Microbial Isolates

The Crimson Core handles a variety of requests for microbiological materials and additional testing of microbial isolates to phenotype and determine antibiotic susceptibility and resistance profiles.

Clinical isolates may be collected for investigators performing epidemiological studies, basic research into microbial pathogenesis, studies of microbial resistance to antibiotics, and microbiome or metagenomic analyses.


To request materials, fill out a Service request form.

  • Requesting groups must have a valid biosafety protocol or certificate for receiving and handling materials at biohazard level 2 (BL2).
  • An IRB protocol may be needed if clinical data is to be released with isolates, and/or sequencing of primary samples containing pathogens will be performed.

    The following represent common types of isolates identified in the BWH Clinical Microbiology Laboratory:

    • Aerobic and facultative anaerobic bacterial pathogens including Staphyloccoal, Streptococcal species, Escherichia coli, and other Gram-negative organisms.
    • Microaerophilic organisms including Campylobacter species.
    • Strict anaerobes such as Bacteroides and Prevotella
    • Candida and other monomorphic yeasts.
    • BL-3 materials including Mycobacterium tuberculosis and fungal isolates require review and approval of the request by the microbiology lab, and proof from investigators that they maintain appropriate facilities within the Longwood Medical Area for the storage and handling of such materials.
    • Viral lysates from clinical cell cultures for CMV, HSV I and II, Adenovirus.
    • Primary source materials (blood only) containing CMV, EBV, HIV or HCV. These materials are collected after completion of viral antigen or viral load studies.
    • Blood containing malarial or Babesial parasites.