Section: Clinical Microbiology

Duration: 2 months

Goals & Objectives

1. Be familiar with indications for seeking microbiologic diagnosis and the proper type of specimen to obtain for each possible clinical situation. Be able to troubleshoot specimen collection both in terms of improper specimens or requests and assist the physician as to proper specimen collection and transport procedures.
2. Be familiar with staining and culture methods for successful microbial growth and identification of the organisms associated with the clinical disease.
   1. Specimen processing:
      • Methods of streaking specimens for isolation.
      • Protocol for all cultures: routine, mycology, mycobacteriology, and parasitology.
      • Preparation of smears for staining.
   2. Media:
      • Ingredients - use and principles of formulation.
      • Methods of subculturing and inoculation of biochemicals.
      • Atmospheric and temperature requirements.
      • Interpretation of results.
3. Be able to use the appropriate equipment needed in microbiologic diagnosis (fluorescent microscope, biosafety hood, etc.) and perform all appropriate staining procedures.
4. Be able to read and interpret all stains performed in Microbiology and Virology: Gram, AFB, India ink, KOH, FA, trichrome.
5. Reading of Cultures: 1. Urine -- quantitation, culture kits. 2. Stool -- specific organisms identified include: Salmonella, Shigella, E. coli 0157, Campylobacter, staphylococci, Candida albicans, and Yersinia enterocolitica. 3. Respiratory tract -- including cultures from the nose, nasopharynx, throat, sputum, transtracheal aspirate. Culture techniques for Corynebacterium diphtheriae, Bordetella pertussis, and Neisseria meningitidis. 4. Miscellaneous cultures: a. Cerebrospinal fluid. b. Body fluids. c. Wounds, abscesses, etc. d. Genitourinary tract: routine and Neisseria gonorrhoeae. e. Eye, ear.
6. Identification of microorganisms: 1. Select appropriate media and methods for identification. 2. Interpret results. 3. Distinguish between normal flora and pathogens. 4. Flow charts for gram-positive and gram-negative bacteria. 5. Perform susceptibility tests and interpret results. 6. Correlation of growth and type of organism.
7. Blood cultures: Be familiar and understand the proper collection and processing of blood cultures, the BACTEC instrument, other means for culturing blood, turnaround time for work up of isolates, and rapid methods.
8. Parasitology: 1. Direct macroscopic and microscopic techniques. 2. Formalin-ethylacetate sedimentation technique. 3. Trichrome stain. 4. Acid-fast stain for Cryptosporidium/Isospora 5. Observe trichrome slides and wet preps of known organisms and be able to identify unknown parasites from trichrome in concentration procedures. 6. EIA for Giardia and Cryptosporidium 7. Wright's Giemsa stain for bloodborne parasites, e.g. Plasmodium, Babesia, etc.
9. Mycology: 1. Yeasts. a. Distinguish different types of yeast. b. Select appropriate media and/or methods for identification - - assimilation and fermentation, API, Vitek. c. Interpret results. 2. Molds: a. Lactophenol cotton blue scotch tape techniques. b. Slide cultures. c. Septate and aseptate hyphae.
10. Mycobacteriology: 1. Process specimen. 2. Perform acid-fast stain. 3. Examine slides for acid-fast bacilli. 4. Interpret culture results and biochemicals. 5. DNA probe identification technology. 6. Learn principles, pros & cons of molecular amplification methods.
11. Anaerobes: Observe and participate in identification of anaerobes, including processing and special growth requirements. Know limitations of anaerobic susceptibility testing.
12. Chlamydia: 1. Observe and participate in detection of chlamydia by cell culture methods. 2. Learn principles and limitations of all methods for detecting chlamydia including cell culture, direct fluorescent monoclonal antibody detection, and serology (EIA), and amplification methods.
13. Be able to perform and interpret the results of various antibiotic sensitivity studies and to select the method appropriate for the given situation: 1. Be able to troubleshoot and interpret various methods of susceptibility testing: Beta-lactamase Vancomycin-resistant enterococci Kirby-Bauer Penr S. pneumoniae MIC Time kill Serum killing titers Inducible -lactamases ESBLs Methicillin-resistant staphylococci E-test
14. Understand and be familiar with specimen processing, culturing, and staining of fastidious organisms or those with culturing requirements differing from routine bacteriological culture methods including Mycobacteria, Legionella, or other unusual organisms.
15. Understand all laboratory methods used to either detect, identify or quantitate organisms using molecular biological methods.
16. Be able to work up the various types of specimens and identify the organisms isolated; this includes identification of bacteria, myco-bacteria, yeasts, fungi, viruses, and parasites.
17. Be familiar with the hospital infection control program. Attend infection control meetings.
18. Become familiar with and understand the requirements for proper collection and transport of specimens for all tests performed in the Virology Laboratory.
19. Observe and perform the various methodologies used by the Virology Laboratory in culturing and/or otherwise testing specimens received. Understand the underlying principles for all methods including the basics of any instrumentation involved.
20. Determine a set of Virology unknowns which will include cytopathic effects and FA stains.
21. Be able to interpret correctly the results of all tests performed both in Virology and Microbiology and convey that information to clinical colleagues.
22. Understand the computer so inquiries can be made via the CRT.
23. Review quality control and quality assurance practices performed by both laboratories.
24. At the end of the rotation, determine a set of Microbiology unknowns which include Mycobacteriology and Parasitology.

Duties and Responsibilities

1. Correlate bacteriological results with clinical data and write inter-pretative notes in the patient's records when indicated.
2. Provide clinical consultation for such problems as methods of ob-taining cultures, transporta-tion of specimens, bacteriological sensitivity testing, and handling of specimens for isolation of anaerobic bacteria and viruses.
3. When indicated, provide instruction in proper techniques for the collection of bacteriological specimens to residents and medical students.
4. Present one inservice or case to the technologists on a topic of his/her choice.
5. Participate in the monthly Virology journal club.
6. Attend the weekly Infectious Disease Grand Rounds (September through June, every Wednesday at 4:00 p.m.).
7. Attend and participate in daily infectious disease laboratory rounds (1:30-2:00 p.m.).
8. Attend the monthly Infection Control Committee meetings (First Friday of each month in the administrative conference room).
9. Participate in laboratory rounds with director and supervisor during the 2ND month of the rotation. (Training with the bench technologist is the first priority.)
10. Responsible for handling clinical microbiology STAT requests. The information below is to be used by the Pathology resident to guide the decision as to the acceptability of a STAT request: 1. For SUNY-Upstate pediatric inpatients (including peds ER), any STAT requests are approved through peds ID. The pathology resident should contact the pediatric attending on-call. In most cases, the lab would be notified in advance by peds ID if any of these tests would be expected to fall onto evening/night shift and weekends. 2. For SUNY-Upstate adult inpatients (including ER), call the ordering physician to determine whether the STAT request is clinically appropriate using the guidelines below. 3. If a physician insists that a STAT request be processed but the reason is not clinically sound, refer the issue to the microbiology director. For any requests that are taken to the director level, the pathology resident must provide the director with pertinent clinical information about the patient, including current therapy, previous test results, and how the STAT request would change patient management. TEST TEST OFFERED STAT APPROVALS RSV antigen 7d/wk - day shift (to 2:30 pm) Hem-Onc/Bone Marrow Transplant patients. No STAT outpatient requests. Influenza A antigen 7d/wk - day shift (to 2:30 pm) Patients admitted for therapy, rarely for placement issues (peds). No STAT outpatient requests. Pneumocystis DFA 5d/wk - day shift (non-BAL) BALs (adults, peds) 7d/wk for STATs (accepted until 9 pm) Endotracheal aspirates (peds) CMV Antigenemia 5d/wk - day shift No STATs (specimen must be received by 9 am) Weekend requests require director approval. AFB smear 7d/wk No STATs (same day TAT if received by 7 am) Legionella urine antigen 7d/wk - day shift (to 2:30 pm) No STATs
11. For any approved STAT request, call the next person on the list that does not have a check by their name (current lists are posted in the Microbiology lab on the file cabinet and in Virology). If that person cannot be reached, go down the list in sequence skipping any names that already have checks by them. If no one can be reached, call those who do have checks. Leave messages on answering machines when available but do not wait for the person(s) to call back - continue down the list of names until someone can be reached.

Evaluation

Residents are involved during their two-month rotation in learning the interpretation of culture results. Subsequent to their assimilation of this information, the resident will then become involved in the clinical interpretation of these data and their relevance. Pathology residents interact with clinicians during weekly case conferences and on special or urgent cases.

1. During the first month of their rotation, the resident is expected to spend the majority of time at the various laboratory areas and reading; once the basic core curriculum is accomplished during this first month, technologists or the director will bring questions and problems to the attention of resident. Initially, these problems are handled by interacting with the director or other laboratory personnel. Once the resident has demonstrated competency in handling certain situations, they assume greater and more independent responsibilities.
2. During the second month of rotation, the resident is expected to run the daily Infectious Disease rounds which includes teaching some aspect of Clinical Microbiology 5 days per week during the rotation.
3. Successfully complete a set of bacteriology unknowns.
4. Residents will be evaluated by the attending clinical microbiologist as to their base of knowledge during bench work consultations and conference presentations.

Recommended Reading

1. Manual of Clinical Microbiology
2. Microbiology and Virology Laboratory Manuals
3. Cumitechs (in chief resident's office)
4. Pertinent microbiology literature
5. National Committee for Clinical Laboratory Standards. Methods for Dilution Antimicrobial Susceptibility Tests for Bacteria that Grow Aerobically -Fifth Edition; Approved Standard. NCCLS Document M7-A5. NCCLS, Villanova, Pennsylvania 19085.
6. National Committee for Clinical Laboratory Standards. Performance Standards for Antimicrobial Disk Susceptibility Tests - Sixth Edition; Approved Standard. NCCLS Document M2-A6. NCCLS, Villanova, Pennsylvania 19085.
7. Murray, P. et al., ed. Manual of Clinical Microbiology, 7th edition. American Society for Microbiology; Washington, D.C. 1999.
8. Forbes, B.A., D. Sahm and A. Weissfeld, ed. Bailey and Scott's Diagnostic Microbiology, 11th edition. Mosby; St. Louis, 2002.
9. Koneman EW, Allen SD, Janda WM, Schreckenberger PC, Winn WC. Color Atlas and Textbook of Diagnostic Microbiology, 4th edition. J.B. Lippincott; Philadelphia, 1992.
10. Mandel GL, Douglas RG, Bennett JE, Dolan, R. ed. Principles and Practice of Infectious Diseases, 3rd edition. Churchill Livingstone; New York, 2000