Clinical Pathology Program

Clinical Microbiology

Rotation Director:
David W. Craft, PhD D(ABMM)

The clinical microbiology rotation consists of three 4-week blocks and is designed to provide an in-depth exposure to the laboratory diagnosis of infectious diseases in the clinical microbiology laboratory. The rotation consists of observation and performance during bench rotations, didactic lectures, organ system centric discussion and mentoring, participation in laboratory rounds and cases with the Infectious Disease Service and attendance at the Infection Control Committee meeting. Opportunities for research are available and are performed under the guidance of the Supervisor or Director. While on rotation, the resident is expected to serve as a resource for the microbiology laboratory in communicating with the clinical staff on unusual or critical test requests or reports and recommending the most appropriate course of action when required.

Goals and Objectives:

Patient Care:

Residents must understand the technical requirements necessary for medical decision-making and the role of the medical director in ensuring that the needs of the patient and the ordering clinician are served. Residents are expected to:

  • Recognize and correctly interpret the clinical significance of common microbiology test results, to include therapeutic and infection control consultation
  • Advise clinical staff on appropriate specimen collection for disease states and pathogen detection
  • Assess atypical laboratory findings and unusual test requests and develop strategies to evaluate and resolve
  • Demonstrate proficiency in microscopy, culture and molecular detection of bacteria, molds, yeasts and parasites
  • Demonstrate proficiency in antimicrobial susceptibility testing, interpretation and limitations of susceptibility test results, and therapeutic consultation

Medical Knowledge:

Residents must demonstrate knowledge about infectious disease presentation and application of this knowledge to advise health care providers and infection control personnel on appropriate laboratory support. Residents are expected to:

  • Develop knowledge of microscopic, molecular and phenotypic identification algorithms of the laboratory through observation, discussion and reading as described in the Components section of this rotation description
  • Understand the relationships between clinical and anatomic laboratory test findings, the underlying pathophysiology, and infectious disease presentation
  • Understand the clinical presentation of infectious disease and differential diagnosis of disease and apply to appropriate laboratory workup and result reporting
  • Serve as a resource to the clinical and laboratory staff for test selection, utilization and interpretation

Practice-based Learning and Improvement:

Residents must be able to demonstrate the ability to evaluate and improve their clinical practices based on new and evolving scientific evidence. Residents are expected to:

  • Apply current medical knowledge and recent literature to unusual cases
  • Recognize the value and limitations of resources that can be used to understand and evaluate laboratory findings (manufacturer's instructions for use, proficiency testing results, quality control data, reference laboratory manuals)
  • Understand the science of current diagnostic systems and how to evaluate their role in patient care and use in the clinical laboratory
  • Utilize library, web-based, and other educational sources to evaluate methodologies and laboratory findings

Systems-based Practice:

Residents must demonstrate an awareness and responsiveness to the system of healthcare, and the public health implications, by utilizing appropriate resources to provide optimal infectious disease laboratory services. Residents are expected to:

  • Understand state and public health reportable disease requirements
  • Understand federal, state and local regulatory issues and compliance requirements
  • Become involved with management issues in the laboratory, including lab utilization, quality control, quality assurance and unusual findings
  • Become involved with institution level consultation to antibiotic stewardship and infection control and communicate their significance to other health care professionals as necessary
  • Recognize and develop management and technical skills necessary to serve as medical director of a microbiology laboratory
  • Consider cost-effectiveness in laboratory testing, including implications for referral services, without compromising patient care
  • Understand the pathologist's role and professional practices in relation to other health care professionals

Interpersonal and Communication Skills:

Residents must be able to demonstrate interpersonal and communication skills that result in effective information exchange and learning with other health care providers, patients, and patients' families. Residents are expected to:

  • Exhibit effective listening and interactive communication skills within the laboratory
  • Provide accurate communication of pathology information using verbal and appropriate electronic communication media
  • Interact with departmental and extra-departmental personnel, including healthcare professionals, healthcare administrators and operators, resource managers, logisticians and other staff in an appropriate manner
  • Provide effective and professional consultation to other health care professionals demonstrating care and respect for them, and sustain ethically sound professional relationships with colleagues, staff, patients, and patients' families as necessary
  • Work effectively as a team with other health care professionals and other staff


Residents must demonstrate a commitment to fulfilling professional responsibilities and ethical principles and sensitivity to a diverse patient population. Residents are expected to:

  • Demonstrate commitment to ethical principles pertaining to confidentiality of patient information, informed consent, and business practices
  • Demonstrate respect, compassion and integrity in all interactions with patients, their families, faculty, other trainees, technologists, and other staff
  • Demonstrate sensitivity and responsiveness to the ethnicity, diversity, age, gender, sexual orientation, and disabilities of patients, colleagues, and staff
  • Demonstrate a commitment to excellence and on-going professional development
  • Demonstrate adherence to guidelines and regulations set forth by regulatory and accrediting agencies
  • Demonstrate ability to identify deficiencies in peer performance


  • No prerequisites are necessary

Duration and Timing of the Rotation:

  • Three four-week blocks, not necessarily contiguous

Teaching Staff:

  • David Craft PhD D(ABMM), Medical Director of Microbiology
  • Debbie Myers, MS, MT(ASCP)SM Supervisor of Microbiology


1.  Reading (background reading covered independently by resident)

The standard text for this rotation is Koneman's Color Atlas and Textbook of Diagnostic Microbiology, 6th edition. Selected chapters will be covered through monthly and recurring didactic presentations. Case studies in infectious diseases text is Cases in Medical Microbiology and Infectious Diseases, 3rd edition. by Gilligan, Smiley and Shapiro. Selected cases will be discussed with Director.

First block (8 consecutive weeks):

  • Specimen processing
  • Blood culture, smear interpretation, rapid tests
  • Bacterial (aerobes & anaerobes) and Yeast identification and susceptibility testing
  • AFB and Mold identification (culture and microscopy)
  • Individual discussion of organ system and case approaches with Director (weekly)
  • Infectious Disease team case presentations (weekly)
  • Infectious Disease lab rounds (weekly)
  • Infection Control Committee meeting (monthly)

Second block (4 weeks):

  • Review of identification and susceptibility testing method and interpretation
  • Individual and tailored mentoring with Director (weekly)
  • Infectious Disease team case presentations (weekly)
  • Infectious Disease lab rounds (weekly)
  • Infection Control Committee meeting (monthly)
  • Project: Case presentation or Research project

Method(s) of Evaluation:

  • Technologist observation and work-up of unknowns
  • Supervisor and Director observation
  • Didactic instruction of case presentation to assess knowledge base
  • Review of research (as applicable)
  • Director assessment
  • Residents will be evaluated based on direct observation by faculty
  • After each rotation, residents will be evaluated by faculty in New Innovations

 Updated: 3/2015 DWC