Respiratory specimens – approach to analysis and interpretation

Guest posting: Ms Tessa Oakley, Senior Bacteriology Scientist with the Timor-Leste Fleming Fund Country Grant and PRIDA member. 

This excellent lecture is from a March 2022 session during the PRIDA Scientific Officer Microbiology Diploma course.

A useful adjunct to this talk is the practical 20 minute video masterclass provided by Dr Ashhurst-Smith here.

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Urinalysis, crystals and casts – annotated photographic guides

Produced by Dr Henry Butt, Senior Hospital Scientist, Newcastle, Australia in 1998. 

See also:

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COVID-19 – Infection Prevention and Control literature: Aug – Sept 2021

Selected 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 gaps – @mdjkf.

Peer reviewed

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COVID-19 update and the effectiveness of the AstraZeneca vaccine – Dr Ian Marr

Guest posting from Dr Ian Marr –MBBS FRACP FRCPA Infectious Disease Physician and Microbiologist

This is a recent lecture provided under the auspices of PRIDA to Samoan physicians and students.   Samoa COVID Marr July 2021

Please add questions to Dr Marr by a posting comment. 

 

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Yeast 101 – species of medical importance – Dr N Townell

Yeast summary April 2021 Townell

  • Candida species
  • Cryptococcus species
  • Trichosporon species
  • Talaromyces marneffei (previously Penicillium marneffei)
  • Rhodotorula species
  • Malassezia furfur
  • Pneumocysitis jiroveci

Dimorphic fungi not included.

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COVID-19 – Infection Prevention and Control literature – March 2021

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 gaps – @mdjkf .

Peer-reviewed

  • Wai-Shun et al.  CCM: Transmission of Severe Acute Respiratory Syndrome Coronavirus 1 and Severe Acute Respiratory Syndrome Coronavirus 2 During Aerosol-Generating Procedures in Critical Care: A Systematic Review and Meta-Analysis of Observational Studies here 
  • Wilson et al The effect of respiratory activity, ventilatory therapy and facemasks on total aerosol emissions here 
  • Li et al.  Build Environ.  Probable airborne transmission of SARS-CoV-2 in a poorly ventilated restaurant here [A return to the previously famous chinese restaurant event to analyse airflows. 
  • Johnson et al. BDJOpen. Dental periodontal procedures: a systematic review of contamination (splatter, droplets and aerosol) in relation to COVID-19 here

  • Quigley et al.  Estimating the burden of COVID-19 on the Australian healthcare workers and health system during the first six months of the pandemic here
  • Katalaris et al. EID: Epidemiologic Evidence for Airborne Transmission of SARS-CoV-2 during Church Singing, Australia, 2020 here

Editorial

  • The safety of anaesthetists and intensivists during the first COVID-19 surge supports extension of use of airborne protection PPE to ward staff here
  • Brophy et al. Sacrificed: Ontario Healthcare Workers in the Time of COVID-19 here 
  • MacIntyre et al.  Scientific evidence supports aerosol transmission of SARS-COV-2 here

Preprints

  • Lee et al Airborne dispersion of droplets during coughing: a physical model of viral transmission here 

Commentary

  • CDC(USA): Science Brief: SARS-CoV-2 and Surface (Fomite) Transmission for Indoor Community Environments here

  • Lewis, Nature.com.  Why indoor spaces are still prime COVID hotspots here 

  • Damazar et al. BMJOpinion. The challenge of keeping hospitals safe in the era of covid here
  • ABC News:  Australian researchers find COVID-19 aerosol spread that puts some healthcare workers at risk over others here 

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COVID-19 – Infection Prevention and Control literature – February 2021

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 gaps – @mdjkf .

Peer reviewed journals

  • Systematic review on the efficacy of face masks in preventing viral transmission here and associated commentary here [An increasing number of ecological studies have also provided persuasive evidence that universal mandatory mask wearing policies have been associated with reductions in the number or rate of infections and deaths]. 
  • SARS-CoV-2 setting-specific transmission rates: a systematic review and meta-analysis here

  • SARS-CoV-2: a systematic review of indoor air sampling for virus detection here 

  • Observational study on the burden of COVID-19 on Australian healthcare workers here [… identified 36 hospital outbreaks or HCW infection reports between January 25th and July 8th, 2020. According to our estimates, at least 536 HCW in Australia had been infected with COVID-19, comprising 6.03% of all reported infections.]

  • Downsides of face masks and possible mitigation strategies: a systematic review and meta-analysis here [There are insufficient data to quantify all of the adverse effects that might reduce the acceptability, adherence and effectiveness of face masks.]
  • Airborne dispersion of droplets during coughing: a physical model of viral transmission here

Pre-prints

  • A systematic review and meta-analysis on the impact of PPE use on healthcare workers here [14 studies with 11,746 HCWs from 16 countries. The estimated overall prevalence of adverse events among HCWs was 78%]
  • Estimating the Failure Risk of Hotel-based Quarantine for Preventing COVID-19 Outbreaks in Australia and New Zealand here  [ 16 failures examined up to 12 Feb 21; The overall failure risk for those transiting quarantine was estimated at one failure per 20,702 travelers]

Letters, commentary and correspondence

  • Rapid spread of multidrug-resistant gram-negative bacteria in COVID-19 units in the US here
  • SARS-CoV-2: eye protection might be the missing key here
  • Risk for Fomite-Mediated Transmission of SARS-CoV-2 in Child Daycares, Schools, Nursing Homes, and Offices here [… used a transmission model to explore the potential for fomite transmission without other pathways. ]

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COVID-19 – Infection Prevention and Control literature – January 2021

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 gaps – @mdjkf .

Peer reviewed journals

  • An experimental study on the stability of SARS-CoV-2 on critical personal protective equipment here  “…viable SARS-CoV-2 in the presence of a soil load persisted for up to 21 days on experimentally inoculated PPE, including materials from filtering facepiece respirators (N-95 and N-100 masks) and a plastic visor. Conversely, when applied to 100% cotton fabric, the virus underwent rapid degradation and became undetectable by TCID50 assay within 24 h. “
  • An observational study on aerosol-based transmission of SARS-CoV-2 in hospital rooms and community isolation facilities here “While SARS-CoV-2 is readily captured in aerosols, virus culture remains challenging despite optimized sampling methodologies to preserve virus viability.”
  • A simulation study on fluid dynamics of COVID-19 airborne infection here A complex study:  “Our simulations demonstrate that currently available information is inadequate to design social distancing recommendations on a solid scientific basis. … The relative humidity of the environment has a particularly dramatic effect [on droplet size and transmission potential].” , 
  • Unintended consequences of hand sanitiser use in COVID-19 pandemic here  “…JAMA Ophthalmology, authors1,2 from 2 different countries report eye injuries in children from inadvertent contact with alcohol-based hand sanitizer. Martin et al1 found a 7-fold increase in ocular exposure in children in 2020, with a corresponding increase in surgeries required to manage severe injuries resulting from these exposures.”
  • Recommendations for residential aged care in Australia post-COVID-19 here  [ a perspective from Victoria, pre second wave ]

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PRIDA Infectious Diseases and Microbiology Journal club: Pacific and SE asia 2021

These will be run with a 45-60 min Zoom session each fortnight on Friday and focus on an article of relevance to the Pacific and SE asia.   This will focus on Infectious Disease and Microbiology.  We will also use it to discuss any topics of interest at the time. Various PRIDA faculty members will moderate the sessions.

First session: February 12th FRIDAY – 12pm Port Moresby, PNG time

  • 745am: Kathmandu, Nepal
  • 9am: Phnom Penh, Cambodia
  • 11am: Dili, Timor-Leste
  • 1pm: Honiara, Solomon Islands
  • 1pm: Port Vila, Vanuatu
  • 2pm: Suva, Fiji
  • 3pm: West Samoa Time, WST

A WhatsApp group will be used to remind everyone each fortnight and send the zoom conference link.   To enrol, please email Ian_Marr[at]gmx.com

Dr Ian Marr – MBBS FRCPA FRACP,  Infectious Disease physician and Microbiologist

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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

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