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

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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

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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%
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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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Practical bacteriology bench reading – wound swabs – video masterclasses from Dr Chris Ashhurst-Smith

  20 minutes. Filming and production Felix Ferguson.

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Malaria diagnostics- what’s new and why is it important?

Guest posting: Dr Ian Marr, Microbiology Registrar, NSW Health Pathology. 

Malaria diagnosis Marr August 2018 v2

Short questions for postgraduates:

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Posted in Module - Parasitology, Protozoa | Tagged | Leave a comment

Genetics presentations L/Professor Rodney Scott, Bir Hospital, Nepal August 2018

Guest posting with permission from Laureate Professor Rodney Scott : these are his presentations provided to post-graduates in Nepal during his recent visit to inspect the new cytogenetics laboratory at the National Academy of Medical Sciences,  Bir Hospital, Kathmandu. Most presentations have annotations. 

BRCA1 and BRCA2 Structure:

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Parasitology overview and helminth infection


Posted in Helminths, Module - Parasitology, PNG | Tagged | Leave a comment