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Guidelines for LSU Clinical Microbiology Rotation

Goals and Learning Objectives of Rotation

BACTERIOLOGYo 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 transportingspecimens for microbiologic analysis.

o Know the colonial morphology and hemolysis patterns of commonlyisolated bacterial pathogens. Be aware of the key biochemical tests used inthe bacteriology laboratory and their importance in organism

identification.

o Understand the principles of media utilization. Learn the uses of selectiveand 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 ofbacteriologic cultures, the difference between evaluating specimens

obtained from sterile and non-sterile sites, and the use of quantitativecultures.

o Know the principles upon which determining the susceptibility of bacteriato antimicrobial agents by antimicrobial dilution, disk diffusion, and

gradient diffusion are based. Be able to relate the advantages anddisadvantages 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 specificexamples where the use of such assays has particular value.

o Be aware of the basic concepts of anaerobic bacteriology, including theparticular specimen collection and transport requirements necessary foroptimal recovery of anaerobic bacteria.

o Understand the importance of quality control and be able to describe theessential components of an effective quality control program.

MYCOBACTERIOLOGYo Be able to describe the role of the laboratory in controlling the spread of

tuberculosis both nosocomially and in the community. Understand thespecific safety issues associated with working with M. tuberculosis.

o Be familiar with the types of specimens submitted to the laboratory formycobacterial culture. Understand how, why, and which specimens are

processed prior to culture. Know which specimen types are and are notappropriate for mycobacterial culture.

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o Be able to describe the principles of the acid-fast and modified acid-fastsmears. 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 mycologylaboratory. 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 mycologylaboratory (dimorphic molds, hyaline molds (especially Aspergillus sp.),

zygomycetes, dermatophytes, dematiaceous molds). Know the keydistinguishing features and clinical significance of the most commonly

isolated members of each group. PARASITOLOGY

o Be familiar with the appropriate techniques for identifying intestinalparasites. 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 humanpathogens 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

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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 theiridentification 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.

VIROLOGYo 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, andrecognition of toxicity, senescence and contamination.

o Understand the principles of viral isolation. Be able to recognizecytopathic effects produced by the most commonly isolated viruses.

oUnderstand the principles of shell-vial culture.

o Understand the use of rapid antigen-based detection methods in thevirology laboratory (both DFA and EIA).

o Understand the theory and practical value of viral serology, in particularits 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 thefollowing activities:

Observe and assist in the analysis of clinical specimens under the supervision of thelaboratory 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 orlaboratory 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 appropriatefaculty member. No on-call duties outside of regular laboratory working hours areassigned 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

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o Clinical Microbiology Conference: 8:30AM at Ochsner Brent HouseConference Center

o Tulane-LSU AIDS Clinical Treatment Unit Meeting: TBAo 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 arerequired, 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 presentationsto the staff at conferences. The Fellows are provided with continuous feedback on theirperformance during the rotation. In general, only deficiencies are noted in writing.

Fellows are evaluated on their demonstrated ability to provide informative consultation tothe 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 ofDiagnostic Microbiology (Koneman, EW et al.); Principles and Practice of

Infectious Diseases (Mandell, G et al. eds.); Medically Important Fungi, A GuideTo Their Identification (Larone, DH); Diagnostic Medical Parasitology (Garcia,

LS and DA Bruckner); Color Atlas of Diagnostic Microbiology (de la Maza, LMet al.).

Slides. Collections of teaching slides are available for the Fellows to use in a self-instructional manner.

Computer software. Self-instructional CD-ROM titles are available for use by theFellows. 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 topicscovered during the rotation are maintained by the faculty.