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Oxford University Hospitals NHS Foundation Trust
Microbiology

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Molecular testing

The Microbiology Department is divided into a number of sections.

Level 7 of the John Radcliffe is home to:

  • autoclaving
  • microbiology specimen reception
  • antibiotic susceptibility testing / bacterial identification (AST/ID)
  • specialised bacteriology
  • general bacteriology
  • the containment level 3 laboratory.

Viral serology and the molecular laboratory are situated on Level 6, although the immunoanalysers used by viral serology are part of the Core Automated Laboratory on Level 4.

The Molecular laboratory is located on Level 6 of the John Radcliffe Hospital. It is divided between two main rooms with extraction performed within one and amplification of product performed within the other.

This section primarily analyses blood samples for the presence of viral, or some bacterial, DNA to help diagnose diseases. Other sample types that can be analysed in this way include cerebral spinal fluid (CSF), faeces, tissue, urine, sputum and swabs of lesions of suspected viral aetiology.

The first process for most of the assays requires any viral or bacterial DNA / RNA present within the sample to be extracted from the patient sample. This is done using the QIAGEN QIAsymphony instrument which allows the process to be automated. Following extraction, the product is added to the relevant PCR assay before the PCR reaction is performed using the Rotor Gene, which is a Qiagen real time PCR cycler.

The department has the Roche COBAS®/ TaqMan® system to perform viral loads, quantitative analysis, on human immunnodeficiency virus (HIV), Hepatitis B virus (HBV) and Hepatitis C virus (HCV).

The Roche COBAS® is used to prepare the samples and then the TaqMan® is used to perform the real time PCR reaction.

We also have the Roche COBAS® X480 system to process clinical material for high-risk human papilloma virus (HPV). These samples are cervical cytology samples that are taken as part of the cervical screening programme.