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Chapter 13

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

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.
Figure 13-1. Diagrammatic representation of the steps
involved in the diagnosis of infectious diseases
Patient with symptoms of Patient is monitored
an infectious disease by the clinician for
consults with clinician success or failure.

Clinician makes Clinician interprets


preliminary diagnosis and report and prescribes
writes order for
treatment.
laboratory tests.

Appropriate specimen(s) Subcultures and


are collected and definitive identification
transported to the systems are examined
laboratory. and report issued.

Cultures are examined


Specimen and patient
and subcultures or
data are entered into the
definitive identification
laboratory computer or
systems set up.
log book.

Specimen is examined Preliminary or Specimen is


macroscopically and presumptive report may be cultured, and plates
microscopically. issued are incubated.
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.
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.
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, 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.

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


Pathology Department include Anatomical Pathology, ehere they
pathologists, chemists, perform autopsies in the morgue
microbiologists, medical and examine diseased organs,
technologists, medical laboratory stained tissue sections, and
technicians. cytology spcimen.
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
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.
To isolate bacteria and fungi from
clinical specimens, specimens are
inoculated into liquid culture media of
onto solid culture media.
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.
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.
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.
The overall responsibility of the Virology Section of
the CML is to assist clinicians in the diagnosis of
viral diseases.
The overall responsibility of the Mycobacteriology
Section of the CML is to assist clinicians in the
diagnosis of Toberculosis.

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