Molecular Microbiology Acceptable Specimens

Acceptable Specimens

The following describes the type of sample that is appropriate for each of our tests. Please refer to Molecular Microbiology Specimen Submission for more information.

Broad-Range PCRs

Acceptable Specimens

Bacteria

Acceptable

  • Fresh frozen tissue
  • Fresh frozen fluid. Common examples include: cerebrospinal fluid, pleural fluid, pericardial fluid, urine, bronchial lavage, joint fluid, bone marrow, vitreous fluid, etc.
  • Formalin Fixed Paraffin-embedded tissues (FFPE, PET): blocks, scrolls, and unstained slides
  • eSwabs, UTM (universal transport media), body fluid/bone marrow in EDTA (not including blood)
  • Sodium polyanethol sulfonate (SPS, Wampole Isolator Tubes) acceptable with disclaimer
  • Respiratory and genitourinary samples may be submitted if Bacterial PCR reflex NGS [BCTDNA] is selected

Unacceptable

  • Sputum
  • Blood, serum, plasma
  • Stool/rectal swabs
  • Citrated or heparinized solutions
  • Tissues floating in formalin
  • Swab/fluid collected in tube containing agar
  • Specimens treated with strong acid Decalcifying/Chelating agents such as Hydrochloric acid and formic acid
  • Specimens incubated above room temperature

Fungi

Acceptable

  • Fresh frozen tissue
  • Skin scrapings
  • Fresh frozen fluid. Common examples include: cerebrospinal fluid, pleural fluid, pericardial fluid, urine, bronchial lavage, joint fluid, bone marrow, vitreous fluid, etc.
  • Formalin Fixed Paraffin-embedded tissues (FFPE, PET): blocks, scrolls, and unstained slides
  • Sodium polyanethol sulfonate (SPS, Wampole Isolator Tubes) acceptable with disclaimer
  • eSwabs*, UTM (universal transport media), body fluid/bone marrow in EDTA (not including blood)

*Fungal PCR may have interference due to some lots of eSwabs which have been found to contain Saccharomyces cerevisiae DNA, resulting in false positive detection. Clinical correlation and/or retesting with a different collection method is advised. The detection of S. cerevisiae from eSwab specimens can interfere with our ability to rule out other fungal DNA.

Unacceptable

  • Sputum
  • Upper respiratory specimens
  • Blood, serum, plasma
  • Stool/rectal swabs
  • Genitourinary specimens
  • Citrated or heparinized solutions
  • Tissues floating in formalin
  • Swab/fluid collected in tube containing agar
  • Specimens treated with strong acid Decalcifying/Chelating agents such as Hydrochloric acid and formic acid
  • Specimens collected in Thioglycolate medium
  • Specimens incubated above room temperature

AFB

Acceptable

  • Fresh frozen tissue
  • Fresh frozen fluid. Common examples include: cerebrospinal fluid, pleural fluid, pericardial fluid, urine, bronchial lavage, joint fluid, bone marrow, vitreous fluid, etc.
  • Formalin Fixed Paraffin-embedded tissues (FFPE, PET): blocks, scrolls, and unstained slides
  • Sodium polyanethol sulfonate (SPS, Wampole Isolator Tubes) acceptable with disclaimer
  • eSwabs, UTM (universal transport media), body fluid/bone marrow in EDTA (not including blood)

Unacceptable

Pathogen Specific Assays

Acceptable Specimens

Bacteria

AFB

Fungi

Parasite

Acceptable

  • Fresh frozen tissue
  • Fresh frozen fluid. Common examples include: cerebrospinal fluid, pleural fluid, pericardial fluid, urine, bronchial lavage, joint fluid, bone marrow, vitreous fluid, etc.
  • Sputum
  • Formalin Fixed Paraffin-embedded tissues (FFPE, PET): blocks, scrolls, and unstained slides
  • eSwabs, UTM (universal transport media), body fluid/bone marrow in EDTA (not including blood)
  • Sodium polyanethol sulfonate (SPS, Wampole Isolator Tubes) acceptable with disclaimer
  • Buffy Coat with stain positive whole blood for Leishmania species DNA detection by PCR [LSHDNA] only
  • Whole blood/cord blood for Treponema pallidum DNA detection by NAAT [TPLDNA] only: Director approval is required for submission of blood samples due to logistical & specimen batching considerations. Submit in a lavender/purple top EDTA tube

Unacceptable

  • Blood, serum, plasma
  • Stool/rectal swabs
  • Citrated or heparinized solutions
  • Tissues floating in formalin
  • Swab/fluid collected in tube containing agar
  • Specimens treated with strong acid Decalcifying/Chelating agents such as Hydrochloric acid and formic acid
  • Specimens incubated above room temperature

Testing on Cultured Organisms

Acceptable Specimens

Organisms Identified by DNA Sequence-Based Methods

Detection of Specific Genes

Strain Typing

Acceptable

  • Pure culture: organism growth on plate or slant
  • blood culture bottle or broth (pure, organism seen on stain)

Unacceptable

  • Mixed Culture
  • No Organism seen on stains from culture bottles/broths
  • No growth on/in culture media

Associated Tests

Code Name Specimen
ASEQID AFB ID by Sequence Analysis Pure Culture
ASPDNA Aspergillus fumigatus DNA detection by PCR Tissue (Fresh frozen or paraffin-embedde...
BSEQID Bacteria ID by Sequence Analysis Pure Culture
NGS16S Bacterial detection by 16S NGS This only available as a reflexive test,...
NRBDNA Bacterial DNA Detection by PCR (without reflex to NGS) Tissue (Fresh frozen or paraffin-embedde...
BWGSID Bacterial ID by Whole Genome Sequencing Pure Culture
BCTDNA Bacterial PCR reflex NGS Tissue (Fresh frozen or paraffin-embedde...
NGSTYP Bacterial Strain Typing by Whole Genome Sequencing Pure culture of bacterial organisms
BRTDNA Bartonella DNA detection by PCR Tissue (Fresh frozen or paraffin-embedde...
COCDNA Coccidioides DNA detection by PCR Tissue (Fresh frozen or paraffin-embedde...
CRYDNA Cryptococcus DNA detection by PCR Tissue (Fresh frozen or paraffin-embedde...
ENBDNA Enterobacterales DNA Detection This only available as a reflexive test,...
NGSITS Fungal DNA Detection by ITS Next Gen Seq This only available as a reflexive test,...
NRFDNA Fungal DNA Detection by PCR (without reflex to NGS) Tissue (Fresh frozen or paraffin-embedde...
FUNDNA Fungal PCR reflex NGS Tissue (Fresh frozen or paraffin-embedde...
HISDNA Histoplasma DNA detection by PCR Tissue (Fresh frozen or paraffin-embedde...
LEGDNA Legionella DNA detection by PCR Tissue (Fresh frozen or paraffin-embedde...
LSHDNA Leishmania species DNA detection by PCR Tissue (Fresh frozen or paraffin-embedde...
MECPCR mecA by PCR Pure culture
MSEQID Mold ID by Sequence Analysis Pure Culture
MTBWGR MTB Resistance by Whole Genome Sequencing Pure Culture
TBCDNA M. tuberculosis complex DNA Detection Tissue (Fresh frozen or paraffin-embedde...
MAVDNA Mycobacterium avium complex DNA Detection Tissue (Fresh frozen or paraffin-embedde...
MCHDNA Mycobacterium chimaera DNA detection by PCR Tissue (Fresh frozen or paraffin-embedde...
MPLDNA Mycoplasma and Ureaplasma DNA Detection by PCR Tissue (Fresh frozen or paraffin-embedde...
NTMDNA Nontuberculous Mycobacteria DNA Detection Tissue (Fresh frozen or paraffin-embedde...
PNEDNA Pneumocystis DNA detection by PCR Tissue (Fresh frozen or paraffin-embedde...
TOXDNA Toxoplasma DNA detection by PCR Tissue (Fresh frozen or paraffin-embedde...
TPLDNA Treponema pallidum DNA detection by NAAT Tissue (Fresh frozen or paraffin-embedde...
TWHDNA Tropheryma whipplei DNA detection by PCR Tissue (Fresh frozen or paraffin-embedde...
YSEQID Yeast ID by Sequence Analysis Pure Culture

Last updated 2024-10-10T21:58:56.255263+00:00