Bacterial and Fungal PCR
ABOUT OUR SERVICE
Our molecular bacteriology service aids in the diagnosis of
bacterial infection by detecting bacterial DNA present in
biological specimens or isolates.
Details of the assays we offer can be found in the
Microbiology User Guide.
Samples must be accompanied by a completed Microbiology
PCR Request Form.
Results are accessed via the
Outreach Results Portal.
SPECIMEN REQUIREMENTS
We accept any fluid or tissue from a normally sterile site,
including formalin-fixed paraffin embedded (FFPE) tissue and blood
culture fluid. Blood culture fluids are only suitable if they have
flagged positive or if organisms have been seen on gram stain.
Specimens should be sent in a sterile, dry container with no
added fluids or transport media.
Sample type
|
Minimum volume required
|
Fluids (excluding blood culture fluid)
|
500 µL
|
Tissue
|
50 mg
|
FFPE tissue
|
10 rolls (10 µm)
|
Blood culture fluid
|
1 mL
|
Please note that samples from non-sterile sites,
including sputum, bronchoalveolar lavage and skin biopsies are not
suitable for broad-range bacterial PCR and will not be
processed. Alternatively targeted real-time PCR or
broad-range fungal PCR can be performed on these specimen types if
requested.
TURNAROUND TIME
Our turnaround time (TAT) for 16S, 18S, Mycobacterial and
Enterobactericeae spp PCRs is 7 days. All other targeted real-time
PCRs have a TAT of 72 hours. FFPE and blood culture fluid samples
are batch-processed weekly, therefore TAT is increased for these
sample types. Please note that our service runs Monday-Friday.
OUR TESTING STRATEGY
Broad range bacterial PCR is a powerful technique that can
detect an extensive range of bacterial pathogens, however it has
reduced sensitivity compared to targeted real-time PCR. For this
reason our
testing strategy combines broad-range and targeted
bacterial PCRs to maximise the diagnosis of infection. Specimens
for which broad-range bacterial PCR is requested will additionally
be tested by relevant targeted PCR depending on specimen type
and/or clinical history, including where available real-time PCR
targeting the most common causative organisms. This combined
approach benefits from the broad range nature of 16S rRNA gene PCR
and the sensitivity of targeted real-time PCR; using them together
increases the diagnostic yield for bacterial infections (Harris
& Brown, 2022).
Harris KA and Brown JR (2022). Diagnostic yield of
broad-range 16S rRNA gene PCR varies by sample type and is improved
by the addition of qPCR panels targeting the most common causative
organisms, Journal of Medical Microbiology¸71 (12). (https://doi.org/10.1099/jmm.0.001633)
If you do not require
additional targeted real-time PCRs, for example if you have
already
performed these
in-house, please indicate this clearly on the request
form.
CONTACT US
For queries please contact:
Technical queries (specimen and test selection, results
interpretation):
Clinical Scientists: laura.atkinson@gosh.nhs.uk (Ext.
0437)
julianne.brown@gosh.nhs.uk (Ext.
5929)
Clinical queries (clinical advice, results
interpretation):
Microbiology consultants: surjo.de@gosh.nhs.uk (Ext.
8661)
james.hatcher@gosh.nhs.uk (Ext.
4583)
General queries (specimen receipt, availability of results):
Microbiology lab: 020 7829 8661 (ext 8661)