1. Chapter 13

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

3. Clinical Specimens
Specimens collected from patients, such as blood, urine, feces, and cerebrospinal fluid (CSF), are known as clinical specimens.
Specimens commonly submitted to the hospital’s Clinical Microbiology Laboratory (CML) include blood, bone marrow, bronchial washings, sputum, CSF, cervical and vaginal swabs, feces, hair and nail clippings, pus, skin scrapings, sputum, synovial fluid, throat swabs, tissue specimens, urethral discharge material, urine, and urogenital secretions.
All specimens should be of the highest possible quality!

4. Importance of High-Quality Clinical Specimens
High-quality clinical specimens are required to achieve accurate, clinically relevant laboratory results.
The three components of specimen quality are:
Proper specimen selection
Proper specimen collection
Proper transport of the specimen to the laboratory
The laboratory must provide written guidelines (“Laboratory Policies and Procedures Manual”).
The person who collects the specimen is ultimately responsible for its quality.

5. Proper Selection, Collection, and Transport of Clinical Specimens
The acute stage of the disease is the most appropriate time to collect a specimen.
Specimen collection should be performed with care and tact to avoid harming the patient.
A sufficient quantity of the specimen must be obtained to provide enough material for all required diagnostic tests.
Specimens must be properly selected.
Specimens must be properly collected.
Material (i.e., specimens) should be collected from a site where the suspected pathogen is most likely to be found.
Specimens should be obtained before antimicrobial therapy, if possible.

6. Proper Selection, Collection, and Transport of Clinical Specimens (cont.)
Whenever possible, a sterile, disposable specimen container should be used.
The specimen container must be properly labeled and accompanied by an appropriate request slip with adequate instructions.
Specimens should be collected and delivered to the laboratory as early in the day as possible to allow sufficient processing time.
All specimens should be placed or collected into a sterile container to prevent contamination.
Specimens should be protected from heat and cold and promptly delivered to the laboratory.
Hazardous specimens must be handled with even greater care to avoid contamination of couriers, patients, and healthcare professionals.

7. Types of Clinical Specimens Usually Required to Diagnose Infectious Diseases
Blood
Blood is usually sterile.
The presence of bacteria in the bloodstream is known as bacteremia.
Septicemia is a serious disease characterized by chills, fever, prostration, and the presence of bacteria or their toxins in the bloodstream.
To prevent contamination of a blood specimen with indigenous skin microbiota, extreme care must be taken to use aseptic technique.

8. Types of Clinical Specimens Usually Required to Diagnose Infectious Diseases (cont.)
Urine
Urine is normally sterile in the bladder, but becomes contaminated by indigenous microbiota of the distal urethra during voiding.
Contamination is reduced by collecting a clean-catch, midstream urine.
Urine culture involves three parts:
A colony count (using a calibrated loop)
Isolation and identification of the pathogen
Antimicrobial susceptibility testing

9. Urine Colony Count
The colony count is a way of estimating the number of viable bacteria that are present in a urine specimen.
A calibrated loop, either 0.01 or mL, is used to inoculate the entire surface of a blood agar plate.
After incubation at 37C overnight, the colonies are counted and the number is multiplied by the dilution factor (either 100 for the 0.01-mL loop, or 1,000 for the mL loop) to determine the number of colony-forming units (CFUs).
No. of colonies  dilution factor = No. of CFU/mL

10. Types of Clinical Specimens Usually Required to Diagnose Infectious Diseases (cont.)
Cerebrospinal Fluid (CSF)
Meningitis is inflammation or infection of the membranes (meninges) that surround the brain and spinal cord.
Encephalitis is inflammation or infection of the brain.
Meningoencephalitis is inflammation or infection of both the brain and the meninges.
CSF is collected by lumbar puncture (spinal tap) into a sterile tube; this is a surgically aseptic procedure performed by a physician.
CSF is considered a STAT (emergency) specimen in the lab!

11. Types of Clinical Specimens Usually Required to Diagnose Infectious Diseases (cont.)
Sputum
Sputum is pus that accumulates deep within the lungs of a patient with pneumonia, tuberculosis, or other lower respiratory tract infection.
Often, specimens labeled “sputum” are actually just saliva; saliva specimens don’t provide clinically relevant information.
If TB is suspected, extreme care should be taken!
Better specimens can be obtained by bronchial aspiration or transtracheal aspiration.

12. Types of Clinical Specimens Usually Required to Diagnose Infectious Diseases (cont.)
Throat swabs
Routine throat swabs are used to determine whether a patient has strep throat.
Specific cultures may be necessary when Neisseria gonorrhoeae or Corynebacterium diphtheriae are suspected.
Wound specimens
Whenever possible, a wound specimen should be an aspirate (i.e., pus collected by needle and syringe) rather than a swab.
Specimens collected by swab are frequently contaminated with indigenous microbiota.

13. Types of Clinical Specimens Usually Required to Diagnose Infectious Diseases, cont.
Gonococci (GC) cultures (for Neisseria gonorrhoeae)
N. gonorrhoeae is a fastidious, microaerophilic, and capnophilic bacterium.
Only Dacron, calcium alginate, or nontoxic cotton swabs should be used to collect GC specimens.
Specimens (e.g., vaginal, cervical, urethral, throat, and rectal swabs) are cultured on special medium (e.g., Thayer–Martin medium) and incubated in a CO2 incubator.
Special transport media are available, and GC swabs should never be refrigerated.

14. Types of Clinical Specimens Usually Required to Diagnose Infectious Diseases, cont.
Fecal specimens
Ideally, fecal (stool) specimens should be collected at the laboratory and processed immediately to prevent a decrease in temperature, which would allow the pH to drop and cause the death of many Shigella and Salmonella species.
Bacteria in fecal microbiota are obligate, aerotolerant, and facultative anaerobes.
A combination of direct microscopic examination, culture, biochemical tests, and immunologic tests may be performed to identify Gram-negative and Gram-positive bacteria, fungi, intestinal protozoa, and intestinal helminths isolated from fecal specimens.

15. The Pathology Department (“The Lab”)
Clinical specimens are submitted to the CML, which is a part of the Pathology Department.
The Pathology Department (often referred to as “the Lab”) is under the direction of a pathologist (a physician who has specialized training in pathology).
The pathology department is divided into two major divisions:
Anatomical Pathology
Clinical Pathology

16. The Pathology Department (cont.)
Anatomical Pathology
Diseased organs, stained tissue sections, and cytology specimens are examined here.
Cytogenetic technologists, cytotechnologists, histologic technicians, histotechnologists, and pathologist’s assistants are employed in this division.
In addition, autopsies are performed in the morgue and some Pathology Departments have an Electron Microscopy Laboratory.

17. The Pathology Department (cont.)
Clinical Pathology
It consists of several laboratories in addition to the CML: Clinical Chemistry, Urinalysis, Hematology/Coagulation, Blood Bank, and Immunology.
Personnel include pathologists, chemists and microbiologists, medical laboratory scientists (also known as medical technologistsMTs), and medical laboratory technicians (MLTs).

18. The Clinical Microbiology Laboratory (cont.)
Responsibilities
Primary mission of the CML is to assist clinicians in the diagnosis and treatment of infectious diseases.
The four major day-to-day responsibilities are to
Process various clinical specimens that are submitted to the CML
Isolate pathogens from those specimens
Identify (speciate) the pathogens
Perform antimicrobial susceptibility testing, when appropriate to do so

19. Isolation and Identification (Speciation) of Pathogens
Bacteriology Section
Bacterial pathogens are isolated from specimens, tests are performed to identify them, and antimicrobial susceptibility testing is performed whenever appropriate to do so.
CML professionals are very much like detectives and crime scene investigators, in that they gather clues about a pathogen until they are able to identify it.
Numerous phenotypic characteristics are used to identify the bacteria (e.g., Gram reaction, cell shape, motility, presence and location of spores, presence or absence of various enzymes, etc.)

20. Isolation and Identification (Speciation) of Pathogens (cont.)
Mycology Section
Responsibility is to assist clinicians in the diagnosis of fungal infections (mycoses).
The specimens processed here are the same as those that are processed in the Bacteriology Section, with the addition of hair and nail clippings and skin scrapings.
A variety of procedures are used to identify fungal pathogens, including special media, KOH preps, tease mounts, biochemical tests (for yeasts), and a combination of microscopic and macroscopic observations (for moulds).

21. Isolation and Identification (Speciation) of Pathogens (cont.)
Parasitology Section
Assists clinicians in the diagnosis of parasitic diseases
Parasites are identified by observing and recognizing various parasite life cycle stages (e.g., trophozoites, cysts, microfilariae, eggs, larvae, adult worms) in specimens identified primarily by their physical appearance (e.g., size, shape, internal details).
Virology Section
Assists clinicians in the diagnosis of viral diseases
Techniques used in the identification of viruses include immunodiagnostic tests, cytologic or histologic examination, electron microscopy, molecular techniques, virus isolation by cell cultures, and cytopathic effect (CPE).

22. Isolation and Identification (Speciation) of Pathogens (cont.)
Mycobacteriology Section (also called the TB Lab)
Assists clinicians in the diagnosis of tuberculosis (TB)
Various types of specimens are submitted, but sputum is the most common type.
Mycobacterium spp. are identified by the acid-fast staining procedure and by using a combination of growth characteristics (e.g., growth rate, colony pigmentation, photoreactivity, and morphology) and a variety of biochemical tests.