Bacterial PCR reflex NGS

General Information

Lab Name

Bacterial PCR reflex NGS

Lab Code

BCTDNA

Epic Name

Bacterial DNA detection by PCR

Description

Detection and identification of Bacterial DNA (16S rRNA target).

Accurate identification of bacterial isolates is an essential task of the clinical microbiology laboratory that enables initiation of proper antimicrobial therapy. For many organisms, traditional phenotypic identification may be difficult, laborious and time-consuming. This issue is further confounded by phenotypic variation within species, many newly described pathogenic species and the limited battery of phenotypic tests available to distinguish among established and potential bacterial pathogens. It is sometimes essential to identify bacterial isolates to species level in order to rule out species that are drug resistant or more pathogenic, to detect unsuspected pathogens, ascribe pathogenicity to species so far considered to be nonpathogenic and to identify new bacterial species.

With more than 20,000 sequences available in public databases (e.g. NCBI), 16S ribosomal RNA gene (rRNA) sequencing is considered by current taxonomists to be the gold standard in bacterial identification and classification. 16S rRNA gene contains conserved regions useful for the design of broad-range PCR primers that can amplify various fragments of the 16S rRNA gene from pathogenic and nonpathogenic bacteria. These fragments include hypervariable regions containing species-specific signature sequences useful for bacterial identification to species level.

In many specimens bacteria 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 antimicrobial therapy. Some specimens may never reveal the presence of a bacterial pathogen because of low abundance and/or lack of viability. The use of PCR to detect this DNA extracted directly from clinical specimens facilitates the identification of these pathogens.

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.

• Bartonella DNA detection by PCR [BRTDNA]
• Enterobacterales DNA Detection [ENBDNA]
• Legionella DNA detection by PCR [LEGDNA]
• Mycobacterium avium complex DNA Detection [MAVDNA]
• Mycoplasma and Ureaplasma DNA Detection by PCR [MPLDNA]
• M. tuberculosis complex DNA Detection [TBCDNA]
• Treponema pallidum DNA detection by NAAT [TPLDNA]
• Tropheryma whipplei DNA detection by PCR [TWHDNA]
• Bacterial detection by 16S NGS [NGS16S]

Forms & Requisitions

Molecular Microbiology Order Form

Synonyms

16S PCR, 16S sequencing, bacteria 16S, bacteria identification, bacteria PCR, bacteria sequencing, bacterial 16S, bacterial identification, bacterial PCR, bacterial sequencing, broad range bacteria PCR, broad range bacterial PCR, molecular bacteria, molecular bacterial

Components

Code	Name
BT16RS	Bacterial PCR: Detection, 16S rDNA
BT16ID	Bacterial PCR: Identification, 16S rDNA
BTSI	Bacterial PCR: Specimen Description
BTSPI	Bacterial PCR: External Identifier
BTSR	Bacterial PCR: Special Requests
BTSC	Bacterial PCR: Specimen Comments
BTNAE	Bacterial PCR: Specimen DNA Extraction
BTREV	Bacterial PCR: Pathologist Review
BTME	Bacterial PCR: Method Note