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 sessions April 2020

Session 1, 22/4/20 

  1. A/Prof J Ferguson: AMR, AMS overview, Knowing your antimicrobials AMS PRIDA Course April 2020 1
  2. Mr Joe Hessell (Pharmacist, Diagnostic Micro Development Program, Cambodia) PRIDA how to implement AMS JH (002)
  3. Recording https://zoom.us/rec/share/xdJnEunz3T9Jfqvk1nzvRKgvDr_Caaa8gyYdrPBZyB2rltDVZaLBRdl3ibhxSJ1p?startTime=1587511492000

Session 2, 24/4/20

  1. Ferguson: AMS clinical issues AMS PRIDA Course April 2020 2
  2. Ferguson: Role of Clinical Microbiology Lab & AMS / Infection Control The role of the clinical microbiology service in antimicrobial stewardship Ferguson
  3. Recording   https://zoom.us/rec/share/xpd-BJ7P5klIX7PszhjBWbRxBZbbX6a8hykf8_QNy01XTy7nL1ngha2ez5u_zGdE?startTime=1587693028000

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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Local production of alcohol hand rub for hospital use (WHO guidance)

Here is excellent straightforward WHO guidance required to set up a cost-effective production facility within an LMIC hospital. Commercial product will usually cost 5-10 times the price.

Hand hygiene by staff before and after every patient interaction is one of the key ways in which to save lives from hospital acquired infection.  If you need to know more, read about Ignaz Semmelweis, the father of infection control who first demonstrated that disinfecting hands saved lives in 1840s Vienna or see one of the references below.



Image credit : Donskey et al, NEJM.  Hand contaminated with MRSA after examining an abdomen (A), and after use of ABHR (B).


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Epidemiology and surveillance 101 – tutorial notes

Epidemiology and surveillance 101 Ferguson 2019  From the John Hunter Hospital 2019 Infectious Diseases tutorial program.


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Artemisinin derivatives for malaria – tutorial notes from Dan Lennon

Guest posting from Dr Dan Lennon, Microbiology Registrar.

Here is another excellent overview of important antimalarials.  Artemisinin Derivatives Lennon 2019.

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Staphylococcus aureus complex – S. argenteus – bug of the week

Guest posting from Dr Dan Lennon, Microbiology Registrar, Pathology North.

This species is increasingly recognised now that MALDITOF  mass spectrometry is widely used for bacterial identification. Here is a useful short summary : S argenteus Lennon 2019 Sept. These species should be regarded as clinically equivalent to S. aureus.

Here is a beautiful  photo taken by Dan. Staphylococcus argenteus on the left. S. aureus on the right. Chocolate agar.


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Cryptocococcal infection bibliography – PNG and Cambodia

I have assembled bibliographies of Cryptococcal literature relevant to:

Two PNG PhD theses of relevance date from the 1990s – summaries here – the authors published several papers that are within the collection above:

Rapid testing of serum and CSF using the current ICT card tests is a reliable diagnostic measure for both C. neoformans and C. gattii.  See also – https://idmic.net/2016/04/02/saving-lives-by-routine-cryptococcal-antigen-screening-and-pre-emptive-fluconazole-in-patients-with-advanced-hiv/

I have not located literature relevant to other Western Pacific Nations. Please let me know if anything is located.

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