Guidelines for LSU Clinical Microbiology Rotation Goals and Learning Objectives of Rotation

BACTERIOLOGY o Be able to accurately interpret Gram-stained smears made from direct specimens and isolated colonies. Understand the importance of microscopic morphology in identifying commonly isolated bacteria. o Be able to describe appropriate methods for collecting and transporting specimens for microbiologic analysis. o Know the colonial morphology and hemolysis patterns of commonly isolated bacterial pathogens. Be aware of the key biochemical tests used in the bacteriology laboratory and their importance in organism identification. o Understand the principles of media utilization. Learn the uses of selective and differential media in the laboratory and be able to identify organisms based on their appearance on such media. o Understand and be able to discuss modern blood culture practices. Become familiar with automated instrumentation for microbial identification. o Be able to determine the clinical significance of microbiology laboratory reports. Understand the principles governing the extent of work-up of bacteriologic cultures, the difference between evaluating specimens obtained from sterile and non-sterile sites, and the use of quantitative cultures. o Know the principles upon which determining the susceptibility of bacteria to antimicrobial agents by antimicrobial dilution, disk diffusion, and gradient diffusion are based. Be able to relate the advantages and disadvantages of automated antimicrobial susceptibility systems. Understand how resistance screening tests are used in the laboratory. o Understand how assays using antigen recognition by antibodies are used for identifying bacteria and their products. Be able to describe specific examples where the use of such assays has particular value. o Be aware of the basic concepts of anaerobic bacteriology, including the particular specimen collection and transport requirements necessary for optimal recovery of anaerobic bacteria. o Understand the importance of quality control and be able to describe the essential components of an effective quality control program. MYCOBACTERIOLOGY o Be able to describe the role of the laboratory in controlling the spread of tuberculosis both nosocomially and in the community. Understand the specific safety issues associated with working with M. tuberculosis. o Be familiar with the types of specimens submitted to the laboratory for mycobacterial culture. Understand how, why, and which specimens are processed prior to culture. Know which specimen types are and are not appropriate for mycobacterial culture.

o Be able to describe the principles of the acid-fast and modified acid-fast smears. Know the difference between Ziehl-Nielsen, Kinyoun, and Auramine-Rhodamine acid-fast stains. o Know the principal methods used for recovering mycobacteria in culture, including the use of radiometric and continuous-monitoring culture systems. o Have a general understanding of the methods used for identifying mycobacteria in the clinical laboratory. This should include the following: Use of growth characteristics to group mycobacteria. Use of conventional biochemical tests to differentiate M. tuberculosis from other mycobacteria. Principle and use of the NAP test. Use of DNA probes to identify mycobacteria. Methods for identifying rapidly-growing mycobacteria. Methods for identifying nocardiae. Understand the methods used for performing susceptibility testing on mycobacteria. MYCOLOGY o Be familiar with the types of specimens submitted to the mycology laboratory. Understand how specimens are handled in the laboratory. o Understand the principles and use of the cryptococcal antigen test. o Know the techniques used for the identification of Pneumocystis carinii. o Be familiar with the techniques used to identify commonly isolated yeasts, including: Colonial and microscopic morphology. o Understand the methods available for, and uses of, antifungal susceptibility testing. o Know the techniques used to identify mycelial fungi, including: Colonial and microscopic morphology. Scotch tape preparation (lactophenol cotton blue stain). o Be familiar with the major groups of fungi isolated in the mycology laboratory (dimorphic molds, hyaline molds (especially Aspergillus sp.), zygomycetes, dermatophytes, dematiaceous molds). Know the key distinguishing features and clinical significance of the most commonly isolated members of each group. PARASITOLOGY o Be familiar with the appropriate techniques for identifying intestinal parasites. This should include a knowledge of the following: o Criteria for evaluating specimens. o Use of specimen preservatives. o Concentration methods. o Be able to differentiate the major groups of intestinal parasites (protozoa, nematodes, cestodes, trematodes). Be able to identify the principal human pathogens in each of these groups and describe in general terms the life cycle, clinical and epidemiological characteristics of these organisms. o Understand the utility of antigen detection methods in the parasitology

laboratory. Be aware of the impact of patient population on test utilization. o Be able to identify the major blood and tissue parasites (plasmodia, filaria, trypanosoma, leishmania) and describe the methods used for their identification in the laboratory. Know the critical elements of the life cycles of these organisms and their clinical and epidemiological significance. o Be able to recognize the most commonly encountered ectoparasites. VIROLOGY o Be familiar with the types of specimens submitted to the virology laboratory. Understand how specimens are processed in the laboratory, and know the criteria upon which specimen acceptability is based. o Have a basic understanding of the principles of cell culture, including familiarity with growing, splitting and maintaining cell cultures, and recognition of toxicity, senescence and contamination. o Understand the principles of viral isolation. Be able to recognize cytopathic effects produced by the most commonly isolated viruses. o Understand the principles of shell-vial culture. o Understand the use of rapid antigen-based detection methods in the virology laboratory (both DFA and EIA). o Understand the theory and practical value of viral serology, in particular its use in the diagnosis of infectious hepatitis and HIV infection.

Overview of Daily Duties and Responsibilities

Precise daily assignments vary; however, Fellows are expected to participate in the following activities: Observe and assist in the analysis of clinical specimens under the supervision of the laboratory technical staff. Interact with clinical staff to evaluate the appropriateness of laboratory test requests. Participate in laboratory rounds, conducted by the microbiology laboratory director and attended by Infectious Disease staff, Fellows, and medical students. Participate in didactic teaching sessions coordinated by the faculty. These sessions may involve reviewing assigned reading material, discussing interesting cases or laboratory findings, and correlating microbiological results with results from other diagnostic investigations (for example surgical pathology).

On-call Duties
During the microbiology rotation, Fellows are only on-call during normal working hours at the laboratory they are rotating through and are supervised directly by the appropriate faculty member. No on-call duties outside of regular laboratory working hours are assigned to the Fellow.

Conferences
ID Conference Attendance is STRONGLY recommended: o ID conference: Thursday, 8:30AM at 136 S. Roman St, 2nd Floor conference room

o Clinical Microbiology Conference: 8:30AM at Ochsner Brent House Conference Center o Tulane-LSU AIDS Clinical Treatment Unit Meeting: TBA o Citywide ID Conference: Friday, 8:30 AM at Ochsner Foundation Hospital Auditorium

Scholarly Activities/ Research Activities During the Rotation

Since the Fellows spend no more than 4 weeks of the rotation in any individual laboratory, opportunities for conducting research projects are limited. Fellows are required, however, to carry out literature searches on unusual cases or new diagnostic modalities and present their findings at the appropriate conferences. In addition, discussion of pertinent articles and other reading materials with the faculty is an ongoing activity throughout the rotation.

Basis, Method and Criteria for Fellow Evaluation

Fellows will be evaluated on performance of daily activities (described previously), participation in required meetings, laboratory rounds and conferences, and presentations to the staff at conferences. The Fellows are provided with continuous feedback on their performance during the rotation. In general, only deficiencies are noted in writing. Fellows are evaluated on their demonstrated ability to provide informative consultation to the clinical service teams, their medical knowledge, their application of this knowledge to efficient/quality patient care, and their diagnostic, technical and observational skills. Fellows are also evaluated on their interpersonal skills, professional attitudes, reliability, and ethics with members of the teaching faculty, peers, laboratory staff, and clinicians. They are further evaluated on their initiative in fostering quality patient care and use of the medical literature, as it relates to their assigned cases.

Educational Resources
Textbooks. A variety of standard and specialized microbiological texts are available for use by the Fellows. These include the latest editions of the Manual of Clinical Microbiology (Murray, PR et al., eds.); Color Atlas and Textbook of Diagnostic Microbiology (Koneman, EW et al.); Principles and Practice of Infectious Diseases (Mandell, G et al. eds.); Medically Important Fungi, A Guide To Their Identification (Larone, DH); Diagnostic Medical Parasitology (Garcia, LS and DA Bruckner); Color Atlas of Diagnostic Microbiology (de la Maza, LM et al.). Slides. Collections of teaching slides are available for the Fellows to use in a selfinstructional manner. Computer software. Self-instructional CD-ROM titles are available for use by the Fellows. Currently available titles are Gram-Stain Tutor, Parasite Tutor, Wheel of Bacteriology, Wheel of Mycology, Wheel of Parasitology. Journal articles. Collections of original journal articles pertinent to the topics covered during the rotation are maintained by the faculty.