Important updates and changes in Microbiology

Please see below for any recent changes in Microbiology. 


Since 2023 there has been a resurgence of measles cases in England and cases continue to increase. Of note, there are ongoing measles outbreaks in London and the West Midlands and it is highly likely that local cases will be seen.

Measles is a notifiable disease and all suspected measles cases should be reported immediately to the local UK Health Security Agency (UKHSA) health protection unit on 0344 225 4524. The health protection unit will organise for measles testing via an oral fluid sample and trace and manage contacts accordingly.

In specific cases where a rapid result is required for patient management or public health interventions, a viral throat swab (green or red top) can be referred to the NUH Microbiology laboratory for PCR testing but this must be discussed with the duty virologist prior to sending (0115 9249924 x83524).

Serology (IgM and IgG) is of limited utility in diagnosing acute measles infection and an oral fluid sample (or viral throat swab) for measles PCR is preferable.

To test for measles immunity in the context of an exposed individual, please request ‘measles IgG’ testing.

Update on BK Virus and Adenovirus PCR Testing - November 2023

From week commencing 6th November BK virus and adenovirus PCR testing will be repatriated into the NUH microbiology laboratory, and will no longer be referred to Micropathology.

There will be no change to the sample requirements, ordering process or the turnaround time for these results.

There will be a change to the reportable units of BK viral load, which will now be reported in international units (IU/ml). Unfortunately we are not able to provide a conversion factor to convert the Micropathology results (copies/ml) into international units. If any advice is needed in comparing copies/ml results with those reported in IU/ml please call the duty virologist on x83524.

Many thanks

Gemma Clark (Consultant Clinical Scientist in Virology)

Louise Berry (Consultant in Virology and Infectious Diseases)

Benjamin Canning (Consultant in Virology and Infectious Diseases)

Change to Giardia testing on faecal specimens - November 2023

From 6th November, the Microbiology department is changing methodology for the detection of Giardia lamblia from stool specimens.

Traditional microscopy techniques have poor sensitivity, which may be as low as 30-50% on single stool specimens.

We are introducing a Giardia Antigen lateral flow (RIDA®Quick Giardia, RBioPharm) which will offer improved sensitivity as compared to traditional microscopy. Results will be reported via the usual electronic systems.

We appreciate your ongoing support in providing the laboratory with sufficient clinical details on requests, in order for the laboratory to perform appropriate testing (e.g. immunocompromised, detailed travel history, duration of symptoms, clinical suspicion).

If you have any questions, please contact the department and we would be happy to help.


Graham White (Deputy Service Manager, Bacteriology)

Dr Annie Joseph (Consultant Microbiologist)

Changes to Aspergillus galactomannan and Beta-D-glucan testing January 2023

Please click on the link below to read the document:

GM BDG letter to users Jan 2023.pdf [pdf] 675KB

Update on Mycology Service August 2022

Update on Mycology Service September 2021

24/7 Working in Microbiology from 6th December

From the 6th December 2021 the Microbiology Service is changing, below is some useful information you need to know about the updated Service:


  • The Microbiology Laboratory will have on site cover 24 hours a day. However, there will be very limited staffing providing essential work between 17:00 and 09:00.


Requests for urgent samples between 5pm and 9am must be made via switchboard asking for the Microbiology Biomedical Scientist (BMS).

  • Urgent samples are as follows:
  • Cerebrospinal fluids (CSFs)
  • Operative specimens (pus/tissue)
  • Fluids from normally sterile sites e.g. joint/pleural/peritoneal fluids
  • Mid stream urines from children where management will be affected by microscopy result and suprapubic aspirate (SPAs)
  • Broncho-alveolar lavage (BAL) for bacteriology
  • Corneal scrapes and vitreous taps


  • New blood cultures will be loaded and positive blood cultures will be processed 24/7. Therefore, please ensure all new blood cultures are sent to the Pathology Department at City and QMC as soon as they have been taken to avoid any delays in them being loaded to the analyser. There is hourly transport in place from Pathology at City to Pathology at QMC, 7 days a week.
  • Guidance on the interpretation of blood culture Gram film results is available on the intranet Antibiotics pages under the ‘Microbiology’ tab, to support clinicians who are reviewing patients out of hours.
  • Routine Bacteriology specimens will now be processed 7 days a week between 09:00 and 20:00.
  • Microbiology samples should be sent/taken to the Microbiology Reception Monday to Sunday between 08:00 and 17:00. Outside of these times please send via the airtube or deliver samples to Specimen Reception in Clinical Pathology, where Microbiology will collect them from.
  • There will be no changes to the medical advice service which will still be an on-call service via switchboard outside of Monday to Friday 09:00 until 17:00, but there will now be onsite presence 7 days a week between 09:00 and 17:00.
  • Please do not phone the lab for results. All results once finalised will appear on Medway/NotIS. If the result is not available it will still be undergoing processing in the laboratory.
  • If you are needing some general Microbiology related information, maybe what specimen container to use, how long should it take for results to come back or possibly some antibiotic guidance, then here are a couple of useful links that should help:

Interpreting Sensitivity Results

In line with new European reporting requirements, the microbiology laboratory report susceptibility results in three categories: S, I or R.

 For some bug-drug combinations, there is no "S" category. Susceptibilities will be reported as either "I" or "R".

·         "S" = susceptible at a standard dosing regimen.

This means there is a high likelihood of therapeutic success using standard doses and dosing intervals.

·         "I" = susceptible at increased drug exposures.

This means there is a high likelihood of therapeutic success if antibiotic exposure is optimised by using higher doses or increasing dosing frequency.
Click here for recommended doses and frequency for organisms with "I" susceptibility.

·         "R" = resistant.
This means there is a high likelihood of therapeutic failure using this antibiotic.

For paediatrics where susceptibilities are reported as "I" and a dosing range is given in the BNFc, the dose at the higher end of the range should be used.

Improvements in reporting of Genital samples - Implemented on 10/09/2018

Female genital samples that are received in the department have a set of default tests performed which include; culture for Candida species and Neisseria gonorrhoea/microscopic detection for Trichomonas vaginalis and if of child bearing age microscopic detection of clue cells an indicator of bacterial vaginosis. Other bacterial pathogens will be investigated dependant on patients demographics or documented clinical details. The department separately reports on Trichomonas and clue cells and a separate report on culture is issued with a standard report “No pathogens isolated” for negative bacterial cultures.

Following a recent audit the department has decided to improve its culture reporting and now issues two negative culture reports based on the investigations performed:

  • Neisseria gonorrhoea and Candida not isolated – for samples that only have the default  investigations performed
  • No pathogens isolated – for samples that have had the default investigations as well as additional pathogens based on clinical information supplied.

Please note: Chlamydia testing is a separate molecular test that will be reported on a separate report if tested.

Update on Sample acceptance and specimen / request labelling within Microbiology - April 2020

From April 2020, The Department of Microbiology will be strictly enforcing the Trust policies and procedures (Sample acceptance in Pathology laboratories procedure - CL/CGP/049 & Request and Specimen labelling policy – CL-CGP/018) on the minimum number of patient identifiers required and will reject any specimens that do not meet this requirement.

Info about change to Chlamydia PCR Collection device

RE: Change of collection device for Chlamydia trachomatis and Neisseria gonorrhoeae molecular (NAAT) testing

The Department of Clinical Microbiology is always seeking ways to improve the services we offer.  We are in the process of implementing a new molecular NAAT’s test for Chlamydia trachomatis and Neisseria gonorrhoeae. The new system will help to improve the efficiency within our laboratory and ultimately improve the time taken to generate a patient result.  In order to take full advantage of the efficiency of the new Abbott Alinity m System, we will require you to start using a different collection kit.

From the 10th August the specimen collection kit that will be sent out for Chlamydia trachomatis and Neisseria gonorrhoeae molecular (NAAT) testing will be the Alinity m multi-Collect Specimen Collection kit (Product number: 09N19-001), see pictures below.  



Kit as it will be received


Picture showing contents of kit


The benefit of the new kit is it is one collection kit for male and female samples. The kit contains a transfer pipette for adding approximately 2.1 ml of urine to the transport tube, urines should be added until the liquid falls within the fill window on the tube label, and an individually packaged sterile specimen collection swab that is placed into the transport tube, utilising the breakpoint on the shaft, after swab sampling. This swab can be either self-taken by the patient or taken by the clinician.  Do not place multiple swabs or a combination of swab and urine in the transport tube.  The transport tube contains 1.35 ml of specimen transport buffer and is used to stabilize DNA until sample preparation.  After collection, transport and storage conditions should be between 2°C to 30°C for up to 14 days.

Please see the product information that has been included with this communication for details on specimen collection procedures and use the new Alinity m multi-Collect Specimen Collection kit.

Please note due to this change any swabs requiring MC&S for bacterial culture MUST now be sent on a separate request form as these are no longer processed within the same laboratory as the Chlamydia/Gonorrhoea NAAT samples.

The current BD swabs (Self Taken Product code: 441122, Male urethral swab Product code: 441358, Female endocervical swab Product code: 441357) and also urine samples in plain universals will no longer be accepted for testing after the 1st September and the new collection device must be used. If you have remaining stocks of any of the above BD swabs then please return to the Microbiology Department at QMC.

If you had previously been using the BD swabs for taking samples for Herpes Simplex Virus testing, then you will now need to use the viral transport media (VTM) kits.  The current VTM being supplied by Pathology is the green top swab kits by Medical Wire (Product code: MW951S).  This may be subject to change as all VTM is currently being nationally supplied and therefore this may be subject to change with no notice.

Thank you for your co-operation and if you have any questions regarding the transition, please do not hesitate to contact the department on Ext: 64950.

Alinity Multi-Connect Specimen Collection Kit instructions[pdf] 1010KB