The document discusses clinical microbiology and the diagnosis of infectious diseases. It covers the following key points in 3 sentences: Clinical specimens must be properly collected, transported, and processed to accurately diagnose infectious diseases. A variety of specimen types can be used to identify different types of bacterial, fungal, parasitic and viral infections. The clinical microbiology laboratory works to isolate, identify, and test pathogens from specimens to assist clinicians in diagnosing and treating infectious diseases.

1. Chapter 13
Hoshino, Lyotta
Reyes, Floreva

2. 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.
• Implementing the proper selection, collection, transport,
and processing of appropriate clinical specimens.

4. The clinical specimens that are
collected from patients are used to
diagnose or follow the progress of
infectious disease.
The clinical specimens that
are used to diagnose
infectious diseases must be
of the highest possible
quantity.

5. Table 13-1. Types of Clinical Specimens Submitted to the Clinical
Microbiology Laboratory
Type of Specimen Type(s) of Infectious
Disease that The
specimen is Used to
Diagnose
Type of Specimen Type(s) of Infectious
Disease that The
specimen is Used to
Diagnose
Blood
B, F, P, V “Scotch tape prep”
P
Bone marrow
B Skin scrappings
F
Bronchial and
Bronchoalveolar washes
V Skin snip
P
Cerebrospinal fluid (CSF)
B, F, P, V Sputum
B, F, P
Cervical and Vaginal swabs
B Synovial (joint) fluid
B
Conjuctival swab or
scraping
B, V Throat swabs
B, V
Feces and rectal swabs
B, P, V Tissue (biopsy and autopsy)
specimens
B, F, P, V
Hair clippings
F Urethral discharge material
B
Nail (fingernail and toenail)
clippings
F Urine
B, P, V
Nasal swabs
B Urogenital secretions (e.g.,
vaginal discharge material,
prostatic secretion
B, P
Pus from a wound or
abscess
B Vesicle fluid or scraping
V
B, bacterial infection; F, fungal infection; P, parasitic infection; V, viral infection

6. Their Role in the
Submission of
Clinical Specimens

7. Should exercise extreme caution during the collection and
transport of clinical specimens to avoid sticking themselves with
needle s, cutting themselves with other types of sharps, or coming
in contact with any type of specimen.
Laboratory professionals make laboratory observations and generate
test results which are used by clinicians to diagnose infectious diseases
and initiate appropriate therapy.
According to the Clinical Laboratory Standard Institute, “All specimens should be
collected or transferred into a leakproof primary container with a secure closure.
Care should be taken by the person collecting the specimen not to contaminate the
outside of the primary container... Within the institution, the primary container
should be placed into a second container, wich will contain the specimen if the
primary cotainer breaks or leaks in transit to the laboratory

8. Figure 13-1. Diagrammatic representation of the steps
involved in the diagnosis of infectious diseases
Patient with symptoms of
an infectious disease
consults with clinician
Clinician makes
preliminary diagnosis and
writes order for
laboratory tests.
Appropriate specimen(s)
are collected and
transported to the
laboratory.
Specimen and patient
data are entered into the
laboratory computer or
log book.
Specimen is examined
macroscopically and
microscopically.
Preliminary or
presumptive report may be
issued
Specimen is
cultured, and plates
are incubated.
Cultures are examined
and subcultures or
definitive identification
systems set up.
Subcultures and
definitive identification
systems are examined
and report issued.
Clinician interprets
report and prescribes
treatment.
Patient is monitored
by the clinician for
success or failure.

10. High-quality clinical specimens are required to achieve
accurate, clinically relevant laboratory results.
Three components of specimen
quality:
Proper specimen collection
Proper specimen collection
Proper transport of the specimen to the
laboratory.

12. The specimen must be properly selected Must be properly and carefully collected.
The material should be collected from a site where he 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
agent(S) the patient is receiving.
The accute stage of disease is 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 require diagnostic tests.
All specimen must be placed or collected into a sterile container to prevent
contamination of the specimen by indigenous microflora and airborne
microbes.
Specimen must be protected from heat and cold and promptly delivered to the
laboratory.
Must be handled with great care to avoid contamination of the patients,
couriers, and healthcare professionals.
Specimens 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
as in the day as possible.

14. Blood
Within the body, the liquid portion of blood
is called plasma.
But if the blood specimen is allowed to clot,
the liquid portions is called serum.
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.

15. Figure 13-2. Composition of Whole Blood

16. Urine The ideal specimen for a urine culture
is a clean-catch, midstream urine
specimen.
Three parts to a urine culture:
A colony count
Isolation and identification of the
pathogen.
Antimicrobial susceptibility counting

17. Urine Composition

19. Cerebrospinal Fluid
Cerebrospinal fluid specimens
are treated as STAT
(emergency) specimens in the
CML, where workup of the
specimens is initiated
immediately upon receipt.

20. Sputum
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.

21. Throat Swabs
If a clinician suspects a pathogen
other that S. pyogenes to be causing a
patient’s pharyngitis, that
information must be included on the
laboratory test requisition.

22. Wound swab
The laboratory test requisition that
accompanies a wound specimen
must indicate the type of wound
and its anatomical location.

23. GC Culture
When attempting to culture Neisseria
gonorrhoeae, one should rember that it is a
fastidious, microaerophilic, and capnophilic
organisms.

24. Fecal specimen
In gastrointestinal infections, the
pathogens frequently overwhelm the
indigenous intestinal microflora, so that
they are the predominant organisms
seen in smears and cultures.

25. The Pathology Department
“The Lab”

26. Within a hospital, the CML is an integral
part of the Pathology Department.
The CM is located in the Clinical
Pathology division of the Pathology
Department.
Clinical Pathology
Personnel working on the Clinical
Pathology Department include
pathologists, chemists,
microbiologists, medical
technologists, medical laboratory
technicians.
Anatomical Pathology
Most Pathologists work in
Anatomical Pathology, ehere they
perform autopsies in the morgue
and examine diseased organs,
stained tissue sections, and
cytology spcimen.

27. Organization
Depending on the size of the hospital, the CML may
be under the directtion of a pathologist, a
microbiologist, or, in a smaller hospital, a medical
technologist who has had many years of experience
working in microbiology.
Responsibilities
The primary mission of the CML is to assist
clinicians in the diagnosis and treatment of
infectious diseases

28. Process clinical specimens
Isolate pathogens
Identify pathogens
Perform antimicrobial
susceptibility testing when
appropriate to do so.
Examining the specimen macroscopically
Examining the specimen microscopically
Inoculating the specimen to appropriate
culture media.

29. To isolate bacteria and fungi from
clinical specimens, specimens are
inoculated into liquid culture media of
onto solid culture media.

30. The overall responsibility of the Bacteriology
Section of the CML is to assist clinicians in the
diagnosis of bacterial diseases.
CML professionals gather “clues” (phenotypic
characteristics) about a pathogen until they have sufficient
information to identify (speciate) it.

31. The overall responsibility of the Mycology
Section of the CML is to assist clinicians in the
diagnosis of fungal infections (mycoses)
When isolated from clinical specimens, yeasts are
identified using various biochemical tests, primarily
based on their ability to catabolise various
carbohydrates.
When isolated from clinical specimen, moulds are
identified using a combination of rate growth and
macroscopic and microscopic observation.

32. The overall responsibility of the Prasitology
Section of the CML is to assist clinicians in the
diagnosis of parasitic diseases. Parasites are
identified primarily by their characteristics
appearances.

33. The overall responsibility of the Virology Section of
the CML is to assist clinicians in the diagnosis of
viral diseases.

34. The overall responsibility of the Mycobacteriology
Section of the CML is to assist clinicians in the
diagnosis of Toberculosis.