Fingerprinting mycobacteria quicker

MANTRA, a rapid genotyping method for Mycobacterium tuberculosis by multiplex PCR and microfluidic labchip. Merritt AJ, Keehner T, O’Reilly LC, McInnes RL, Inglis TJ.  J Clin Microbiol. 2010 Aug 11. [Epub ahead of print]

In this short report we described a method for rapid field genotyping of Mycobacterium tuberculosis. The name MANTRA was chosen to indicate that this is only a nominal tandem repeat analysis, and not the definitive analysis of M. tuberculosis tandem repeats on which MIRU-15 and MIRU-24 are based. Our intent is to use this easily run, single tube method for preliminary field work in resource-limited settings that lack Mycobacterial reference laboratory support close by.

The drive to come up with a field genotyping method was prompted by experience in places where tuberculosis is much commoner than in Australia, and where clinical laboratory services are limited to microscopy and culture – i.e. most places where tuberculosis is common. Publication of the method implies an intent to use the MANTRA method in future overseas development work such as the capacity-building projects we’ve been involved in before. It also leaves us with a need to investigate how best to run this field genotyping method alongside molecular detection/identification assays. Direct application to smear-positive sputa is a priority so that both detection and genotyping assays can be run much closer to the patient in endemic locations.

Definitive M. tuberculosis genotyping methods other than VNTR/MIRU are in current use in Mycobacteriology reference laboratories. These include IS6110 ribotyping and spoligotyping. It is common practice in the developed world to combine at least two different genotyping methods when delineating isolate clusters.

Leaving aside the potential application of whole bacterial genome sequencing to molecular epidemiology, the immediate need in M. tuberculosis genotyping is to combine shorter time-to-genotype with genotyping of a higher proportion of clinical isolates. VNTR/MIRU typing has helped on both counts but is currently hampered by a discussion on whether to use MIRU-15 or MIRU-24. While MIRU-24 may be a little more discriminatory, recent work shows that MIRU-24 and spoligotyping both miss some strain lineages.

Until the optimal method has been identified there will be a continuing discussion over genotype nomenclature.  That discussion will inevitably slow down the roll-out of a standard initial M. tuberculosis genotyping method.  While it was not our intention to replace either reference method of VNTR/MIRU typing, the MANTRA approach may have some merit due to its pragmatic avoidance of genotype labels. It is a de facto plea to molecular epidemiologists to concentrate their collective efforts on populations that suffer the bulk of the global tuberculosis burden.

Parasitology Masterclass

The ASM/ACTM Parasitology & Tropical Medicine Masterclass earlier this month was an excellent opportunity to catch up with leading experts in the field. The MicroGnome brings you a series of snapshots highlighting the weekend’s teaching. The edited highlights will be presented at the next QEIIMC Tropical Medicine Breakfast:

Wilderness & Expedition Medicine conference

If you haven’t registered yet for the Ends of the Earth Wilderness & Expedition Medicine Conference in Bunbury, WA on 2nd October yet, here is a fresh registration form.

The main update on the form is a line encouraging users of PayAnybody to put their surname on the reference line so that the ACTM Secretariat can quickly add you to the list of paid registrants – easily done when you’re one of the early birds, but a bit more tricky if your rego comes in at the same time as the main flood.

Wilderness & Expedition Medicine

Registration is now open for the forthcoming day conference on Wilderness & Expedition Medicine in Bunbury, on Saturday 2nd October.

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  • As interest in the conference is running high, we recommend early registration to ensure your place.
  • Preliminary programme information can be found here. All speakers have been secured for the day.
  • Programme details will be posted on this site as they become available.

FACTM exam briefing


When: March, 2011. Exact date to be announced in New Year.

  • Paper 1 at 09:45-12:15pm
  • Paper 2 at 13:45-16:15hrs
  • including 15” instruction & reading time, 2hr writing time and 15” administration window


In Townsville and Perth, plus any other major Australian centre, in accordance with demand and availability of exam supervisors/venue.


  • A   FACTM (Clinical) Medical graduates qualified and registered to practice in Australia or New Zealand. Overseas qualified medical practitioners currently licensed to practice in either Australia or New Zealand (e.g. as trainees or on conditional registration) will be eligible to enter for the FACTM examination. At least two years of medical practice and some experience in tropical or travel medicine are advisable. Those with less clinical experience will be expected to make a case for early entry in order to avoid disappointment.
  • B   FACTM (Paraclinical). The Paraclinical Fellowship exam is designed for other health care professionals qualified and licensed to practice in Australia or New Zealand with an interest in tropical or travel health e.g. paramedics, remote area nurses, travel health clinic staff, medical laboratory scientists, epidemiologists, veterinary medical and scientific officers, pharmacists and other professions allied to medicine


  1. Register your expression of interest with the College Secretariat and apply for the Affiliate category of membership (the application form can be found on the ACTM website) before 30th September, 2010. If you have recently completed a Diploma in Tropical Medicine recognised by the College, you may apply for recognition in lieu and exemption from the part 1 exam (Clinical).
  2. Indicate your preferred exam centre, your 2 referees and the names of any senior ACTM members who are willing to act as local exam supervisors.
  3. The College will contact you with detailed exam instructions including an invoice for exam fees ($500)
  4. Complete your exam revision
  5. Attend examination centre and complete papers 1 and 2
  6. Results will be communicated to candidates via the College Secretariat after completion of marking, audit by the external examiner and review by the College Examination Board.
  7. Candidates must achieve an overall mark of 50% in both papers to be granted a pass and MUST achieve an aggregate score of at least 60% in their preferred topic. For FACTM (Clinical) candidates, the preferred topic is automatically Clinical Tropical Medicine.
  8. No grades other than PASS or FAIL will be given, however the highest scoring successful candidates in each of the Clinical and Paraclinical streams will be recognised with a College award.


  • Paper 1 will comprise different multiple choice question formats, including 30 x 5 subquestion T/F from a bank of 45 arranged by topic area (i.e. 150 x T/F) with negative marking, and 20 x 5 objective structured questions from a bank of 25 without negative marking. Total marks will be expressed as a final mark out of 50 plus a subtotal for the preferred topic.
  • Paper 2 will comprise 10 data interpretation questions arranged by topic of which 8 must be attempted, and 10 short notes questions of which 8 must be attempted. Short notes questions will be designed to be answered succinctly in table, dot point, annotated list, graph or sketch diagram form. Total marks will be expressed as a final mark out of 50 plus a subtotal for the preferred topic.

Recommended revision plan:

  • A    Clinical: use the Oxford Handbook of Tropical Medicine as a baseline, supplemented by the respective chapters in 22nd edition of Manson’s Tropical Diseases, and the core text books for your chosen three other topics. Aim for a DTM&H standard of knowledge and use the sample questions with worked answers on the College website to assess your knowledge. Supplementary revision material can also be found on the MicroGnome website. When using other study materials, seek an Australasian perspective on the subject matter.
  • B      Paraclinical: use the core textbooks in the recommended list to master each of the four topics. Priority should be given to health issues of direct relevance to the Australasian region, as applied by health practitioners in Australia and New Zealand. Ensure a good grasp of the common, the serious and life threatening. The part 1 exam will emphasise breadth of knowledge with practical use in our region. Sample questions with worked answers can be found on the College website. These examples are not exhaustive, nor are revision materials.

If in doubt about the scope of knowledge required, use the recommended textbook for that topic as a guide.

TJJI for the IEB, 13-AUG-10