Molecular Microbiology Acceptable Specimens
Acceptable Specimens
The following describes the type of sample that is appropriate for each of our tests. Please refer to How to Submit a Specimen instructions for more information.
Test Type: Broad-Range PCRs
Target Organism: Bacteria
Component tests:
Bacterial PCR reflex NGS [BCTDNA]
Bacterial DNA Detection by PCR (without reflex to NGS) [NRBDNA]
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
Target Organism: Fungi
Component tests:
Fungal PCR reflex NGS [FUNDNA]
Fungal DNA Detection by PCR (without reflex to NGS) [NRFDNA]
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
Target Organism: AFB
Component tests:
Nontuberculous Mycobacteria DNA Detection [NTMDNA]
M. tuberculosis complex DNA Detection [TBCDNA]
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
- Sputum specimens can be tested for M. tuberculosis complex DNA Detection [TBCDNA] and/or Mycobacterium avium complex DNA Detection [MAVDNA] only
- 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
Test Type: Pathogen Specific Assays
Target organisms: Bacteria
Bartonella DNA detection by PCR [BRTDNA]
Legionella DNA detection by PCR [LEGDNA]
Mycoplasma and Ureaplasma DNA Detection by PCR [MPLDNA]
Treponema pallidum DNA detection by NAAT [TPLDNA]
Tropheryma whipplei DNA detection by PCR [TWHDNA]
Target organisms: AFB
Mycobacterium avium complex DNA Detection [MAVDNA]
M. tuberculosis complex DNA Detection [TBCDNA]
Target organisms: Fungi
Aspergillus fumigatus DNA detection by PCR [ASPDNA]
Coccidioides DNA detection by PCR [COCDNA]
Cryptococcus DNA detection by PCR [CRYDNA]
Histoplasma DNA detection by PCR [HISDNA]
Mucorales DNA detection by PCR [MUCDNA]
Pneumocystis DNA detection by PCR [PNEDNA]
Target organisms: Parasite
Acanthamoeba and Balamuthia species PCR [AMBPCR]
Leishmania species DNA detection by PCR [LSHDNA]
Toxoplasma DNA detection by PCR [TOXDNA]
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
Test Type: Testing on Cultured Organisms
Organisms Identified by DNA Sequence-Based Methods:
Bacteria ID by Sequence Analysis [BSEQID]
AFB ID by Sequence Analysis [ASEQID]
Mold ID by Sequence Analysis [MSEQID]
Yeast ID by Sequence Analysis [YSEQID]
Bacterial ID by Whole Genome Sequencing [BWGSID]
Detection of Specific Genes:
mecA by PCR [MECPCR]
MTB Resistance by Whole Genome Sequencing [MTBWGR]
Strain Typing:
Bacterial Strain Typing by Whole Genome Sequencing [NGSTYP]
Acceptable
- Pure culture: organism growth on plate, slant, or blood culture bottle (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 | Comments |
---|---|---|---|
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 2024-09-20T18:14:05.506731+00:00