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.

Kulkarni MV, Zurita AN, Pyka JS, Murray TS, Hodsdon ME, Peaper DR. Use of imipenem to detect KPC, NDM, OXA, IMP, and VIM carbapenemase activity from gram-negative rods in 75 minutes using liquid chromatography-tandem mass spectrometry. J Clin Microbiol. 2014 Jul;52(7):2500-5.

Boyce JM, Lee L, Topal J, Peaper DR, Balcezak T. Response to mold contamination of intravenous magnesium sulfate produced by a compounding pharmacy. JAMA Intern Med. 2014 Apr;174(4):630-1.

Peaper DR, Kulkarni MV, Tichy AN, Jarvis M, Murray TS, Hodsdon ME. Rapid detection of carbapenemase activity through monitoring ertapenem hydrolysis in Enterobacteriaceae with LC-MS/MS. Bioanalysis. 2013 Jan;5(2):147-57.

Elinav E, Strowig T, Kau AL, Henao-Mejia J, Thaiss CA, Booth CJ, Peaper DR, Bertin J,Eisenbarth SC, Gordon JI, Flavell RA. NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell. 2011 May 27;145(5):745-57.

Ichinohe T, Pang IK, Kumamoto Y, Peaper DR, Ho JH, Murray TS, Iwasaki A. Microbiota regulates immune defense against respiratory tract influenza A virus infection.Proc Natl Acad Sci U S A. 2011 Mar 29;108(13):5354-9.