COVID-19 – infection prevention and control literature – December 2020

Papers that related to COVID-19 infection prevention and control from the daily COVID-19 Critical Intelligence Unit  listings and other identified literature.  This posting does not assess the specific evidence or its quality. Please let me know of any significant gaps – @mdjkf .

Peer reviewed journals

  • Meta-analysis: Effectiveness of N95 respirators and surgical/face masks in preventing airborne infections in the era of SARS-CoV2 here  . Yet another go over the pre-SARS-COV-2 evidence with little change to the findings.  [There is only one currently registered RCT of medical masks vs respirators for COVID-19 care underway worldwide- completes in April 2021 and apparently enrolling well] 
  • SARS-Coronavirus-2 cases in healthcare workers may not regularly originate from patient care: lessons from a university hospital on the underestimated risk of healthcare worker to healthcare worker transmission [outbreak ix]  here
  • A systematic review and meta-analysis on household transmission of SARS-CoV-2 here
  • Classification of aerosol-generating procedures: a rapid systematic review here 
  • Detection of SARS-CoV-2 within the healthcare environment: a multicentre study conducted during the first wave of the COVID-19 outbreak in England here
  • COVID-19 and its impact in the dental setting: A scoping review here 
  • Risks of Aerosol Contamination in Dental Procedures during the Second Wave of COVID-19-Experience and Proposals of Innovative IPC in Dental Practice here
  • Hearing the voices of Australian healthcare workers during the COVID-19 pandemic here
  • Surgical Mask Partition Reduces the Risk of Noncontact Transmission in a Golden Syrian Hamster Model for Coronavirus Disease 2019 (COVID-19) here
  • Evidence of Long-Distance Droplet Transmission of SARS-CoV-2 by Direct Air Flow in a Restaurant in Korea here
  • Assessment of Air Contamination by SARS-CoV-2 in Hospital Settings (JAMA evidence review) here 
  • Non-COVID area of a tertiary care hospital: A major source of nosocomial COVID-19 transmission here 
  • A Serious Game Designed to Promote Safe Behaviors Among Health Care Workers During the COVID-19 Pandemic: Development of “Escape COVID-19” here

Continue reading

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Top 10 Infectious Diseases papers 2020 from Prof Josh Davis

Guest posting from Josh Davis, Infectious Diseases Physician, John Hunter Hospital,  Newcastle,  NSW.

Thanks Josh! He has selected the Top ID papers of 2020 Davis based on:

  • Deal with diagnosis or Rx of infectious diseases (COVID excluded)
  • Relevant to clinical practice
  • Practice-changing, paradigm-shifting, or dogma-challenging

Posted in Infectious diseases, Journal club | 1 Comment

REVIVE Antimicrobial Encyclopaedia

The Global Antibiotic Research & Development Partnership (GARDP) has announced the launch of their new resource, the Encyclopaedia – REVIVE ( A great new resource!   

This resource includes definitions of terms from the field of antimicrobials including ‘Active Pharmaceutical Ingredient’, ‘Bacterial efflux’ and ‘Minimum Inhibitory Concentration’. Each term has links for users to find more information on the subject and wherever available there are also links to REVIVE content such as webinar recordings and
Antimicrobial Viewpoints on the subject. Some terms also include bespoke explanatory videos with clear diagrams featuring REVIVE experts.

Posted in A/m resistance, Module-basic microbiology and AMR | Tagged | 1 Comment

COVID-19 – infection prevention and control literature – November 2020

Papers that related to COVID-19 infection prevention and control from the daily COVID-19 Critical Intelligence Unit  listings and other identified literarure.  This posting does not attempt to assess the specific evidence or its quality. Please let me know of any significant gaps – mdjkf[at] or @mdjkf .

Peer reviewed journals

  • COVID-19 in health-care workers in three hospitals in the south of the Netherlands: a cross-sectional study here . “Interpretation: Although direct transmission in the hospitals cannot be ruled out, our data do not support widespread nosocomial transmission as the source of infection in patients or health-care workers.”
  • Systematic review: Surface contamination, stability, and disinfection data on SARS-CoV-2 here
  • Outbreaks of COVID‐19 in health care workers at the Royal Melbourne Hospital here. Previously available as preprint.  “We describe the largest institutional outbreak of SARS‐CoV‐2 health care worker infections reported in Australia to date. Our response was necessarily iterative and pragmatic and advice often pre‐dated formal state and federal recommendations. During these outbreaks, a number of key factors emerged that shaped our responses, extending well beyond a focus on PPE alone.”
  • Effectiveness of Face Masks in Preventing Airborne Transmission of SARS-CoV-2 – manikin simulation experiments here
  • Hospital-acquired COVID-19 and risks to healthcare workers here. Discusses the effectiveness of universal masking by HCW and patients as a control measure. 
  • Investigation into COVID-19 transmission in hospitals (UK Healthcare Safety Investigation Branch) – report 29/10/20  Commentary on report here
  • A single site, cross sectional survey of frontline healthcare professionals on symptoms associated with personal protective equipment use hereNew-onset symptom rate was 66% (n=208). The most common new-onset symptom was headache (n=115, 36.5%) followed by breathing difficulty-palpitation (n=79, 25.1%) and dermatitis (n=64, 20.3%). “
  • A prospective observational study on airborne SARS-CoV-2 in hospital rooms with optimised ventilation here 
  • Airborne COVID-19 inactivation using low dose far-UVC lighting here 
  • Long-distance airborne dispersalof COVID-19 in wards at Uppsala University Hospital here (PCR detected, culture negative) 
  • A comparative study of mid-turbinate and nasopharyngeal swabs for SARS-CoV-2 detection here
  • Observational study of surveillance and identification of clusters of health care workers with COVID-19 hereIn this report, we describe three clusters of COVID-19 infections among health care workers (HCWs), not associated with patient exposure, and the interventions undertaken to halt ongoing exposure and transmission at our cancer center.”
  • BMJ Open Triaging of respiratory protective equipment on the assumed risk of SARS-CoV-2 aerosol exposure in patient-facing healthcare workers delivering secondary care: a rapid review here  There is a paucity of evidence on the comparison of facemasks and respirators specific to SARS-CoV-2, and poor-quality evidence in other contexts. The use of surrogates results in extrapolation of non-SARS-CoV-2 specific data to guide UK Government PPE guidance. The appropriateness of this is unknown given the uncertainty over the transmission of SARS-CoV-2.This means that the evidence base for UK Government PPE guidelines is not based on SARS-CoV-2 and requires generalisation from low-quality evidence of other pathogens/particles. There is a paucity of high-quality evidence regarding the efficacy of RPE specific to SARS-CoV-2.”
  • A literature review on the effectiveness of surgical masks and respirators for COVID-19 here   No new data cited.
  • A Lancet Resp Med editorial on COVID-19 transmission and infective microdroplets here “Public health guidance now needs to advise people how to navigate risk in indoor settings and wearing facemasks is becoming mandatory in many countries for travelling on public transport, indoor shopping, and gatherings. Facemasks and shields offer protection from larger droplets but their effectiveness against airborne transmission is less certain. Advice on spending time indoors should also focus on improved ventilation and avoiding crowded spaces.”
  • A cohort study on the risk of hospital admission with COVID-19 in healthcare workers and their households in Scotland here and associated editorial here
  • A laboratory simulation study on the effect of draping during surgical procedures here
  • Systematic review- The organotropism of COVID-19 here
  • Environmental analysis of COVID-19 air and surface contamination inside an Italian city bus here  “After two weeks of measurements and more than 1100 passenger travelling on the bus the virus was never detected both on surfaces and on air, suggesting that the precautions adopted on public transportation are effective in reducing the COVID-19 spreading.”


  • A rapid systematic review of measures to protect older people in long term care facilities from COVID-19 here; 38 studies included. Reported interventions include mass testing, use of personal protective equipment, symptom screening, visitor restrictions, hand hygiene and droplet/contact precautions, and resident cohorting. 

Letters and correspondence discussed:

  • SARS-CoV-2 in the U.S. Military — Lessons for Civil Society – NEJM Editorial discussing two recent papers here (Parris Island quarantine outcomes and U.S.S. Theodore Roosevelt outbreak). High rates of asymptomatic carriage in both studies. 
  • “Controversial” (DANMASK)  trial may show that masks protect the wearer here  (BMJ blog posting) Bayesian analysis of the DANMASK-19 trial alone shows an 81% probability of fewer infections among those encouraged to wear a mask 
  • Healthcare worker perceptions and attitudes on N95 respirator reuse here
  • Update to a living rapid review on COVID-19 in health care workers here “There was no new evidence for masks, other personal protective equipment, or other risk factors, including infection control training and education” 
  • Cycle threshold (Ct) values and infectivity of SARS-CoV-2 on surfaces here
  • Silver linings of the COVID-19 pandemic from an infection prevention and control perspective here  Canadian data- we present local data demonstrating reduction in hospital acquired infection, recognizing that our hospitals’ acuity and volumes reduced due to pandemic preparation.


  • The Cochrane Library released a systematic review on interventions to support resilience of healthcare workers during and after a pandemic here
  • The Canadian National Collaborating Centre for Methods and Tools released an update on the risk of COVID-19 transmission across different indoor settings here

Guidance and reports

  • Cochrane review: Physical interventions to interrupt or reduce the spread of respiratory viruses here and associated editorial here
  • The World Health Organization published guidance on technical PPE specifications here
  • The US Agency for Health Research and Quality (AHRQ) updated its living rapid review on masks for prevention of COVID-19 in community and healthcare settings hereNo new evidence cited.
  • The World Health Organization released interim guidance on:
    • Prevention, identification and management of health worker infection in the context of COVID-19 here
    • Infection prevention and control health-care facility response for COVID-19 here
    • Safe environments for patients and staff in COVID-19 health-care facilities here
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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
Posted in Infection prev & control, Journal | Tagged , | 1 Comment

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


Posted in Module- Mycobacteria, Mycobacteria tuberculosis, Pacific Island nations, Presentations | Tagged , , | Leave a comment