Bacterial and Fungal PCR


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.



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


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.



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.



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).  (


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.



For queries please contact:

Technical queries (specimen and test selection, results interpretation):

Clinical Scientists: (Ext. 0437)       

                     (Ext. 5929)   


Clinical queries (clinical advice, results interpretation):    

Microbiology consultants: (Ext. 8661)

                                 (Ext. 4583)


General queries (specimen receipt, availability of results):

Microbiology lab: 020 7829 8661 (ext 8661)

© 2011 Great Ormond Street Hospital for Children NHS Trust