You are here

Specimen Collection

Primary patient specimens

Respiratory specimens should be submitted in the approved 50 ml conical centrifuge tubes that are included in the mailers provided by the Wadsworth Center. A minimum of 1 ml of specimen is required. Acceptable specimens for M. tuberculosis complex and M. avium complex PCR assay include:

  • Expectorated sputum
  • Induced sputum
  • Bronchial aspirates
  • Tracheal aspirates
  • Bronchoalveolar lavage
  • Fine needle aspirates
  • Lung biopsies
  • Tissues (NOT paraffin embedded)
  • CSF

In order to submit any other specimen type for PCR testing, the submitting laboratory must obtain permission from CLEP using the non-permitted laboratory test request application form. FAX this form to CLEP at the number shown on the form. CLEP will FAX back an approval or denial of your request.  Once approval is obtained, include a copy of CLEP’s approval form with the specimen when it is shipped.

Unacceptable specimens include:

  • Formalin fixed/paraffin embedded tissues
  • Stool (feces)
  • Whole blood
  • Swabs
  • Non-human specimens
  • Already processed (concentrated) specimens (see note below)
  • Respiratory specimens with a volume of less than 1 ml
  • Broken or leaking tubes
  • Sputa collected >7 days from date of receipt

NOTE:  Specimens that are >7 days old, specimens with smaller volumes and already processed (concentrated) specimens may be accepted on a case-by-case basis as deemed appropriate by the Mycobacteriology Laboratory Director.

Mycobacterial isolates

Isolates of growing acid fast bacilli may be sent on slants of culture media (LJ, 7Hl0, etc.) in screw capped tubes or in liquid culture media.  Place a single piece of parafilm or tape around the cap to prevent opening in transit. If liquid media is submitted, 3 ml is the optimal volume (1 ml minimum). Liquids may be submitted in the 50 ml screw capped conical tubes provided with the mailing kits, or in gasketed cryovials. Place a single piece of parafilm or tape around the cap to prevent opening in transit. 
Unacceptable: Growth sent on culture plates.

Required Specimen Submission Information

Specimens will not be processed without the required submission information. Information may be submitted in two ways:

  • If you have access to the Health Commerce System (HCS) and the Clinical Laboratory Information Management System (CLIMS), follow the steps below:

    1. Log onto the New York State Health Commerce System
    2. Select 'CLIMS'
    3. Select 'Remote Order'
    4. Click on the tab that indicates the type of sample you would like to submit (i.e. human, animal, environmental, etc.)
    5. Fill in the screens, ‘Place the Order’, print form and submit with specimen.

This method provides many advantages over paper submission including specimen tracking, notification when results become available, online access to results, and access to testing catalog. Should you encounter difficulty, please access the Reference Guide in the Remote Order application or contact CLIMS.

NOTE: If you are from a licensed clinical laboratory with a valid PFI number or county or regional health department your HIN/HCS coordinator can grant you access to CLIMS (and create your HCS account if needed). For all other access, the Request for Access to the Wadsworth Center Laboratory Information Management System (CLIMS) form must be completed, signed and faxed to (518) 474-8140 or (518) 473-1326.