Skip to Main Content

Clinical Microbiology Laboratory

The Clinical Microbiology Laboratory is certified by the American College of Pathology as an Extent 4 [highest] in the following areas: Bacteriology; Mycology; Mycobacteriology; and Parasitology. Extent 4 means that the Laboratory has passes periodic proficiency tests and unannounced inspections so that it is licensed to perform the most complex diagnosis in these areas. The Clinical Virology Laboratory is likewise certified.

The Laboratory utilizes a mixture of molecular diagnostic and agar-based techniques. Its “theme” has, and is, “rapid” (less than 4 hour) diagnostic methods. It has an extensive publication history concerning these methods, which are now used world-wide. Approximately 85% of pathogenic bacteria are identified from an agar plate within 4 hours of colony observation using MALDI-ToF.

Routine molecular techniques directly from patient specimens include genetic amplification for M. tuberculosis, Neisseria gonorrhoeae, Chlamydia, Group A Streptococcus, Group B Streptococcus, MRSA, Anaplasma and Ehrlichia, and Candida auris, as well as a panel of GI pathogens. Additionally, rapid molecular methods are used in conjunction with traditional culture for identification of blood stream infections and antimicrobial resistance markers.

Routine rapid antigen tests include Giardia, Cryptosporidium, H. pylori, and Cryptococcus.

The laboratory is in the process of converting to total laboratory automation (TLA). After construction, validation, and implementation, culture-based bacteriology will be standardized with automated plate inoculation and incubation. Interpretation of colonies and semi-automated MALDI-ToF processing will occur on a computer screen as opposed to physically holding plates.


Specialized testing

The Laboratory routinely sequences from 16s ribosomal bacterial DNA for identification. In addition, the Laboratory has developed and implemented Sanger sequencing for identifying mycobacterial and fungal species.

Special services

Clinical Infectious Diseases Rounds are held in the Microbiology Laboratory on Monday, Tuesday, and Friday. A faculty member conducts the rounds in conjunction with the Clinical Microbiology Fellow and Laboratory Medicine Resident. Rounds include patient case histories followed by a discussion of the laboratory methods and results. Didactic sessions on specific topics may also be presented.


  • Associate Professor of Laboratory Medicine; Director, Clinical Microbiology Laboratory, YNHH; Director, Virology Reference Laboratory, VACT; Director, Medical Microbiology Fellowship Program