Flashcards
Week 4 Nov 4-8
Cards in this deck (97)
- 1Laboratory FunctionsDiagnosis (culture / serology / molecular / proteomics)
Guidance for treatment
Outbreak detection
Support for infection control
Collect & Collate information (follow trends in resistant pathogens/ anntimicrobial susceptibility summaries)
Epidemiological studies - 2Lab members provide advice on..- Appropriate specimen collection / transport
- Interpretation of laboratory results
- Managing patients (antimicrobial therapy)
- Infection control issues - 3Laboratory Work-flowYou (the doctor) directly affect these
•Collection
•Transport / storage
•Accessioning
Quality Control
•Processing
•Interpretation / Identification
•Susceptibility testing / Molecular testing
•Reporting / Documentation - 4Specimen Collection Issues to consider•Will the specimen provide useful information.
•Choice of the type of specimen
•Instructions for collection by patient
•Transport time to the laboratory = some specimens are okay for a limited amount of time
•Need for transport media
•Quality of the specimen
•Risk of false positive or false negative results
•Specimens for culture are NEVER placed in formalin = trying to grow something not preserve it, sometimes used for stool looking for pathogen eggs - 5Accessioning•Process of identifying the specimen
- is the specimen properly labelled?
- has the specimen been properly collected?
- time / date of collection / transport
Specimen accepted and processed or rejected?
- Rejection criteria?
•Is the specimen a “STAT” (dont usually say this anymore) or “Life Threatening” specimen, red stickers for people on the operating table, drop what youre doing life or death
•Processed in-house (99% in house) or referred out (rare testing send out)?
•Each specimen received must be coded and entered into the Lab Information System - 6Why will we reject your specimen!- Missing information (name, specimen type etc)
- Info on specimen does not match requisition
- Specimen is too old, improper transport
- Swab / transport media expired
- Inappropriate specimen
- Poor quality specimen
- Specimen is leaking
- Duplicate specimens
• You MUST NEVER submit a specimen on yourself or family member!! - 7Transport of Specimens• Transport time to the laboratory
• Specimen type - swabs, urine, blood, stool, fluids, scrapings
• Transport media
- Maintain viability but inhibit growth (usually)
- Cary Blair Transport Media
- SAF (parasites)
• Incubation / refrigeration / storage - 8Processing of Specimen•Type of specimen - swab, fluid, blood, stool etc
•What tests are required? - culture / serology / molecular / POC /
Microscopy (gram stain, AFB stain etc)
•Does the specimen require additional processing
- decontamination
- centrifugation
•What media are required?
•Incubation conditions? - 9Sputum / Specimen Grading- depends on number of neutrophils and number of epithelial cells
Q0 - Very Poor Quality Specimen: Microscopic examination shows oropharyngeal contamination.
Specimen not processed.
Q1 - Poor Quality Specimen: Microscopic examination shows oropharyngeal contamination. This specimen has been processed but results should be interpreted with caution. Repeat if possible.
Q2 - Good Quality Specimen
Q3 – Very Good Quality Specimen - 10Interpretation / Identification•Microscopy (0.5 hour - same day)
•POC (0.5-1 hr)
•Culture (24 hr – 3 weeks)
•Direct MALDI-TOF (same day)
•Serological (same day / week)
•Molecular
- same / next day for diagnostics
- same / next week for epidemiological studies
•Susceptibility testing (additional 24-72 hours)
- longer for Mycobacteria - 11Blood Culture Collection• A minimum of “one set” (set = two blood cultures) [preferably 2 sets = 4 bottles] per septic episode should be obtained. (A set originates from the same venipuncture) so you might be taking blood from both arms to have 2 sets
• 95% of bacteremias detected when ≥ two blood cultures are drawn.
• Ensures an adequate volume of blood is cultured.
•Helps distinguish between clinically important and contaminant microorganisms
• A finite percentage of blood cultures are typically contaminated (3 to 5%) in SJ its 0.9% which is awesome. Discard the first few mls because it might contain skin plug - 12Lab requisitionPhysician’s name / contact info
Patients Name
Patients Birthday
Unique Identifier
- Health card number
- Passport number
Specimen Type
Method of collection - there are three different types of ways to collect urine, have to be specific
Date / time of collection
Required analysis
Relevant Clinical Information
Drug allergies (i.e. Pen allergy) - 13Susceptibility Testing- used as a guide for treatment
- tracking emergence of resistance
Breakpoint = is the bug susceptible to antibiotic, intermediate or resistant
Dependent on the bug, the drug (depends on distribution), and the site of the infection (blood of CSF? for example)
MIC = minimum inhibitory concentrations
stops visible growth of bacteria
Lab will tell you specific answers for antibiotics, dont give all the information - 14Susceptibility Test Methods•Kirby-Bauer (disk diffusion)
•Broth / agar microdilution
•E-Test
•Automated systems (Vitek / Microscan)
•Proportion method (Mycobacteria)
•Screening methods
- agar based
- nitrocephin disks - 15Disc Diffusion Methodmost common method
◼ Interpretation of results
◼ By comparing the zones of inhibitions diameters with “standard tables”, measurement is important just a zone isn't significant
Report back as susceptible or resistant no the diameter size because doctors dont care - 16e-testMIC = minimum inhibitory concentration
The point where the soze of inhibition intersects the plastic strip which is full of antitiocs. Just wait to see where the zone intercepts the strip
very quick and easy great method - 17Dilution Method•Broth dilution/ Agar dilution methods
•Permit quantitative results:
•Indicates concentration of drug necessary to inhibit (bacteriostatic
activity) or kill (bactericidal activity) the microorganisms tested
◼ Minimum Inhibititory Concentration (MIC)
◼ Minimum Bactericidal Concentration (MBC)
Diluting until tubes you can produce inhibitory and then plate the last three after you dilute in tubes - 18Automated systems Vitek- Broth dilution based system
- Limited breakpoints
- Useful for common (most) pathogens
- May not be reliable for more fastidious (need to be accurate or detailed) pathogens - 19Gram positive CocciIn pairs and chains
- Enterococcus
- Streptococcus
- Peptostreptoccus = anaerobe posititve
In clusters
- Staph aureus
- Staph lugdunensis
- Staph epidermidis
- Staph saprophyticus
- other coagulase negative staphylocci - 20Catalasetest to differentiate Staph and Staph to see the chains
Off an agar plate onto a glass slide you have to add hydrogen peroxide to figure out the difference
STAPH = Catalase positive with bubbles breaking up into water and oxygen
STREP = Catalase negative NO bubbles - 21Staphylococci• Catalase positive
• Facultative anaerobes = can do with or without oxygen
• Commonly found on skin & mucous membranes
• >20 species recognized
• Species commonly associated with human disease:
- S. aureus
- S. lugdunensis
- S. epidermidis
- S. saprophyticus - 22How to Differentiate Staph aureusPresence of coagulase
The coagulase different is why aureus is talked about so specifically on its own, very significant in clinical practice
Take fibrinogen and turns it to fibrin
When blood clots one of the steps is fibrinogen to fibrin so when staph is present it can clot your blood = BAD
After you determine its staph not strep the first question is if its aureus
Add a little bit of the colony of agar and add it to a plasma tube and let it incubate see if there is a fribin visible clot - 23S aureus Virulence factors1. Coagulase = most important marker of Staph virulence.
2. Protein A
3. Enterotoxins = preformed toxins
4. Toxic shock toxin = superantigen
5. Exfoliative toxin - 24Pathogenesis of Staphylococcal Infections• Cellulitis
• Abscesses
• Impetigo
• Scalded Skin Syndrome
• Endocarditis
• Osteomyelitis
• Pneumonia
• Food poisoning
• Toxic Shock - 25Coagulase-negative staph• Everyone carries coagulase-negative staphylococci on their skin
• Virtually impossible to eradicate CoNS, even with disinfectant use and vigorous hand washing
• Because of affinity for synthetic materials, devices inserted through the skin are frequently infected
• A polysaccharide; this is secreted into the area around the staphylococcal micro-colony = slime production
- Slime allows coagulase-negative staph to adhere to synthetic material
• Slime is also anti-phagocytic and inhibits chemotaxis - 26S. lugdunensis- coagulase negative staph
- considered as virulent as S. aureus
- produces clumping factor on slide coagulase test, producing bound coagulase so we dont consider it positive on coagulase test like Staph aureus is but it is similar to aureus because it can do the bound coagulase thing - 27S. saprophyticusUropathogen associated with young women
- 28Pustular impetigo• Vesicles at different stages of development
• Pus-filled vesicles on erythematous base
• Also dry and crusted lesions
Seen in younger kids - 29Toxic shock syndrome• Initially described in menstruating women and persons with localized staphylococcal infections
• Systemic absorption of TSST-1 = toxin forms bridge between T cell receptor and APC receptor. The formation causes incredible cytokine cascade that is very unwanted because the immune system freaks out causing the below problems
• TSS produces fever, blood vessel dilation, and a sunburn-like rash
• cytokine stimulation
- hypotension
- multi-organ failure
• fatality rate is ~5% - 30Food poisoning (heat stable toxin)• Acute onset - 2 to 4 hours after ingestion
• Severe nausea, vomiting, abdominal pain and diarrhoea
• Self-limiting and resolves in 12 to 24 hours
• Occurs when food is contaminated with enterotoxin producing staphylococci from a food handler - 31Osteomyelitis from Staph- Infection in bones and joints may occur as a result of bacteremia or because of direct inoculation
- 32Endocarditis / bacteremia- S. aureus is one of the most frequent causes of bacteremia
- Frequently in IV drug users
- S. aureus may stick to heart valves (damaged and undamaged) and produce endocarditis
- may seed other organs of the body, producing localized or multiple abscesses - 33Streptococcus speciesBeta hemolytic strep = zone of clearance
- S pyogenes Group A
- S agalactiae Group B
- Groups C, F, G
Non-beta-hemolytic streptocci
- S. pneumoniae
- Strep viridans group
- Enterococcus - 34Viridans Streptococcus• S. mutans, S. mitis, S. sanguis, S. salivarius
• Bacteremia = in the bloodstream
• Endocarditis
• Dental caries - 35S. pyogenes: Group A Streptococcus• Pharyngitis (Strep throat)
• Necrotizing fasciitis
• A more simple cellulitis 99% are caused bt Staph aureus on group a strep
• Toxic shock similar to superantigen with staph infection - 36Community acquired pneumonia- S. pneumoniae
- H. influenza
- M. pneumoniae
- C. pneumonia
- Legionella pneumophilia
some other anaerobes - 37Pneumococcal Virulence Factors• Capsule is the most important virulence factor
• Pneumolysin (hemolysin)
• Secretory IgA protease = found in the airways and the protease can break down the IgA help protect itself - 38S. pneumonia commonly causes- Community-acquired pneumonia (CAP)
- Acute sinusitis
- Otitis media
- Bacterial meningitis - 39Enterococci cause...Cause...
- Urinary tract infections
- Bacteremia & endocarditis
- Intra-abdominal infection
**Vancomycin resistance an increasing concern ** - 40Clostridium Types• C. perfringens = Wound & soft tissue infection. Caused gangrene.
• C. botulinum = botulism. Sometimes used for Botox other medical purposes. Stops the ability of muscles to contract
• C. tetani = Tetanus. Contraction of muscles
• C. difficile = colitis. - 41Listeria• Aerobic
• Gram positive bacillus
• Non-spore forming
• Beta-hemolytic
• Tumbling motility at room temperature
• Intracellular pathogen
• Can hijack cytoskeleton of the cell and moves through cells while taking membrane with it making a vacuole
It is an intracellular pathogen
Related to food outbreaks on the media - 42Listeria and Non Pregnant adults• Transient asymptomatic GI carrier state
• Sepsis
• CNS
- Meningitis
- Meningoencephalitis
- Rhomboencephalitis = posterior part of brain being infected
• Focal lesions due to haematogenous spread (through the blood stream) - 43EnterobacteriaciaeGlucose fermenter Oxidase negative
- E. coli
- Klebsiella speices
- Proteus species
- Salmonella species
- Shigella species - 44MacConkey Agar• A selective agar plate to help differentiate
• Crystal violet and bile salts = inhibits gram positives
• Neutral red and lactose = helps differentiate - 45Cytochrome Oxidase- really quick test to do
- Oxidate positive = P.aeruginose and Vibrio species
- Oxidase negative = enterobacteriaceae - 46UTIs that are concerning and should be treated if asymptomic- patients about to go for an invasive urinary tract procedure
- Renal transplant patients
- Pregnant women
Normally no symptoms = DONT treat - 47CystitisUTI presumed to be confined to the bladder
- 48Pyelonephritisa more invasive infection
inflammation of the kidney and renal pelvis - 49Intrarenal abscess / perinephric abscesscollection of pus in the kidney or in
the soft tissue surrounding the kidney
Intrarenal = inside the kidney
Perinephric abscess = near or around the kidney - 50Most common causes of UTIs= KEEPS
K pneumoniae
E coli = THE BIG PLAYA 80% infections
E nterococcus
P roteus
S taphulococcus saprophticus - 51Catheter associated Nosocomial (hospital stetting) UTISShort term hospital UTI
- E. coli, enterococcus, proteus, pseudomonas, and S. aureus
Long term hospital
- E. coli, enterobacter, proteus, candida, pseudomonas, morganella, providencia, candida - 52Uropathogenic E. coli-Adherence is major virulence factor
- P fimbria = bind to the P antigen present on urothelial cells
- K antigen associated with upper tract infections
- Type 1 fimbria associated with increased inflammation
- Hemolysins promote pores in cell membrane
-Flagella promote motility - 53Proteus, Morganella, Providencia major virulence factorsurease producing organisms = crytal formation
biofilms
highly motile
use fimbriae for attachment - 54Virulence Factors Associated with Enterobacteriaceae- E.coli has many characteristics
- Proteus, Morganella, Providencia produce urease associated with kidney stones
- Biofilms = colonizing a catheter protects from host defenses
- Highly motile moving up the urinary tract using fimbriae for attachment - 55Etiology of GastroenteritisGram negatives are important cause but not the only causes
•E.coli = negative
•Salmonella = negative
•Shigella spp. = negative
• Campylobacter
• Yersinia enterocolitica
• Listeria monocytogenes
• Vibrio spp.
• Parasites
• Viruses - 56Enterohemorrhagic E. Coli (EHEC)•Produce shiga-toxins = Also called verocytotoxins
- bloody diarrhea
- very not good - 57Shigella• Shigellosis = bacillary dysentery
- Most communicable of the bacterial diarrhoeas HIGHLY INFECTIOUS
S. dysenteria typically most virulent
- Shiga toxin - 58Salmonella Virulence Factors~2000 serovars, different antigens are associated with it
• Very Motile
• fimbriae
• Biofilm formation
• Invasion of Peyer’s patches in the colon
• Emergence of drug-resistance - 59Salmonella Pathogenesis• Gastroenteritis
• Bacteremia without GI symptoms
• Enteric Fever = Classically bimodal course
• Carrier state - 60Epidemiology of P. aeruginosa• Glucose non-fermenter oxidase positive, will grow on MacConkey
•Environmental organism found in soil & water
•Opportunistic, nosocomial (originating in the hospital) pathogen of
immunocompromised individuals
•Typically infects the respiratory tract, urinary tract, burns & wounds - 61Epidemiology of P. aeruginosa• Pneumonia with people who have Cystic fibrosis & bronchiectasis
• Septic shock with Neutropenic (low neutrophils with chemo) patients
• Urinary tract infections with Catheterized patients
• GI tract like colitis with Premature infants & neutropenic patients
• SSTI with patient Burns & wounds
OPPORTUNISTIC PATHOGEN!! - 62Major Virulence Factors Associated with P. aeruginosa•Antibiotic resistance
•Pili
• Mucoid polysaccharide
• Special Pigments - 63P. aeruginosa Treatment Options:Challenging organism to treat
Only 1 oral option, many are highly toxic
Ceftazidime
Cefepime
Piperacillin
Carbapenem
Aminoglycoside
**Ciprofloxacin = oral option, fluoroquinolones
Colistin
Aztreonam - 64How antibiotic resistance can occur- Loss of porins = antibiotics cant get in
- Over-expression of transmembrane efflux pump
- B-lactamases in periplasmic space
- Bypass targets
- Mutations in lipopolysaccharide structure
- Ribosomal mutation or modification
- Antibiotic modifying enzymes - 65Nosocomial(of a disease) originating in a hospital.
- 66Gastroenteritis caused by bacterial toxins- Staphylococcus aureus
- Bacillus cereus
- Clostridium perfringens
- Clostridium difficile - 67Bacteriostatic vs BactericidalBacteriostatic = inhibits growth MIC
Bactericidal = kills organism MBC
Don't always need to use bactericidal, but sometimes like with endocarditis you HAVE to kill it all - 68Differential toxicitybased on the concept that the drug is more toxic to the infecting organism that to the host
Majority of antibiotics are based on naturally occurring compounds or may be semi-synthetic or synthetic. - 69What is the ideal antibiotic•No / low toxicity to the host, well tolerated.
•Low chance of development of resistance.
•Does not induce hyper-sensitivities
•Rapid and extensive tissue distribution.
•“Relatively” long half-life.
•Free of interactions with other drugs.
•Convenient for administration / relatively inexpensive. - 70Empiric Therapyinfectious diseases are frequently acute processes and requite immediate treatment before having answers from the lab, treat based on other factors before getting the results back
- 71Threats of Antimicrobial Resistance- Avian influenza
- HIV/AIDS
- Respiratory disease, pneumococci
- Enteric disease, shigella
- Multidrug resistant TB and Extensively drug resistant TB
- Multidrug resistant gonorrhea
- Multidrug resistant malaria
- Community acquire MRSA
- MRSA, VRSA, VRE and other nosocomial infections - 72Factors that may accelerate the development of resistance-inadequate levels of antibiotics at the site of infection.
-duration of treatment too short / long
-overwhelming numbers of organisms
-overuse / misuse of antibiotics
-poor quality counterfeits
-animal husbandry
-no prescription requirement (OTC).
-frequent exposure to the same class - 73Cellular Targets of Antibiotics Cell wall synthesis inhibitors-Beta lactams = penicillins, cephalosporins, carbapenems
-Glycopeptides = Vancomycin
-Fosfomycin = inhibits cell wall but does it very differently - 74Cellular Targets of Antibiotics Nucleic Acid Synthesis-Folate synthesis = sulfonamides and trimethoprim
-DNA gyrase = quinolones
-RNA polymerase = Rifampin - 75Cellular Targets of Antibiotics Protein Synthesis-50S subunit = macrolides, clindamycin, linezolid, chloramphenicol, streptogramins
-30S submit = tetracyclines and aminoglycosides - 76General Mechanisms of Resistance-Altered permeability
-Inactivation/destruction of antibiotic
-Altered binding site
-New binding sites
-Efflux pumps mechanisms
-Bypass of metabolic pathways - 77Penicillins1. Penicillin V, G
2. Amoxicillin/ ampicillin
3. Cloxacillin = anti-staphlycoccal
4. Piperacillin = Anti-pseudomonal - 78B-lactam resistance mechanisms1. Production of a -lactamase = most common resistance method
2. Altered PBP = happening with S. pneumoniae
3. Novel PBP = happening with MRSA
4. Altered permeability = gram negatives approach - 79Natural Penicillins (Pen G Benzylpenicillin/V)- β-haemolytic Streptococci (NEVER RESISTANT!) never ever been described
- α-haemolytic Streptococci (if susceptible i.e. not predictable)
- Treponema pallidum (syphilis)
- Cannot be used against Staphlycoccus, gram negatives or gut anaerobes - 80AminopenicillinsExcellent: Enterococcus faecalis, Listeria, H. pylori, non beta-lactamase producing H.influenzae
Good: many coliforms like E. coli, salmonella, and shigella
Poor: staphylococci and gut anaerobes - 81First-Generation Cephalosporins- Used to treat skin and soft tissues infections because it is likely staph and strep infections. Convenience drugs for S. aureus and streptococci
- In patients allergic to penicillins
- Surgical prophylaxis - 82Second-Generation CephalosporinsCefuroxime – respiratory drug treating Hemophilus or M. catarrhalis.
- 83Third-Generation Cephalosporins- Really good for gram negatives and reasonable for gram positive
- Used for meningitis, Community Acquired Pneumonia (CAP) or nosocomial pneumonia, gonorrhea, Lyme, and febrile neutropenia which is suppressed bone marrow (pseudomonal coverage) - 84Carbapenems = they kill everything EXCEPT- MRSA and MRSE
- Enterococcus faecium
- Stenotrophomonas maltophilia
- Pseudomonas cannot be killed by Ertapenem, have to use Meropenem or Imipenem - 85GlycopeptidesVancomycin
Can treat gram positive cocci like…
- MRSA and coagulase negative Staphylococci. Still drug of choice for MRSA
- Penicillin resistant S. pneumoniae
- Penicillin resistant Enterococcus
Can treat gram positive rods like…
- C. jeikeium
- C. difficule which must be given orally - 86Fosfomycinprevents the synthesis of the building blocks for peptidoglycan
uncomplicated cystitis in females caused by E. coli/ E. faecalis - 87FluoroquinolonesMechanism
- DNA gyrase, DNA cant reform
Resistance
- Spontaneous mutations in parC and gyrA *** results in AA substitution – reduced affinity for the antibiotic TWO mutations and they are step wise
- Down regulation of porins and up regulation of pumps
Use
- good oral availability.
- 1-3rd generations - 88Metronidazole (Flagyl)Mechanism
- anaerobic conditions = produces free radicals
- Inhibits nucleic acid synthesis by disrupting/damaging DNA
Resistance
- Reduced drug activation
- Reduced permeability and increased efflux
- Altered DNA repair
Use
- Anaerobic infections
- C. difficule
- H. pylori
- Antabuse effect - 89MacrolidesMechanism
- inhibitors of protein synthesis
- binds to ribosomes
Resistance
- efflux pump
- modify the target site
Use
- mild community acquired pneumonia
- pertusis
- atypical pathogens
**can prolong QT cardiac cycle and processed by Cyto P-450 - 90ClandamycinWorst cause of C dificile as a side effect
Used for
- Orofacial infections
- Necrotizing pneumonia = typically from aspiration
- Intra-abdominal infections
- Diabetes/ischemic feet
- Gram positive infections = necrotizing fasciitis treated - 91TetracyclinesMechanism
- Bind reversibly to 30S ribosomal subunits
- Inhibits protein synthesis
Resistance
- Energy dependent efflux
- Enzymatic inactivation
- Ribosomal protection
Use
- Atypical bacteria
- Zoonotic
- most gram positives
- can lead to discoloration of teeth - 92AminoglycosidesGentamicin, Tobramicin, Amikacin
Mechanism
- Excellent gram negative
- Binds to ribosomal subunit, enter through energy dependent transport system
Resistance
- enzymatic modification
Use
- Complicated UTIs (Pyelonephritis), highly concentrate in urine!!!
- Mixed infections without abscess formation
- Endocarditis treatment = penicillin and gentamycin treating enterococcus have synergistic effect
- Pseudomonas infections
- For resistant Gram Negative bacilli - 93Trimethoprim/SulfathoxaleMechanism
- blocks folic acid synthesis at two points
- Ultimately blocks production of DNA
Resistance
- Chromosomal
- Plasmids
Use
- GI infections
- PCP pneumonia
- Very active anti staph agent!! - 94Colistin- Work against bacterial membrane
- Displaces divalent cations from phosphate groups of membrane lipids
- Disrupts outer membrane
- Useful in treating Multi Drug Resistant gram negative infections (afghan/Iraq war)
- Renal, neurotoxicity - 95Daptomycin- Great against gram positive agents and resistant (MRSA)
- Insertion into bacterial cell membrane
- Rapid membrane depolarization and K+ ion flux
- Bactericidal concentration-dependent killing
- CANNOT use with respiratory tract infection because mucous takes away effect
- Currently very expensive but hopefully one day be used instead of vancomycin - 96Approach to ID triangle1. Host
2. Environment
3. Agent = type of pathogen, virulence factors, resistance - 97—
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- Med 1 Host Defense Flashcards on Week 4 Nov 4-8, created by Sarah Purcell on 07/11/2019.
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