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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
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Hello, my name is Theo Gouliouris and I’m a consultant in microbiology and infectious diseases here in Cambridge. Welcome to this virtual tour of the Clinical Microbiology and Public Health Laboratory at Addenbrooke’s Hospital. The lab here is one of the PHE regional laboratories, part of a network of eight labs in England. As such, it has a dual role. It serves, firstly, as a diagnostic microbiology lab for patients at Addenbrooke’s Hospital in the Rosie, but also for two linked hospitals– Papworth and Lister at Stevenage, along with the GP practises in the area.
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In addition, as part of its public health role, it’s ready to respond to community outbreaks, but also to receive tests from the region for specialist tests or molecular tests that do not require sending to a national reference lab. For example, Clostridium difficile ribotyping. But it’s also ready to respond to national threats, such as bioterrorist incidents or significant epidemics. Well, we had one of these recently– as you know– as part of the COVID-19 pandemic. This lab was one of the first labs to be able to test for SARS-COV-2 PCR.
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Then, as tests were rolled out in the NHS and lighthouse mega-labs were set up, it has its role in the diagnosis of SARS-COV-2 has been limited more in the local population as part of what we call pillar one testing. Scientists from this lab are also involved in setting up labs abroad as part of crisis. For example, during the Ebola crisis in West Africa, scientists went to Sierra Leone to set up and help run labs over there. In addition, scientists from this lab have been involved in validating and setting up assays which have then be rolled out in the wider PHE.
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The lab is an extremely busy part of the hospital, yet invisible to the outside. It is critical, though, for the diagnostic evaluation of patients with infection. It operates 24/7, all year round, and receives over a million specimens split between bacteriology, virology, but also with some work that goes to mycology and parasitology. The best place to appreciate this is when looking at the reception area where all samples are received, packed in boxes, and it’s the job of the scientists here to pack them out according to sample type. And you can see groups of them into stool, urine, sputum, or blood, for example.
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Then, these are moved to the booking area where biomedical scientists will check the details and complete what is called the pre-analytical stage of analysis. So here, they will check that the samples are labelled properly, that the clinical details are available, that there hasn’t been any spillage or contamination of the sample. And if there are any concerns, they will reject the sample at this point. Next, they will decide what are the appropriate tests to set up. For example, the types of plates that need to be set up for bacterial cultures. Now, big labs like this are well set up for large scale, high throughput work. However, amongst the samples, there will be always very precious specimens.
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For example, say, a brain biopsy from an immunocompromised patient. This will require very different work compared to, say, a superficial swab from a wound, which is likely to be contaminated with skin bacteria. So, it’s clearly very important for the clinicians on the wards to include as much detail so that appropriate tests can be set up. The other piece of information that’s very critical for us to have is if there is any suspicion from the clinical history of organisms that could pose a risk to our lab staff.
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For example, this could include tuberculosis or a travel history to tropical areas which might increase the risk of organisms, such as salmonella, typhoid, or brucella, and this is the point for the biomedical scientists to tag the sample so it can be processed safely in a bio safety level three lab.

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.

Testing

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.

Biosafety

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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