MICROBIOLOGY
DIAGNOSING INFECTIOUS
DISEASES:
INTRODUCTION
●
The proper diagnosis of an
infectious disease requires
○ taking a complete patient
history,
○ conducting
a
thorough
physical examination of the
patient,
○ carefully
evaluating
the
patient’s
signs
and
symptoms, and
○ implementing the proper
selection,
collection,
transport, and processing of
appropriate
clinical
specimens.
CLINICAL SPECIMENS
● The various types of specimens,
such as blood, urine, feces, and
cerebrospinal fluid, that are
collected from patients and used
to diagnose or follow the
progress of infectious diseases
are referred to as clinical
specimens.
● The clinical specimens that are
used to diagnose infectious
diseases must be of the highest
possible quality.
● The most common types of
clinical specimens that are sent
to the hospital’s microbiology
laboratory (hereafter referred to
as the Clinical Microbiology
Laboratory or CML)
ROLE OF HEALTHCARE PROFESSIONALS IN
THE SUBMISSION OF CLINICAL SPECIMENS
● laboratory professionals do not
themselves make diagnoses,
● Laboratory professionals make
laboratory
observations
and
generate test results which are
used by clinicians to diagnose
infectious diseases and initiate
appropriate therapy.
IMPORTANCE OF HIGH-QUALITY CLINICAL
SPECIMENS
● High-quality clinical specimens
are required to achieve accurate,
clinically
relevant
laboratory
results.
● The laboratory must provide
written instructions for the proper
selection,
collection,
and
transport
of
clinical
specimens.
● When clinical specimens are
improperly collected and handled,
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○ the
etiologic
agent
(causative agent) may not
be found or may be
destroyed,
○ overgrowth by indigenous
microflora may mask the
pathogen, and/or
○ contaminants
may
interfere
with
the
identification of pathogens
and the diagnosis of the
patient’s
infectious
disease.
PROPER SELECTION, COLLECTION,
TRANSPORT OF CLINICAL SPECIMENS
●
●
AND
When collecting clinical specimens
for microbiology, these general
precautions should be taken:
● The specimen must be properly
selected.
● The specimen must be properly
and carefully collected.
● The material should be collected
from a site where the suspected
pathogen is most likely to be
found and where the least
contamination is likely to occur.
● Whenever possible, specimens
should be obtained before
antimicrobial therapy has begun.
● The acute stage of the disease
when the patient is experiencing
the symptoms of the diseaseis
the appropriate time to collect
most specimens.
● Specimen collection should be
performed with care and tact to
avoid harming the patient,
causing discomfort, or causing
undue embarrassment.
● A sufficient quantity of the
specimen must be obtained to
provide enough material for all
required diagnostic tests.
● All specimens should be placed
or collected into a sterile
●
●
container
to
prevent
contamination of the specimen
by indigenous microflora and
airborne microbes.
Specimens should be protected
from heat and cold and promptly
delivered to the laboratory so that
the results of the analyses will
validly represent the number and
types of organisms present at the
time of collection.
Specimens must be handled with
great care to avoid contamination
of the patients, couriers, and
healthcare professionals.
The specimen container must be
properly
labeled
and
accompanied by an appropriate
laboratory
test
requisition
containing adequate instructions.
Ideally, specimens should be
collected and delivered to the
laboratory as early in the day as
possible
CONTAMINATION OF CLINICAL SPECIMENS
WITH INDIGENOUS MICROFLORA
● Clinical specimens must be
collected in a manner that
eliminates, or at least reduces,
contamination of the specimens
with members of the indigenous
microflora.
TYPES OF CLINICAL SPECIMENS USUALLY REQUIRED TO
DIAGNOSE INFECTIOUS DISEASES
Specific techniques for the collection
and transport of clinical specimens vary
from institution to institution and are
contained in the institution’s Lab P&P
Manual.
BLOOD
● Within the body, the liquid portion
of blood is called plasma, but if a
blood specimen is allowed to clot,
the liquid portion is called serum.
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(Thus, serum is plasma that no
longer contains clotting factors.)
● Bacteremia—the presence of
bacteria in the bloodstream—may
or may not be a sign of disease.
Septicemia, on the other hand, is
a disease.
URINE
● Urine is ordinarily sterile while it
is in the urinary bladder.
However, during urination, it
becomes
contaminated
by
indigenous microflora of the distal
urethra.
● The ideal specimen for a urine
culture
is
a
clean-catch,
midstream urine specimen.
● A complete urine culture consists
of a colony count, isolation and
identification of the pathogen,
and
Antimicrobial
susceptibility testing.
CEREBROSPINAL FLUID
● Cerebrospinal fluid specimens
are treated as STAT (emergency)
specimens in the CML, where
workup of the specimens is
initiated
immediately
upon
receipt.
● Information obtained as a result
of examining a Gram stain of the
spinal fluid sediment will be
reported by telephone to the
clinician immediately; this is what
is known as a preliminary report.
SPUTUM
● Sputum is pus that accumulates
deep within the lungs of a patient
with pneumonia, tuberculosis, or
other lower respiratory infection.
● Laboratory workup of a good
quality sputum specimen can
provide important information
about a patient’s lower respiratory
infection, whereas workup of a
patient’s saliva cannot.
WOUND SPECIMENS
● Whenever possible, a wound
specimen should be an aspirate
(i.e., pus that has been collected
using a small needle and syringe
assembly), rather than a swab
specimen.
● The laboratory test requisition
that accompanies a wound
specimen must indicate the type
of wound and its anatomical
location.
GC CULTURES
● The initials GC represent an
abbreviation for gonococci, a
term referring to N. gonorrhoeae.
As
mentioned
earlier,
N.
gonorrhoeae is a fastidious
bacteria that is microaerophilic
and capnophilic.
● When attempting to culture
Neisseria
gonorrhoeae,
one
should remember that it is a
Fastidious, microaerophilic, and
capnophilic organism.
FECAL SPECIMENS
● Ideally, fecal specimens (stool
specimens) should be collected
at the laboratory and processed
immediately
to
prevent
a
decrease in temperature.
● In gastrointestinal infections, the
pathogens frequently overwhelm
the
indigenous
intestinal
microflora, so that they are the
predominant organisms seen in
smears and cultures.
THE PATHOLOGY DEPARTMENT
(“THE LAB”)
● Within a hospital, the CML is an
integral part of the Pathology
Department.
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○ isolate pathogens,
○ Identify
(speciate)
pathogens, and
○ perform
Antimicrobial
susceptibility testing when
appropriate to do so.
● In general, the processing of
clinical specimens in the CML
includes
○ examining the specimen
Macroscopically,
○ inoculating the specimen
to
appropriate
culture
media.
ISOLATION
AND
IDENTIFICATION
(SPECIATION) OF PATHOGENS
ANATOMICAL PATHOLOGY
● Most
pathologists
work
in
Anatomical Pathology, where
they perform autopsies in the
morgue and examine diseased
organs, stained tissue sections,
and cytology specimens.
CLINICAL PATHOLOGY
● Clinical pathologists are essential
for
diagnosing
diseases,
managing patient care, ensuring
lab test accuracy, conducting
medical research, and training
healthcare professionals.
● To isolate bacteria and fungi from
clinical specimens, specimens
are inoculated into liquid culture
media or onto solid culture
media.
BACTERIOLOGY SECTION
● The overall responsibility of the
Bacteriology Section of the CML
is to assist clinicians in the
diagnosis of bacterial diseases.
THE CLINICAL MICROBIOLOGY
LABORATORY
● The four major responsibilities
of the CML are to
○ process
clinical
specimens,
Flowchart illustrating the sequence of events that
occur within the Bacteriology Section of the Clinical
Microbiology Laboratory.
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MYCOLOGY SECTION
● The overall responsibility of the
Mycology Section of the CML is
to assist clinicians in the
diagnosis of fungal infections
(mycoses).
PARASITOLOGY SECTION
● The overall responsibility of the
Parasitology Section of the CML
is to assist clinicians in the
diagnosis of parasitic diseases.
Parasites are identified primarily
by
their
characteristic
appearance.
VIROLOGY SECTION
● The overall responsibility of the
Virology Section of the CML is to
assist clinicians in the diagnosis
of viral diseases.
MYCOBACTERIOLOGY SECTION
● The primary responsibility of the
Mycobacteriology Section (“TB
Lab”) of the CML is to assist
clinicians in the diagnosis of
tuberculosis.
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