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Interpretation of
Microbiology Results
Harm
patient
GARBAGE IN,
GARBAGE OUT
QUALITY IN,
QUALITY OUT
Test ordering
Result transcription
Order transcription
Patient preparation
Result delivery
Sample testing
Specimen collection
Result review
Action taken on basis
of result
Specimen identification
Specimen transport
Pre analytical
Analytical
Post analytical
Important requirements
Adequate collection, transport, and
processing of clinical specimens
Cooperation among medical team members :
Clinical practitioners
Nurses
Laboratory practitioners
Specimen Collection
Important data
Patient identity (name, age, sex, ward)
Clinician identity (name, adress, ph-no.)
Specimen (type, source, time of
collection)
Relevant clinical information
Antibiotics usage
Laboratory test required
Patient-Collected Specimens
Urine, Sputum, Stool, Semen
Never be assumed that the patient
knows how to collect
Printed instruction: will be read?
understand?
Verbal, pictures and written
Urine
Mid stream urine ( Clean catch urine,
urin porsi tengah)
Urine Supra pubic puncture
Urinary Catheter
Swab
Upper respiratory tract, external ear,
eye, genital tract
Tips of swab:
Cotton: excessive fatty acids, toxic to
certain bacteria
Dacron or polyester
Sputum
Bronchial washing
Bronchial brushing
Bronchoalveolar
lavage
Transtracheal
aspiration
Tracheal aspiration
Juni 2006
Genital Specimens
Specimen
source
Potential
Pathogens
Primary plating
media
Cervix
Chlamydia; GC;
herpes
Cul-de-sac
Endometrium
Mixed aerobes
/anaerobes
Vagina
Group B strep;
Mixed aerobes
anaerobes BV
Room temperature:
Abscess, lesion, wound, body fluids, CSF for
bacteria, inner ear, genital, nasal, throat,
tissue
Bacteremia
When ?
Draw blood cultures as close as possible to the episode of
chills or fever. Do NOT delay, as recovery of
microorganisms diminishes with time after the fever spike.
Chills
Blood Cultures
Bacteremia
Level
Temp
30
0
Time (min)
60
Effect of Volume
100
90
80
70
60
% Relative 50
Yield
40
30
20
10
0
5
10 15 20 25 30 35 40 45 50 55 60
ml
*Reprinted from Infectious Disease Clinics of North America, Vol 16, M.L. Towns and L. B.
Reller, Diagnostics methods: Current best practices and guidelines for isolation of bacteria
and fungi in infective endocarditis, p. 363-376(2002) with permission from Elsevier.
Blood volume
Adults: bacteria <30 CFU/ml, more blood that is
cultured, the greater the chance of isolating the
organism
Infants: bacteria >1000 CFU/ml
26
Anticoagulation
Entrapped bacteria within a clot may go
undetected
Inoculated into sterile tube containing an
anticoagulant for transport to the laboratory
Heparin, EDTA, Citrate : not recommended
SPS (Sodium polyanethol sulfonate)
0,025-0,03%
SPS : anticoagulant, anti-complementary, antiphagocytic, interferes activity of some antibiotics
Inhibit Neisseria spp., Gardnerella vaginalis,
Streptobacillus moniliformis, Peptostreptococcus
anaerobius
Specimen Rejection
Suboptimal specimens
Require a phone call to the person in charge of
collecting specimen
Lab never discharge specimen before contacting
the health care team
In certain situation it may be necessary to process
suboptimal specimen
notation in final report!
Microbiology Investigation:
Microscopic
Culture and susceptibility tests
Serology:
Antigen detection
Antibody detection
Molecular:
Detection of nucleic acid
Result review
Action taken on basis of result
Pharyngitis
Normal pharyngeal flora:
Nose cultures
Not predictive of the etiologic agents of
sinus, middle ear, or lower respiratory tract
infections
Pathogen directed:
Screening of MRSA
Detection of Bordetella pertusis
Urine culture
105 CFU/ml urine in asymptomatic patient
102 CFU/ml urine in patient with clinical
sign and symptom of UTI
group B streptococci:
Pregnant women: any amount have
implications for the fetus
Female 12-55: >50 CFU/ml urine
Interpretative Reading of
Antibiotics Susceptibility Test
MDROs
Resistant Staphylococcus aureus : MRSA, VISA, VRSA
Vancomycin Resistant Enterococcus (VRE)
Gram Negatif Bacteria (GNB):
Other MDROs
Plasmid mediated AmpC -lactamases
Factors,
affect transmission and spread
environmental factors, both in the
hospital and the community
the use of antibiotics
the antimicrobial fitness of the
pathogen
Cultivation-dependent
methods entail long
delays for many
pathogens (fastidious)
Legionella pneumophila
Problem Solving?
Alternative tests:
Serology
Nucleic Acid Amplification : PCR
Antigen detection
Microbial-specific structural components (antigens) are
identified in specimens obtained from an infected host
Can be used to identify microorganisms once they have
been recovered in culture
Methods depends on the fact that some microbial
components are chemically unique and form areas on
the molecule known as antigenic determinants
Antigen can be recognized by and can combine
specifically with antibody molecules to form stable
products
Antibody detection
IgM antibodies
detected earlier in the infection (7-10 days)
Usually indicative of active, as opposed to past,
infection
IgG antibodies
Previous infections or immunization
Serodiagnosis of an infectious diseases requires
measurement of IgG concentration on both acutephase and convalescent-phase serum specimens
Chronic infections, epidemiology
Limitations of PCR: