Molecular Genetic Pathology Fellowship

Molecular Microbiology Laboratory Rotation


Medical Knowledge

On completing the Molecular Microbiology laboratory rotation(s), the fellow is expected to be able to:

  1. Demonstrate an understanding of viral and prokaryotic molecular biology and biochemistry relevant to development, performance and interpretation of nucleic-acid based tests for the identification and evaluation disease causing microorganisms.
  2. Demonstrate an understanding of the technical, interpretive, quality control, and validation aspects as well as the clinical implications of the various tests performed in the molecular microbiology laboratory, including:
    1. Viral load tests.
    2. Direct molecular detection of viruses, bacteria and fungi in various body fluids.
    3. Identification of cultured bacteria by sequencing of rRNA genes.
    4. Antimicrobial resistance testing by directed mutation testing, or nucleic acid sequencing.
    5. Tests performed in the molecular epidemiology laboratory.
  3. Demonstrate an understanding of the pre-analytical, analytical and post-analytical issues relevant to accurate performance of the tests performed in the laboratory.

Patient Care

  1. Perform, review, interpret and report tests performed in the molecular microbiology laboratory
  2. Understand the clinical implications and limitations of these tests and, when appropriate, communicate these to ordering physicians.
  3. When these tests are inadequate to answer relevant clinical questions, help the treating physician identify clinically appropriate tests, laboratories performing such tests, and assist the clinician in interpreting these tests.

Practice Based Learning and Improvement

  1. Regularly collect and study the literature relevant to testing performed in molecular microbiology and demonstrate the ability to critically evaluate and compare published material.
  2. Evaluate published literature to determine the clinical value of tests performed in the molecular microbiology laboratory and identify future directions in testing to improve the ability of the molecular microbiology laboratory to assist in patient care.

Interpersonal and Communications Skills

During the rotation, fellows must demonstrate interpersonal and communication skills that result in effective information exchange and teaming with other health care providers, laboratory personnel, patients, and patients' families. Towards this end they shall:

  1. Develop effective working relationships with professional and technical staff in the molecular microbiology laboratory, and outside consultants.
  2. Demonstrate effective verbal communication skills when communicating results to clinicians, at the appropriate level for the information being transmitted; convey and explain test results clearly, precisely, and concisely to physicians in direct conversations, or at conferences; communicate effectively with technical personnel when troubleshooting assays, or when managing the laboratory.
  3. Develop excellent written skills for communication of complicated results when issuing reports, for the development and implementation of new laboratory policies and procedures, and for presentation of scientific research data, as appropriate.
  4. Develop presentation skills that include selection of appropriate presentation materials and visual aids, good oral presentation and mannerisms, and the ability to answer questions effectively.


Demonstrate habits leading to excellence in professional performance, which includes:

  1. Perfect attendance at all laboratory activities;
  2. Reliability in each assigned duty;
  3. Completeness of work-up of each case;
  4. Dedication to patient care;
  5. Maintaining appropriate and cordial relationships with laboratory and clerical personnel, with attending-staff and with other fellows and residents.

Systems Based Practice

Fellows must demonstrate an awareness of and responsiveness to the larger context and system of health care and the ability to call on system resources to provide molecular microbiology services that are of optimal value. Towards this they shall, where appropriate:

  1. Provide guidance to clinicians to ensure that testing in the molecular microbiology laboratory is used and integrated into patient care in an appropriate and cost-efficient manner.
  2. Demonstrate knowledge of scientific, legal, and ethical issues relating to molecular microbiology testing.
    1. Understand the implications not only to patients, but also to the community at large, of results of molecular microbiology tests.
    2. Understand the ethical basis and the legal requirement for informed consents for HIV related tests in NY State.
    3. Monitor the compliance of the laboratory with these requirements in cases that the fellow is involved with.
    4. Demonstrate an understanding of the regulatory issues governing the operations of the laboratory, including CLIA regulations, NY State regulations, CAP implementation of CLIA regulations, and the various guidelines of the Clinical Laboratory and Standards Institute (CLSI) to help laboratories meet these guidelines and provide optimal testing services to patients.
  3. Demonstrate knowledge of the impact of laboratory management and activities on other health care professionals, organizations, and society.
  4. Understand financial and economic systems in which the molecular microbiology laboratory operates, including billing, the appropriate use of current procedural terminology codes, diagnostic codes, and health insurance and reimbursement issues.
  5. Practice cost-effective health care and resource allocation that does not compromise quality of care.
  6. Demonstrate an understanding of the impact of nucleic acid based organism identification and typing on infection control activities of the hospital and the mitigation of the spread of infections in the community at large.
  7. Be an advocate for quality patient care and contribute to clinician education.
  8. Demonstrate the ability to assess, understand, and use the resources, personnel, and health care systems necessary to provide optimal care.

Administration Contact

  • Ms. Casey Schadie
  • Coordinator, Residency Training Program
  • Department of
    Pathology & Cell Biology

    Columbia University College of
    Physicians & Surgeons

    630 W. 168th Street
    New York, NY 10032
  • Tel: 212 305-5697

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