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

  • Capon et al. Bondi and beyond. Lessons from three waves of COVID-19 from 2020. “To describe local operational aspects of the coronavirus disease 2019 (COVID-19) response during the first three waves of outbreaks in New South Wales (NSW), Australia, which began in January, July and December 2020”  [pre-delta outbreak confidence!]
  • Santarpia et al. The size and culturability of patient-generated SARS-CoV-2 aerosol. “Size-fractionated aerosol samples and aerosol size distributions were collected from 6 x COVID-19 positive patients. Aerosol samples were analyzed for viral RNA, positive samples were cultured in Vero E6 cells. “
  • Bergand et al. Variation of National and International Guidelines on Respiratory  Protection for Health Care Professionals During the COVID-19 Pandemic
  • Oster et al.  Association Between Exposure Characteristics and the Risk for COVID-19 Infection Among Health Care Workers With and Without BNT162b2 Vaccination (during Alpha, Israel). “This case-control study found that exposure to SARS-CoV-2–positive household members was a risk factor associated with infection among vaccinated HCWs”
  • Keehner et al. Resurgence of SARS-CoV-2 Infection in a Highly Vaccinated Health System Workforce [Delta experience, California]
  • Read et al.  Hospital-acquired SARS-CoV-2 infection in the UK’s first COVID-19 pandemic wave

  • Ingram et al. COVID-19 Prevention and Control Measures in Workplace Settings: A Rapid Review and Meta-Analysis

Preprints

  • Conway-Morris et al. The removal of airborne SARS-CoV-2 and other microbial bioaerosols by air filtration on COVID-19 surge units. “Crossover study of portable air filtration and sterilisation devices in a repurposed ‘surge’ COVID ward and ‘surge’ ICU. Filtration significantly reduced the burden of other microbial bioaerosols. “
  • Wachinger et al.  Highly valued despite burdens: qualitative implementation research on rapid tests for hospital-based SARS-CoV-2 screening [German experience with admission RDTs ] “Despite challenges, RDT-based screening for all incoming patients was observed to be feasible and acceptable among implementers and patients, and merits continued consideration in the context of rising infections and stagnating vaccination rates.”
  • Thornton et al.  The impact of heating, ventilation and air conditioning (HVAC) design features on the transmission of viruses, including SARS-CoV-2: an overview of reviews. “Ventilation, humidity, temperature, and filtration can play a role in viability and transmission of viruses, including coronaviruses. Recommendations for minimum standards were not possible due to few studies investigating a given HVAC parameter.”

  • Shirreff et al. How well does SARS-CoV-2 spread in hospitals? “We estimate the patient-to-patient R0 and daily transmission rate of SARS-CoV-2 using data from a closely monitored hospital outbreak in Paris, March-April 2020… An obligatory mask-wearing policy introduced during the outbreak is likely to have changed the R0, and we estimate values before (8.7) and after (1.3) its introduction, corresponding to a policy efficacy of 85%.” 
  • Linsenmeyer et al. Cryptic Transmission of the Delta Variant AY.3 Sublineage of SARS-CoV-2 among Fully Vaccinated Patients on an Inpatient Ward. “An inpatient was diagnosed with asymptomatic DV infection on routine pre-discharge testing. Contact tracing detected infection in 6 of 38 (unmasked) patients (15.8%), 1 of 168 staff (0.6%).”

  • Lindsey et al. Characterising within-hospital SARS-CoV-2 transmission events: a retrospective analysis integrating epidemiological and viral genomic data from a UK tertiary care setting across two pandemic waves [pre-delta study].  “Staff-to-staff transmission was estimated to be the most frequent transmission type during Wave 1 (32% of observed hospital-acquired infections; decreasing to 13% in Wave 2. Patient-to-patient transmissions increased from 27% in Wave 1 to 52% in Wave 2, to become the predominant transmission type.  Hospital-acquired cases appeared to drive most
    onward transmissions. ” “Most of our transmission hotspots were wards built over two decades ago, with 6 – 8 beds per bay, and shared toilet facilities between every 1 to 2 bays.”
  • Byambasuren et al.  The effect of eye protection on SARS-CoV-2 transmission: a systematic review.  [limited poor quality evidence]

Commentaries

  • Doherty Institute COVID-19 modelling : key findings (10Sep21) ; report to cabinet 17Sep21 and revised report 10Aug21

  • BMJ 28Sep21:  Covid-19: Fully vaccinated patients no longer need to test or isolate before elective procedures, hospitals are told. “Fully vaccinated patients no longer need to have a polymerase chain reaction covid-19 test or to isolate before elective procedures, as long as they have a negative lateral flow test on the day, the UK Health Security Agency (UKHSA) has told hospitals.”

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COVID-19 evidence-based Australian treatment protocol examples

These are the current treatment protocols that HNE Health, NSW has in place:

The evidence base is as per the Australian National Covid-19 Evidence Taskforce  which has a robust approach to evidence assessment (strength and quality).

Important recent updates from them : 

Conditional recommendation: “Consider using inhaled budesonide for the treatment of symptomatic COVID-19 in adults who do not require oxygen and who have one or more risk factors for disease progression.”

“The Taskforce has issued a strong recommendation against the use of ivermectin outside of randomised trials:  Do not use ivermectin for the treatment of COVID-19 outside of randomised trials with appropriate ethical approval. “

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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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COVID-19 – Infection Prevention and Control literature – May to July 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.

Evidence summaries from the IPC Panel of the Australian National COVID19 Evidence Taskforce on respirators, masks and eye protection  published here in May 2021 on MagicApp.  Updated continuously.

Peer reviewed

  • Wilson et al. JHI.  What is the evidence that medical procedures which induce coughing or involve respiratory suctioning are associated with increased generation of aerosols and risk of SARS-CoV-2 infection? A rapid systematic review. “There was an absence of evidence to suggest that the procedures included in the review were associated with an increased risk of transmission of respiratory infection.”

  • Deol et al, PLOS ONE. Estimating ventilation rates in rooms with varying occupancy levels: Relevance for reducing transmission risk of airborne pathogens . “..demonstrate two methods that can be used to estimate ventilation rate in busy congregate settings, such as clinic waiting rooms.”

  • Gregson et al, Endoscopy. Identification of the source events for aerosol generation during oesophago-gastro-duodenoscopy. “Coughing was evoked in 60% of the endoscopies, with a greater peak concentration and a greater total number of sampled particles than the patient’s reference voluntary coughs (11 710 vs 2320 L−1 and 780 vs 191 particles, n=9 and p=0.008). Endoscopies with coughs generated a higher level of aerosol than tidal breathing, whereas those without coughs were not different to the background. “

Preprints

  • Deng et al medRxiv. Viral infection and transmission in a large well-traced outbreak caused by the Delta SARS-CoV-2 variant. “…first local transmission of the Delta SARS-CoV-2 variant in mainland China. All 167 infections could be traced back to the first index case.” Relevant to the current NSW situation; high presymptomatic viral loads and transmission’ 1000-fold higher viral loads seen than previous strain
  • Wang et al. medRxiv. Comparative evaluation of the transmissibility of SARS-CoV-2 variants of concern.  
  • Ferris et al. Authorea.  FFP3 respirators protect healthcare workers against infection with SARS-CoV-2 . Important observational evidence from Cambridge in the setting of rampant spread of B.1.1.7 (Alpha variant).  “After the change in respiratory protection, cases attributed to ward-based exposure fell significantly, with FFP3 respirators providing 31-100% protection (and most likely 100%) against infection from patients with COVID-19.”
  • Grout et al. MJA. Estimating the failure risk of quarantine systems for preventing COVID-19 outbreaks in Australia and New Zealand . Good lessons from this analysis!

  • Coleman et al. medRxiv. Viral Load of SARS-CoV-2 in Respiratory Aerosols Emitted by COVID-19 Patients while Breathing, Talking, and Singing.  The largest proportion of SARS-CoV-2 RNA copies was emitted by singing (53%), followed by talking (41%) and breathing (6%). Overall, fine aerosols constituted 85% of the viral load detected in our study. Virus cultures were negative. Singapore 2021 data ; most patients had VOC infections though only one with Delta. 

Commentaries

  • Wark et al MJA. We are not doing enough to prevent the spread of COVID-19 and other respiratory viruses in Australian hospitals.
  • McMorrow CDC (USA). Improving communications around vaccine breakthrough and vaccine effectiveness.  USA vaccine efficacy evidence in setting of Alpha and Delta variants. “Risk of severe disease or death reduced 10-fold or greater in vaccinated and Risk of infection reduced 3-fold in vaccinated.”
  • Wei et al. JAMA.  Nine Lessons Learned From the COVID-19 Pandemic for Improving Hospital Care and Health Care Delivery. Wisdom from New York’s experience.
  • Hyde et al. MJA. Australia must act to prevent airborne transmission of SARS‐CoV‐2.

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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 – April 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.

Evidence summaries from the IPC Panel of the National COVID19 Evidence Taskforce on respirators, masks and eye protection will be published soon on MagicApp (comment made 15/5/21).

Peer-reviewed

  • Thompson et al. Transmission rates of SARS-CoV-2 in specific settings: systematic review and meta-analysis here [Twenty-eight studies reported healthcare-based contacts, 10 of which met inclusion criteria for meta-analysis]
  • Aghalari et al. A systematic review on SARS-CoV-2 transmission prevention in hospital air here [11 articles were included in this study]
  • Nasiri et al Comparing saliva and nasopharyngeal swab specimens for SARS-CoV-2 detection here [14 studies ; no significant difference in detection]
  • Katelaris et al Airborne transmission of SARS-CoV-2 during church singing in Sydney here [This cluster occurred despite adherence to guidelines requiring microphone use and a 3-m cordon around singers]
  • Hogan et al.  Acquisition of COVID‐19 by healthcare workers in Western Australia here [26 locally acquired cases examined. Ten health care workers acquired the infection in the workplace – direct HCW to HCW transmission implicated in 7 cases.]
  • Genomic characteristics and clinical effect of B.1.1.7 (UK / Kent) variant in London here [No difference in illness severity. Viral load by proxy was higher in B.1.1.7 samples than in non-B.1.1.7 samples, as measured by cycle threshold value]
  • Karimzadeh et al. A rapid review on infective dose, routes of transmission, and outcome of COVID-19 compared with other respiratory viruses here [An accurate quantitative estimate of the infective dose of SARS-CoV-2 in humans is not currently feasible and needs further research. Our review suggests that it is small, perhaps about 100 particles]
  • Goldstein et al.  A systematic review on the risk of transmitting COVID-19 during nebuliser treatment here [..Case series raise concern of transmission risk, and simulation studies demonstrate droplet dispersion with virus recovery, but specific evidence that exposure to nebulizer treatment increases transmission of coronaviruses similar to COVID-19 is inconclusive]
  • Carazo et al. Infection control practices in SARS-CoV-2 infected healthcare workers in Canada here
  • Spada et al. The role of climate on the spread of SARS-CoV-2 here  […this study demonstrates that climatic factors significantly influence the spread of SARS-CoV-2]

Editorial

  • BMJ Tang et al.  COVID-19 and the definition of airborne transmission here [“..It is now clear that SARS-CoV-2 transmits mostly between people at close range through inhalation”]  

Preprints

  • Buising et al. Portable air cleaners to reduce aerosol transmission on a hospital COVID-19 ward here [Aerosols rapidly travelled from the patient room into other parts of the ward. Air cleaners were effective in increasing the clearance of aerosols from the air in clinical spaces and reducing their spread to other areas (experimental study)] 
  • Galanis et al. 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 frequency of adverse events amongst HCWs due to PPE use is very high.]
  • Bazant et al. Carbon dioxide monitoring to quantify risk of indoor airborne transmission of COVID-19 here
  • Lyngse et al. Increased Transmissibility of SARS-CoV-2 Lineage B.1.1.7 by Age and Viral Load: Evidence from Danish Households here [Primary cases infected with B.1.1.7 had an increased transmissibility of 1.5-1.7 times that of primary cases infected with other lineages]
  • Hyde et al.  Commentary from Australia on airborne transmission of SARS-CoV-2 here

Commentary and correspondence

  • Greenhalgh et al.  Ten scientific reasons in support of airborne transmission of SARS-CoV-2 here
  • BMJ Barniuk.  Airborne transmission of SARS-CoV-2 here
  • UK SAGE advice Mahase. Wider use of FFP3 masks may be needed for airborne transmission here.
  • Allen et al.  Indoor air changes and potential implications for SARS-CoV-2 transmission here
  • Kuehn, JAMA:  COVID-19 in clinicians here [The investigators examined reports of 152 888 infections and 1413 deaths among health care workers in 195 countries ]
  • Mehta et al. Lancet Resp Med:  The toll of COVID-19 on healthcare workers here
  • Rapid spread of multidrug-resistant gram-negative bacteria in COVID-19 units in the US here
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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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