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How are samples processed at a laboratory?

This lab tests the local population through pillar 1 testing, defined as swab testing of those in clinical need, and health and care workers

In the video above, Dr. Theo Gouliouris takes us on a virtual tour around the clinical microbiology and public health laboratory at Addenbrookes hospital, Cambridge.

This laboratory is part of a network of eight Public Health England (PHE) regional laboratories in England and serves a dual role.

Firstly, it acts as a diagnostic microbiology lab for patients in hospital and local GP practices.

Secondly, it plays a role for public health, receiving specialist molecular tests from the region that do not require sending to a national reference laboratory, such as Clostridium difficile, for ribotyping.

Additionally, it is ready to respond to community disease outbreaks and national threats such as bioterrorism or significant epidemics.

Pillar 1 testing

As part of the COVID-19 pandemic, this laboratory was one the first to be able to test for SARS-CoV-2 using PCR.

As the NHS rolled out more tests and large-scale labs were set up, the laboratory now tests the local population through pillar 1 testing, defined as swab testing of those in clinical need, and health and care workers.

During the Ebola crisis in West Africa, labs were also set up in Sierra Leone to help with the outbreak.

The laboratory plays a critical role in the diagnostic evaluation of patients with infection, receiving over a million specimens annually, spanning over the fields of bacteriology, virology, mycology, and parasitology.

Processing samples

All samples are received in reception where scientists will sort them by sample type — urine, stool, sputum, or blood.

They are then moved to the booking area, where biomedical scientists will check the details before conducting the pre-analytical stage of analysis, consisting of checking for proper labelling of samples, availability of clinical details, ensuring no spillage of contamination of samples.

If there are any concerns, the sample will be rejected at this stage.


Next, the appropriate tests for the samples will be set up — for example, the types of plates that need to be prepared for bacterial cultures.

Large labs like this one are capable of large scale high throughput work — the use of automated equipment to rapidly test many samples at once.

However, there will always be samples that require more attention and a different testing procedure, for instance, a brain biopsy from an immunocompromised patient compared to a superficial swab from a wound.

This highlights the importance for clinicians to include as much detail as possible so that appropriate tests can be set up.


It’s also important to note any information from the clinical history which may suggest the presence of organisms that could cause harm to laboratory staff, for example, tuberculosis, or a travel history to certain areas which may increase the risk of contracting organisms such as Salmonella typhi or Brucella.

This information should be tagged onto the sample so that it can be processed safely in a Biosafety level 3 laboratory.

To see a brief tour around Dr. Theo’s laboratory, click here.

These videos were produced by the CUH Media Studio.
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Introduction to Practical Microbiology

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