Introduction to MALDI-TOF Mass Spectrometry – two webinars

These presentations are targeted to new medical micro lab users, especially those within Fleming Fund LMIC countries.

Lecture 1: Principles of MALDI-TOF – Tuesday 16th June 1200-1300hr, AEST, Dr Tony Elias, Senior Microbiology Registrar, Pathology NSW

Overview of the theory and process of MALDI-TOF, a method capable of rapid identification of micro-organisms, revolutionising diagnostic microbiology.

Lecture 2: Practicalities of MALTI-TOF – Tuesday 23rd June 1200-1300hr, AEST

Discussion of reporting, QC, troubleshooting and further applications


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Spirometry and case studies – recent presentations in PNG

Guest posting from Dr John D. Brannan PhD, Scientific Director , Dept Respiratory & Sleep Medicine, JOHN HUNTER HOSPITAL, NSW, Australia

Spirometry theory and practice from someone who really knows! Accurate measurement the key to diagnosis and treatment- lots of potential traps.

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Asthma and COPD- updates from Professor Wark – PNG 2020 March

Guest posting: Professor Peter Wark, University of Newcastle

These presentations highlight the important issues for clinicians concerning these common conditions.  Note the limited role for antibiotics in the management of acute exacerbations of these conditions.

  1. Challenges and opportunities in Asthma in 2020 Wark PMGH Grand rounds March 2020

  1. Challenges and opportunities in COPD in 2020 Wark PMGH Grand rounds March 2020

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

Under construction (May 2020)

SECOND CLINICIAN CALL: Confirmed culture identification with susceptibility available

  • Prior to calling, check the isolate antibiogram to see that species and susceptibility are consistent with each other – 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).

Specific advice by organism:

Enteric Gram negative – an Enterobacterales species – e.g. E. coli, Klebsiella species, Enterobacter species Continue reading

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Blood culture tutorials: May 2020 PRIDA course

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Positive blood culture clinician liaison process (microbiology) part 1

Updated summary of Gram stain appearances, microbiological and clinical implications. Updated blood culture collection and liaison approach.

Microbiology and Infectious Diseases postgraduate teaching (PRIDA)

Stop press: Gram stain appearance and implications ver 2 2020 Ferguson


  • Always note down all clinician discussions in a large personal diary or preferably on the electronic pathology record for the patient’s sample if this exists.
  • Categorise and record the clinical relevance of the positive culture – a standard template to be shared soon.

Improve blood culture collection practice

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Antimicrobial stewardship – LMIC focus – PRIDA course references and e-learning

References – AMS core element guides 

Recommended E-learning courses

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COVID19 – PRIDA Course sessions: Overview, IPC, Diagnosis, Outbreak response

8/4/20 Presenters: Drs Nikki Townell  – Coronavirus overview ; John Ferguson – Infection control COVID19

8/4/20 Journal Club: Townell 

17/4/20 Presenters: Drs Townell, Marr and Ferguson (90 minutes total)

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Coronovirus – realistic optimism from Chinese experience – Dr Bruce Aylward, WHO

Dr Bruce Aylward also was on an Australian webinar on 6/3/20 – recording here.

2 March 20:30 GMT — Transmission details emerge from WHO China analysisCOVID

China has mounted “perhaps the most ambitious, agile and aggressive disease containment effort in history” against a new infectious disease, the World Health Organization (WHO) said in a report released on 28 February, after a 9-day meeting in China, 16–24 February. The report analyses data from the outbreak in China, and recommends steps that China and other countries should take to curb COVID-19.

New daily cases are declining in the country, the WHO confirmed, so much so that authorities are now having problems recruiting patients for the more than 80 clinical trials being run there that test potential treatments for the coronavirus. Some experimental treatments should be prioritized over others, the health agency recommended.

The report’s analysis of data from China finds that 104 strains of the coronavirus, named SARS-CoV-2, collected from people between December 2019 and mid-February 2020 are 99.9% similar, meaning that the virus is not significantly mutating. The median age of people infected is 51 years old. And most cases that have spread from person to person are within hospitals, jails or households, which implies close contact is often required for the virus to spread between people. Airborne spread is not believed to be a major driver of transmission, the report says. In one preliminary study from the province of Guangdong, people who shared the same household as someone with COVID-19 had 3–10% chance of being infected.

The WHO credits China’s ability to reign in the epidemic to a variety of measures. One is that 1,800 teams of epidemiologists have rapidly tracked tens of thousands of contacts of people infected with the virus in the Hubei province, where the outbreak emerged. Up to 5% of these contacts ended up having the disease and were diagnosed quickly. And the report says the lockdown on travel out of Hubei — an unprecedented measure in a province of this size — curbed wider spread of the disease to China’s 1.4 billion citizens.

References (with thanks to Dr Craig Dalton)

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Quality microbiological diagnostics and antimicrobial susceptibility testing explained

Our recent ‘Lessons from the Field’ paper is now (freely) available via the Western Pacific Surveillance and Response journal It is focused on implementation of quality testing in Pacific Island nations. 

Clinicians and others may be interested in the answers to these questions which are seldom explained:

  • How does quality microbiological culture and AST enable better patient care?
  • What are the meanings of minimum inhibitory concentration and clinical breakpoints?
  • How is AST usually performed?
  • What challenges occur with AST?
  • What are recent AST data from Pacific Nations showing about AMR?

Ferguson JK, Joseph J, Kangapu S, Townell N, Duke T, Manning L, et al. Quality microbiological diagnostics and antimicrobial susceptibility testing, an essential component of antimicrobial resistance surveillance and control efforts in Pacific island nations. Western Pac Surveill Response J. 2020 Feb;11(1). doi:10.5365/wpsar.2018.9.3.004

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