Annual Report April (2010) March (2011)

Transcription

1 Annual Report April (2010) - March (2011) Laboratory Service: Scottish Mycobacteria Reference Laboratory Author: Dr I F Laurenson, Alan Rayner & the Team Date: May 2011 Page 1 of 22

2 1. Summary with key points for consideration: received 966 Mycobacteria (including 3 from animal samples) and identified 960 isolates during the year The 18% over SLA number of cultures identified and susceptibility tested has maintained significant pressure on the service. A further nine loci were added to the panel of fifteen MIRU-VNTR loci used for routine genotyping of Mycobacterium tuberculosis complex in mid-november Twenty four digit MIRU-VNTR profiles are now reported to users on a weekly basis and used for epidemiological investigations where available. We plan to retrospectively genotype all MTBC strains from Changes in available technology have lead to major and ongoing changes in methodology for susceptibility testing. During the past year there was only 1 MDR and no XDR Mycobacterium tuberculosis patients diagnosed. (See Table 3) The Scottish Clinical Guideline on Tuberculosis and the proposed Scottish TB Action Plan are likely to shape future TB and laboratory services in Scotland, particularly through recommending: i) rapid liquid culture for all specimens, in addition to solid for at least precious samples ii) iii) minimum quality standards, being cognisant of laboratory mycobacterial throughput. review the role of new diagnostic tools (e.g. easy to use molecular tests direct on specimens to diagnose TB and resistance). 2. Activity data 2.1 Contracted activity: Table 1 Test Type Contracted number Page 2 of 22 Actual number Number Positive

3 Phenotypic Culture Sensitivities 1 st 2 nd + 3 rd line Rapid isolation techniques Molecular Typing MIRU-VNTR Rapid Molecular on film 200 (current funding) positive sputa 400 (agreed funding) TOTAL It has been agreed with HPS that from we will count all cultures received by 31 st March rather than specimens and cultures by that date, to allow more time to prepare the report. The impact of this on annualised figures is negligible. Table 2 Mycobacteria identification and sensitivity testing. est Category 2010/ / / / / / / /04 dentification irst line ensitivity econd line ensitivity hird line ensitivity tests for rapid rowers M. tuberculosis complex: 1 st Line Sensitivities = Isoniazid, Ethambutol, Rifampicin & Pyrazinamide 2 nd Line Sensitivities = Ciprofloxacin, Rifabutin Clarithromycin, Amikacin & Streptomycin 3 rd Line Sensitivities = Capreomycin, Clofazamine and Prothionamide Page 3 of 22

4 Table 3 Patients with drug resistant Mycobacterium tuberculosis isolates Year MDR TB* XDR TB** Isoniazid only Isoniazid & Streptomycin only Pyrazinamide only Streptomycin only Pyrazinamide & Streptomycin only Rifampicin & Rifabutin only Isoniazid, Streptomycin & Clofazamine Isoniazid, Ciprofloxacin, Amikacin & Capreomycin Isoniazid & Clarithromycin Ethambutol Clarithromycin Clofazamine Isoniazid, Clarithromycin & Capreomycin Isoniazid, Clarithromycin & Streptomycin Pyrazinamide & Clarithromycin Isoniazid, Clarithromycin, Streptomycin & Prothionamide *Multidrug-resistant tuberculosis (MDR TB) = Resistance to at least rifampicin and isoniazid. **Extensively drug-resistant tuberculosis (XDR TB) = MDR TB that is also resistant to any fluoroquinolone, and to at least one of three injectable second-line anti-tb drugs used in TB treatment (amikacin, capreomycin and kanamycin). Page 4 of 22

5 2.2 Activity by Health Board: Annual Report April (2010) March (2011) Table 4 Requests for identification and sensitivity testing by Health Board Test / Investigation Mycobacteria Cultures All Mycobacteria MTBC# NTM## Health Board Ayrshire & Arran Borders Dumfries & Galloway Fife Forth Valley Grampian Greater Glasgow & Clyde Highland Lanarkshire Lothian Orkney, Shetland Tayside Western Isles Total for Scotland NEQAS and internal QC #MTBC = Mycobacterium tuberculosis complex (Note the MTBC for consisted of 493 M. tuberculosis, 6 M. bovis, 6 M. bovis (BCG), and 7 M. tuberculosis complex- some pending) ##NTM = Non-tuberculous mycobacteria Page 5 of 22

6 Identification Methods All strains of Mycobacteria are tested using the GenoType Kits manufactured by Hain Lifescience. If this fails to give a result the PCR Restriction Assay (PRA) method is performed. If this fails to identify the mycobacterium, sequence analysis of the hsp65 PCR product (a 439bp fragment of the gene encoding the 65kDa heat shock protein (hsp65) which is common to all mycobacteria) is increasingly performed. Table 5 Identification PCR Restriction Assay & Sequencing PRA Sequenced PRA Sequenced PRA Sequenced PRA Sequenced Page 6 of 22

7 Table 6 Film positive respiratory and non respiratory samples tested by direct molecular detection April March 2011 Health board Respiratory Samples tested (all samples tested) M. tuberculosis complex positive respiratory samples (all samples) Ayrshire & Arran 6 (6) 1 (1) Borders 3 (3) 2 (2) Dumfries & Galloway 5 (6) 1 (1) Fife 5 (11) 4 (4) Forth Valley 9 (10) 6 (7) Grampian 23 (30) 12 (17) Greater Glasgow & Clyde 70 (84) 54 (63) Highland 11 (13) 9 (11) Lanarkshire 15 (19) 12 (16) Lothian 35 (44) 22 (28) Orkney, Shetland 0 0 Tayside 8 (14) 5 (7) Western Isles 0 0 Total 190 (240) 128 (157) Rapid Direct Molecular Testing on film positive sputa This is carried out weekly, currently on a Wednesday. All film positive respiratory samples received up to the preceding Tuesday morning are included in the weekly run. Page 7 of 22

8 Table 7 Mycobacteria specimens for rapid isolation by Health board Health Board Former Argyll & Clyde Ayrshire & Arran Borders Dumfries & Galloway Fife Forth Valley Grampian Greater Glasgow Greater Glasgow & Clyde Highland Lanarkshire Lothian Orkney, Shetland Tayside Western Isles Total for Scotland Page 8 of 22

9 Typing Since August 2005, 15-locus MIRU-VNTR typing has been performed routinely on all MTBC isolates. Since mid-november 2010, a 24-locus MIRU-VNTR typing protocol has been in use and the results fed back to users. Following the introduction of the nine additional loci there have been three requests from TB services to investigate putative TB clusters, one from Grampian (two clusters involving 14 and 7 patients), one from Lothian (three clusters involving 9, 5 and 5 patients and one from Greater Glasgow & Clyde involving two patients. During the year , 227 Scottish patient isolates were genotyped using 15-locus MIRU-VNTR. An additional 133 patient isolates were genotyped using the 24-locus MIRU-VNTR protocol. Laboratory Contamination Clusters: During we have not been involved in the investigation of any laboratory contamination events in Scotland. This may in part reflect emphasis on this issue at the last two audit-study days and support given over recent years to Scottish Laboratories by. 3. Quality assurance report 3.1 Turn around times Table 8 Target turnaround times st Page 9 of 22

10 inical specimen amination, culture, lation and ntification where the late is subsequently wn to be MTB mplex. tomated liquid and nventional solid lture on all samples ing processed for cobacterial culture. visional ntification of MTB mplex by nucleic d amplification test nsitivity testing of B complex mpleted. Annual Report April (2010) March (2011) Target turnaround time agreed (working days) Actual turnaround time 95% completed by: working days (mean) Actual turnaround time 95% completed by: working days (mean) </= 42d from receipt in at least 95% of specimens 33 (11) 37 (17) Set up </= 1 working day from receipt (5d/ week reference Laboratory Service) at least 95% of specimens 1 (1) 1 (1) </= 7d from receipt of a positive culture in 95% of specimens 4 (2) 8 (3) </= 28d of isolate receipt/ isolation in 95% of instances 35 (15) 35 (17) RU-VNTR typing d transmission to tional database </= 63d from receipt of isolate in 95% of specimens (with a view to brining this down across time) 43 (17) 31 (15) Table 8A All Mycobacteria turnaround times and ranges from time of culture receipt Test/Investigation Mean turnaround time Range Mycobacteria Identification 10.5 days 1-82 days Mycobacteria susceptibilities 13 days 5-63 days Identification as MTBC 2 days 1-32 days Page 10 of 22

11 M. tuberculosis complex final identification M. tuberculosis complex susceptibility testing Non-tuberculous Mycobacteria identification Non-tuberculous Mycobacteria susceptibility testing 15 days 1-63 days 15 days 6-63 days 4 days 1-82 days 11 days 5-48 days Identification and front line sensitivity testing The time interval between receipt of a culture and the issue of the final identification and first line sensitivity report varies greatly from 1-12 weeks, depending on factors such as the nature of the culture medium used by the sending laboratory, paucity of organisms in the culture, the species of mycobacterium and the presence or absence of contamination. Typing PCR-based genotyping results MIRU-VNTR can be available in 2-5 days once the DNA is extracted although samples are also normally batched before these tests are performed. Where a result is already available the time to respond to a request can be almost immediate. 3.2 Internal audit: a) Horizontal audits. One audit completed. Minor non-compliances addressed. b) Vertical audits. One audit completed. Minor non-compliances addressed. c) Examination audits. Three audits completed. One audit with non-compliances addressed. Two audits currently being addressed. d) Internal Quality Assurance has been performing IQA since November One sample and one culture per month are selected at random by the IQA co-ordinator, anonymised and retested for all appropriate investigations with a new lab number. The original identity of the sample or culture is only known to the IQA co-ordinator until all results are reviewed. For the period 1 April 2010 to 31 March 2011 a total of 4 samples and 4 cultures were assessed. This falls short of the expected number for the year. Previously we had performed between 6 and 10 IQA samples and cultures in any year. The reason for performing so few IQA tests is partly due to implementation of new technologies and typing, busy periods in the lab and staff intermittent sickness. IQA for Clinical Specimens All 4 specimens were sputum samples. All 4 specimens were smear negative, which was in agreement with the findings from the original samples. One of the 4 specimens was culture negative after 8 weeks incubation which was in full agreement with the result from the original sample. One of the 4 specimens was culture Page 11 of 22

12 negative after 8 weeks incubation whereas the original sample was reported as contaminated. This could be due to the aliquot of sample used for the IQA culture containing fewer contaminating bacteria thus decontamination was more successful. One of the 4 specimens was culture negative after 6 weeks incubation as the egg slopes were contaminated. This result is in full agreement with the findings from the original sample which also had contaminated egg slopes. One of the 4 specimens grew M. celatum whereas the original sample was negative on culture. The patient from whom the original sample was taken only ever had the one sputum sample cultured for mycobacteria. The M. celatum from the IQA sample grew on egg media only. The failure to isolate the M. celatum organism in the original sample could be due to very small numbers of organisms being present. IQA for Mycobacterial Cultures Of the 4 cultures assessed all 4 grew M. tuberculosis. All 4 M. tuberculosis isolates were in full agreement with the original cultures for the identification test results, for susceptibility test results and for MIRU-VNTR typing results. 3.3 Accreditation schemes Scheme Status Date of last full inspection. Date of last visit CPA Full May 2008 Surveillance visit May 2010: minor non compliances addressed. as part of Microbiology was inspected by CPA (Registration Number 2496) in May No critical non-compliances were identified. The next inspection is due in External audit schemes NEQAS Quality Control AAFB Microscopy: our score for microscopy was 16 points out of a possible total of 24. This was due to the late return of one batch of our results, we had the correct answer. A system has been put in to place to prevent this from happening again. Culture for M. tuberculosis: we scored 24 points out of a possible 24. Molecular detection: One NEQAS distribution was received for direct and post culture detection and rifampicin resistance in April 2010, containing two specimens. We scored full marks (28 out of a possible 28). MIRU-VNTR typing for both MTBC isolates was correct. During the last year has participated twice in the HPA EQA for MTBC genotyping which is coordinated by the Mycobacterium Reference Unit, London. Each panel consists of 8 samples. Review of results due June requested the RIVM EQA panel from the Netherlands to assist with evaluation of the 24-locus MIRU- VNTR protocols. This is a large panel of 30 samples that has not been fully tested to date. WHO first line Mycobacterium tuberculosis sensitivity testing. Round 16: we have returned our results and await feedback. Page 12 of 22

13 QCMD MTB EQA Panel One distribution for MTBC nucleic acid detection was received in August 2010, containing 10 specimens. We scored full marks. Collaboration We actively assist the Irish Reference and other Laboratories with difficult isolates, on a charged basis. This is valuable in increasing the depth and complexity of our work as a Reference Laboratory. 3.5 Incidents and complaints Incidents: Following a typing query a review of results from revealed errors affecting 13 loci from 9 patients. This changed clustering status of 3 patients. Relevant CPHMs were informed and amended reports issued. Preventative steps have been taken. A fuller report is available on enquiry. Complaints: None received. Compliments: Laboratory visitors and users have expressed informal thanks, in the form of s, for training and service, although no formal letters were received. 3.6 Equality and diversity impact assessments We have worked with NHS Lothian and other Lothian reference laboratories to implement equality and diversity impact assessments for our services. 4. New developments 1. Progress with molecular typing methods For the period 1st April 2009 to 31 st March 2011, 360 Scottish strains have been genotyped using MIRU- VNTR methodology. Data is stored in a BioNumerics database (Applied Maths) which contains various genotyping results from > 5000 MTBC strains. MIRU-VNTR typing data is sent regularly to the National TB Typing Database held at the HPA CfI at Colindale. Scottish typing data is also distributed in a paper format to CPHMs approximately four monthly (last distribution April 2011). Comment is also made on request from TB services. The typing results are fed back weekly to HPS and CPHMs as well as on patient reports, often available ahead of sensitivity results. Approximately 56.6% of all genotyped strains are clustered, with each cluster containing between 2-75 patients. Eighty-seven of 110 clusters cross boundaries between Health Boards. The HPA UK TB Diagnosis and Molecular Epidemiology (DAME) Group are considering introduction of a naming scheme for all clusters. 2. Progress with molecular detection methods. Real-time PCR The Xpert MTB/RIF real-time PCR assay (Cepheid UK) for MTBC detection and rifampicin resistance directly from sputum samples was evaluated as part of an Honours BSc student project during early The assay performed well with 100% sensitivity and specificity for MTBC detection in routine respiratory samples. It is a fairly expensive test but no specific sample extraction stage is required, thus the assay does confer the advantage of being able to perform daily single tests on concentrated and NALC-treated smear positive samples which would improve sample turnaround times compared to weekly batch testing. In addition, the technical time required is much reduced compared to the current strategy of real-time PCR for MTBC detection followed Page 13 of 22

14 by MTBDRplus testing for RIF/INH susceptibility testing (the total hands-on time is approximately 20 minutes). Two kits (10 tests each) have been purchased to allow continuing use and evaluation of this system. Susceptibility Testing As the radiometric Bactec 460 support ceased during we reviewed susceptibility and introduced extended testing to some second and third line agents in the MGIT 960 system. In addition we reintroduced the capability to undertake testing on solid media as a confirmatory back-up. We are assessing microtitre systems and have streamlined susceptibility testing of rapidly growing mycobacteria. These changes have taken considerable effort and resource to undertake, but are essentially cost neutral to NSS in terms of equipment and consumables. Molecular resistance testing on isolates to first and second line agents is used as an adjunct when there is clinical need. 3. Gamma interferon testing for the diagnosis of latent tuberculosis. This was introduced in September 2008 on a pay as you go basis. During the period, 1 st April 2010 to 31 st March 2011, blood samples from 422 patients were received. A total of 387 patient tests were performed. These are generally batched and performed fortnightly by Lothian Specialist Serology staff in conjunction with TB lab staff. Lothian and Ayrshire and Arran Health Board areas are the most frequent users of this service with 54.5% and 12% of submitted specimens respectively. The role of interferon gamma release assays is outlined in NICE and Scottish TB Guidelines as well as FAQs being available on the HPA Website. NICE updated guidance in March These ex-vivo assays are based on the detection of gamma-interferon production by the peripheral blood mononuclear cells in response to stimulation by specific M. tuberculosis antigens. Unlike the tuberculin skin test, the assays available are highly specific for M. tuberculosis as they do not respond to previous BCG vaccination. Such assays have proved to be sensitive and specific for detection of tuberculosis in various patient groups. 4. Other activities UK MDR advice service This was set up during and continues to participate in this service. Scottish TB Action Plan Owing to a statistically significant upturn in Scottish TB cases and the introduction of the Scottish TB Guidelines the Scottish Government instituted the construction of a TB Action Plan for Scotland. The plan was endorsed by the Minister for Public Health in March 2011 and will shape future TB services in Scotland. contributed to the main group and subgroups, including providing the chair for the laboratory services subgroup. Implication for finance and staffing The financial implications of the assessment and introduction of new identification and typing methods are difficult to predict, and these can partly replace current techniques. Reagents and kit prices have been subject to inflation. This factor and the rises in specimen numbers have contributed to rising costs. New developments impose a relatively greater demand on senior BMS, clinical scientist and medical staff time than on consumables and equipment. Planning and collaboration with colleagues in other centres is essential, and are demanding of medical time, as is discussion with colleagues on the management of MDR TB patients. Page 14 of 22

15 National Guideline and Action Plan progression has been demanding of medical time. 5. Future developments Changing molecular technologies require us to reassess those currently used and make the most of collaboration with laboratories to develop better and more cost-effective testing. Rapid molecular confirmation, particularly from specimens, of species identity and sensitivity remains of importance in the era of MDR TB we intend to continue to assess and develop such techniques. One laboratory is performing a kit based real time PCR test on all specimens prior to referring them on to NHS Lothian for further processing. If others choose to go down this pathway this will affect Scottish TB services configuration. Requests to take on primary diagnostic work for some smaller laboratories is under consideration by NHS Lothian. 6. Teaching The laboratory provides support for undergraduate science and medical students and for dissertation projects for Trainees/ MSc s. Attachments, usually for about a week, are arranged for visiting BMS, clinical scientist and medical staff from hospitals in Scotland and occasionally elsewhere. Medical and Scientific staff from contribute regularly to several teaching programmes for medical, nursing and technical staff throughout Scotland and at international meetings and seminars. See also student projects below. a) Internal Staff Training Several Lothian staff participated in the study day (c below). BMS have been trained in primary processing of mycobacterial specimens during the past year. b) Individual placements Visitors to April 2010 March /5/2010 Dr Rebecca Gilson, StR from GUM RIE for 1 day 13/5/2010 Dr Jean Walker, LAT StR from Micro RIE for 1 day 22/6/2010 Dr Badriya Al Adawi, from Micro Lab Glasgow Yorkhill Childrens Hosp for 4 days 6/9/2010 Dr Chin Lim, StR from Micro Lab RIE for 1 week 23/9/2010 Karen Craik, BMS from Micro Lab Dumfries Royal for 1 day 27/9/2010 Dr Noha Elsakka, StR from Micro Lab RIE for 1 week 11/10/2010 Dr Linsay Batchelor, from Micro Lab SGH Glasgow for 1 week 11/10/2010 Dr Naomi Gadsby, Clinical Scientist from Micro Lab RIE for 1 week 31/1/11 Dr Surhabi Taori, SpR from Micro Lab RIE for 1 week Page 15 of 22

16 c) External Training Our biennial audit study day in June 2010 covered a range of mycobacterial topics, including laboratory contamination, the audit of laboratory services, talks on various laboratory methods and the epidemiology of Mycobacteria. Mrs Claxton, Mrs Doig and Dr Seagar participated in and contributed to a workshop hosted by the National Mycobacterium Reference Unit in London for all UK and Irish Laboratories on susceptibility testing and typing. 7. Research Collaborative research projects include: Thesis: The application and impact of DNA fingerprinting on the epidemiology of Mycobacterium tuberculosis in Scotland (with PhD student Abigail Hopkins and supervisor Dr Jim McMenamin at HPS). September 2002 to September This thesis was awarded in the autumn of Thesis: Lessons for the control of tuberculosis in Scotland from Molecular fingerprinting of Mycobacterium tuberculosis. (with University of Glasgow MPH student Dr Catherine Benton under the supervision of Dr Jim McMenamin, HPS). Thesis accepted in May Thesis: Epidemiology of Multi-Drug Resistant Tuberculosis in Scotland. Masters in Public Health. collaborated with colleagues at HPS and Lothian Health supervising a student at the University of Edinburgh (see publication below). Thesis accepted September Thesis: Tuberculosis and alcohol misuse in Scotland. Masters in Public Health Project. collaborated with colleagues in the University of Edinburgh supervising a student. Thesis accepted September Collaborations are ongoing with the Veterinary Laboratory Agency on M. bovis and microti infections, the Scottish Thoracic Society on management of infections caused by non-tuberculous mycobacteria. University of Edinburgh PhD-Dr Laurenson co-supervised and staff supported a student who commenced a thesis studying the evolution and typing of Mycobacterium abscessus. She had to withdraw for family reasons after 1 year s work A MSc student has taken up the project Collaboration with Oxford University on evolution of Mycobacterium tuberculosis. Collaboration with TB colleagues at HPA CfI, Colindale to investigate the sequence characterisation of M. tuberculosis VNTR loci. November 2009 onwards. Collaboration with Professor Stephen Gillespie, University of St Andrews on mycobacterial agents. has continued to maintain good links with colleagues at other TB reference centres in the UK. Staff have contributed to Health Protection Agency hosted workshops with Irish and other UK colleagues. The HPA TB Diagnosis and Molecular Epidemiology (DAME) Working Group has formed a strain typing meeting by teleconference to assist in keeping all areas abreast of developments. A list of recent publications and posters is included in Appendix E Page 16 of 22

17 8. Staffing Annual Report April (2010) March (2011) Mr Alan Rayner continued as BMS Team Manager, Mrs Pauline Claxton and Christine Doig as BMS Team Leaders, and Gary Davidson, Fiona Mathewson and Lukman Elabor as BMSs. Dr Louise Seagar continued as Clinical Scientist. Mrs Shona Hannan continued as full time secretary. A review of her agenda for change outcome has resulted in an upgrade of her position to a Band 3. Dr Laurenson and Dr Olson continued as Director and Deputy Director respectively. Dr Gibb has occasionally provided cover, for which we are grateful. Due to the increase in samples from other health boards Lothian Microbiology has stopped rotating staff through the Mycobacteria Unit to reduce the training load, which allowed the increase in samples without increasing staffing. Sandra Houston (BMS) volunteered to fill this post and started on 1 st May Local staff training will continue. We are grateful to all those who have supported us during the periods of staff absence and training of new staff, maintaining a high level of service. 9. Financial report The finance report as for the review year provided by UHD of Lothian Health Board is shown in appendix F. Budgeting for molecular tests is made difficult for a number of reasons: 1. These budget lines have been in use for several years, and during the period there have been many changes in the molecular methods and test protocols. 2. The volume and methods of typing work has varied considerably over this period. 3. We have continued with MIRU-VNTR typing during the current financial year. The introduction of further loci leads to some increase in cost, but is almost entirely offset by savings on direct testing of sputa for Mycobacterium tuberculosis complex and resistance. Some aspects of molecular work seem to be more demanding of staff time than consumables. 4. The cultures received were ~18% more that contracted, putting pressure on laboratory budgets and staff to maintain the costs and service. In view of these difficulties with the short-term forecasting of spending on molecular reagents, we feel that the allocation for this should be left unchanged for the coming year. 10. Summary and conclusions continues to provide an essential laboratory, clinical and epidemiological service to the population of Scotland and supports relevant teaching and research. It endeavours to keep abreast of the most recent scientific, clinical and epidemiological trends in Mycobacterial infections and to provide a cost effective and quality assured service. There have been major developments in this field in the last few years and predicting the financial implications for the service is a challenge. Requirement for senior biomedical scientist and medical input is likely to increase, and the workload relating to resistant M. tuberculosis infection and nontuberculous mycobacteria may increase over the coming years. For the forthcoming year we hope to keep within the forecast budget, dependent on greater staffing stability and a fall in specimens received. Acknowledgements Page 17 of 22

18 We are grateful for the support given by Lothian Health, the NSS and HPS over the past year as well as Consultant colleague Dr AP Gibb who has occasionally provided cover. Lothian Microbiology Clinical Manager, Mr Mike Gray continues to support. We are particularly grateful to Dr ES Olson for his support as Deputy Director, and the team in the production of this report. Dr IF Laurenson, Alan Rayner and the Team Date: May 2011 Page 18 of 22

19 11. Appendices Appendix A (Internal audit reports and updated risk register) Risk Register: Formal Directorate Laboratory Risk Register available. Generic High risk areas: difficulty in recruitment and retention of MLA and BMS staff. Staff sickness abated at present. Appendix B (External Accreditation Schemes: Summary of findings including areas of commendation and concern) See 3.4 Appendix C (External QA exception reports) None Appendix D (Evaluation of new methods) Different methods of susceptibility testing to replace the Bactec 460 are currently being evaluated. Appendix E Publications ( ) 2007 Enhanced Surveillance of Mycobacterial Infections (ESMI) in Scotland: annual report for Scotland for the years HPS Weekly Report 41; 44:2007. ( contributor of data) (Accessed 29 th May 2008) Tuberculosis in the UK. Annual report on tuberculosis surveillance and control in the UK Health Protection Agency November 2007 ( contributor of data) (Accessed 29 th May 2008) Xavier Emmanuel F, Seagar AL, Doig C, Rayner A, Claxton P, Laurenson IF. Human and animal infections with Mycobacterium microti, Scotland. Emerg Infect Dis 2007; 13: Seagar AL, Prendergast C, Emmanuel FX, Rayner A, Thomson S, Laurenson IF Evaluation of the GenoType Mycobacteria Direct assay for the simultaneous detection of the Mycobacterium tuberculosis complex and four atypical mycobacterial species in smear-positive respiratory specimens. J Med Microbiol. 2008; 57: Warwick RM, Magee JG, Leeming JP, Graham JC, Hannan MM, Chandwick M, Crook DW, Yearsley CP, Rayner A, Parker R. Mycobacteria and allograft heart valve banking: an international survey. J Hosp Infect. 2008; 68: Murray MP, Laurenson IF, Hill AT. Outcomes of a standardised triple therapy regime for Non tuberculous mycobacterial pulmonary infection. Clinical Infectious Diseases2008: 47:2, Page 19 of 22

20 2009 Annual Report April (2010) March (2011) Jackson AD, Seagar AL, Reid ME, Doig C, Forbes KJ, Laurenson IF, McMenamin J.Characterising transmission of a tuberculosis genotype in Scotland: a qualitative approach to social network enquiry. Int J Tuberc Lung Dis Apr; 13(4): Anderson LF, Laurenson IF, Blatchford O, Shakir E, McMenamin J, Johnston F, Stevenson J. Trends in multidrug-resistant tuberculosis in Scotland, Euro Surveill. 2009:14; 11: pii Tuberculosis in the UK: Annual report on tuberculosis surveillance in the UK Tuberculosis: Clinical diagnosis and management of tuberculosis, and measure for its prevention and control in Scotland. Health Protection Network, NHS NSS. March Accessed 26th May 2009 Eisin Shakir, Fiona Johnston, Alan Rayner, Ian Laurenson, Oliver Blatchford and Jim McMenamin. Enhanced Surveillance of Mycobacterial Infections (ESMI) in Scotland: 2007 tuberculosis annual report for Scotland. 2008:42; 49 Accessed 26th May Claire McGoldrick, Caroline Coghlin, Amie-Louise Seagar, Ian F Laurenson, Noel H Smith, William Stewart, Keith Kerr, J Douglas Mycobacterium microti infection associated with spindle cell pseudotumour and hypercalcaemia a possible link with an infected alpaca. BMJ Case Reports 2010; doi: /bcr Tuberculosis in the UK: Annual report on tuberculosis surveillance in the UK 2010http:// Eisin Shakir, Fiona Johnston, Alan Rayner, Ian Laurenson, Oliver Blatchford. Enhanced Surveillance of Mycobacterial Infections (ESMI) in Scotland: 2010 tuberculosis annual report for Scotland. 2010:44; Saunders NJ, Trivedi UH, Thomson ML, Doig C, Laurenson IF, Blaxter ML. Deep resequencing of serial sputum isolates of Mycobacterium tuberculosis during therapeutic failure due to poor compliance reveals stepwise mutation of key resistance genes on an otherwise stable genetic background. J Infect Mar; 62(3): Epub 2011 Jan 13. PubMed PMID: Mandal S, Bradshaw L, Anderson LF, Brown T, Evans JT, Drobniewski F, Smith G, Magee JG, Barrett A, Blatchford O, Laurenson IF, Seagar AL, Ruddy M, White PL, Myers R, Hawkey P, Abubakar I. Investigating transmission of Mycobacterium bovis in the UK, J Clin Microbiol Mar 23. [Epub ahead of print] PubMed PMID: Scottish TB Action Plan March 2011: Page 20 of 22

21 List of posters and presentations present Venkatesh H, Seagar AL, Neish B, Laurenson IF. Evaluation of the Genotype Mycobacteria Direct assay for detection of Mycobacterium tuberculosis complex and four atypical mycobacteria in smear positive specimens ICAAC Abstract D-1574 Chicago September Lim YC, Willson P, Laurenson IF, Rayner A, Claxton P. Non-tuberculous mycobacterial infection in South East Scotland. Federation of Infection Societies. Abstract 149: Cardiff November Seagar A-L. Appropriate use of IGRA?: a laboratory perspective. IGRA Echo Symposium presentation. Birmingham March Seagar A-L, Rayner A, Claxton P, Laurenson I. Assessment of the GenoType MTBDRplus assay performance compared to culture using respiratory and non-respiratory samples in Scotland. Abstract European Congress on Clinical Microbiology and Infectious Diseases, Vienna, 10 th -13 th April Seagar A-L, Doig C, McSparron C, Hill A, Laurenson I. Assessment of the use of the Quantiferon-TB gold intube assay for the diagnosis of TB infection in Lothian, Scotland. Abstract European Congress on Clinical Microbiology and Infectious Diseases, Vienna, 10 th -13 th April Prasad Palani Velu, Gilhooley S, McSparron C, Hill A, Stevenson J, Laurenson IF. Trends in HIV testing amongst TB patients in Lothian, Scotland ( ) British Infection Society Association of Medical Microbiologists 13 th Annual Meeting London May Abstract 7. Oral presentation. An epidemiological study of a cluster of Mycobacterium tuberculosis in Lothian. Ng B, McSparron C, Gilhooley S, Doig C, Seagar A-L, Laurenson IF. Abstract 0212, Federation of Infection Societies, Edinburgh November Student projects performed at ( ) PFGE typing of Mycobacterium intracellulare isolates from suspected laboratory contamination. (MSc project March 2006) Development of a Real-time PCR for the detection of Mycobacterium tuberculosis complex (BSc Microbiology Hons. Project, 2007) Review of management of patients with Non-tuberculous mycobacteria (MB ChB SSC student project, Spring 2007) Development of real-time PCR for the detection of mycobacteria in clinical samples. (BSc Microbiology Hons. Project, 2008) Epidemiology of multi-drug resistant tuberculosis in Scotland (MPH project, June- August 2008) Real-time PCR for the detection of rifampicin and isoniazid resistance in M. tuberculosis strains (BSc Infectious Disease Hons. Project, 2010). Tuberculosis and alcohol misuse in Scotland. (MSc in Public Health Research Project 2009) Page 21 of 22

22 Review of susceptibility testing for non-tuberculous mycobacteria in Scotland during (MBChB SSC4 student project ) An epidemiological study of a cluster of Mycobacterium tuberculosis in Lothian. (MBChB SSC4 student project 2010) Evaluation of a Pyrosequencing approach for the rapid identification of rifampicin and isoniazid -resistant Mycobacterium tuberculosis (BSc Infectious Disease Hons. Project, 2011). Further oral presentations see under teaching above. Page 22 of 22