentage of true positives in a sample population that are correctly identified as positive by a test.
Specificity
percentage of true negatives in a sample population that are correctly identified as negative by a test.
Positive predictive value
percentage of all positive test results that are true positives.
Negative predictive value
percentage of all negative test results that are true negatives.
Predictive values associated with individual test results vary
Predictive values associated with individual test results vary with disease prevalence
In a high prevalence herd, you will have a
more accurate results.
Specimen collection
- Collect from actual site of infection
- Minimise contamination
- Collect early in the stage of disease process
- Use appropriate transportation
- Collect before the initiation of antimicrobial therapy
Can you submit a swab for a bx?
better to submit the material itself
What happens if you submit a fecal sample in a serum tube?
the bacteria will produce lots gas
Gram Staining
Gram Positive Purple(Crystal violet)
Eg: Streptococcus pyogenes
Stapylococcus aureus
Gram Negative- Pink (Safranin)
Escherichia coli Pasteurella multocida
Gram stain -Gram Positive = Thick Peptidoglycan
Acid Fast Staining (Kinyon’s stain)
Acid fast positive organism stains: Pink Acid fast negative organism stains: Blue
Acid fast stain –Acid fast + =mycolic acid
Largest Problem with direct staining
Sensitivity is very poor
Blood
• CSF
• Mycoplsama, spirochetes( can not be stained)
Urine
Collection,
• Cystocentesis preferred over catheterization
• Urethral contamination occurs in free catch and catheterized samples • <105/ml- probable contamination(
• Gram staining(2 bacteria/ oil immersion)
• Capped syringe, sterile container
• Refrigerate if cannot be cultured if cannot be cultured immediatly
• May use Urine preservation tubes
Transudates and exudates
- Syringe
- Remove air
- Anaerobic transport medium
•Lavages or washes use a buffered solution •Saline vs. lactated ringer’s solution
Feces
- 2-3 gms
- Leak proof container
- Repeated culture needed in shedding/chronic infections
Blood
- Several specimens over a period of time, onset of fever,
- 3- 4 in first 1.5 -3 hours
Tissue samples
- Portion of a tissue
- Multiple specimens
- Collect first during necropsy
- Sealed leak proof container
- Refrigerate if delivery delayed
Interpretation
Normal flora Vs. Pathogens
Correlate with clinical signs and the organism
Quantitation- light, moderate, heavy
(Isolation of four or more organism; Most likely contamination)
False negative results
May be due to sampling, transport, storage issues, antimicrobial therapy, Fastidious organisms or when specific procedures needed
Consult with clinical microbiologist
The most dangerous pathogens are classified as
BSL-4
Principle of Secondary Containment
transport in secondary container that is leakproof, puncture proof and contains liquid absorbent
Rare bacteria are
Gram Negative cocci
Polymerase Chain Reaction
• Non culture based from clinical samples • For identification of isolates.
- Conventional PCR
- Real Time PCR
- What is the limitation for PCR identification? You have to know what you are dealing with
Antigen detection
(EIA, agglutination, FA, etc.)
(tests use antibody reagents to detect antigens in serum, feces, urine, tissue.)
Chemical detection
(HPLC, GLC, MALDI-TOF- MS) (analysis of total cell fatty acids/proteins; limited use on clinical specimens)
Biological detection
(Limulus amoebocyte assay) (test for LPS, adapted from clotting mechanism of horseshoe crab)
Detection of Specific Immune
Response to a bacteria or fungus
• Humoral (antibody) Response
Eg: Agglutination, precipitation, ELISA
• Cell mediated immune response
Eg: Tuberculin reaction, Interferon gamma test
Generation of an immune response requires time and immune response may persist
False positives for immune tests can mean
prior antigen exposure, vaccination, cross-reactions
False negatives for immune tests can mean…
anergy, immunosuppression
Beta Lactam(b-Lactam) antimicrobials
All have a b-Lactam Ring
Members of the group
Penicillins,( Ampicillin, Amoxicillin, Ticarcillin) Cephalosporins(1st, 2nd,3rd, 4th Generations) Carbapenems (Imipenem)
Monobactams (Aztreonam)
Mechanism of action
Inhibit Cell wall synthesis(transpeptidation step) in the peptidoglycan synthesis, Stimulate autolysins which degrade peptidoglycan
b-Lactam antimicrobials differ in their spectrum of activities
Some are effective against both Gram Negatives and Gram positives
Some are effective against only Gram Negatives than Gram positives or vice versa
Vary in their absorption, toxicity, and their ability to penetrate tissues or blood brain barrier
Bactericidal antimicrobials- KILL THE BACTERIA
Excretion through kidneys
Time Dependant killing- you have to have a concentration over a period of time
Mechanism of action of Beta Lactam antimicrobials
Mechanism of action
Inhibit Cell wall synthesis(transpeptidation step) in the peptidoglycan synthesis, Stimulate autolysins which degrade peptidoglycan
Resistance mechanisms of b-Lactamase
Resistance mechanisms;
• b-Lactamase(enzyme which cleaves b lactam ring) production • Extended Spectrum b lactamase
• Alteration in penicillin binding proteins
cell wall synthesis inhibitors
- Glycopeptides(Vancomycin, daptomycin)
- Last resort antimicrobial in S. aureus, and Enterococcus
• Fosfomycin, bacitracin
Gram positive cocci
Staphylococcus
Streptococcus
Enterococcus
Micrococcus
Staphylococcus
Facultative anaerobic catalase positive cocci
Exceptions: Anaerobic species;S.sacharolyticus, S.aureus
subsp.anaerobius
Classic opportunistic pathogens
Natural habitat is skin and mucous membranes
May be a part of resident or transient flora
Staph in a dog is is almost always…
S. pseudintermedius
What is Coagulase?
Enzyme which Convert fibrinogen to Fibrin
Staph causes
Suppurative conditions
• Superficial: skin and soft tissue infections
pyoderma, folliculitis, furunculosis, wound infections
• Deep infections
Abscess, cellulitis, mastitis, pyomyositis, Necrotizing fasciitis and myositis
- Infections of other body systems
- Empyema, osteomyelitis, arthritis, endocarditis, pneumonia,otitis,sinusitis, meningitis
• Invasive bacteremia
pyogranulomatous
Chronic persistent relapsing infections in staph infections
Toxin Mediated Diseases from Staph
- Toxin mediated diseases:
- Staphylococcal toxic shock syndrome(TSST-1)
- Staphylococcal food poisoning(Staphylococcal enterotoxin)
•Staphylococcal scalded skin syndrome (Exfoliative toxins)
All of these are superantigens!
Superantigen
Causes indiscriminate binding to MHC Class II receptor and releasing lots of cytokines and T cells
Virulence factors of Staph
- Protein A: Bind to FC portion of IgG- prevents phagocytosis
- Hemolysins: lyse RBC and other body cells
- Proteases: Destroy tissues
- Hyaluronidase: destroy connective tissue
- Lipases
- Alpha toxins: membrane damaging toxin
- Leukocidin (role in necrotizing fasciitis and pneumonia in dogs)
- Exfoliative toxins
- Biofilm formation
Staph in Dogs
Wound infections, surgical site infections, septic arthritis, osteomyelitis, Urinary tract infections, endocarditis, peritonitis, ocular infections, ear infections
- Necrotizing fasciitis and necrotizing pneumonia
- Bacterial folliculitis and furunculosis
Why do dogs get staph so easily?
“Epidermal barriers are less well developed” ???
Thin stratum corneum Lack of Follicular Plug
Diagnosis of Staph
Direct examination of the specimen
Gram positive cocci in clusters are indicative
Evidence of inflammation with abundance of neutrophils is highly suggestive
Culture (infection or contamination especially when CoNS is isolated)
Semiquantitative culture is useful (heavy, moderate, few)
PCR
(What are the issues associated with PCR in diagnosing Staphylococcal skin infections?- There is LOTS OF CONTAMINATION)
What kind of culture do you use with Staph
anerobic
Greasy Pig Disease
Exudative epidermitis caused by S. hyicus
Cattle: S. aureus
• Sub-acute chronic or acute mastitis
• Per-acute mastitis (Gangrenous mastitis)
Ulcerative Pododermatitis (S. aureus)
BIRDS Bumble foot; S. aureus
Botryomycosis
Botryomycosis- Rodents, Human, Horses Chronic pyogranulomatous inflammation Most common isolate : S. aureus
Treatment of staph
Antimicrobial susceptibility testing is a critical component
Variability in susceptibility pattern
Emergence of multidrug resistant Staphylococci
Make sure that the labs follow appropriate guidelines CLSI or EUCAST
Inducible Clindamycin resistance in macrolide resistant Staphylococcus
Nothing will substitute culture and AST
Therapy depends on Infection site and severity
Species variation and geographic variations,
1st generation Cephalosporins (Cephalexin) are the first line of treatment choice
Quinolones Not the first line of choice(resistance efficacy not well documented, and due to rapid development of resistance
All staphylococcus isolates which are macrolide(erythromycin) resistant should be
All staphylococcus isolates which are macrolide(erythromycin) resistant should be considered Clindamycin resistant unless otherwise confirmed by a D-test