University of Cincinnati

Microbiology

Duration: Three months

Rotation Director(s): Judith Rhodes, PhD

Faculty/ Instructor(s):
Amy Frey, DO
Donna Oblack, PhD
Joel Mortensen, PhD 

Description of Rotation

The sequence of the learning experience in bacteriology generally mimics the philosophical approach to the microbiological workup of specimen material, i.e., the infectious disease systems approach. Thus the resident progresses through work groups devoted to the assessment of urinary tract infections, sepsis, respiratory infections and so forth. Fundamental skills in organism recognition and identification, common to all work groups are integrated early in the experience. Reading assignments, videotape presentations, cognitive and performance educational objectives are integrated into this systems approach.

Organism groups requiring specialized environments, such as fungi, acid-fast bacteria, viruses and parasites, are presented with a focus on their unique laboratory problems and the processes required for their recognition, recovery, and characterization. Likewise, antibiotic testing, from susceptibility testing through therapeutic drug monitoring, is presented from the laboratory perspective of fundamental drug/organism interactions and the integration of these data to clinical application. Finally, cost-effective management in the clinical microbiology laboratory is presented.

Rotation Objective

• Understand the concept of normal microbial flora at specific anatomic sites and discuss cultural approaches to detect infection at such sites, including transport and media selection.
• Be familiar with key reactions required to identify common pathogens in each sub-specialty area of microbiology.
• Be able to read and interpret Gram stains, acid fast and fluorochrome stains, KOH and other wet preps and Trichrome stains.
• Outline an appropriate algorithm for submission of blood cultures and their workup in the lab, stressing the factors necessary for interpretation of positive cultures.
• Describe the principle and operation of commercially available, automated blood culture systems.
• Understand the advantages and limitations of both cultural and biochemical methods of determination of urinary tract infections.
• Categorize the infectious and toxic microbial causes of gastroenteritis.
• Identify the major groups of antibiotics, their modes of action and the group(s) of organisms for which they are indicated.
• List the various types of antibiotic tests used in the laboratory for testing susceptibility of bacteria, mycobacteria and fungi. Include those tests designed to monitor drug levels.
• Be familiar with the role played by the microbiology laboratory in hospital infection control.
• Define the advantages and limitations of direct and colony probe technology in clinical microbiology.
• Understand the concept of primary and opportunistic pathogens as it applies to mycology and how that influences specimen choice, culture methods and culture interpretation.
• List the dimorphic pathogens and describe their two forms and geographic ranges.
• Describe the principles of viral diagnosis from culture, including methods for viral isolation and confirmation.
• Relate the clinical manifestation of malaria to the species of the parasite involved.
• Define and characterize three common protozoans, intestinal helminths and tissue helminths.
• Categorize the four major groups of mycobacteria and the types of infections associated with each. Define the safety practices required to handle AFB specimens and cultures in the diagnostic lab.
• Define the benefits and caveats of direct amplification techniques for detecting microbial agents.

Level of Training

At the end of the 12-week rotation, the residents will be tested on their knowledge and understanding of microbiology. A Gram stain reading and interpretation examination will be administered by Dr. Rhodes.  Minimum Pass = 80 percent.  A written examination will be administered by Dr. Mortensen.  Minimum Pass = 85 percent.  Residents must pass both examinations in order to pass the rotation.

Daily Responsibilities

During the first nine weeks of the rotation, the resident is expected to meet with Dr. Oblack once a week to discuss reading assignments in the various microbiology content areas. During the three weeks that the resident spends at CCHMC, there will be additional weekly meetings with Dr. Mortensen. 

Conferences:  During the 12-week rotation in microbiology, the residents are required to attend microbiology conferences. Residents are expected to attend any CE conferences or teleconferences scheduled during the rotation. Residents are expected to attend an infection control meeting with Dr. Rhodes at University Hospital, Dr. Oblack at VAMC or Dr. Mortensen at CCHMC.

Infectious Diseases Consult Team: During the third month of the microbiology rotation, the pathology resident will round with the Adult ID team. The resident is expected to attend the pre-rounds review of patients, as well as accompany the team while it sees patients at UH and VAMC. During the course of the month, the resident is expected to be the liaison between the team and the microbiology laboratory and anatomic pathology. For example, if the team sends out a test and needs to know the laboratory’s normal range, sensitivity, PPV etc., the pathology should be responsible for obtaining the information and presenting to the rest of the team. Likewise, if a biopsy is obtained in the course of making the diagnosis, the resident should make the arrangements to have the slides reviewed with the team.  For junior residents this will probably involve the attending on the case, but for more senior residents, they may wish to review the slides themselves with the team. Finally, during the consult month, the pathology resident is expected to assist the ID fellow by preparing and presenting any anatomical pathology aspect of the case. If there is no specific AP material on the patient, the resident may present a short (three or four image) review of the key pathologic features of the disease.

Evaluation

Presentations/manuscripts: Each resident is expected to present a 30-minute CE talk related to microbiology at the VAMC during his or her 12-week rotation. Residents will work with Dr. Oblack to select a topic and schedule their presentations. 

Each resident is expected to write a case study on a microbiology case during the rotation. Residents will work with Dr. Mortensen to identify a suitable case and prepare a publication ready case study.

• Oral discussion with the directors
• Correct interpretation of 10 slides at the 80 percent level
• Satisfactory attendance at infectious diseases conference on Tuesdays
• Satisfactory presentation (30 minutes) of a microbiological topic to laboratory staff
• Satisfactory performance serving on Infectious Diseases Consult Team during the third month of the rotation