Bacteriology and Mycology Flashcards
Specimen collection is collected during:
acute phase of illness; within 72 hours of illness
Collected samples must be transported without delay within _________
30 mins to 2 hrs
Level of prioritization: Critical/Invasive specimen (1)
CSF
Amniotic fluid
Blood
Pericardial fluid
Heart valves
Level of prioritization: Unpreserved (2)
Feces
Sputum
Wound drainage
Level of prioritization: Quantitation required (3)
Catheter tip
Urine
Tissues for quantitation
Level of prioritization: Preserved (4)
Urine
Feces
Swab in holding media
Level of prioritization: Batch processing (5)
Sputum
AFB culture
Specimen for culture:
Blood
CSF
Sputum
Throat swab
Nasopharyngeal swab
Cotton swab
Endotracheal aspirate
Calcium alginate swab
Stool
Specimen to rule out bacteremia, septicemia, and sepsis
Blood
Most common cause of sepsis normal flora:
E.coli, S. aureus
Blood pathogen that is never a normal flora
P. aeruginosa
Cleansing procedure before collecting blood for blood culture
70-95% alcohol -iodine scrub- alcohol rinse
Common contaminants of blood culture
Viridans
S.epidermidis
Cutibacterium acnes (P. acnes)
Dilution of blood to media
1:10
Result for blood culture:
7 days
Detection days for Brucellosis:
3-4 weeks
Detection days for leptospirosis
8 weeks
Microscopic agglutination test for leptospirosis uses:
Live leptospira antigen to patient’s serum
Macroscopic identification test for leptospirosis
Heat killed leptospira
Rapid Test for Brucellosis
Serum Agglutination Test
4 significant Brucella (scam)
B. Suis
B. Canis
B. Abortus
B. Melitensis
of sets to be collected for blood culture
2-3 sets
Hours of interval for blood cultures collected at 2 different sites
1 hour
Amount to be collected for blood culture: Adult
> 20 mL
Amount to be collected for blood culture: Pediatric
1-10 mL
Amount to be collected for blood culture: infants
0.5 mL to 1.0 mL
Anticoagulant for blood culture
0.025% SPS
SPS disadvantages
Inhibits other bacteria: Neisseria, G. vaginalis
Remedy for SPS inhibition
1% gelatin
Anticoagulant not used for bacterial culture
EDTA and Citrate
Procedure for blood culture that uses white top tube with EDTA
PCR procedure
Volume collected in blood culture in emergency cases
40 mL
Collect blood sample during:
peak of fever
Media for Blood culture (bacte)
TSB
BHI
Brucella broth
Castañeda bottle (biphasic media- both liquid and solid)
specimen to rule out meningitis
CSF
CSF tube intended for micro
Tube 2
Storage for CSF
37 deg C
Specimen for CSF smear preparation and culture
sediments
Cause of neonatal meningitis
S. agalactiae
Cause of meningitis for children < 5 years old
H. influenzae serotype b
Cause of meningitis for adult meningitis >29 years old
S. pneumoniae
Cause of meningitis for 5-29 years old
N. meningitidies
Cause of meningitis for elderly/immunocompromised
L. monocytogenes
Added to CSF collection from a shunt
thioglycollate
Thioglycollate allows the growth of
Facultative anaerobes
Strict aerobes
anaerobes
Specimen of choice for urine
clean catch midstream
Unable to void urine specimen
catheterized
Specimen of choice for anaerobic culture of urine
Suprapubic urine
Specimen for molecular studies like PCR in urine
1st morning urine
Usual request for urine
culture and sensitivity
1 cause of UTI
E. coli
UTI in females and elderly women with catheter
S. saphrophyticus
Other causes of UTI:
Klebsiella, E. faecalis (gram positive cocci)
Media used for susceptibility test for kirby bauer
MHA
Used for determining the dilution factor of urine sample
Calibrated loop
1 ul loop dilution factor
1000
10 ul loop dilution factor
100
Computation for colony count:
Colonies x dilution factor = colony count/mL of urine
Colony count considered as UTI
> 100,000
Urine without preservative: ___ priority
2nd
Urine with preservative: ______ priority
4th
Preferred preservative for urine culture
boric acid
Maintains accurate colony count preservative
Boric acid
Sputum is used to rule out:
Lower respiratory tract infections (pneumonia, bronchitis, TB)
Patient must be instructed to _______ with water prior to collection and cough deeply into container
rinse/gargle
Sputum volume requirement:
5 to 10 mL
Bartlett’s classification is used to differentiate
sputum and saliva
Bartlett’s classification: not a respiratory sample
no of SEC and PMN
no of SEC: >10
no of PMNs: <25
Cell that can be seen to confirm for true respiratory sample
Alveolar macrophage
Usual cause of pneumonia
K. pneumoniae
P. Aeruginosa
S. pneumoniae
H. influenzae
Causes pneumonia to those with cystic fibrosis
P. aeruginosa
1 cause of ventilator associated/intubated pneumoniae
P. aeruginosa
Process that should be done to sputum for detecting M. tuberculosis
Decontamination and Digestion
Process of removing contaminants and normal flora
Decontamination
Process of liquefying sample and free any trapped organism to make it detectable
Digestion
Gold standard for decontamination and digestion
N-acetyl-L-cysteine (mucolytic agent to digest) + NaOH (acts as decontaminant)
Other agents for decontamination and digestion
Z-TSP
4% NaOH
Cetylpyridium chloride Sodium chloride method
5% oxalic acid
BSL for contaminants
BSL 1
BSL for mucous membrane, ingestion, exposure
BSL 2
BSL for acquired aerosol transmission, inhalation
BSL 3
Specimen collection of SPUTUM according to Bailey’s and positive result
1 sputum in 3 days (1 per day)
positive: 2/3
DOH collection of SPUTUM; positive result
1st collection: morning
2nd collection: random
Positive: 1/2
Specimen of choice for detecting streptococcal infection and C. diphteriae
Throat swab
Major throat pathogen
S. pyogenes
Pharyngitis is caused by bacteria
S. pyogenes
Major throat flora
Viridans strep (S. mitis, S. mutans, S. salivarius)
No.1 cause of SBE and causes dental caries
Viridans
Viridans produces ______ and ______ which enhances attachments to teeth
Glucans and Dextrans
Specimen of choice for detecting B. pertussis
Nasopharyngeal swab
Causes whooping cough
B. pertussis
N. meningitidies is a normal flora from
nasopharynx, oropharynx
N. meningitidis is pathogen seen
CSF
Capsulated form of N. meningitidis
pathogenic
No capsule form of N. meningitidis
normal flora
Toxic to neisseria
Cotton swab
To collect N. meningitidis use:
Dacron
Calcium alginate
Component of cotton swab that is toxic to Neisseria
Fatty Acids
Specimen to collect when patient is on ventilator/intubated
Endotracheal aspirate
Not to be used for viruses as inhibits/prevent replication
Calcium alginate
Primarily used for aerobic bacteria
Swab
Anaerobic specimen should be rejected if it is collected using
SWAB
Specimen of choice for detecting GIT pathogens
Stool
Normally detected GIT pathogens
salmonella, shigella
Invasive bloody diarrhea
Shigella
4 serogroups of Shigella (d,f,b,s)
A: S. dysenteriae
B: S. flexneri
C: S. boydii
D: S. Sonnei
Serogroup of shigella that is a late lactose fermenter
S. Sonnei
Human pathogen of Salmonella
S. enterica
Animal pathogen of Salmonella
S. bongori
If stool specimen is not possible, specimen can be collected in
rectal swab
Media for stool specimen
EMB
MAC
SSA
Semi-quantitation technique for stool:
isolation streak (4 quadrants)
Critical values in Microbiology:
Positive
blood culture
CSF gram stain or culture
Cryptococcal antigen test or culture
blood smear for malaria
S. pyognes from a sterile site
Acid-fast smears or Mycobacterium culture
S. agalactiae or herpes simplex from genital site of a pregnant woman at term
Detection of significant pathogen (i.e., B. pertussis, Brucella, Legionella)
mostly used in laboratory; readily available for decontamination and digestant of sputum
4% NaOH
Agent added to sputum likely to contain P.aerugenosa
5% oxalic acid
Types of bacteria that is usually encountered in laboratory
Facultative anaerobes, aerobes, strict aerobes
Aerobes requirement:
21% O2 and 0.03% CO2
CAPNOPHILIC bacteria requires:
↑CO2
indicators of Gaspak Jar
Methylene blue and
Resazurin
Color of Resazurin in presence of oxygen
Pink
Color of Methylene blue in presence of oxygen
Blue
Absence of oxygen color in gaspak jar
colorless
Component of Gaspak Jar that maintais anaerobiasis
Palladium pellets
Common failure of gaspak jar
inactivation of catalyst due to repeated use
Anaerobic culture % of components
5% CO2
10%H2
85% N2
For detecting capnophylic (Neisseria) and microaerophilic
Candle Jar
microaerophilic requirements
5-10% CO2
5% O2
Darting motility
causes gastroenteritis
wings of seagull appearance
both microaerophilic and capnophilic
Campylobacter
Lowest concentration that inhibited bacterial growth of Antibiotic Susceptibility Testing
MIC (minimum inhibited)
Lowest concentration of antibiotic that can kill bacteria antibiotic susceptibility test
MBC (minimum bactericidal) /MLC (Minimum Lethal)
AST: can act against many bacteria
Broad Spectrum
AST: limited range of action
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