Clinical Microbiology Training and Competencies

Anatomic and Clinical Pathology Residency Program


To assure that clinical pathology residents attain the general competencies in clinical microbiology expected of a new practitioner as defined by the ACGME.


The trainer is defined as a staff member of the Section of Clinical Microbiology who has been specifically designated to perform pathology resident training and to assess his/her competency. Trainers will generally include the Medical Director and one or more of the following: Administrative Specialist, Technical Specialist, or a Senior Technologist (Med Tech II).


For each item listed on the CLINICAL MICROBIOLOGY TRAINING CHECKLIST, the trainer will assure that the general competencies (as listed and defined below) are covered when applicable:

Patient Care: Working under the direction of the Medical Director of Clinical Microbiology, the pathology resident will be involved in the following:

  • Assessment of the appropriateness and quality of clinical specimens submitted for testing based on specimen source and type of suspected pathogen (i.e. bacterial, mycobacterial, fungal, viral)
  • Interpretation of clinical significance of positive cultures and other abnormal test results
  • Confirmation of unusual patterns of antibiotic susceptibility (e.g. extended spectrum beta-lactamase producers)
  • Review of smear/culture discrepancies
  • Correlation of urine dipstick results with microscopic findings on urine sediment examination
  • Provision of clinical consultation relevant to microbiology and urinalysis. The resident will also participate in section-specific quality control and process improvement processes to ensure the provision of patient-focused and cost-effective care.
  • In addition, he/she will be expected to attend and actively participate in the Department of Medicine Morning Report and Infectious Disease Rounds. Specifically, the resident will be expected to:
    • Develop an understanding of established specimen acceptance standards specific to the Section of Clinical Microbiology (including adequacy of sputa, limits on the number of blood cultures per hospital admission and guidelines for stool evaluation for ova/parasites)
    • Initiate contact and discussion with clinicians and other health care professionals regarding specimen problems, clinical requests that deviate from established policies/procedures, and orders for esoteric tests
    • Gather essential and accurate clinical information as needed to provide clinical consultation in microbiology, including interpreting the clinical significance of patient test results and making appropriate recommendations for antibiotic therapy and/or follow-up laboratory tests
    • Educate fellow (peer) residents in other clinical disciplines about the proper use of microbiology laboratory tests by participating in Morning Report, Infectious Disease Rounds and other interdisciplinary conferences.
Methods of evaluation:
  • Review of training checklist and task-specific credentialing logs
  • Oral examination
  • Written examination
  • Completion of questionnaire by trainer(s)

Medical Knowledge: The resident is expected to have or acquire the necessary basic science and clinical medicine knowledge to apply an analytic approach to clinical situations (see Patient Care activities outlined above). This will include a thorough understanding of laboratory methods for the detection of microbial pathogens (including culture isolation, antigen detection and molecular probes), presumptive and definitive identification of clinical isolates, and determination of antibiotic susceptibilities. Specifically, the resident will be expected to:

  • Acquire a working knowledge of culture requirements (including media selection, incubation temperature atmospheric environment) for all specimen sources/sites and type of suspected pathogen (i.e., bacterial, mycobacterial, fungal, viral)
  • List the normal bacterial flora of various body sites
  • Describe the principles and utility of selective and differential growth media
  • Explain the potential effects of pre-analytical variables on test results
  • Evaluate the diagnostic utility of laboratory tests in a given clinical situation, interpret the test results, and correlate with available clinical data
Methods of evaluation:
  • Review of training checklist and task-specific credentialing logs
  • Oral examination
  • Written examination
  • Completion of questionnaire by trainer(s)

Practice-Based Learning & Improvement: The resident will develop a systematic approach to the investigation and evaluation of clinically relevant testing and how to make appropriate decisions resulting in improved patient care. This involves the integration of individual clinical expertise with the best available external clinical evidence from systematic research. To the attain the above goals, the resident is expected to:

  • Proactively seek examples of abnormal, interesting, and unusual laboratory findings and correlate these data with clinical diagnoses and disease states via chart review and contact with clinicians
  • Develop proficiency in the performance of medical literature searches and demonstrate the effective use of these tools
  • Apply knowledge of research study design and statistical methods to evaluate published scientific literature
  • Demonstrate the ability to efficiently retrieve patient clinical information and laboratory data via the Hospital and Laboratory Information Systems
  • Present interesting cases to fellow residents, faculty and laboratory staff
  • Actively participate in laboratory quality assurance and improvement activities
  • Actively participate in research activities
Methods of evaluation:
  • Review of training checklist and task-specific credentialing logs
  • Oral examination
  • Written examination
  • Completion of questionnaire by trainer(s)

Interpersonal and Communication Skills: The resident will learn how to be effective when exchanging information with other healthcare professionals. Specifically, the resident must:

  • Demonstrate the ability to communicate effectively and efficiently, both orally and in writing
  • Demonstrate the ability to interact constructively and negotiate effectively with others on issues requiring resolution
  • Demonstrate appropriate utilization of available communication technologies to communicate effectively with others (e.g., voice mail, electronic mail)
  • Demonstrate the ability to prepare and deliver effective presentations utilizing a variety of presentation methods (overheads, slides, presentation graphics, and multimedia)
  • Attend and participate in interdisciplinary teaching activities and Infection Control committee meetings
Methods of evaluation:
  • Review of training checklist and task-specific credentialing logs
  • Completion of questionnaire by trainer(s)

Professionalism: The resident will be expected to show a commitment to ethical principles when carrying out professional responsibilities. He/she will exhibit behavior appropriate to their activities related to the clinical microbiology rotation. Specifically, the resident will be expected to:

  • Maintain strict patient confidentiality with respect to all clinical and personal information: diagnosis, prognosis, test results, etc.
  • Demonstrate compassion and empathy for patients
  • Demonstrate respectful behavior toward other healthcare professionals
  • Behave appropriately when involved in stressful/emotional situations by maintaining self-control and attempting to defuse the situation
  • Respond to pager and telephone calls promptly and courteousl
  • Regularly and punctually attend conferences, meetings, assigned rotations, and other obligations, and contribute whenever possible
  • Demonstrate a commitment to ongoing professional and personal development by keeping abreast of developments in the medical literature
Methods of evaluation:
  • Completion of questionnaire by trainer(s)

Systems-Based Practice: The resident will be aware of and responsive to the larger context and system of healthcare as it relates to their assigned responsibilities. Specifically, the resident must:

  • Demonstrate awareness and understanding of the role of the laboratory in the healthcare delivery system and the importance of reliable, cost-effective, and timely laboratory data in clinical decision-making
  • Demonstrate awareness of the integral role of the microbiology laboratory in public health and epidemiology, including statutory requirements for laboratory-based reportable diseases
  • Demonstrate the ability to work effectively with clinicians and other healthcare professionals to achieve high=quality and cost-effective care
  • Demonstrate familiarity with different models for health care delivery and their impact on laboratory reimbursement
  • Demonstrate knowledge of methods for cost analysis and accounting and cost containment measures
  • Demonstrate understanding of the budget preparation and tracking proces.
Methods of evaluation:
  • Review of training checklist and task-specific credentialing logs
  • Oral examination
  • Written examination
  • Completion of questionnaire by trainer(s)

The general competencies will be taught using a combination of the following methods:

  • Direct observation
  • Assigned reading and other learning aids (test procedure manuals, textbooks, medical journals, computer-based tutorials, pre-recorded and live audio- and teleconferences)
  • Completion of specific learning activities and learning objectives
  • Departmental and interdisciplinary teaching conference.
  • Review of previous interesting case.
  • Attendance at various monthly meetings: Microbiology section staff meetings, Microbiology section management meetings, Clinical Laboratory Administration, Clinical Pathology Quality Assurance and Improvement Committee, Infection Control Committe.
  • Manage mentorship by the section Medical Director.

Completion of each resident training activity will be documented on the Microbiology Training Checklist as well as task-specific credentialing logs. In addition to the methods of evaluation specified above, the resident's overall performance will be assessed at the completion of each rotation through Clinical Microbiology by the section Medical Director in consultation with the resident's designated advisor and other departmental faculty.

For More Information

Please contact us if you have questions about the Anatomic and Clinical Pathology Residency Program at Danbury Hospital, or would like more information.