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Jan 24, 2024

NMRS

Updated 25 August 2023 © Crown copyright 2023 This publication is licensed under the terms of the Open Government Licence v3.0 except where otherwise stated. To view this licence, visit

Updated 25 August 2023

© Crown copyright 2023

This publication is licensed under the terms of the Open Government Licence v3.0 except where otherwise stated. To view this licence, visit nationalarchives.gov.uk/doc/open-government-licence/version/3 or write to the Information Policy Team, The National Archives, Kew, London TW9 4DU, or email: [email protected].

Where we have identified any third party copyright information you will need to obtain permission from the copyright holders concerned.

This publication is available at https://www.gov.uk/government/publications/national-mycobacterium-reference-laboratory-nmrl-user-manual/nmrs-south-user-handbook

This user handbook is intended for use by laboratories referring samples and cultures to the National Mycobacterium Reference Service (NMRS)-South.

NMRS-South is an accredited constituent reference laboratory of specialised microbiology and laboratories of UK Health Security Agency (UKHSA). With its sister laboratory, the NMRS – Central and North based in Birmingham, it provides mycobacterial reference services to the NHS in England, and works closely with mycobacterial reference services in the devolved administrations.

The principal activities of the unit include:

Phenotypic drug susceptibility testing (DST) is carried out for selected M. tuberculosis and non-tuberculosis mycobacteria (NTM) isolates. Extended testing is carried out for M. tuberculosis complex isolates with resistance to first line agents.

The laboratory also offers a primary isolation service, including microscopy and culture, and a Fastrack (polymerase chain reaction (PCR)) service for detection of M. tuberculosis complex and rifampicin resistance.

NMRS-South provides information and advice to clinical and public health teams, assisting in the identification and investigation of TB transmission and actively supporting outbreak investigation and surveillance activity within the UK.

Since January 2018, NMRS-South has utilised WGS for the identification of all mycobacterial isolates and detection of resistance for M. tuberculosis. The laboratory no longer provides MIRU-VNTR typing as WGS provides improved discrimination based on single nucleotide polymorphism (SNP) differences between all sequenced isolates. By implementing WGS within a single management structure across both laboratories in the NMRS for England the new service improves the diagnosis, treatment and public health management of TB and plays a significant role in delivering England’s TB strategy.

NMRS-South understands that it may take some time for users to establish familiarity with report formats; clinical and scientific support is always available from NMRS-South to guide users through the change to WGS.

The WGS service includes:

Identification of NTM continues to be a core part of our service. We are working to standardise our testing methods and costs across the service, including DST. We are monitoring turnaround times as part of the service, aiming to report full WGS results within 7 working days of the receipt of pure positive cultures.

The unit is a World Health Organization (WHO) Supranational Reference Laboratory for M. tuberculosis DST. Together with centres in Germany, Sweden and Belgium, it co-ordinates External Quality Assurance (EQA) for DST across the EU and non-EU states in the WHO Euro region.

It is also a member of WHO’s Global Laboratory Initiative (GLI) involved with the development of WHO and International Union Against Tuberculosis and Lung Disease (IUATLD) strategies for management of mycobacterial diseases and participates in international EQA schemes receiving samples and dispatching to designated regions.

Ownership and accountability of the user handbook lies with the Laboratory Manager and Clinical Lead for NMRS-South. This is version 13, 21 August 2023, Qpulse MYRUW239.

National Mycobacterium Reference Service-South (NMRS-South)

National Infection Service, 61 Colindale AvenueLondonNW9 5EQ

Email [email protected]

Telephone 020 832 76957

DX address DX 6530016, Colindale NW

Service will be provided between 9am to 5pm, Monday to Friday (excluding Bank holidays).

Each request referred from a stakeholder to the laboratory for testing is considered to be an agreement under UKHSA terms and conditions of business.

General results enquiries are initially addressed by our administrative staff who will direct clinical and technical enquiries to the appropriate staff. There is daily cover for clinical and technical issues.

Complex cases are discussed further internally and the advice given will often be a product of this discussion, not just the opinion of the person answering the telephone call. We record the advice given for continuity and must know the identity of both the patient and the caller.

For the NMRS-South pricelist, please contact the laboratory by:• email: [email protected], [email protected]• telephone: 020 8327 6957, 020 8327 7708

If you want to speak to the Laboratory Safety Officer, please contact the Laboratory Manager.

Complaints can be submitted by post, email or telephone to the Laboratory Manager and Clinical Lead of NMRS-South. If contacting by email, please also include [email protected] as a recipient.

The complainant will be initially responded to within 5 working days of the complaint being raised. Full investigations and corrective actions will be applied within 20 working days wherever possible.

NMRS-South provides the following services:

* Genotypic drug susceptibility predictions are made for all isolates; however, routine phenotypic susceptibility testing for first line agents is no longer performed – this includes isoniazid, rifampicin, pyrazinamide and ethambutol. If WGS predicts resistance or if WGS data is not sufficiently clear to accurately make a prediction, phenotypic testing of first line agents will be performed. Testing for second and third line agents will be performed for multi-drug resistant (MDR) isolates when clinically indicated.

Further information concerning services or matters of interest is available from UKHSA on GOV.UK

All turnaround times are dependent upon the receipt of 3mls of pure culture containing sufficient bacteria for analysis; we will attempt to purify contaminated cultures where possible.

[note 1] Testing of further agents can be performed if clinically indicated. Please contact NMRS-South to discuss individual cases.

Reported within one working day of specimen receipt.

Final negative result reported after 30 working days (6 weeks) or 40 working days (8 weeks) for blood and cerebrospinal fluid (CSF) samples.

Note, cultures that are negative at 6 or 8 weeks that were positive on either Fastrack or microscopy are incubated further for a total of 12 weeks. A report is only issued if the culture subsequently becomes positive. A further incubation comment is also added to the report for such cases.

Clinical samples received by 9:30am are analysed on the same day and results communicated to the sending laboratory within one working day.

A minimum volume of 0.5ml cerebrospinal fluid (not supernatant) is required for Fastrack.

If culture is specifically requested, we will also culture the residual material but the minimum volume required would be >0.5 ml. The chances of obtaining a positive smear and culture result are increased when a large volume of CSF is submitted for examination.

Paraffin wax embedded samples are no longer accepted for processing.

Clinical and technical advice is available between 9am and 5pm, Monday to Friday.

NMRS-South will endeavour to process all samples received irrespective of any delay between sample collection and arrival at NMRS-South. However, test performance, particularly of primary culture, may well be reduced by significant delays following sample collection, and we recommend service users make transport arrangements that minimise such delays.

Please make sure samples are kept at the appropriate temperature (2°C to 8°C for primary specimens and 36°C to 37°C for positive cultures) while awaiting transportation.

Note, if a specimen is submitted to NMRS-South for an investigation that we do not offer, we will temporarily archive the sample or isolate and issue a report to the sender explaining the reasons for the sample’s rejection. The specimen will then be sent back to the referring laboratory or referred on if within UKHSA Colindale.

Turnaround times for bacterial identification and DSTs are dependent upon the receipt of viable, pure cultures. Cultures that are no longer viable will necessitate the sending of a second isolate, thus significantly increasing turnaround time.

Mixed or contaminated cultures in which acid-fast bacillus (AFB) has been seen require purification and subculture to obtain final results. NMRS-South will undertake such processes whenever possible rather than rejecting contaminated cultures; however, this will again result in a significantly increased turnaround time. If no AFB has been seen in the submitted culture whether contaminated or not, no further work will be carried out.

Submitting a second pure culture will often allow final results to be obtained more quickly and we always recommend that a second sample is sent when the first is mixed or contaminated.

If an aliquot of a liquid culture is to be sent then a minimum volume of a 3ml smear positive sample is required. Transfer 3ml of deposit from a settled positive sample to a sterile non-glass leak-proof universal for transport, and store the rest of the sample at your laboratory.

If a volume of between 2ml to 3ml is received, NMRS-South will attempt WGS but there will be insufficient sample volume to perform any required phenotypic testing; for this reason, we strongly advise referring laboratories to send at least 3ml. Samples of less than 2ml will be not be processed.

Solid cultures can be submitted when there is visible growth on the slope. Leaking cultures will not be processed and a report will be issued informing the user of this.

Please do not submit culture plates. These will be not be processed and a report will be issued informing the user of this.

Please do not submit Mycobacteria Growth Indicator Tubes (MGIT).

Though NMRS-South will not reject samples that are subject to significant delay between collection and receipt, clinical specimens submitted for culture should be as fresh as possible. We strongly recommend that specimens are refrigerated if any delays in submission to NMRS-South are likely.

Do not add diluent to specimens.

This service offers rapid molecular detection of M. tuberculosis complex and rifampicin resistance from primary specimens.

If testing is required, please make sure that samples are sent and received at NMRS-South by 9:30am for it to be included in that day’s testing.

Ideal specimens are smear positive primary respiratory specimens as these have the highest load of acid fast bacilli (AFBs); the assay sensitivity in smear negative specimens is significantly lower due to the lower bacillary load.

Sensitivity is lower again for fluid specimens, such as CSF, pleural fluid and ascitic fluid. The minimum volume of CSF (not supernatant) that can be examined is 0.5ml. The minimum volume of other fluids required is 1.0ml; however, submitting the largest possible volume of CSF and other fluids will increase the sensitivity. For respiratory specimens, at least 1ml of sample is required.

Please note that lysed blood, heavily bloodstained samples or pus containing samples can interfere with PCR based reactions. DNA in specimens requesting molecular tests may degrade if stored for too long before referral. We no longer offer this service for paraffin wax embedded samples. Urine samples have not been validated for this method.

We also offer PCR-based testing for detection of resistance to isoniazid, quinolones and aminoglycosides in primary samples under certain circumstances. Please contact NMRS-South clinicians to discuss cases where you feel this may be required.

If the sample is received and requires decontamination, this will delay PCR testing. If resistance to isoniazid, quinolones and aminglyocsides is detected, the specimen will also be cultured on solid and liquid media if this was not requested originally to maximise the detection and subsequent testing for drug-resistant tuberculosis.

No specimens or cultures are routinely referred by NMRS-South to other laboratories, except for particular MDR M.tuberculosis isolates that require testing to Bedaquiline, Clofazimine and Delamanid, which will be sent to the Emerging bacterial pathogens unit, San Raffaele Scientific Institute, Milan, Italy for testing.

In exceptional circumstances, the NMRS-South Business Continuity Plan (BCP) may be invoked and samples will need to be referred to another laboratory. Should this occur, the work shall be placed with a competent laboratory which complies with ISO15189:2012 or other accreditation standard as appropriate and NMRS-South will request assurance from the referral laboratory about quality assurance practices for monitoring purposes. If other investigations are required at another laboratory then it is strongly recommended that a further specimen or culture is sent directly to that laboratory.

Additional requests for Primary Fastrack testing must be accompanied by an NMRS Fastrack request form (N2).

Requests can be processed, on receipt of sufficient and suitable material, within the time periods specified below:

All first isolates of M. tuberculosis have resistance prediction by WGS; phenotypic susceptibility testing is only performed for first line agents if WGS predicts resistance or fails to make a prediction.

All new multi-drug resistant isolates (MDRs) are processed for phenotypic reserve DST. Repeat phenotypic testing will only be performed on isolates received more than 2 months after previous testing.

Additional susceptibility testing on M. tuberculosis isolates must be discussed with NMRS-South before requests are submitted.

The following samples will receive sensitivities as part of routine protocol:

NTM isolates will be set up for an appropriate panel of phenotypic testing depending on the species based on the organism identification and the patient’s clinical status. Full and accurate completion of the request form aids in this process.

Additional susceptibility testing on NTM isolates can be requested by contacting us.

Specimens must be labelled with the following:

Request forms must match the corresponding specimen and include the above information on the sample as well as the following details:

The name and contact information of the requester (telephone number is vital for urgent requests) should also be included.

NMRS-South request forms are available on GOV.UK including:

Order pre-labelled request forms with your requestor code and address from the laboratory information management system (LIMS) department via email ([email protected]). This will reduce clerical errors.

Make sure the appropriate NMRS-South request from is fully completed for the sample being submitted with the required information as stated above (under Specimen and sample submission guidelines) as well as the correct telephone number, particularly for primary Fastrack requests.

Each sample must be accompanied by an individual request from, even if more than one sample is submitted from the same patient.

The UKHSA NMRS-South laboratory advises users where forms are poorly completed and in these instances, the user will be charged. Please state clinical details when they are provided. Wherever possible, NMRS-South supports its users by not rejecting referred specimens and cultures.

The space marked ‘For NMRS-South Use Only’ is intended for use by NMRS-South staff. Please do not write in this space.

If a reference service is required urgently, please contact NMRS-South to discuss prior to dispatch. Always mark as urgent clearly on the request form.

A small but significant proportion of samples received by UKHSA are poorly or inappropriately packaged. This often leads to samples leaking or being damaged during transport, therefore posing a serious risk to UKHSA staff handling them. UKHSA hopes to eliminate this risk by helping laboratories to understand basic packaging requirements.

The following guidelines are intended to cover the transport of clinical samples from humans, or cultures of micro-organisms isolated from such samples to another laboratory for diagnostic or other clinical testing within the UK where the micro-organisms suspected of causing the disease are all either hazard groups 2, 3 or 4.The terms Category A and Category B are limited to classifying samples or microbial cultures being transported to another laboratory.

These guidelines are not intended as a substitute for reading the advice given by the Department for Transport (DfT) and the Department of Health and Social Care (DHSC).

For further information, visit:

NMRS-South will report any leaking containers and improperly packaged parcels to users.

Leaking cultures will not be processed by NMRS-South. Users will be informed and a repeat sample requested.

NMRS-South will endeavour to process primary material if leakage occurs. However, this is likely to compromise the chance of successful culture and we will request the user to send us an additional specimen.

Repeated offences may be escalated to the UKHSA corporate health and safety department.

Label the specimen or culture bottle with the name of the patient (or unique identifier) and the laboratory number. All specimens and cultures sent to NMRS-South must be packed in accordance with IATA regulations 650/602.

The packaging should consist of 4 components:

For liquids, each leak-proof primary receptacle should be wrapped in absorbent material sufficient to absorb all contents of the sample and placed inside a polythene bag. There should be one sample per bag. The use of parafilm is not recommended.

The bagged samples may then be placed together inside a rigid, leak-proof plastic container. This container is placed inside a fibreboard box or approved DX plastic outer packaging. This outer packaging should be of sufficient size for its capacity, mass and intended use, and with at least one surface having minimum dimensions of 100mm by 100mm.

Documentation must be placed between the secondary container and the outer packaging. Do not place it inside the plastic container.

Do not submit positive cultures on agar plates. These will be discarded and not processed.

To minimise delays, we recommend specimens, especially those sent for our Fastrack molecular diagnostic service, are sent by routine courier, for example DX or other specialised courier.

Please make sure that the courier is able to reach NMRS-South before 5pm.

Cultures can only be sent by courier.

NMRS-South issues acknowledgement of receipt reports on the date of receipt of the samples.

NMRS-South reports are routinely sent out via LabPortal. Printed reports will only be sent out if the referring laboratory is not registered to PHE-eLab. For details on how to register and further information, please email [email protected]

Users can access archived reports on PHE-eLab using the search function for up to 2 years.

It is our policy that reports containing patient data should not be sent by routine email.

Emails cannot be relied on to guarantee security of patient data because they can be intercepted by a third party on route, unless encrypted.

NMRS-South is accredited in accordance with International Standard ISO15189:2012 – Medical Laboratories with Laboratory No.10080.

All tests are in scope with the exception of:

View the certificate of accreditation and schedule of accreditation for NMRS-South, issued by the UK Accreditation Service (UKAS).

NMRS-South participates in numerous EQA schemes, including those run by:

The quality of our systems is also checked by our Internal Quality Assurance (IQA) schemes, which requires selection of referred samples for ‘blinded’ testing at a later date. After processing, the results for IQA samples are ‘unblinded’ and are assessed against the results originally reported to the sending laboratory. Any discrepancies are fully investigated as to their root cause before remedial action is implemented.

Any discrepancies leading from EQA or IQA are fully investigated as to their root cause before corrective action is implemented. Results of our EQA and IQA performance are discussed at departmental meetings as appropriate.

The UKHSA Microbiology Services is licensed by the Human Tissue Authority (HTA) (licence number 12459) to store tissues from deceased people for scheduled purposes. Post mortem samples are submitted to UKHSA by coroners or pathologists for examination to help them determine the cause of death.

As part of our public health remit, we sometimes need to retain these samples for the purpose of public health monitoring, which is defined as a scheduled purpose within the Human Tissue Act 2004. Further analysis of these samples may help determine the cause of an outbreak due to an infectious disease or may allow identification of new strains of infectious agents at a later date.

Obtaining consent to remove, store and use human tissues for a scheduled purpose is one of the underlying principles of the Human Tissue Act. UKHSA Microbiology Services receives post-mortem samples from coroners’ post-mortems or from NHS establishments across the UK and therefore we are not in a position to either seek consent ourselves or have arrangements in place to confirm that the requirements of the Act have been complied with by the sender.

We would ask coroners and pathologists who send post mortem samples to UKHSA Microbiology Services to provide us with details of consent, and would also ask that consent includes retention of the samples for the purpose of public health monitoring.

When tissue samples from deceased people are received at the UKHSA Microbiology Services. They are retained securely and confidentiality is maintained in compliance with Caldicott principles as are all samples received at this centre.

It is normal practice for tissue samples from the deceased to be disposed of in the same way that all other clinical samples we receive are disposed of. However, we will adhere to any specific requirements regarding disposal or returning tissue samples if requested by the sending coroner or pathologist.

The recommendations of the Caldicott report (1997) and the subsequent Information Governance Review (2013) have been adopted by UKHSA as a whole. These recommendations relate to the security of Patient Identifiable Data (PID) and the uses to which they are put.

NMRS-South observes Caldicott guidance in handling PID. The Clinical Lead of NMRS-South and others are advised on confidentiality issues and for the monitoring the physical security of PID in all parts of the NMRS-South site. This also applies to the transfer of results of investigations to and from the site whether by mail services, electronically or by telephone. The value of ‘safe haven’ arrangements, or other means by which the sender and receiver of information can identify themselves to each other before data is transferred, is emphasised. See the reports section of this user manual.

NMRS-South audits the security of its PID in collaboration with its customers. Customers are invited to review our arrangements in conjunction with individual laboratory directors and/or the UKHSA Caldicott Guardian. Customers are also asked to draw to the Caldicott Guardian’s attention any instances where PID security has been threatened or has broken down.

Any uses that PID are put to outside the clinical diagnostic services generally allow patient identifiers to have been removed beforehand, and when PID is used for research purposes the proposals are considered first by the appropriate Ethics Committee. All enquiries regarding the security and use of PID should be addressed to the Laboratory Manager at [email protected]