Diagnosing Infectious DiseasesChapter 13

Hoshino, LyottaReyes, 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.

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 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 VB, bacterial infection; F, fungal infection; P, parasitic infection; V, viral infection

Their Role in the Submission of Clinical Specimens

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

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.

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 collection

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 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.

Types of Specimens Usually Required to Diagnose Infectious

Diseases

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

SputumLaboratory 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 SwabsIf 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 swabThe laboratory test requisition that accompanies a wound specimen must indicate the type of wound and its anatomical location.

GC CultureWhen 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

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.

The Clinical Microbiology Laboratory

OrganizationDepending 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.

ResponsibilitiesThe 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:

Process clinical specimensIsolate pathogens

Identify pathogens

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 SectionThe 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 SectionThe 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 SectionThe 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.

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