UPNG MMED Revision week sessions – Sepsis, AMR, Antimicrobial stewardship and neurology

Here are the presentations from Drs Ferguson and Miteff at the 2019 sessions.



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Entamoeba histolytica

Note that if someone is a carrier (passes cysts of Entamoeba), then if they develop diarrhoea from some other cause, the cysts will form trophozoites – this does NOT mean the patient has amoebic dysentery!

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Antimicrobial susceptibility testing – video masterclasses – Fiona Courtney

  1. Consumables for AST –
  2. Set up of AST –
  3. Reading of the AST result –

Thank you Fiona for these excellent explanations!


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How to do a minor research thesis (for instance an M. Med study report)

Here is an excellent overview from Professor Trevor Duke who is a conjoint academic with UPNG.  Follow his advice when setting up the study and writing its report.

Abstract:  Many universities and colleges in low-income and middle-income countries require a masters dissertation or thesis for as part of postgraduate training, and some
colleges offer a 1-year to 2-year diploma of child health as a clinical qualification to enable skills in child health for generalists, or as part of the early phase of paediatric
training. This paper describes the stages of doing a research project for such a masters or diploma, and describes in detail how to write a minor thesis. The paper is designed to provide a practical approach for junior researchers, and their supervisors. Colleges differ in their formal requirements of a minor thesis (word count, line spacing, referencing style), but this paper outlines the principles and practical issues rarely covered elsewhere.

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Bacteriology 101

Pre-analytical issues

  • Correct indication for testing – concept of ‘diagnostic stewardship’
  • Patient identification and sample labelling
  • Correct specimen collection- avoid contamination- esp. blood culture
  • Correct transport and storage
  • Reject poor samples – sputum with no PMNs squames++, urinary catheters, wound drains, other

Continue reading

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Enzyme immunoassays (EIA) unpacked

There are many types of EIA used in microbiology and biochemistry.  Depending on the format of the test, some have alternative names such as ELISA and CLIA (chemoluminescent immunoassay). Continue reading

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Laboratory diagnosis of fungal disease- selective overview

Organism Microscopy Culture and identification Non-culture methods
General Histopath PAS & silver stains etc.

K0H with Parker ink (skin scrapings/nails)

SAB (Saborauds dextrose agar) medium +/- antibiotics +/- cycloheximide

For other media, see here.

Blue thymol blue sticky tape preparation from cultures for examining hyphae and fruiting structures


Invasive fungal disease: 1-3 Beta-D-Glucan assay (serum) – broad spectrum but not incl. Cryptococcus

Candida albicans and other similar species Characteristic yeast shapes larger than bacteria; appear Gram positive Colonies with ‘feet’ (C. albicans)

Chromogenic candida agar – usually sufficient for ID. Several types.

Yeast sugar assimilation panels e.g. API , VITEK etc



C. neoformans

C. gattii

India ink preparation for capsule (CSF)

NB. capsule production media dependent

Presumptive: capsule+yeast= Cryptococcus (no other species has a capsule)

Urease positive

Bird seed agar – pigmented colonies = Cryptococcus

CGB medium- (L-Canavanine, glycine, 2 bromthymol blue agar) distinguishes C. gattii from C. neof.

Crypto antigen lateral flow assay (serum/CSF)


IF serotyping of isolates- research only

Aspergillus species Histopath – narrow septate hyphae; acute angle branching Culture appearance- pigmentation

Species ID by sticky tape preparation

Galactomannan EIA  (serum, BAL)

Serum precipitins used in ABPA Dx


Pneumocystis jirovecii(PJP) Bronchial lavage / induced sputum – IF / silver / Giemsa stains Usually a clinical diagnosis

No culturable


PCR more sensitive than IF

Continue reading

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Tuberculosis update 2018 from A/Prof Anna Ralph

Guest posting: Associate Professor Anna Ralph, Director of Global and Tropical Health at Menzies School of Health Research, Darwin, Northern Territory, Australia. 

News :  UN General Assembly first ever High-Level Meeting on the fight against tuberculosis, September 28th 2018.

New(ish) WHO strategy and targets: 

 SDGsEnd TB Strategy
Reduction in number of deaths vs 201590%95%
Reduction in TB incidence vs 201580%90%
TB-affected families facing catastrophic costs0%0%
Continue reading
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Video masterclass- part 3- Faeces plate reading- Dr Chris Ashhurst-Smith

Guest posting: Dr Chris Ashhurst-Smith, Pathology North.

Part 3: Faeces culture plate reading.  Video Felix Ferguson. 8 minutes.

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Video masterclass – Dr Chris Ashhurst-Smith – part 2- urine culture reading

Guest posting: Dr Chris Ashhurst-Smith, Pathology North.

Here is part 2 about urine culture reading. Video by Felix Ferguson. Thank you Chris! Enjoy.

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