CHAPTER 13 DIAGNOSING INFECTIOUS DISEASE

Prepared by: Lovelle Easter C. Macaraan Ma. Eloisa A. Alcantara Justine C. Sales Angelou H. Brinas

Introduction
The proper diagnosis of disease requires: 1. Taking a complete patient history 2. Conducting through physical examination of the patient. 3. Carefully evaluating the patients sign and symptoms 4. implementing the proper selection, collection, transport and processing of clinical specimen

Clinical Specimen
It is the various types of specimens (e.g. blood, urine, feces and cerebrospinal fluid) that are collected from patients and used to diagnose or follow the progress of infectious disease.

Type of Specimen

Type (s) of infectious disease that the specimen is to used to diagnose B, F, P, V B

Type of Specimen

Type (s) of infectious disease that the specimen is to used to diagnose P F P B, F, P, B B, V B, F, P, V, B

Blood Bone marrow

scotch tape prep Skin scrapping Skin snip Sputum Synovial (joint) fluid Throat Swabs Tissue specimen Urethral discharge material

Bronchial and V bronchoalveolar washes Cerebrospinal fluid Cervical & Vaginal Swab Conjunctival Swab or scraping Feces and Rectal Swab Hair clippings B, F, P, V B, B, V B, P, V

F
F
B B

Nail (finger nail and toe nail) clippings

Nasal Swab Pus form a wound or abcess

Urine

B, P, V
B, P V

Urogenital secretion
Vesicle fluid or scraping

B, bacterial Infection; F, Fungal infection; P, Parasitic Infection; V, Viral Infection

Role of healthcare professionals in the submission of clinical specimen

A close working relationship among the members of healthcare team is essential for the proper diagnosis of infectious disease. Laboratory findings must then be conveyed to the attending physician as quickly as possible to facilitate the prompt diagnosis and treatment of infectious disease. Healthcare professionals who collect and transport clinical specimen s should exercise extreme caution during the collection and transport of clinical specimen to avoid sticking themselves with needles, cutting themselves types of sharps or incoming contact with any type of specimen.

According to the Clinical and Laboratory Standards 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 containerWithin the institution, the primary container should be placed into a second container, which will contain the specimen if the primary container breaks or leaks in transit to the laboratory

Importance of High-Quality Clinical Specimens

High-quality clinical specimens are required to achieve accurate, clinically relevant laboratory results (i.e. results that provide information about the patients infectious disease.)It has often been stated that the quality of the laboratory work performed in the CML can be only as good as the quality of specimens that are received. The three components of specimen quality: 1. Proper specimen selection(e.g. the correct type if specimen must be submitted) 2. Proper specimen collection 3. Proper transport of the specimen to the laboratory.

 Laboratory Policies and Procedures Manual or lab P&P (manual for short).Copies of the Lab P&P Manual must be available to every ward, floor, clinic, and department. Often it accessible through the hospitals computer system. However, the person who collects the specimen is ultimately responsible for its quality.

When clinical specimens are improperly collected and handled: 1. The etiologic(causative) agent may not be found or may be destroyed 2. Overgrowth by indigenous microflora may mask the pathogen 3. Contaminants may interfere with the identification of pathogens and the diagnosis of the infectious disease.

Proper Selection, Collection, and Transport of Clinical Specimens

When collecting clinical specimens for microbiology, these general precautions should be taken: The specimen must be properly selected. The specimen must be properly and carefully collected. The material should be collected from a site where the suspected pathogen is most likely found and where the least contamination is likely to occur. Whenever possible, specimens should be obtained before antimicrobial therapy has begun. The acute stage of the disease is the most 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 required diagnostic tests. All specimens should be placed or collected into a sterile container to prevent contamination of the specimen by indigenous microflora and airborne microbes. Specimens should be protected from heat and cold and promptly delivered to the laboratory so that the results of the analyses will validly represent the number and types of organisms present at the time of collection. Hazardous specimens must be handled with even greater care to avoid contamination of the courier, patients and healthcare professionals.

 Whenever possible, sterile, disposable specimen containers should be used. The specimen container must be properly labeled and accompanied by appropriate request slip containing adequate instructions. Specimens should be collected and delivered to the laboratory as early in the day as possible to give the technologist sufficient time to process the material especially when the hospital or clinic does not have 24-hour laboratory service.

Types of Clinical Specimens Usually Required To Diagnose Infectious Diseases

Blood Blood is usually sterile. The presence of bacteria in the bloodstream may indicate a disease, although temporary or transient bacteremias may occur after oral surgery, tooth extraction or even aggressive tooth brushing. Bactermia may occur during certain stages of many infectious diseases. 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 the blood specimen with indigenous skin flora, extreme care must be taken to use sterile technique when collecting blood for culture.

Urine Urine is ordinarily sterile while it is in the urinary bladder. However during urination, it becomes contaminated by indigenous microflora of the distal urethra. Contamination can be reduced by collecting a clean-catch, midstream urine (CCMS urine). Clean-catch refers to the fact that the area around the external opening of the urethra is cleansed by washing with soap and rinsing with water before urinating. This removes the indigenous microflora that live in the area. Midstream refers to the fact that the initial portion of the urine stream is irected into a toilet or bedpan, and then the urine stream is directed into a sterile container.

There are actually three parts to urine culture: 1. A colony count 2. Isolation and identification of the pathogen 3. Antimicrobial susceptibility testing.

The colony count is a way of estimating the number of viable bacteria that are present in the urine specimen. A calibrated loop is a bacteriologic loop that has been manufactured so that it contains a precise volume of urine. The mere presence of bacteria in the urine (bacteriuria) is not significant, as urine always becomes contaminated with bacteria during urination (voiding).

Cerebrospinal Fluid Meningitis, encephalitis and meningoencephalitis are rapidly fatal diseases that can be caused by a variety of microbes, including bacteria, fungi, protozoa and viruses. Meningitis is inflammation or infection of the membranes that surround the brain and spinal column. Encephalitis is inflammation or infection of the brain.

 Meningoencephalitis is inflammation or infection of both the brain and the meninges. To diagnose these diseases, cerebrospinal fluid must be collected into a sterile tube by a lumbar puncture under surgically aseptic conditions. Preliminary reports are laboratory reports that are communicated to the requesting physicians before the availability of the final report. Preliminary reports containing CSF Gram Stain observation frequently enable physicians to make diagnoses and initiate therapy and often save patients lives. Sputum

Sputum is pus that accumulates deep within the lungs of a patient with pneumonia, tuberculosis, or other lower respiratory infection. Unfortunately many of the sputum specimens that are submitted to the CML are actually saliva. A laboratory workup of a patients saliva will not provide clinically relevant information about the patients lower respiratory infection. This situation can be avoided if someone takes a moment to explain to the patient what is required.

 Throat Swabs

Routine throat swabs are collected to determine whether a patient has strep throat. If any other pathogen is suspected by the physicians to be causing the patients pharyngitis, a specific culture for that pathogen must be noted on the request slip, so that the appropriate culture media will be inoculated. Wound Specimens Whenever possible, a wound specimen should be an aspirate, rather than a swab specimen. Specimens collected by swab are frequently contaminated with indigenous microflora and often dry out before they can be processed in the CML.
GC Cultures The initials GC represent an abbreviation for gonococci, a term referring to Neisseria gonorrhoeae. As mentioned earlier, N. gonorrhoeae is a fastidious bacterium that is microaerophilicc and capnophilic. Only Dacron, calcium alginate, or nontoxic cotton swabs should be used to collect GC specimens.

 Fecal Specimen Ideally fecal specimens (stool specimen) should be collected at the laboratory and processed immediately to prevent a decrease in temperature, which allows the pH to drop, causing the death of many Shigella and Salmonella species. Alternatively, the specimen may be places in a container with a preservative that maintains a pH of 7.0.

The Pathology Department

The Pathology Department is under is under the direction of a pathologist (a physicians who has had extensive, sprecialized training in pathology, the study of the structural and functional manifestations of disease).

Organization

Pathology Department

of typical Pathology
Department

Anatomical Pathology

Clinical Pathology

Morgue

Clinical Chemistry Laboratory Hematology Laboratory

Histopathology Laboratory

Cytology Laboratory

Immunology Laboratory

Cytogenetic Laboratory Electron Microscope Laboratory

Blood Bank

Clinical Microbiology Laboratory

Pathology Department consists of two major divisions:

Anatomical Pathology Most pathologist work in Anatomical Pathology, where they perform autopsies in the morgue and examine diseased organs, stained tissue sections, and cytology specimens. Clinical Pathology Clinical Pathology consists of several other laboratories: the Clinical Chemistry Laboratory ; the Hematology Laboratory ; the blood bank; and the immunology Laboratory .

The Clinical Microbiology Laboratory

Organization Depending on the size of the hospital. The clinical microbiology laboratory may be under the direction of a pathologist, a microbiologist or in smaller hospitals, 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. To accomplish this mission, the four major, day-to-day responsibilities of the CML are to:

-Process the 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.

The exact steps in the processing of clinical specimens vary from one specimen type to another and also depend on the specific section of the CML to which the specimen is submitted, In general, processing includes the following steps: -Examining the specimen macroscopically and recording pertinent observations(e.g cloudiness or the oresence of blood, mucus or an unusual odor) -Examining the specimen microscopically and recording pertinent observations( e.g the presence of white blood cells or microorganisms) -Inoculating appropriate culture media in an attempt to isolate the pathogens from the specimen and get them growing in pure culture in the laboratory.

Isolation and Identification (Speciation) of Pathogens

In an effort to isolate bacteria and fungi from clinical specimens, the specimens are inoculated into liquid culture media or onto solid culture media. The goal is to get any pathogens that are present in the specimen growing in pure culture and in large number, so that there will be a sufficient quantity of the organism to inoculate appropriate identification and antimicrobial susceptibility testing systems.

Clinical Microbiology Laboratory

Bacteriology Section

Mycobacteriology Section (TB Lab)

Mycology Section

Immunology Section

Virology Section

Parasitology Section

 Bacteriology Section The overall responsibility of the Bacteriology Section of the CML is to assist clinicians in the diagnosis of bacterial diseases.

The various phenotypic characteristics (clues) useful in identifying bacteria include the following: > Gram reaction > Cell shape > Morphologic arrangement of cells > Growth or no growth on various types if plated media > Colony morphology > Presence or absence of a capsule > Motility > Number and location of flagella

> Ability to sporulate > Location of spores > Presence or absence of various enzymes > Ability to catabolize various carbohydrates and amino acids > Ability to reduce nitrate > Ability to produce indole from tryptophan > Atmospheric requirements > Type of hemolysis produced

 Mycology Section The overall responsibility of the Mycology Section of the CML is to assist clinicians in the diagnosis of fungal infections. In the Mycology section, various types of clinical specimens are processed, fungal pathogens are isolated and tests are performed to identify the fungal pathogens. Parasitology Section The overall responsibility of the Parasitology Section of the CML is to assist clinicians in the diagnosis of parasitic diseases-specially, infections caused by endoparasites, such as parasitic protozoa and helminthes (parasitic worms).

 Virology Section The overall responsibility of the Virology Section of the CML is to assist clinicians in the diagnosis viral diseases. Mycobacteriology Section The primary responsibility of the Mycobacteria Seciton of the CML is to assist clinicians in the diagnosis of tuberculosis. In the mycobacteriology section, various types of specimens are processed, acid fast staining is performed.