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General Information

Course ID (CB01A and CB01B)
HTEC D083A
Course Title (CB02)
Clinical Microbiology Lecture
Course Credit Status
Credit - Degree Applicable
Effective Term
Fall 2023
Course Description
This course addresses microorganisms of medical microbiology with emphasis on the characteristics of clinically significant microorganisms and their biochemical profile, media for isolation, and identification methods for selected pathogens. The student will be introduced to various identification methods, theories, and techniques used in basic microbiology, parasitology, virology, and mycology. This course will emphasize routine organism identification, and correlating test results with disease states.
Faculty Requirements
Course Family
Not Applicable

Course Justification

This course is CSU transferable and part of a CTE program. This is a course that was developed based on the National Accrediting Agency of Clinical Laboratory Sciences and California State Department of Public Health accreditation standards required for Medical Laboratory Technicians' training programs. This course belongs on the Certification of Achievement-Advanced in Medical Laboratory Technology. This course introduces the basic knowledge for understanding the relationship between pathogens and disease. This course must be successfully completed in order to qualify for the clinical externship and take the exam.

Foothill Equivalency

Does the course have a Foothill equivalent?
No
Foothill Course ID

Course Philosophy

Formerly Statement

Course Development Options

Basic Skill Status (CB08)
Course is not a basic skills course.
Grade Options
  • Letter Grade
  • Pass/No Pass
Repeat Limit
0

Transferability & Gen. Ed. Options

Transferability
Transferable to CSU only

Units and Hours

Summary

Minimum Credit Units
4.5
Maximum Credit Units
4.5

Weekly Student Hours

TypeIn ClassOut of Class
Lecture Hours4.59.0
Laboratory Hours0.00.0

Course Student Hours

Course Duration (Weeks)
12.0
Hours per unit divisor
36.0
Course In-Class (Contact) Hours
Lecture
54.0
Laboratory
0.0
Total
54.0
Course Out-of-Class Hours
Lecture
108.0
Laboratory
0.0
NA
0.0
Total
108.0

Prerequisite(s)

Corequisite(s)

HTEC D083.

Advisory(ies)

Limitation(s) on Enrollment

Entrance Skill(s)

General Course Statement(s)

Methods of Instruction

Lecture and visual aids

Discussion of assigned reading

Discussion and problem solving performed in class

Collaborative learning and small group exercises

On-line question  sites to help evaluate comprehension

Assignments

  1. Required reading from text and homework assignments.
  2. Collaborative learning exercises such as analysis of case studies, completion of investigative activities and other exercises designed to reinforce course content and allow for the application of subject matter.  Some of these assignments may involve group work.

Methods of Evaluation

  1. Class activity - Discussions and oral question and answer sessions that test comprehension and require synthesis and application of course material.
  2. Written Assignments - Worksheets designed to evaluate the student's performance and understanding of the course material.
  3. Comprehensive Final Exam - Written test requiring the student to demonstrate their ability to summarize, integrate and critically analyze concepts examined throughout the course.
  4. Problem solving - Case studies and/or written questions to evaluate the students ability to apply critical thinking skills to a clinical situation.
  5. Objective test - Written test examination designed to demonstrate student's understanding of the course material presented.
  6. Quizzes - Quizzes will measure the student's understanding of the course material on a regular basis and help identify any areas that may need extra attention. Quiz questions may be incorporated into the lecture presentation.

Essential Student Materials/Essential College Facilities

Essential Student Materials
  • Computer and access to the internet
Essential College Facilities
  • None.

Examples of Primary Texts and References

AuthorTitlePublisherDate/EditionISBN
Mahon, Connie R.Textbook of Diagnostic MicrobiologyWB. Saunders2018/6th edition9780323613170
Tille, PatriciaBailey and Scott's Diagnostic MicrobiologySt. Louis: Elsevier Science2021/15th editionISBN: 9780323681056
Delost, Maria DannessaIntroduction to Diagnostic Microbiology for the Laboratory SciencesJones & Bartlett Learning2022 2nd editionISBN: 978-1284199734

Examples of Supporting Texts and References

None.

Learning Outcomes and Objectives

Course Objectives

  • Discuss the topics of: safety, standard precautions, isolation procedures, specimen collection, microscopy, and gram stains as they relate to the clinical microbiology laboratory.
  • Summarize the fields of study included in microbiology.
  • Describe the basic theory of molecular testing.
  • Categorize microorganisms seen in the clinical microbiology laboratory as normal flora or clinically significant given their source.
  • Describe the mechanism of action of the different classes of antimicrobials.
  • Compare and contrast the various methods for susceptibility testing including advantages and disadvantages.
  • Evaluate general characteristics of medically important fungi.
  • Evaluate general characteristics of medically important parasites.
  • Associate clinically significant viruses with their prospective infections or diseases.
  • Categorize the organisms that are required to be reported to the state's Department of Health Services and describe how this is accomplished.
  • Given clinical laboratory data and patient's clinical symptoms, solve presented case studies covering all material presented throughout this lecture course.

CSLOs

  • Given patient history information, specimen source and laboratory results including biochemical profile, media used, gram stain, and other selected identification results identify the microrganism isolated from the patient.

Outline

  1. Discuss the topics of: safety, standard precautions, isolation procedures, specimen collection, microscopy, and gram stains as they relate to the clinical microbiology laboratory.
    1. Identify the issues that need to be addressed when forming a comprehensive safety program for the microbiology laboratory.
    2. Differentiate the three types of biosafety cabinets and their uses.
    3. Correlate the most common agents associated with laboratory-acquired infections and identify their corresponding disease, routes of infection and source.
    4. Given the type of isolation used for a patient and their diagnosis, choose the appropriate isolation procedure to be used in specimen collection.
    5. Examine the microscope, locate each of the components and describe the function of each identified component.
    6. Suggest the proper mechanism(s) for maintaining organism viability relating to storage, transport, and preservation of specimens by responding with appropriate suggestions when asked.
    7. Examine the steps involved in the gram stain procedure. Explain the principle of each step.
    8. Suggest limitations and precautions when performing a gram stain and recommend viable solutions.
  2. Summarize the fields of study included in microbiology.
    1. Differentiate the specialty fields of: bacteriology, virology, mycology and parasitology.
    2. Compare and contrast the procedures for identification, including molecular, for the above areas of microbiology.
  3. Describe the basic theory of molecular testing.
    1. Illustrate the components needed to perform NAT (nucleic acid testing) including base pairs and DNA structure
    2. Describe the principle of MALDI (matrix assisted laser desorption/ioniztion)
    3. Compare and contrast conventional biochemical testing for identification to molecular tests and MALDI.
  4. Categorize microorganisms seen in the clinical microbiology laboratory as normal flora or clinically significant given their source.
    1. Identify which pathogens are of concern in the organs presented, i.e. (respiratory tract, urinary tract, central nervous system, etc.)
      1. Correlate a particular infectious disease with its major characteristics, causative agent, reservoir, mode of transmission and diagnostic laboratory procedures.
      2. Select the appropriate biochemical tests for identifying an organism and interpret the chemical reaction that occurs.
      3. Compare conventional identification methods to molecular where appropriate.
    2. Compare and contrast normal flora from these different sites:

      mouth and oral cavity, nasopharynx, stomach and small intestine, and colon.
      1. Create a chart of the above sites and list possible normal flora organisms for each site.
    3. Identify the general characteristics of respiratory and gastrointestinal infections and bacteremia.
      1. Describe the basic anatomy of the respiratory tract and explain the mechanical defenses of each anatomic site and how alterations to these defenses may lead to infection disease.
      2. Identify normal flora of the respiratory tract and explain how alterations in the normal flora may lead to infectious diseases.
      3. Discuss the basic pathogenic mechanisms of infectious diseases of the respiratory tract and the virulence factors of the organisms that cause respiratory diseases.
      4. Identify the normal host defenses at each level of the gastrointestinal tract in preventing infection.
      5. Explain the major mechanisms by which bacteria can cause diarrhea.
      6. For each of the bacterial agents presented in lecture, predict the results of direct microscopy of the stool specimen and select media for maximal recovery of the pathogen.
      7. Differentiate bacteremia from septicemia.
      8. Classify each type of bacteremia and associate specific organisms with each type.
      9. Highlight the advantages and disadvantages of each procedure used for the detection of bacteremia including: using selective media, blood culture additives and the various methods for removing antimicrobials.
    4. Identify the general characteristics of central nervous system and urinary tract infections and sexually transmitted diseases.
      1. Describe the proper procedure for specimen collection, transportation and processing CSF samples.
      2. Identify common bacterial pathogens in meningitis along with one host-related factor and one virulence-related factor for each pathogen.
      3. Compare and contrast the physical, chemical, and cellular features of bacterial, mycobacterial, fungal, syphilitic, viral and parasitic central nervous system infections.
      4. Identify the various urinary tract infections and their location within the urinary tract system.
      5. Identify the variety of pathogens and select the most common pathogens responsible for urinary tract infections.
      6. Interpret urinalysis results based on bacterial colony count, pyuria and symptoms and signs presented by the patient.
      7. Describe the clinical manifestations produced by the following, discuss the epidemiology and pathogenesis of each of the infections: N.gonorrhoeae, C. trachomatis, T. pallidum, and H. ducreyi.
      8. Interpret specific and non specific serologial testing results used to diagnose syphillis.
    5. Describe the general characteristics of the genus Staphylococcus.
      1. Compare the characteristics of the staphylococci to other gram-positive cocci.
      2. Describe the virulence factors associated with staphlyococci.
      3. Differentiate between endotoxins and exotoxins.
      4. Given clinical infections, correlate with possible staphylococci species.
      5. Develop an algorithm of key tests to differentiate among the clinically relevant Staphylococcus species.
      6. Describe the principle of key test for differentiating Staphylococcus species.
      7. Explain the mechanism of action of MRSA and why it is a serious clinical problem.
    6. Differentiate between streptococci and related organisms.
      1. Develop an algorithm of key tests to differentiate among the clinically relevant Streptococci and Enterococci species.
      2. Classify streptococci using the Lansfield classification system.
      3. Compare and contrast the different virulence factors associated with staphylococci, enterococci and streptococci including their mode of action.
      4. Assess the value of molecular testing on direct specimens for  identification
    7. Compare and contrast the gram negative cocci presented: Neisseria, Moraxella and Haemophilus.
      1. Identify the general characteristics of the genus Neisseria.
        1. Distinguish pathogenic from nonpathogenic Neisseria species including their source.
        2. Discuss the virulence factors of the Neisseria species including pili and the polysaccaride capsule.
        3. Develop an identification flowchart for the identification of pathogenic Neisseria.
        4. Compare and contrast the clinical presentation of gonorrhea in male and female patients.
        5. List risk groups of epidemic menigococcal meningitis and discuss the usefulness of the meningococcal vaccine.
        6. Discuss specimen collection, transport and processing for N. gonorrhoeae cultures and advantages of molecular testing.
      2. Identify the general characteristics of the genus Haemophilis.
        1. Correlate the Haemophilus species with their associated infection, clinical manifestations and mode of transmission.
        2. Determine the appropriate specimen collection, transport, culture media and growth factor requirements for isolation of each Heamophilus species discussed.
      3. Identify the general characteristics of the genus Moraxella.
        1. Discuss the pathogenic significance of Moraxella catarrhalis in children and adults.
        2. Compare the similarities and differences between Moraxella catarrhalis infections and those caused by Haemophilis and Neisseria species.
        3. Compare and contrast these organisms in respiratory infections.
    8. Identify the general characteristics of the Enterobacteriaceae and Pseudomonas families.
      1. Compare the pathogenesis of the different strains of Escherichia coli strains pathogenic for the gastrointestinal tract.
      2. Develop an algorithm using biochemical tests for presumptive identification of clinically significant Enterobacteriaccea.
      3. Identify the virulence factors associated with the Pseudomonas species.
      4. Describe the general characteristics of nonfermenative gram-negative rods.
    9. Identify the general characteristics of clinically significant anaerobes identified in the clinical microbiology laboratory.
      1. Differentiate the various types of anaerobes with regard to atmospheric requirements.
      2. Select specimens that meet the proper specimen collection and transportation criteria for anaerobic processing.
      3. Given clinical signs and symptoms of an anaerobic infection, predict the most probable etiologic agent from the following: wound botulism, tetanus, gas gangrene, actinomycosis, pseudomembranous colitis, and bacterial vaginosis.
  5. Describe the mechanism of action of the different classes of antimicrobials.
    1. Examine the major mechanisms by which resistance to various antimicrobial agents can occur.
    2. Summarize the major sites of action and their primary mechanism of action for major classes of antimicrobial agents.
    3. Differentiate between bacteriostatic and bactericidal. Relate factors that can influence outcome of specific antimicrobial activity.
    4. Evaluate the basic structure of microorganisms and the specific functions of individual components with the action of antimicrobial agents.
  6. Compare and contrast the various methods for susceptibility testing including advantages and disadvantages.
    1. Examine the rationale behind the performance of antimicrobial susceptibility tests.
    2. Evaluate the method for selection of specific drugs in testing and reporting.
    3. Summarize how zone interpretive criteria used with the disk diffusion test are established.
    4. List the variables that must be controlled when antimicrobial susceptibility testing is performed.
    5. Explain the principles behind automated antimicrobial susceptibility testing methods.
    6. Select the organisms for which B-lactimase testing is useful and explain the principle of the test.
    7. Discuss advantages and disadvantages of molecular testing for resistant genes.
  7. Evaluate general characteristics of medically important fungi.
    1. Evaluate the appropriate specimen collection procedures, staining methods, and culture techniques used in the mycology laboratory.
    2. Differentiate the terms associated with fungal structures.
    3. Categorize fungi in to their respective classes.
    4. List the common opportunistic saprobes associated with infections in immunocompromised hosts.
    5. Discuss the advantages of molecular identification  of fungi.
  8. Evaluate general characteristics of medically important parasites.
    1. Assess the major considerations in collecting and handling of specimens for identification of intestinal, blood, and tissue parasites.
    2. Evaluate the general procedure for performing the direct wet mount, concentration procedures and permanent stained smears.
    3. Recognize the mechanism of pathogenesis, method of infection, clinical symptoms, prevention, and treatment of the major human pathogens.
    4. Examine the morphology, recognize the life cycle and the usual procedure for identification of the parasites covered in lecture.
    5. Classify a particular parasitic infection as a protozoa or helminth disease.
  9. Associate clinically significant viruses with their prospective infections or diseases.
    1. Examine the characteristics of viruses, and differentiate these organisms from bacteria.
    2. Examine how viruses are transmitted or acquired, the infection the virus produces, and the effective method of laboratory diagnosis for viruses presented in lecture.
    3. Evaluate the different methods used in the diagnosis of viral infections, including advantages and limitations of conventional tissue cultures, rapid viral antigen detection methods and molecular testing.
    4. Explain the significance of novel viral strains and the  impact on the world population.
  10. Categorize the organisms that are required to be reported to the state's Department of Health Services and describe how this is accomplished.
    1. List organisms that are required to be reported to CADPH or CDC
    2. Evaluate the required documentation, notification and follow-up required.
  11. Given clinical laboratory data and patient's clinical symptoms, solve presented case studies covering all material presented throughout this lecture course.
    1. Solve case studies involving pathogenic gram positive and gram negative organisms.
    2. Solve case studies involving fungus, parasites and viral agents.
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