MICROBIOLOGY

PRINCIPLES OF DIAGNOSTIC MEDICAL MICROBIOLOGY CONTD.. DIAGNOSIS OF INFECTION BY ANATOMIC SITE: 2). URINE: Bacteriologic examination of the urine is done mainly when signs or symptoms point to urinary tract infection, renal insufficiency ,  or hypertension.  It should always be done in persons with suspected systemic infection or   fever of unknown origin.  It is desirable for women in the first trimester of pregnancy . Urine secreted in the kidney is sterile unless the kidney is infected.  Uncontaminated bladder urine is also normally sterile.  The urethra,  however ,  contains a normal flora,  so that normal voided urine contains small numbers of bacteria.  Because it is necessary to distinguish contaminating organisms from etiologically important organisms,  only quantitative urine examination can yield meaningful results. The following steps are essential in proper urine examination. PROPER COLLECTION OF SPECIMEN Proper collection of the specimen is the single most impor

PRINCIPLES OF DIAGNOSTIC MEDICAL MICROBIOLOGY CONTD.... DIAGNOSIS OF INFECTION BY ANATOMIC SITE Wounds,  Tissues,  Bones,  Abscesses,  & Fluids: Microscopic study of smears and culture of specimens from wounds or abscesses often gives early and important indications of the nature of the infecting organism and thus helps in the choice of antimicrobial drugs.  Specimens from diagnostic tissue biopsies should be submitted for bacteriologic as well as histologic examination.  Such specimens for bacteriologic examination are kept away from fixatives and disinfectants, minced,  and cultured by a variety of methods. The pus in closed,  undrained soft tissue abscesses frequently contains only one organism as the infecting agent; most commonly staphylococci,  streptococci,  or enteric gram-negative rods.  The same is true in acute osteomyelitis,  where the organisms can often be cultured from blood before the infection has become chronic. Multiple microorganisms are frequently enco

PRINCIPLES OF DIAGNOSTIC MEDICAL MICROBIOLOGY CONTD... LABORATORY AIDS IN THE SELECTION OF ANTIMICROBIAL THERAPY The antimicrobial drug used initially in the treatment of an infection is chosen on the basis of clinical impression  after the physician is convinced that an infection exists and has made a tentative etiologic diagnosis on clinical  grounds.  On the basis of this "best guess," a probable drug of choice can be selected .  Before  this drug is administered,  specimens are obtained for laboratory isolation of the causative agent.  The results of  these examinations may necessitate selection of a different drug.  The identification of certain microorganisms  that are uniformly drug-susceptible eliminates the necessity for further testing and permits the selection of  optimally effective drugs solely on the basis of experience. The commonly performed disk diffusion susceptibility test must be used judiciously and interpreted with restraint.  In general,  only one

PRINCIPLES OF DIAGNOSTIC MEDICAL MICROBIOLOGY CONTD... IDENTIFYING BACTERIA USING 16S RRNA The 16S rRNA of each species of bacteria has stable (conserved) portions of the sequence.  Many copies are  present in each organism.  Labeled probes specific for the 16S rRNA of a species are added,  and the amount of  label on the double-stranded hybrid is measured.  This technique is widely used for the rapid identification of  many organisms.  Examples include the most common and important Mycobacterium species,   C immitis,  Histoplasma capsulatum ,  and others.  Portions of the 16S rRNA are conserved across many species of microorganisms.  Amplifying the 16S rRNA using  primers to these conserved regions allows isolation and sequencing of the variable regions of the molecules.  These variable sequences are genus- or species-specific markers that allow identification of microorganisms.   Pathogens that are difficult or impossible to culture in the laboratory have been identified using thi

PRINCIPLES OF DIAGNOSTIC MICROBIOLOGY... CULTURE SYSTEMS:  For diagnostic bacteriology ,  it is necessary to use several types of media for routine culture,  particularly when  the possible organisms include aerobic,  facultatively anaerobic,  and obligately anaerobic bacteria.  The  specimens and culture media used to diagnose the more common bacterial infections.  The standard medium for specimens is blood agar ,  usually made with 5% sheep blood.  Most aerobic and facultatively anaerobic organisms will grow on blood agar .  Chocolate agar ,  a medium containing heated blood  with or without supplements,  is a second necessary medium; some organisms that do not grow on blood agar, including pathogenic Neisseria and Haemophilus ,  will grow on chocolate agar.  A selective medium for enteric  gram-negative rods (either MacConkey agar or eosin-methylene blue [EMB] agar) is a third type of medium  used routinely.   Specimens to be cultured for obligate anaerobes must be plated on

PRINCIPLES OF DIAGNOSTIC MEDICAL MICROBIOLOGY: INTRODUCTION Diagnostic medical microbiology is concerned with the etiologic diagnosis of infection.  Laboratory procedures  used in the diagnosis of infectious disease in humans include the following: 1.   Morphologic identification of the agent in stains of specimens or sections of tissues (light and electron microscopy). 2.   Culture isolation and identification of the agent. 3.   Detection of antigen from the agent by immunologic assay (latex agglutination,  enzyme immunoassay [EIA],  etc) or by fluorescein-labeled (or peroxidase-labeled) antibody stains. 4.   DNA -DNA or DNA -RNA hybridization to detect pathogen-specific genes in patients' specimens. 5.   Detection and amplification of organism nucleic acid in patients' specimens. 6.   Demonstration of meaningful antibody or cell-mediated immune responses to an infectious agent. In the field of infectious diseases,  laboratory test results depend largely on the qual