Fungal PCR reflex NGS

General Information

Lab Name

Fungal PCR reflex NGS

Lab Code

FUNDNA

Epic Name

Fungal DNA detection by PCR

Description

Fungal PCR reflex NGS

Rapid and accurate Identification of pathogenic fungi and at the species level is important for correct therapeutic intervention against an infectious disease. Biochemical or phenotypic methods for identification of a yeast or mold first requires growth of the microorganism in a suitable media. Furthermore, complete identification of organisms can be time consuming in cases where a biochemical reaction needs extended incubation or a phenotype takes a long time to appear on a plate requiring long time viability in the culture media. In many specimens, fungal elements can be seen by microscopy of tissue sections but are very difficult to grow due to their fastidious nature, or are not viable as a result of antifungal therapy. Often, fungal elements are seen on paraffin embedded tissue when a fresh tissue specimen is no longer available.

Identification of pathogenic fungi by PCR amplification of microbial DNA followed by DNA sequencing can by-pass the requirement for growth of microorganism on a media for slow growing or fastidious organisms and the requirement for extended incubation for scoring biochemical or phenotypic results for many other organisms. Therefore, sequence based identification of microorganisms offer a faster turn around time and more accurate result compared to conventional methods based on biochemical and phenotypic tests.

Sequencing of specific gene(s) provides a rapid and accurate identification of clinically significant organism. Judicious primer selection allows amplification of sequences at the species level or at the phylogenetic level. Raw sequences are assembled then classified by comparison to public sequence databases and the UWMC Clinical Microbiology Sequence Database in order to provide organism identification.

Gene sequencing of 28S rRNA gene for molds and ITS for both molds and yeasts provides rapid, accurate identification of clinically significant fungi. The regions contain conserved regions useful for the design of universal primers that amplify the gene from all pathogenic and nonpathogenic fungi in addition to hypervariable regions that contain species-specific signature sequences useful for fungal identification to species level.

Selection of this test will reflex to Fungal DNA Detection by ITS Next Gen Seq [NGSITS] if there is evidence of multiple fungal templates present.

Reflexive Testing

When suspected pathogenic microorganisms are detected, identification procedures are performed, as appropriate for the organism and specimen, including evaluation of polymicrobial specimens using Next Generation Sequencing.

• Coccidioides DNA detection by PCR [COCDNA]
• Cryptococcus DNA detection by PCR [CRYDNA]
• Mucorales DNA detection by PCR [MUCDNA]
• Histoplasma DNA detection by PCR [HISDNA]
• Pneumocystis DNA detection by PCR [PNEDNA]
• Fungal DNA Detection by ITS Next Gen Seq [NGSITS]

Incidental Finding Reflexes

• Acanthamoeba and Balamuthia species PCR [AMBPCR]
• Leishmania species DNA detection by PCR [LSHDNA]
• Toxoplasma DNA detection by PCR [TOXDNA]

Forms & Requisitions

Molecular Microbiology Order Form

Synonyms

28s PCR, 28S sequencing, broad range fungal PCR, broad range fungi PCR, fungal 28S, fungal identification, fungal ITS, Fungal PCR, fungal sequencing, fungi identification, Fungi PCR, fungi sequencing, ITS PCR, ITS sequencing, molecular fungal, molecular fungi, universal fungal PCR, universal fungi PCR

Components

Code	Name
FUNSUM	Fungal PCR: Summary
FU28RS	Fungal PCR: Detection, 28S rDNA
FU28ID	Fungal PCR: 28S Identification
FUITRS	Fungal PCR: Detection, ITS rDNA
FUITID	Fungal PCR: ITS Identification
FUSI	Fungal PCR: Specimen Description
FUSPI	Fungal PCR: External Identifier
FUSR	Fungal PCR: Special Requests
FUSC	Fungal PCR: Specimen Comments
FUNAE	Fungal PCR: Specimen DNA Extraction
FUREV	Fungal PCR: Pathologist Review
FUME	Fungal PCR: Method Note