Samples for Mycobacterial Investigations
Microscopy
All samples except blood, swabs and urine are routinely examined for direct AFB microscopy (provided there is sufficient specimen). Turnaround time 1 day.
Culture
Our current practice is to inoculate all specimens into liquid and solid media. Turnaround time 4-6 weeks average, but incubated for 12 weeks
Rapid confirmation of MTBC is achieved initially using a lateral-flow immunochromatographic assay.
Identification and phenotypic drug susceptibility testing
SMRL uses Whole Genome Sequencing to identify mycobacterial species, predict MTBC drug susceptibility/resistance and assess MTBC strain relatedness from a single test.
The WGS pipeline predicts susceptibility and resistance for four first-line TB drugs with a high degree of accuracy but further phenotypic drug susceptibility testing (DST) may be required depending on the combination of resistance predictions obtained.
There may occasionally be situations where cultures are referred for alternative modes of testing at one of the UKHSA National Mycobacterium Reference Service laboratories.
NTM susceptibility testing is based on the ATS/IDSA criteria for diagnosing NTM infection, modified by local experience and thereafter only repeated at 3 month intervals (exception: Mycobacterium abscessus complex yearly interval). Turnaround time is dependent on isolate. Testing will be performed on:
- all NTM from sterile sites (except for Mycobacterium marinum from skin biopsies);
- first isolates of Mycobacterium abscessus complex, Mycobacterium xenopi, Mycobacterium malmoense, Mycobacterium szulgai and Mycobacterium kansasii. Experience suggests that these are likely to be associated with clinically significant disease.
- patients with cystic fibrosis, HIV or with significant T cell immunosuppression (if we are informed of the clinical features)
For all other pulmonary isolates of NTM we will not do sensitivity testing unless we are informed that the patient meets ATS criteria for NTM lung disease (please indicate which criteria are met). For non sterile sites such as urine or faeces we will not do sensitivity testing unless there is a strong clinical suspicion of infection. To arrange sensitivity testing please email us at Loth.Smrl@nhslothian.scot.nhs.uk
The current BTS NTM Pulmonary Disease advice, including comment on ATS/IDSA criteria is at:
https://www.brit-thoracic.org.uk/standards-of-care/guidelines/bts-guidelines-for-non-tuberculous-mycobacteria (accessed January 2022).
Molecular tests
Pulmonary specimens from NHS Lothian sources fulfilling NICE based criteria will be tested by a rapid molecular test for MTB complex and rifampicin resistance if sufficient sample is received (2ml minimum volume required). In addition, any AFB smear positive samples are also tested. Rapid molecular testing of both pulmonary specimens and positive cultures is also available for MTB complex and isoniazid, fluoroquinolone, amikacin, kanamycin, capreomycin and ethionamide resistance where clinically indicated.
Interferon Gamma Release Assay (IGRA) for detection of latent TB infection is performed ‘in-house’ for NHS Lothian patients by Blood Sciences Autocore using the QuantiFERON-TB Gold Plus (QFT-Plus) test. Other Health Boards may use this facility via a Service Level Agreement with NHS Lothian. Potential users should contact:
Mrs Una Jarrold
Tel: 0131 242 6830
Una.White@nhslothian.scot.nhs.uk
Operational Science Manager, Blood Sciences, NHS Lothian.
Quantiferon 4 tube system and Sarstedt universal blood culture adaptors are available from catalogue on PECOS system for NHS Lothian users (Product No. 622222). If a Safety-Multifly is used, the line must be primed with an empty Sarstedt tube first to ensure the correct volume (1ml) of blood is delivered into each tube. All 4 tubes (Nil, TB1, TB2, and Mitogen) must be inoculated. The black mark on the side of the tubes indicates the validated range of 0.8–1.2 ml. If the level of blood in any tube is outside the range of the indicator mark, a new blood sample should be obtained. It is important to gently agitate the tubes ten times to ensure the entire inner surface of each tube is coated with blood, to dissolve antigens on tube walls. DO NOT shake vigorously.
Samples should be dispatched to the laboratory as soon as possible but must reach the laboratory within 16 hours of collection. Do not refrigerate. See the Edinburgh & Lothians Laboratory Medicine Test Directory for full details. Laboratories out with NHS Lothian may incubate tubes upright for 16-24 hours at 37±1ºC. After incubation, samples may be held between 4 and 27ºC and must reach the laboratory within 72 hours. Samples should be sent according to SLA to the NHS Lothian Specialist Serology/Blood Sciences centre.
The T-spot assay is another IGRA, which is available from:
Oxford Immunotec
115D Milton Park
Abingdon
Oxfordshire
OX14 4RZ
Tel: +44 (0) 1235 442 780
Fax: +44 (0) 1235 442 781
Note that tuberculin skin testing (TST) is an alternative mode of assessing latent TB infection (LTBI). There is no gold standard for LTBI detection.
TST and IGRAs may be negative in patients with active TB infection and LTBI tests have little role in routine assessment of active TB infection.
Technical, Scientific and Health and Safety Advice
The technical and scientific staff at the SMRL are happy to provide advice on all laboratory aspects of microscopy and isolation of Mycobacteria and on the safe running and design of Containment Level 3 laboratories.
Please contact Loth.Smrl@nhslothian.scot.nhs.uk for technical help and advice.
Environmental Testing (NHS Lothian only)
Testing can be performed on water and air from heater/cooler units. For water samples, 50mls are required, sodium thiosulphate should added to the water collection pots to neutralise the hypochlorite before sampling (final concentration of at least 18mg/L).
Air sampling plates supplied by SMRL by prior arrangement.
Clinical, Epidemiological and Infection Control Advice
The primary source of medical advice for the diagnosis, management and public health investigation of TB lies with the consultants in the relevant specialties in the local health board. The consultant microbiologists attached to the SMRL are happy to complement this primary advice where appropriate.
Please contact us via Loth.SMRL@nhslothian.scot.nhs.uk or alternatively Dr Ian Laurenson (Director) Ian.Laurenson@nhslothian.scot.nhs.uk, Dr Olga Moncayo Olga.Moncayo@nhslothian.scot.nhs.uk, Dr Donald Inverarity Donald.Inverarity@nhslothian.scot.nhs.uk, or Dr Naomi Gadsby Naomi.Gadsby@nhslothian.scot.nhs.uk for advice on issues such as microbiological diagnostic tests, antibiotic susceptibility tests, strain typing for contact tracing, and infection control.
Services not provided
Please note SMRL no longer offers PCR for MTBC detection in formalin-fixed, paraffin embedded tissue. Samples for 16S rDNA PCR may be sent directly by the user to a suitably accredited laboratory such as:
Microbiology, Virology and Infection Control Level 4,
Camelia Botnar Laboratories Great Ormond Street Hospital for Children
Great Ormond Street London
WC1N 3JH
DX number: DX6640203
DX Exchange: Bloomsbury 91WC
For histological samples requests a minimum of 4 rolled sections (10µm thick). More preferred if possible to allow repeat extractions.
Department of Microbiology
Leeds General Infirmary
Old Medical School
Thoresby Place
Great George Street
Leeds
LS1 3EX
DX number: DX6281504
DX Exchange: Leeds 90LS
For histological samples requests 10 sections 10µm thick
Antimicrobial Assays
Information on assays on first line TB therapy drugs and other antimicrobial mycobacterial drugs can be found at http://www.assayfinder.com/ (accessed 240622)
Leprosy Diagnosis
SMRL does not undertake investigations for the diagnosis for leprosy. Clinicians should refer all suspected or confirmed cases to one of the national leprosy centres where the case can be reviewed by a Consultant Advisor in Leprosy. Contact in the first instance:
Dr Stephen Walker
Consultant Advisor in Leprosy
Hospital for Tropical Diseases
Mortimer Market Centre
Capper Street
London
WC1E 6JB
Tel: 020 3447 5959