COVID-19 – infection prevention and control literature – October 2020 (complete)

Papers that related to COVID19 infection prevention and control from the daily COVID-19 Critical Intelligence Unit  listings for October.  You can sign up for their full evidence summaries via their website.

Peer reviewed journals

  • A systematic review on airborne transmission of COVID-19 here
  • A simulation study on the effectiveness of face masks in preventing airborne transmission of COVID-19 here 
  • A study on aerosolisation during tracheal intubation and extubation in operating theatres here
  • A rapid systematic review on the classification of aerosol-generating procedures here
  • Update to living systematic review on ventilation techniques and risk for transmission here
  •  Commentary on the transmission of COVID-19 via contaminated surfaces here
  •  The stability of SARS-CoV-2 on different surfaces here
  • The Cochrane Library updated: Clinical answers on COVID-19 infection control and prevention measures
  • An analysis of person-to-person transmission of COVID-19 and super-spreading events  here 
  • An Australian study on flight-associated transmission of COVID-19 using genome sequencing here

Letters and correspondence 

  • An updated living rapid review on epidemiology and risk factors for COVID-19 infection in health care workers here
  • The World Health Organization released guidance on health system considerations for influenza and COVID-19 in the WHO European Region here
  • • The low risk of COVID-19 transmission by fomites in real-life conditions here

Pre-peer review articles 

  • A systematic review and meta-analysis on heterogeneity in transmissibility and shedding COVID-19 via droplets and aerosols here
  • A study on the role of aerosols in the transmission of COVID-19 public spaces here
  • A rapid qualitative appraisal of frontline healthcare workers’ experiences with PPE in the UK here
  • COVID-19 Viral Loads, Environment, Ventilation, Masks, Exposure Time, And Severity : A Pragmatic Guide Of Estimates here 
  • Viable SARS-CoV-2 in the air of a hospital room with COVID-19 patients here
  • A systematic review and individual-pooled analysis of COVID-19 viral load here
  • A national survey on risk factors associated with COVID-19 infection and outbreaks in long term care facilities in England here  


  • The Cochrane Library published:
    •  systematic review on interventions to reduce contaminated aerosols during dental procedures here
    • an update on COVID-19 infection control and prevention measures here

Guidance and reports

  • ANZCA updated its statement on personal protection equipment during COVID-19 here

News and blogs

  • Nature news feature on the effectiveness of face masks here  This is actually quite a broad and sensible discussion of the evidence
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Polioviruses – update 2020

Polio eradication – so close but still not there! Here is an excellent recent 2 page wrap up by Dr S. Naqvi, our senior registrar in Infectious Diseases and Microbiology.  Polioviruses Naqvi 2020 tutorial

See also Circulating vaccine derived poliovirus – Papua New Guinea Disease outbreak news, 2 July 2018 (WHO)

Photo and table: Wikipedia 

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Hepatitis C update – Flaviviridae tutorials 2020

Hepatitis C Virus tutorial JSD JF Sep 2020   Drs J Ferguson and J Davis

Also see Australian HIV, HCV and HBV precribing summary.

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Cumulative antibiogram example – 2018 – Port Moresby General Hospital


Cumulative antibiograms summarise the collective susceptibility of bacterial isolates against various antibiotics. Prepared by Drs Jacklyn Joseph and John Ferguson, August 2019. Isolates were cultured from PMGH inpatients and outpatients served by the PMGH Laboratory. Outpatients came from clinic locations from around the National Capital District.

There is selection bias inherent in the samples included in hospital antibiograms and great care must be taken with its interpretation. Treatment guideline review and modification in the light of this antibiogram needs to take into account specific clinical data that assesses the response to treatment of both culture positive and negative infections across the different patient groups (paediatric, adult) and locations (intensive care, non intensive care, outpatient). Susceptibility rates at other institutions may differ significantly.

Where possible isolates derived from inadequate specimen types such as urinary catheter or endotracheal tube tips, have been excluded from analysis. However it is probable that many urine cultures may not have been collected for the correct reason or in the correct manner leading to the possibility of error due to contamination or sampling of patients with asymptomatic bacteriuria.

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Varicella zoster – three illustrative cases

Guest posting: Dr Holly Jordan, Physician Trainee, John Hunter Hospital, Newcastle, NSW. 

  • Case 1: 76F presents with headache, lethargy and behavioural changes 1 week post developing unilateral vesicular rash of the upper limb.
  • Case 2: u73F presents with 3-4 days history of unilateral (R) frontal headache, associated with (R) ocular pain followed by rash on (R) forehead + inability to open her (R) eye.
  • Case 3: u88M found to have multiple (R) hemispheric acute lacunar infarctions following a slow deterioration post fall 3 months prior.

VZV presentation Jordan June 2020


  1. Albrecht et al. Epidemiology, clinical manifestations, and diagnosis of herpes zoster: UpToDate
  2. Skripuletz et al. Varicella zoster virus infections in neurological patients: a clinical study BMC Infectious Diseases (2018) 18:238
  3. Beaman MH. Community-acquired acute meningitis and encephalitis: a narrative review. MJA. 2018.
  4. Haanpaa M et al. CSF and MRI findings in patients with acute herpes zoster. Neurology. 1998; 51(5):1405-11.
  5. Herpes zoster ophthalmicus: Therapeutic Guidelines (Australia); 2019
  6. Nagel MA. Varicella zoster virus vasculopathy: UpToDate

Picture: Wikipedia 

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Spinal tuberculosis update (Pacific Region)

A recent seminar on orthopaedic infections took place organised by the Pacific Islands Orthopaedic Association.  Here is the presentation: Zoom tutorials – Spine TB Ferguson 2020 final_cb.    References are within the presentation.   Some take home messages: 


  • High burdens of latent TB infection in Pacific Nations
  • Need for clinical vigilance for active TB, especially in those with risk factors (Age, systemic steroids, HIV, smokers, alcohol, diabetes, vitamin D deficiency (active treatment of latent TB optimal)
  • Drug resistant TB is emerging and already at a significant level in PNG

Diagnosis and confirmation

  • Direct molecular detection (sputum and other) of TB and MDR is now the standard of care
  • Special diagnostic considerations for children and those with HIV

Medical management

  • Local clinical expertise required – patient education, close monitoring and drug management (side effects, MDR)
  • Don’t neglect MDR-TB management- must embrace local detection & control
  • Emerging shortened course management regimens for MDR


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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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