 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.
 Clinical Specimens
 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.
 Table 13-1. Types of Clinical Specimens Submitted to the Clinical Microbiology
Laboratory
 B- bacterial infection
 F- fungal infection
 P- parasitic infection
 V- viral infection
Type of Specimen Type(s) of Type of Specimen Type(s) of
Infectious Infectious
Disease that The Disease that The
specimen is Used specimen is Used
to Diagnose to Diagnose
Blood B, F, P, V "Scotch tape P
Bone marrow B Skin scrap F
Bronchial and V Skin snip P
Broncholar washes
Cerebrospinal fluid B, F, P, V Sputum B,F,P
(CSF)
Cervical and Vaginal B Synovial (joint) B
swabs fluid
Conjuctival swab or B, V Throat swabs B,V
scraping

Feces and metal swabs B, V (lepropsy and B, F, P,V

autopsy)specimen
s
Hair clippings I Urogenital
Discharge
material
Nail (fingernail and F B,P,V
toenail)
clippings
Nasal swabs B Urogenital B,P
secretions (e.g
vaginal discharge
material,
prostatic
secretion
B scraping V

 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 container breaks or leaks in
transit to the laboratory
 Should exercise extreme caution during the collection and transport of
clinical specimens to avoid sticking themselves with needles, 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
 Figure 13-1. Diagrammatic representation of the steps involved in the diagnosis
of infectious diseases
 Importance of High Quality Clinical Specimen
 High-quality clinical specimens are required to achieve accurate, clinically
relevant laboratory results.
 Three components of specimen quality:
− Proper specimen selection
− Proper specimen collection
− Proper transport of the specimen to the laboratory.
 Proper Selection, Collection, and Transport of Clinical Specimen
− 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 acute 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 micro-flora 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.
 Types of Specimens usually Required to diagnose Infectious Diseases
♥ 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.
 Figure 13- 2 Composition of Whole Blood

♥ 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
 Urine Composition

♥ Cerebrospinal Fluid
− Cerebrospinal fluid specimens are treated as STAT (emergency)
specimens in the CML, where workup of the specimens is initiated
immediately upon receipt.
♥ 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.
♥ 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.
♥ Wound swab
− The laboratory test requisition that accompanies a wound specimen
must indicate the type of wound and its anatomical location.
♥ GC Culture
− When attempting to culture Neisseria gonorrhoeae, one should
rember that it is a fastidious, microaerophilic, and capnophilic
organisms.
♥ Fecal specimen
− In gastrointestinal infections, the pathogens frequently overwhelm
the indigenous intestinal microflora, they are the predominant so that
organisms seen in smears and cultures.
− Fecal matter is collected to test for the presence of rotavirus
 The Pathology Department "The Lab"
 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 Anatomical Pathology
Personnel working on the Clinical Most Pathologists work in Anatomical
Pathology Department include Pathology, where they perform
pathologists, chemists, microbiologists, autopsies in the morgue and examine
medical technologists, medical laboratory diseased organs, stained tissue sections,
technicians. and cytology specimen.
 The Clinical Microbiology Laboratory
 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
 4 Major Responsibilities of the CML are to
1. Process clinical specimens
2. Isolate pathogens
3. I Identify pathogens
4. Perform antimicrobial susceptibility testing when appropriate to do so.
 In general, the processing of clinical specimens in the CML includes
 Examining the specimen macroscopically
 Examining the specimen microscopically
 Inoculating the specimen to appropriate culture media.
 Isolation and Identification (Speciation) of Pathogens
− To isolate bacteria and fungi from clinical specimens, specimens are
inoculated into liquid culture media of 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.
 CML professionals gather "clues" (phenotypic characteristics) about a
pathogen until they have sufficient information to identify (speciate) it.

♥ Mycology Section
− 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.
♥ Parasitology Section
− 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.
♥ 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 overall responsibility of the Mycobacteriology Section of the CML
is to assist clinicians in the diagnosis of Toberculosis.