Microbiology News

COVID-19 Laboratory Testing Update

March 13th, 2020

COVID-19 testing is performed using PCR technology (i.e. to detect the viral RNA). Test sensitivity is dictated by the amount of virus on the swab and is therefore influenced by (1) the timing of the test in relation to the symptoms and (ii) the quality of the sample (operator-dependent). A test should be interpreted in light of the pre-test probability (severity of symptoms, their level of exposure, the disease in the contact); no test is 100% sensitive or specific.

Serological testing is NOT available currently (27th March 2020).

• COVID19 RNA is detected on a Nasopharyngeal swab (Red COPAN or Yellow COBAS) by PCR (or BAL if on ITU)
• Follow Trust guidelines as on HUB
• All samples need to be requested on Medway using the “COVID-19” request
• Do not send repeat swabs unless agreed by Micro
• If unable to use Medway, use Virology form (we would rather you didn’t)
• If Flu testing is also required, please write this in clinical details
• Place swab into clear bag and then blue bag (i.e. DOUBLE bagged)
• Place sample into rigid red transport boxes (at present on ITU, AMU, MTU, Torridge, Bramble and ED)
• Porters will collect swabs from above wards every two hours starting from 6:00am (this is a 24 hour service) and take directly to Old Path Lab
• No need to telephone Porters for Virology samples (though urgent blood samples will need portering to Blood Sciences in A template)
• All other samples from patients need to have ?COVID in clinical details as they need to be handled separately in the lab
• There is no need to telephone the lab in advance if the patient meets the case definition (the case definition may change so check HUB)
• Samples are processed daily 7 days a week, so expect a result the same day if the sample arrives before 1800
• Positive results will be telephoned; negative results will NOT be telephoned and you need to check Medway or IPS
Please do not ring for results – we are inundated with telephone calls

Microbiology Newsletter January 2020

January 31st, 2020

Microbiology Newsletter Jan 2020

GP Order Communications System (GP OCS)

May 14th, 2019

It is a pleasure to be able to finally advise you that the long awaited implementation of a GP Order Communications System (GP OCS) is now under way.

The aim of the project is to offer an electronic Pathology test ordering system for GP Practices sending samples to the RD&E, with this project both orders and results will be sent and shared electronically with the GP requesting the tests.

The system supplier has estimated it will take approximately 26 weeks to build the system and roll out to 5 pilot GP practices; we therefore are estimating delivery during the latter part of Q3, early part of Q4 of this calendar year.  The team will then roll out to the remaining sites, planning for 3 practices a week to go live; this is expected to take a further 3-4 months.

The project team with the supplier are currently developing the roll out schedule for this new system, should your Practice like to be one of the early adopters of this exciting project please contact the Programme Team at the following address:-

Chris Carr – Pathology Computer Systems Manager
Royal Devon and Exeter NHS Foundation Trust     Email: ccarr5@nhs.net

Should you have any queries relating to the project delivery please contact:

Richard Excell – IM&T Programme Manager
Royal Devon and Exeter NHS Foundation Trust     Email: richard.excell@nhs.net

The team at the Royal Devon & Exeter Foundation Trust look forward to working closely with you on this exciting project.

Sarah Hodder                                                                                                                                                                                                    Diagnostic Cluster Manager

Microbiology User Survey Report

February 15th, 2019

Microbiology User Survey Report 2018

Microbiology Molecular Update

February 10th, 2019

We are delighted to inform our users that we have now taken delivery of and verified a random access Nucleic-Acid-Amplification-Test platform, called EliTech.

As of 4th February 2019, we will be performing NAATs on CSF for the following targets:

  • HSV1 and 2
  • VZV
  • Enterovirus
  • Parechovirus

This will replace the current referred service in Bristol and will give much better turnaround times (currently 2-3 days, down to a next day result). We really hope this will have a good impact on patient care, allowing speedier diagnosis and decision making, and limit the amount of intravenous acyclovir currently being used whilst waiting for results.

Allied to this, using the same technology, we also now offer the following NAATs test on-site, again significantly improving turnaround  times:

  • CMV viral load           ]
  • EBV viral load            ] on patients with severe immunosuppression
  • BK viral load              ]
  • HSV vaginal swabs – on any patient with symptoms

If anyone would like to know more, please contact Microbiology via the email service: rde-tr.Microconsultants@nhs.net

Dr Cressida Auckland

COBAS 6800

December 8th, 2018

Microbiology are pleased to announce the arrival of a new molecular machine – the COBAS 6800.  This all-in-one automation is used for testing samples for chlamydia, GC, Hep C viral loads, HIV viral loads and Hep B viral loads


Royal College of Pathologists User Satisfaction Survey

March 6th, 2017

Latest results available here.

New Cobas e-601 Random Access Analyser

June 27th, 2016

As of Tuesday 21st June 2016, we have moved some Virology  Serology Testing (HIV, Hepatitis B surface antigen, Hepatitis B core antibody, Hepatitis C antibody, Syphilis antibody, HTLV  and Hepatitis B surface antibody)  onto the Cobas e-601 random access analyser.

cobas e601


The only difference you should notice is the wording on some of these reports – please see below for examples:

Negative samples will be reported as Non-reactive

POSITIVE samples will be reported as REACTIVE

Click here for report examples


Microbiology News March 2016

March 14th, 2016

We have recently reviewed the most common e-mail queries sent to rde-tr.MicroConsultants@nhs.net and are in the process of producing some FAQ pages to help which will be posted here.

Currently, the following FAQs are to be added:

  • Recurrent UTIs
  • Lyme Disease
  • Hepatitis serology
  • Impetigo
  • Sputum (various questions)
  • Chlamydia serology
  • PID
  • Wound swabs
  • Clinical details
  • Non-albicans Candida in GU samples
  • Campylobacter


This is a working list, so if there is anything you would like a more in depth fact sheet for, or even just a handy reference guide, please don’t hesitate to e-mail us @ rde-tr.MicroConsultants@nhs.net

Change to Prescription of Fosfomycin

December 9th, 2015

As of 01/12/15 the RD&E pharmacy will no longer supply Fosfomycin 3g sachets for community patients against a GP proforma.

There is now a licensed product available, so if you need to use Fosfomycin, prescribe in the normal way, and the patient can collect from the local pharmacist.



Uncomplicated lower urinary-tract infections caused by multi-resistant organisms when there are no more suitable alternative antibacterial options available

Patients are eligible for treatment with fosfomycin if the following criteria are fulfilled:

  • They must be suffering from a symptomatic UTI;
  • A urine specimen must have been examined by the laboratory;
  • There must be a significant growth of a fosfomycin-sensitive organism in the urine sample; and
  • There must be no other more suitable oral treatment alternative, either because of bacterial resistance, or patient allergy or intolerance to suitable antimicrobials


Adult (female): 3grams orally for 1 dose (a second dose may be given after 72hours with persistent infection and/or on the advice of microbiology)

Adult (male): 3grams orally for 1 dose, then 3grams orally after 3 days

References/Further info

RDE RX antimicrobial pages: http://app.rx-guidelines.com/Viewing/Index/171#W2pUxOTUUH

Product characteristics: http://www.mhra.gov.uk/home/groups/spcpil/documents/spcpil/con1444368450881.pdf