Tuberculosis- drug resistant- online learning, mailing lists and references

Courtesy of Dr Suman Majumdar and others.

Mailing lists

Online Training for drug-resistant TB

Websites / organisatons

Other references & Resources

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Zika transmission prevention not just for men- updated WHO guidance

As well- Zika and risk of microcephaly – see this NEJM report.

AIMED - Let's talk about antibiotics

The World Health Organization (WHO) has strengthened its advice on preventing sexual transmission of the Zika virus. The interim guidance report recommends that both men AND women practice safe sex for six months after returning from an area where an infection is present, even if they have no symptoms. The previous guidelines, published in June 2016, stated that only men needed to practice safe sex for a period of just two months.

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BCG vaccine – more than just protection from childhood tuberculosis

This is a useful BCG systematic review concerning childhood protection against TB- worth reading in detail.

Longterm BCG protection into adulthood – vaccine efficacy (VE) 10-19 years post BCG was 58% (95% CI 27 to 76) p=0·002 and there was still a non-significant signal occurring in the 30-39 year group (VE 42%) in this large observational study from Norway.

BCG halves neonatal mortality – also read this important commentary from Dr Frank Shann in 2012. There are also heterologous protective effects of measles vaccination in infants.

A team is running a current RCT of neonatal BCG in Melbourne to examine immune correlates  and influence on infection and allergy. Existing evidence of BCG influence on childhood allergy was summarised here by Freyne and Curtis – conflicting relatively weak evidence; hence one of the rationales for the trial . Other related papers of interest include:

  • Curtis, N et al. Comparable CD4 and CD8 T cell responses and cytokine release after at-birth and delayed BCG immunisation in infants born in Australia. Vaccine. 2016 Jul 29;34(35):4132-9.
  • Curtis, N Et al.  BCG-associated heterologous immunity, a historical perspective: experimental models and immunological mechanisms. Trans R Soc Trop Med Hyg. 2015 Jan;109(1):46-51.


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Epidemiology – don’t be lost for words!

As part of your systematic review of a micro-organism species or group of species (e.g. Enterobacteriaceae) , knowledge about the ‘epidemiology‘ is essential,  the second element in the ORGANISM knowledge proforma.

“Epidemiology is the study of the distribution and determinants of health-related states or events in specified populations, and the application of this study to the control of health problems.” [ref1]

In your reading or when asked during a viva examination to “describe the epidemiology” of an organism or disease, concern yourself with a few basic questions- always a lot to say about most bugs! :

  • What disease(s) does it cause? What are the reservoirs of the organism? – human, animal, environmental etc
  • Who (age, sex) gets colonised ? Who gets infected? Natural history of colonisation and disease.
  • Where – geographical determinants,
  • When – Are there seasonal differences in disease incidence?
  • Why/how- how is it transmitted?  Is it an obligate pathogen or an opportunist? Risk factors  for disease – immune status, healthcare exposure etc


For an excellent online course see the self learning package from CDC (USA).   Knowledge of epidemiology is essential for pathologists, physicians and others.


  1. Last JM, editor. Dictionary of epidemiology. 4th ed. New York: Oxford University Press; 2001. p. 61.
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Molecular microbiology – recent tutorial references and resources


  1. DNA extraction – essential first step. Quantity of DNA obtained can be assayed spectrophotometrically.
  2. Reverse transcriptase step – for detection of RNA viruses
  3. Nucleic acid amplification –  know how PCR works! This PCR animation is easy to understand.  Many other methods now that are more complex and are isothermal – do not require cyclers to change the temperature of the reaction.
  4. Detection of product – most assays rely on closed tube ‘real-time’ detection of product. There are a variety of nucleic acid probe methods described.   Have a look here for a short video instruction.  Quantification becomes possible and is used widely.
  5. DNA sequencing – this is a basic technique these days (see below)

Excellent background materials from ICPMR, NSW ( circa 2009): 

Molecular-diagnosis-in-microbiology-ferguson-2016: overview presentation.

Important concepts

  • pre-analytical and assay factors that affect sensitivity and specificity
  • quality control (see above presentation)
  • amplification product quantification and its usefulness

N.B. visit your local molecular lab if there is one and examine and understand all of the assays in use – for commercial assays, obtain the product inserts to read.  

Modern methods

  • Next generation sequencing methods: basically a way of doing massive parallel sequencing of short multiple sequences in the same sample
  • GenXpert and similar methods : of great relevance for Nepal, PNG and elsewhere
  • Multiplex commercial molecular platforms – e.g. Biofire filmarray
  • Whole genome analyses


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Outbreaks unpacked- recent tutorial material

The online Field Epidemiological Manual is an essential resource.  Here are the 10 steps, and 10 pitfalls list we went through.

This is a great survey of the wider topic from a local leading thinker:  Outbreak-insights-looke-2012.

EpiInfo is the free CDC software much beloved by field epidemiologists for easy data collection and analysis.  If you want to learn one program, start with this one!

This epi-graph-and-line-list-for-flu provides a simple way to set up a line list and epidemiological curve.  Line lists are based on the Australian CDNA Influenza in Aged care guideline.

See here for some great example epidemic curves with explanations. Excerpts below:



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Lablogatory – medical pathology unpacked – a great clinical resource

This looks like a great site for post grad pathology and medicine trainees -interesting case by case discussions – worth working through one per week.

AIMED - Let's talk about antibiotics

If you have a curiosity about what actually goes on in a medical pathology lab. and matters pathological, then this is the site for you. There are fabulous clinical case presentations with detailed pathological correlation (many great photos) –  just the thing for medical post graduate students but also great for others involved with diagnosis and treatment of infection and other disorders.

The Lablogatory team is a broad church – regular contributors also write about topics such as global health, lab safety, molecular diagnostics, and the daily life of a clinical pathologist. There are short quizzes to test your knowledge. Wherever your interests lie, you’re sure to find something relevant!  It certainly complements what we are trying to do at AIMED.

Please visit  Lablogatory and see what you think! 

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Metapneumovirus (hMPV) – bug of the week

Human-metapneumovirus-sept-2016-path-north summary sheet.

See also this local case reports of severe pneumonia due to hMPV.  Includes discussion of Hunter New England region, NSW,  Australia epidemiology and current knowledge / research in to hMPV.

Note the change to taxonomy that has occurred in 2016 : Pneumoviridae is a new virus family in the order Mononegavirales. It was created in 2016 by elevating the now dissolved paramyxoviral subfamily Pneumovirinae.


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Blood culture liaison process – advice by organism type- Gram positives

SECOND CLINICIAN CALL: Confirmed culture identification with susceptibility available

  • Prior to calling, check the isolate antibiogram to see that species and susceptibility make sense – see EUCAST Expert rules which provide intrinsic resistance characters by species, including unusual phenotypes.
  • If possible speak to the same clinician who you initially contacted about the Gram stain result (look at your diary record !). Make sure your interaction has an proper formality about it – this is essential for building clinician respect for the laboratory service. See previous posting concerning ISBAR process.
  • Document additional clinical data required for completion of an Bloodstream infection event record after your contact (refer to this example template for these records with definitions of key data items). These records of significant BSI events are gold when it comes to analysis of local epidemiology of sepsis (community or hospital acquired/associated).

Specific advice by organism:

Continue reading

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Example template for documenting significant bloodstream infections

Suggested format for documenting significant BSI for later analyses.  Sub documents with key definitions will be provided soon. Print this sheet onto a single A4 page and maintain a records folder. Include documentation of the clinical liaison process as below.  Definitions for significance will be discussed in a future posting.  Continue reading

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