Guidance

NMRS Central and North: user handbook

Published 11 December 2023

The UK Health Security Agency (UKHSA) public health laboratory National Mycobacterium Reference Service – Central and North (NMRS Central and North), is an accredited constituent reference laboratory of the National Infection Service (NIS) of UKHSA.

With its sister lab in Colindale, NMRS-South, it provides mycobacterial reference services to the NHS in England. NMRS works closely with mycobacterial reference services in the devolved administrations, in particular, the Wales Centre for Mycobacteria and the Scottish Mycobacterial Reference Laboratory.

Main activities

The principal activities of the unit include the:

• provision of a mycobacterial reference service based on whole genome sequencing (WGS) for the identification of Mycobacterium spp isolates
• prediction of drug susceptibility and resistance
• determination of relatedness for the detection of transmission and investigation of outbreaks

Phenotypic drug susceptibility testing is carried out for selected M. tuberculosis complex and non-tuberculous mycobacterial isolates if clinically indicated. 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 as well as an urgent polymerase chain reaction (PCR) service for detection of M. tuberculosis complex and rifampicin resistance.

NMRS Central and North provides information and advice to clinical and public health teams for the identification and investigation of outbreaks and tuberculosis (TB) transmission. Our activities support surveillance activity for TB in the UK.

Contact information

Delivery address

Address

UKHSA PHLB National Mycobacterium Reference Service - Central and North
National Infection Service
Heartlands Hospital
Bordesley Green East
Bordesley Green
Birmingham
B9 5SS

DX Address

UKHSA Birmingham
NMRS - Central and North
Heartlands Hospital
DX6780100
Birmingham

Telephone

+44 (0)121 424 0241

Email

uhb-tr.nmrs@nhs.net

Hours of service

For all tests offered, service will be provided between 8am to 4pm, Monday to Friday (excluding bank holidays).

Personnel and contact details

General results enquiries are addressed by our administrative staff initially who will direct clinical and technical enquiries to the appropriate staff. There is daily cover for clinical and technical issues via email and a response will be initiated within 24 hours. Complex cases are discussed further internally and the advice returned will often be a product of this discussion, not just the opinion of the person responding to the enquiry. We record the advice given for continuity. We must know the identity both of the patient and the person making the enquiry.

General enquiries

Email: uhb-tr.nmrs@nhs.net
Telephone: 0121 424 0241

Clinical enquiries

Title	Name	Email	Telephone
	Dr Esther Robinson	Esther.Robinson@ukhsa.gov.uk	0121 424 3725
	Dr Noorann Sheikh	Noorann.Sheikh@ukhsa.gov.uk	0121 424 2464
Laboratory Manager	Mrs Priti Rathod	Priti.Rathod@ukhsa.gov.uk	0121 424 2510
Quality Manager	Mrs Caroline McKeon	Caroline.McKeon@ukhsa.gov.uk	0121 424 2510
Health and Safety Lead	Mrs Priti Rathod	Priti.Rathod@ukhsa.gov.uk	0121 424 2510

Summary of NMRS Central and North services

NMRS Central and North provides the following services:

• identification of Mycobacterium sp. isolates (WGS based identification service from liquid or solid culture media provided free to the NHS)
• drug susceptibility testing and genotypic resistance prediction for M. tuberculosis complex genotypic prediction of resistance and susceptibility from WGS; where indicated, phenotypic susceptibility testing will be performed according to NMRS protocols – this is currently provided free to the NHS but may change in the future – NMRS will test for second and third line drugs on resistant isolates or when clinically indicated
• drug susceptibility testing for non-tuberculous Mycobacteria (NTM) phenotypic culture based testing for clinically significant NTM isolates; this is a chargeable test)
• molecular epidemiological service (for example outbreak investigations, laboratory cross-contamination, based on single nucleotide polymorphism (SNP) differences determined by WGS, provided free to the NHS)
• primary isolation service (including microscopy and culture, this is a chargeable service)
• urgent (PCR) service (molecular detection of M.tuberculosis complex and rifampicin resistance in primary specimens, this is a chargeable service)
• clinical, scientific and technical advice
• clinical advice for case and outbreak investigation and management
• computerised database on laboratory-confirmed cases
• archived collection of Mycobacterium isolates for epidemiological analysis
• training

For further information concerning services or matters of interest, visit the UKHSA homepage.

NMRS Central and North services

Please note all turnaround times are dependent upon the receipt of a pure culture containing sufficient mycobacteria for analysis. At least 90% of all samples will be available at the turnaround times listed below.

We endeavour to assist laboratories by treating contaminated cultures to purify mycobacteria rather than returning them to the sender.

Reference service

Service	Description	Turnaround time
Identification of AAFB positive cultures	DNA sequencing and genotypic tests are performed for identification and first line sensitivities	Reported within 5 to 7 working days of culture receipt
M. tuberculosis sensitivity
First line antibiotics (phenotypic)	Isoniazid, Rifampicin, Ethambutol, Pyrazinamide	Reported within 2 to 3 weeks of culture receipt, if required, based on WGS results.
Reserve antibiotics	Levofloxacin, Moxifloxacin, Amikacin, Kanamycin, Prothionamide, Capreomycin, Linezolid	Reported within 2 to 3 weeks of request for Reserve sensitivities, Identification of rifampicin resistance or MDRTB in referred cultures.
Additional antibiotics	Bedaquiline, Delamanid, Clofazimine	Reported within 4 to 6 weeks of request for these sensitivities or identification of MDR/XDRTB.
Non-tuberculous Mycobacteria (NTM) sensitivity*	Rapid growers: Co-trimoxazole, Linezolid, Ciprofloxacin, Moxifloxacin, Cefoxitin, Amikacin, Doxycycline, Clarithromycin Tobramycin, Imipenem, and Tigecycline. Slow growers – M Avium Group: Clarithromycin, Moxifloxacin, Amikacin, linezolid Slow growers – Non M Avium Group: Clarithromycin, Ciprofloxacin, Moxifloxacin, Rifampicin, Amikacin, Doxycycline, Linezolid, Rifabutin, Co-trimoxazole	Reported within 4 to 6 weeks of WGS ID/sensitivity request from clinicians.

*Please note the antibiotic panel tested for NTM will vary depending on the organism identified.

Primary service

Service	Turnaround time
Fluorescence microscopy on clinical samples	Reported within one working day of specimen receipt
Culture of clinical samples on liquid (BD MGIT) and solid (LJ slopes) media	Final negative result reported after 8 to 10 weeks
Culture of blood and bone marrow samples in BD Bactec Myco/F Lytic culture bottle	Final negative result reported after 6 weeks
PCR service for clinical samples (part of primary service)	Clinical samples received by 9:30am are analysed daily and positive results communicated to the sending laboratory within one working day
Rapid detection of M. tuberculosis complex and rifampicin resistance	TB PCR tested on all children aged under 16 years

Note 1: Minimum cerebrospinal fluid (CSF) (not supernatant) volumes required is greater than or equal to 3ml. We will automatically culture residual material for maximum sensitivity if rifampicin resistance is detected or if an internal patient. In all other cases, culture must be requested.

Note 2: Cut tissue sections with dimensions 5µm (micrometres) by 10µm (micrometres) for TB PCR. Cut sections are preferable.

Note 3: Urine, swabs, blood and bone marrow samples are not suitable for TB PCR.

Advisory service

Clinical and technical advice: available Monday to Friday from 8am to 5pm.

Main factors affecting specimen performance

If a specimen is submitted to NMRS Central and North for an investigation that we do not offer, we will temporarily retain the sample or isolate for one week and issue a report to the sender explaining the reasons for the sample’s rejection.

Reference service for positive mycobacterial cultures (identification, drug resistance testing and genomic relatedness for TB)

If an aliquot of a positive liquid culture is to be sent, then transfer 3 to 5 ml of the sample to a 5ml container for transport, and store the rest of the sample at your laboratory.

Please do not put parafilm around the lid of the container for transport.

A positive LJ culture can be sent as a slope for analysis by WGS and phenotypic drug sensitivity testing (DST) provided it has been labelled with a minimum of 2 patient identifiers.

Turnaround times for bacterial identification and drug susceptibility tests is dependent on the receipt of pure viable cultures.

Turnaround time may increase significantly for cultures that:

• have insufficient volumes
• require purification
• cannot be retrieved because they require decontamination of the culture
• are no longer viable and necessitate a second isolate

Our approach is to assist you wherever possible by not rejecting contaminated cultures; however, submitting a second different or subsequent culture is usually the best strategy.

Leaking, insufficiently labelled and incorrectly packaged cultures will not be processed and a report will be issued informing the user of this. These cultures will not be returned to the sender.

Primary service

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 Central and North are likely. Please send multiple samples for samples recovered through an invasive procedure.

Do not add diluent to specimens. When small pieces of tissue are submitted, sterile saline or sterile water may be added to prevent desiccation.

Do not use formalin as this will kill the mycobacteria.

Blood samples for culture should be sent in a vacutainer containing citrate or lithium heparin (not EDTA, as this inhibits the growth of mycobacteria) or in a BD Bactec Myco/F Lytic culture bottle. The range of blood volume that can be cultured is 1ml to 5ml, with optimum recovery obtained at 3ml to 5ml; therefore, 2 citrated blood tubes or lithium heparin tubes are recommended.

Bone marrow samples should be sent in a sterile universal.

We do not perform microscopy on urine specimens faeces, swabs, bloods and bone marrow; we will culture these specimens.

If you wish to send samples of non-human origin please contact NMRS Central and North before sending.

Urgent PCR

This is our urgent PCR molecular diagnostic service for primary samples to detect Mycobacterium tuberculosis complex (MTBC) and rifampicin resistance. Additional requests for urgent PCR testing must be accompanied by a request form. Requests can be processed, on sufficient and suitable material, usually within 24 hours of receipt of the request.

We do not perform PCR on faeces, urine, swabs, bloods wax blocks and bone marrow.

Ideal specimens are smear positive primary specimens. Other specimens have lower sensitivities for detection (see Zeka and others. ‘Journal of clinical Microbiology’ (2011) 12: 4138-4141; Weyer and others. ‘European respiratory journal’ (2013) 42:252–271). Positive mycobacterial cultures are unsuitable for PCR.

Generally, smear positive samples are more likely to be successfully analysed as they have a higher acid alcohol fast Bacilli (AAFB) load. In line with National Institute for Health and Care Excellence (NICE) guidelines (2019), each specimen type should be tested by PCR in children under 16 years with suspected TB.

In general, fluid samples such as CSF, pleural fluid and ascitic fluid have much lower sensitivities; the minimum amount of CSF that will be examined is 3 ml (not supernatant). However, submitting the largest possible volume of CSF (ideally over 6ml) and other fluids will increase the sensitivity.

Lysed blood or heavily bloodstained samples can interfere with PCR based reactions. DNA in specimens requesting molecular tests may degrade if stored for too long before referral.

Contact tracing and case meeting

We are frequently asked to attend case meetings (or via teleconference) for complex patients and larger contact tracing investigations in institutions such as schools, prisons and healthcare institutions. We will try and assist where possible, but requests with less than 1 to 2 working days’ notice of the meeting are unlikely to be feasible.

Referral of specimens and cultures

Specimens or cultures are referred by NMRS Central and North to NMRS-South for further drug sensitivities, if required. 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.

Requesting additional tests

M. tuberculosis sensitivity

All new multidrug resistant and drug resistant isolates on clinical request will be processed for reserve drug sensitivity testing. Sensitivities will be repeated on isolates more than 2 months apart or where there are clinical concerns, for example poor response or drug intolerance.

Additional sensitivity testing on M. tuberculosis isolates must be discussed with the NMRS Central and North laboratory staff before requests are submitted.

Non-tuberculous Mycobacteria (NTM) sensitivity

All repeatedly isolated, clinically significant NTM isolates as assessed using current published clinical guidelines and where there is an intention to treat will be set up for the appropriate panel based on the organism identification and the patient’s clinical status. Full completion of the request form aids this process.

Additional sensitivity testing on NTM isolates must be discussed with the NMRS Central and North laboratory clinical staff before requests are submitted.

We test NTM sensitivities once a year for established NTM colonisation or infection. For new pulmonary NTM infection, we will test NTM sensitivities on a second isolate after clinical discussion. All sterile site and non-pulmonary site samples requesting NTM sensitivities will receive sensitivities. Please email any retrospective sensitivity requests with the relevant patient and clinical details.

Repeat cultures

We test repeat cultures for TB and NTM if more than 2 months have elapsed since previous identification. Any samples received before the 2-month period will be rejected unless there is a clinical indication provided. For cultures with repeat samples from the same time and site, only one sample will have full identification and sensitivities and cultures will be tested from each site. All other samples will go out with previously isolated comment and will refer to our previous laboratory number with the full results.

Specimen and sample submission guidelines

Specimens must be labelled with the following:

• full name (first name and surname)
• unique patient identifier (hospital number)
• sender’s sample number
• date of birth
• NHS number

Request forms must match the sample and include the above information, as well as the list below. The name and contact information of the requester, such as an NHS.net email address (telephone number is vital for urgent requests) is also required.

• tests required
• sample type, such as primary sample or positive mycobacterial culture
• specimen or isolation site
• date sent
• sex
• full patient address, including postcode
• date and time of collection of specimen
• relevant clinical information
• sender’s location details

Request forms to accompany specimens and cultures

Please ensure the appropriate NMRS Central and North request form is fully completed for the sample being submitted with the required information as stated above, as well as the correct telephone number and email address. See below for guidance on how to fill in the form.

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

Download and print the request form

The UKHSA Public Health Laboratory Birmingham (PHLB) NMRS Central and North laboratory advises users where forms are poorly completed. Wherever possible NMRS Central and North supports its users by not rejecting referred specimens and cultures.

1. Only use this form for mycobacterial related requests. Ensure you are using the most up-to-date version.

2. Our address, including DX number. Mark all packages clearly for CL3/NMRS.

3. Useful contact details for both lab and clinical enquiries.

4. State the lab sender details as this is where reports will be sent to. It also helps clinicians to know this for when patients have been transferred between hospitals.

5. Include a name and contact details of a clinician so our clinicians have a point of contact when discussing results and treatment options.

6. Include all patient details listed here and ensure the sample has at least 2 matching patient identifiers. Your lab number is useful to include, especially as there may be multiple isolates on the same patient.

7. Include the patient’s address and postcode, if it is available, as it aids in contact tracing.

8. State the specimen type and don’t be vague. For example, if a tissue or a fluid, state where from. This will affect how we treat the sample and what work we do on it.

9. Include the date the original sample was collected as this will affect how often we test the sample. The date you cultured/inoculated the sample into MGIT/ LJ and the date it flagged positive is also important. If AAFB positive, send to us.

10. A positive mycobacterial culture refers to either a MGIT liquid culture or a LJ slope. Primary sample is the original, untreated sample.

11. If you have performed any preliminary tests in house, include the results here. This could be a PCR, line probe, TBcID, TB check and so on.

12. The ‘Positive / Negative / Not done’ section refers to your auramine microscopy result on the primary sample.

13. Primary isolation is for the primary sample only and will usually be an auramine smear and a MGIT and LJ culture (if suitable sample type and sufficient volume).

14. Tick the MTB complex / Rifampicin resistance PCR box if you are requesting a TB PCR. Note: not all sample types are suitable for this test so please check specimen requirements before sending.

15. Tick the Positive mycobacterial cultures box if you are sending a positive mycobacterial culture (MGIT aliquot or LJ) for identification and sensitivity. We will process it for WGS. This is not suitable for primary samples.

16. Include any additional requests or information at the bottom of the form, including:

• relevant clinical details that will aid our clinicians
• previous results
• if it is a repeat sample
• if you have spoken to one of our clinicians regarding this request

Guidance on packaging and transport

A small but significant proportion of samples received by the UKHSA National Infection Services 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.

Sample description	Packaging requirement
Category A samples are known or suspected to contain a microbial agent with the following definition: “an infectious substance which is transported in a form that if exposure to it occurs, is capable of causing permanent disability, life-threatening or fatal disease to humans or animals”. The majority are Hazard group 3 or 4.	Assign to UN2814 (Humans). Packaging Instructions PI620. Supporting documentation as per the international agreement on the Carriage of Dangerous Goods by Road (ADR). Transport as category A ADR licensed courier
For practical reasons to allow referral and reference services to continue, a limited number of Category A agents are exempt from being transported as Category A. These are Vero-cytotoxin producing Escherichia coli (VTEC), Mycobacterium tuberculosis and Shigella dysenteriae 1.	Assign UN3373. Packaging instruction PI650. Send by courier; Royal Mail will not accept.
Category B samples are those that do not meet the definitions of Category A.	Assign UN3373. Packaging instruction P1650. Send by post or courier (Royal Mail will accept).

The terms Category A and Category B are limited to classifying samples and 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 and the Department of Health and Social Care.

Use the links below for further information:

• Shipping dangerous goods: overview
• Transporting dangerous goods
• Guidance on regulations for the transport of infectious substances (2021 to 2022)

Reporting incidents during transportation that may affect the safety of personnel

NMRS Central and North will report any leaking containers and improperly packaged parcels to users.

Leaking cultures will not be processed by NMRS Central and North; users will be informed and a repeat sample requested.

Repeated offences will be referred to the UKHSA Safety Committee who may refer to the Health and Safety Executive.

Label the specimen or culture bottle with the name of the patient, unique identifier (for example, hospital number or date of birth) and the laboratory number. All specimens or cultures sent to NMRS Central and North must be packed in accordance with international air transport association (IATA) regulations 650/602.

Place the specimen or culture inside a leakproof plastic container 5ml bijoux polypropylene screw cap labelled container from international scientific supplies (product code PBT200.P04), then place bijoux into a universal as a secondary container. Please place the secondary container with enough absorbent material to be able to absorb all the contents of the bottle in case of leakage.

5ml bijoux containing specimen. The bijoux should then be placed in a universal.

The top of the specimen or culture bottle must be fixed on firmly so that there is no chance of leakage. This will also prevent desiccation of the specimen or culture in transit, which would compromise successful culture. Do not put parafilm around the lid. Wrap the bottle in absorbent material and seal it inside a minigrip bag. NMRS Central and North will endeavour to process primary material if leakage occurs but this is likely to compromise the chance of successful culture, and we will request the user to send us an additional specimen. Leaking cultures will not be processed and a repeat sample will be requested.

Place the plastic container inside a fibreboard box.

Place the form between the plastic container and the outer cardboard box. Do not place it inside the plastic container.

In the event of leakage or breakage, the whole shipment will be destroyed without opening.

Please ensure packaging is clearly labelled for CL3 – NMRS Central and North, so that packages are taken into CL3 to be opened.

Specimens may be sent by Royal Mail or courier.

We recommend that, to minimise delays, specimens, especially those sent for urgent PCR, are sent by routine courier, for example, DX or other specialised couriers.

Please ensure that the courier is able to reach NMRS Central and North before 4pm.

Reports

The NMRS Central and North reports are routinely sent out via E-lab or National Pathology Exchange (NPEx). Printed reports will only be sent out if the referring laboratory is not registered to E-lab. Missing reports and archived reports can be posted if requested.

It is our policy that reports containing patient data should not be sent by routine email.  Emails cannot be relied on to guarantee the security of patient data because they can be intercepted by a third party en route (unless encrypted). Emails can be sent from NHS.net emails to another NHS.Net email account if the need arises.

Submitting tissue samples from deceased people

Compliance with the Human Tissue Act

The UKHSA microbiology services are 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 National Infection Service 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 the 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 receive 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 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.

Compliments and complaints

Compliments or complaints can be referred by email, telephone or post to Dr Esther Robinson, Priti Rathod and Caroline McKeon as well as senior staff (Lisa Jarrett, Rose Allen and Amna Zulfiqar). All complaints will be managed by Caroline McKeon and a final response will be within 20 days of receipt of complaint.

Caldicott recommendations

The recommendations of the Caldicott report (1997) were adopted by Public Health England, now UKHSA. These recommendations relate to the security of patient identifying data (PID) and the uses to which they are put.

UKHSA observes Caldicott guidance in handling PID and has an overall Caldicott guardian who is the Director of Health Protection and Medical Director who reports through the information governance and Caldicott functions and onwards to the National Executive.

The UKHSA microbiology services have a Caldicott guardian who advises the director of microbiology services on confidential issues and is responsible for monitoring the physical security of PID in all parts. This also applies to the transfer of results of investigations to and from UKHSA microbiology services whether by mail services; telephone or fax. The value of ‘safe haven’ arrangements or other means of the sender and receiver information identifying themselves to each other before data is transferred is emphasised.

UKHSA is anxious to audit 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 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.

Download NMRS mycobacteriology form