You can find a new version of the registration form here, or download it directly from this website: Registration Form

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1. Wilderness & Expedition Medicine conference
2. Celebrating 100 years of tropical medicine in Townsville.
3. Wilderness & Expedition Medicine

• Feature in PCR Insider

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.

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The ASM/ACTM

• Introduction to faecal parasite examination (Lynne Garcia)
• Blood parasites (Lynne Garcia)
• Molecular methods in parasitology (Jaco Verweij)
• Medical Entomology (Richard Russell)
• Clinical cases of parasitic infections (clinical centres around Australia)

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1. Leishmaniacs
2. Tropical Medicine Masterclass
3. Missing parasites?

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.

Related posts:

1. Wilderness & Expedition Medicine
2. Expedition & Wilderness Medicine reviewed
3. Conference programme

Download (PDF, 89.45KB)

• 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.

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1. Wilderness & Expedition Medicine conference
2. Expedition & Wilderness Medicine reviewed
3. Conference programme

Friday, 3^rd December, 2010.

• 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

Where:

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

Who:

• 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

How:

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.

What:

• 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 22^nd 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

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Soil-associated infection can be thought of as:

• geoindiginous – native to soil
• geotreatable – inactivated if introduced to soil
• geotransportable – carried via soil e.g. septic tank systems

Three of the four major groups of microorganisms are involved:

1. Bacteria – Bacillus anthracis, Legionella longbeachae, Clostridium perfringens, Burkholderia pseudomallei
2. Fungi – Coccidioides immitis, Histoplasma capsulatum
3. Protozoa – Naegleria fowleri, Balamuthia mandrillaris

Viruses do not feature due to the lack of a human host in the soil. Examples of potentially geotransportable microorganisms include large movements of airborne dust such as the Mongolian dust cloud over the Sea of Japan. The list of biotreatable bacteria, helminths, protozoa and viruses is long since it includes the content of biosolid waste and waste waters e.g. adeno- and Norwalk viruses, Salmonella, E.coli O157:H7, microsporidia, Giardia & Ascaris.

Soil science and its microbial content has yielded antibiotics including penicillin and streptomycin, but soil also contains intrinsically antibiotic resistant bacteria.

• What we breathe: soil particles – fibrous mineral particles including asbestos, silica & radon
• What we drink - arsenic seeping into drinking water in Bangladesh, well design to avoid cholera and other water-borne infections, but benefits from Calcium, Magnesium & Fluoride micronutrients
• What we eat – benefits directly through nutrition, possibly affected by microbial growth kinetics, but potential exposure to geotransported microorganisms
• What we think – e.g. protozoal infections due to free-living amoebae, sporadic  & generally attributed to soil or surface exposure
• What medicates us – soil = treasure chest of natural products, endophytes, metagenomic analysis of soil, possible beneficial impact through microbial respiration on global warning, through carbon sequestration

The MicroGnome’s talk on Sinister Soils & Risky Rhizospheres followed immediately after Dr Pepper’s talk.

Notes by the MicroGnome.

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Perhaps the most surprising bit of the report is that no researchers were harmed in these experiments.

The following bacteria were found around the teeth of the captured sharks:

Gram negative

• Enterobacter cloacae, E.aerogenes
  
• Citrobacter freundii, C. koseri, C.farmeri
  
• Proteus mirabilis, P. vulgaris
  
• Moellerella wisconcensis
  
• Providencia alcalifaciens
  
• Escherichia coli
• Leclercia adecarboxylata
• Pseudomonas aeruginosa, Ps. stutzeri
• Vibrio parahaemolyticus, Vibrio spp.
• Acinetobacter sp.

Gram positive

• Staphylococcus epidermidis, S.sciuri, S.warneri, S.hominis, S.xylosus
  
• Streptoccus (viridans group)
• Enterococcus species

The first reported analysis of bacteria from the mouth of a shark investigated the bacterial flora of a great white and found several marine Vibrios. The presence of these species in the mouths of bull and tiger sharks captured off the coast of northeastern Brazil is interesting, and reinforces the need for  antibiotics effective against marine bacteria such as Vibrio species when treating shark-induced injury.

Not that this is going to happen every day. Shark attacks are rare in the overall scheme of things, fatal attacks occurring in this part of the world only once every few years. Interesting, then that Recife has seen an unusually high rate of shark attacks in recent years. It is also a good place to capture sharks. For those that really need to know the gory details, an international record of shark attacks has been maintained at the University of Florida. The record contains over 4000 investigations with an overall mortality of shark attack at 8.3%.

There are some great resources for worldwide shark attack maps including

• Shark Attack Map Interactive
• Global Shark Attack Map

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is the theme of a day conference on wilderness and expedition medicine we’re running with the Rural Clinical School in Bunbury this coming October. Further details on the enclosed poster, which you may want to download, print off and circulate to anyone interested in medicine, paramedical work or first aid in wild places.

The Romans called the very edge of the known world ‘ultima thule’; a place that probably equates to the Outer Hebrides.

The MicroGnome has been to this particular candidate for the World’s End and found a wild but very beautiful landscape of islands set among fingers of the Eastern Atlantic.

Barra is at the far end of the chain of inhabited outer islands and can be reached by ferry from Oban on the mainland or from  Lochmaddy to the north.

The quicker alternative is to take a British Airways flight and land on the beach – time subject to tides. Here’s what’s in store if you want to get to the end of the earth in a hurry.

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This recently published decade-long study found that after the introduction of 7-valent pneumococcal vaccine, invasive pneumococcal disease due to 7vPCV serotypes fell in aboriginal children to a level similar to non-aboriginal children. However, there was an increasing disparity in rates between aboriginal and non-aboriginal populations, mainly due to a significant increase in invasive pneumococcal disease in aboriginal adults, particularly those between 30 and 49 years old. Non 7vPCV serotypes of Streptococcus pneumoniae increased over the study period in non-aboriginal children and in aboriginal adults.

The most likely explanation for the increase in IPD in aboriginal adults was thought to be serotype replacement, with a possible additional deleterious effect of the 23-valent pneumococcal vaccine in adults functionally immunocompromised by co-morbidities. Alternative explanations considered less likely were net fluctuations in disease due to specific virulent serotypes o changes in disease surveillance methods during the study period.  These findings were largely in line with observations in other parts of Australia.

Invasive pneumococcal disease causes an estimated 1.6 million deaths per annum worldwide, mainly in developing countries. In industrialised countries, aboriginal populations are at significantly higher risk.

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1. All shot up: the flu vaccine controversy

What could be more difficult than trying to work out the cause of a serious pneumonia in time to guarantee successful treatment? Come and find out when we consider some of the more challenging pneumonias seen in tropical Australia and nearby parts of the region during next Tuesday’s Tropical Medicine Breakfast.

There are some useful on-line resources for our colleagues in remote locations:

• ACTM Primer of Tropical Medicine
• Pulmonary Eosinophilias

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Blood culture bottle top

Here are the notes you were promised: BC Med 2010

Download (PDF, 760.47KB)

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Download (PDF, 760.47KB)

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Other recent material on melioidosis and its corresponding priobe can be found either here on the Priobe Net or the MicroGnome site.

An editorial on melioidosis was posted recently by our colleagues at Life in the Fastlane.

Happy digging!

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1. Leishmaniasis 1: clinical tropical medicine
2. Leishmaniasis 2: clinical parasitology & entomology

For those working towards the ACTM Fellowship exam there are some useful on-line learning resources:

• eMedicine
• WHO
• Centers for Disease Control & Prevention
• Medical Journal of Australia

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Prof E Phillips, Department of Infectious Diseases & Tropical Medicine, Sir Charles Gairdner Hospital. Microbiology & Infectious Diseases breakfast meeting, PathWest Laboratory Medicine WA. 29^th July, 2010.

Adverse drug reactions can be classified in terms of occurrence and aetiology as predictable (“Type A”) or extensions of the drugs pharmacological effect which constitute 80% or more of drug reactions or unpredictable (“Type B”)(immunological/idiosyncratic) which make-up 20% or less of drug reactions. These categories act as a useful diagnostic framework for the clinician approaching the patient with a potential adverse drug reaction.

 There is a general need to raise professional awareness of “Type B” adverse reactions to therapeutic agents. The 7 “A”s is an aide memoire:

•  
  • Anticonvulsants
  • Antibiotics
  • Allopurinol
  • Antiinflammatories
  • Antiretroviral agents
  • Alternative medicines
  • Monoclonal Antibodies

 The commoner “Type B”  reactions that come to specialist medical attention are to penicillin/betalactam agents, other antibiotics, aspirin and nonsteroidal anti-inflammatory agents, local anaesthetic agents, corticosteroids, ACE inhibitors and multi-drug reactions.

Penicillin allergy. This is common at least as a label. Up to 10-20% ward charts may note a claim for penicillin allergy.  Of these, only around 10% are truly allergic i.e. < 1% population. Alternatives exist but at increased cost – $s, risk of antibiotic resistance and reduced efficacy e.g. in treatment of serious S. aureus infection, syphilis and meningitis.

Mechanisms – Understanding of this has evolved overtime and currently is thought to be mainly due to interaction with beta-lactam side chains and not the beta-lactam ring itself for many beta-lactam class drugs. True anaphylaxis (Type 1 hypersensitivity reaction, Gell &Coombs) occurs in < 0.01% treatment courses. A simple classification is that immediate reactions are potentially IgE mediated, and late are non-IgE. In IgE mediated, there is prior sensitisation with exposure to treatment agent, generating treatment specific IgE which binds to high affinity IgE Fc receptors on Mast cells.

Diagnosis – benzyl penicillin isomerises into major and minor antigenic determinants. Penicillin skin testing is safe. Only a small percentage with a history of ‘allergy’ prove positive. There is a 97-99% negative predictive value if combined major and minor determinant testing is done with other reagents such as benzyl penicillin (also a minor determinant) and amoxycillin. Of note penicillin allergy is not a life-long diagnosis and 10 % of initially skin test positive patients lose skin test reactivity per year and resensitisation occurs in <1% of patients exposed to repeated oral courses of antibiotics. Unfortunately the major and minor determinants of penicillin, previously commercially available have been off-market since 2004.   Currently non-TGA approved major and minor determinants are available as Diater reagents through for specialist approved prescriber use in clinic and have been successfully used here since mid-2008 Testing now includes multiple skin test reagents followed by an oral challenge. In our clinic’s experience, in keeping with numbers in the literature, 17/150(11.3%) tests were positive to one or more testing reagents, and 4 of these would have been missed if only major and minor determinant testing had been performed. Amoxycillin has been implicated in a high proportion of skin test positives, likely largely related to the act that amoxycililn is one of the most common antimicrobials currently utilised in the community

Occasionally in acute treatment settings we encounter patients who would benefit from treatment with a specific antimicrobial drug such as a penicillin or cephalosporin from which they are being excluded because of an allergic history and because testing cannot be practically applied.   Rapid desensitisation protocols have been devised that entail administration of increasing doses of antimicrobials over a 2-4 hours period and are safe and effective.  These procedures require careful monitoring and are only temporary meaning that after the drug in question has been discontinued redesensitisation would be needed for future exposure. Patient’s who have undergone desensitisation should be referred back to specialty clinics for specific allergy testing after they are clinically stable and have finished the required course of antibiotics.

Cephalosporin cross reactivity – 15% cross reactivity claimed from old data and published non-consecutive case reports. Originally this cross-reactivity was thought to be beta-lactam ring specific but currently evidence supports that it is likely due to side chains shared between cephalosporin and penicillin agents. Recent meta-analyses across different generations of cephalosporins support that < 5% of those penicillin skin test positive will react on oral provocation to cephalosporin class antimicrobials.

Chlorhexidine allergy.  Chlorhexidine is a common and efficacious antiseptic available in a wide array of formulation included impregnated central venous catheters and cleaning solutions.  IgE mediated reactions to chlorhexidine have been more recently described. The most important route for sensitisation has been identified to be mucosal such as the use of gels in urologic procedures.   Chlorhexidine is also available in a wide array of over the counter products such as mouthwashes and toothpaste.

Fluoroquinolones. Fluoroquinolones and particularly ciprofloxacin administered intravenously can cause release of histamine. Moxifloxacin has a greater tendency to cause allergic reactions than Ciprofloxacin and interestingly more recent information suggests that again largely based on side chain differences between these drugs there is not 100% cross-reactivity meaning that some patients who have reactions to moxifloxacin can tolerate ciprofloxacin and vice versa.

Delayed reactions. Around 5% antibiotic takers have a mild rash of some kind. In some cases this may be due to a drug/infection interaction e.g. the well recognised EBV/Amoxycillin interaction. These are common but usually not life threatening as long as there are no other features of drug reaction such as fever, severe rash, mucosal features or internal organ involvement. On the grounds of cost versus benefit, an uncomplicated maculopapular rash or delayed urticarial rash can be tolerated with symptomatic support where the antibiotic at fault is needed for treatment of a severe or life-threatening infection. 

Severe antibiotic reactions. Stevens-Johnson Syndrome or Toxic Epidermal Necrolysis or drug reactions with fever, rash and internal organ involvement are contraindications to desensitisation or reintroduction of the causal agent. Although many in vivo and ex vivo approaches are currently under investigation, no diagnostic tests are routinely available to help implicate specific drugs for these syndromes.

Notes by MicroGnome, edited by E Phillips.

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2. Melioidosis treatment
3. The rest of the world sleeps in. Meanwhile …

Download (DOC, 173.5KB)

For those working towards the ACTM Fellowship exam there are some useful on-line learning resources:

• eMedicine
• WHO
• Centers for Disease Control & Prevention
• Medical Journal of Australia

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> sample collection

We’ve been talking about what a lab without walls might look like for some time. It’s a lot more than sample collection, though, important though that is. Recently, ideas have come together from several different sources and have been tested in the school of hard knocks – well outside our comfort zone, in the field. The serious version got an airing in London recently. Here’s the latest update, presented at a benefit event organised by the Melville Friends of Lete Foho and Hatolia (Timor Leste) in order to raise funds for building and equipping a secondary school there.

Here’s the talk; it came hot on the heels of a humbling description of the health challenges facing the Timorese population. Humbling, because we have so much more back-up with which to tackle a significantly lighter burden of infectious diseases:

Download (PDF, 5.85MB)

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Blastocystis hominis

Here, as promised, is the complete set of teaching units on enteric infection.

1. enteric fever

   Download (PDF, 251.74KB)

2. intestinal protozoa

   Download (PDF, 252.74KB)

3. intestinal helminths

   Download (PDF, 231.72KB)

4. traveller’s diarrhoea

   Download (PDF, 172.54KB)

Other useful sources of information including up to date epidemiology, parasite images and life cycles include:

• the World Health Organization
• the Centers for Disease Control and Prevention
• the CDC Yellow Book on travel health

See also MicroGnome posts on winter diarrhœa , enteric fever and traveller’s diarrhoea.

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the London School of Hygiene & Tropical Medicine

No, not a reference to lyrics from the Waifs. More a matter of ruminating over the consequences of a flying visit to the UK capital; home of the London School of Hygiene and Tropical Medicine. The London School is the larger of the two remaining British centres of tropical medicine and maintains R & D collaborations with partner centres round the world; a truly international centre in more ways than one. The MicroGnome was there to plan yet more field research and deliver a lunch-time talk on the field applications of molecular microbiology [Field Apps LSTM 2010], and was rewarded with a day-long feast of medical microbiology with fellow micrognauts.

Also on the London itinerary was the map reading room at the Royal Geographical Society‘s Kensington Gore site. Think modern university library but switch maps for books. Heaven must have a map room. Micrognome was on a quest for early depictions of tropical Western Australia. He was rewarded by maps from the original John Forrest expedition to the Kimberley and Canning’s survey for the eponymous stock route,. It is so easy to view physical geography through Google Earth or with the aid of a GPS receiver; data which becomes obsolete every times the geosatellite passes by. Not for us the sheer hard, footslogging of travelling survey teams. Which makes the hand drawn survey maps all the more impressive. This may only be the surface with marginal notes on the topography and its flora. But these early geographical surveys are records of systematic exploration, and an expanding state economy. They provide us with time, date and location markers for the start of movements of livestock and other traffic which may have contributed to the distribution of zoonotic and environmental diseases. 

London is a complex city with many faces, and much to occupy the traveller beyond the headline tourist attractions. It brings to mind the sort of list you can probably find somewhere on the Net: 

you know you’re in London when:

• you recognise those old buildings from the label on a sauce bottle
• you hear a clock chime the hour and think it’s the lead in to the news
• the skyline has appeared in the Bill, Spooks and countless other series shown on the ABC
• they warn you to ‘Mind the Gap’ even when it’s only a couple of centimetres
• you can find your way round underground better than you can on top
• there’s a coffee shop, sandwich chain and old world pub on every street
• and the suburbs have names that must have been introduced by early Australian settlers

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3. Paint the map red