Molecular Microbiology Acceptable Specimens

Broad-Range PCRs

Acceptable Specimens

Bacteria

• 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

Fungi

• 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

AFB

• 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

Pathogen Specific Assays

Acceptable Specimens

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]
• Treponema Pallidum DNA detection, Mucocutaneous [TPLSWB]
• Tropheryma whipplei DNA detection by PCR [TWHDNA]

AFB

• Mycobacterium avium complex DNA Detection [MAVDNA]
• M. tuberculosis complex DNA Detection [TBCDNA]

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]

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

Testing on Cultured Organisms

Acceptable Specimens

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 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