Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Among Residents and Employees in a Veterans Affairs Community Living Center: A 42-Month Prospective Cohort Study

Background

Understanding routes of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission in long-term care facilities is essential for the development of effective control measures.

Methods

Between March 1, 2020, and August 31, 2023, we identified coronavirus disease 2019 (COVID-19) cases among residents and employees in a Veterans Affairs community living center that conducted routine screening for asymptomatic COVID-19. Contact tracing was conducted to identify suspected transmission events, and whole genome sequencing was performed to determine the relatedness of SARS-CoV-2 samples.

Results

During the 42-month study period, 269 cases of COVID-19 were diagnosed, including 199 employees and 70 residents. A total of 48 (24.1%) employees and 30 (42.9%) residents were asymptomatic. Sequencing analysis provided support for multiple events in which employees transmitted SARS-CoV-2 to co-workers and residents. There was 1 episode of likely transmission of SARS-CoV-2 from one resident to another resident, but no documented transmissions from residents to employees.

Conclusions

Transmission of SARS-CoV-2 in the community living center predominantly involved transmission from employees to co-workers and residents. There is a need for improved measures to prevent transmission of SARS-CoV-2 by healthcare personnel.

Inactivation and/or physical removal of Candida auris from floors by detergent cleaner, disinfectants, microfiber, and ultraviolet C light (UV-C)

Contaminated surfaces may be a source of transmission for the globally emerging pathogen, Candida auris. Because floors may be a source of C. auris contamination on hands, strategies for inactivating or removing C. auris from floors were investigated. A sporicidal disinfectant and UV-C were most effective in inactivating C. auris on floors.

Evaluation of a mobile disinfection cabinet using ultraviolet-C light and aerosolized hydrogen peroxide for disinfection of medical equipment

In laboratory testing, a mobile enclosed disinfection cabinet using ultraviolet-C light and aerosolized hydrogen peroxide was effective for disinfection of hard and soft surfaces. The addition of aerosolized hydrogen peroxide to ultraviolet-C light resulted in improved disinfection of soft surfaces and Clostridioides difficile spores.

Pulsed dosing and extended daily dosing of oral vancomycin do not facilitate clearance of Clostridioides difficile colonization in mice

Vancomycin taper and pulse regimens are commonly used to treat recurrent Clostridioides difficile infections, but the mechanism by which these regimens might reduce recurrences is unclear. Here, we used a mouse model to test the hypothesis that pulse dosing of vancomycin after a 10-day treatment course enhances clearance of C. difficile from the intestinal tract. Mice with C. difficile colonization received 10 days of once-daily oral vancomycin followed by 20 days of treatment with saline (controls), daily vancomycin, or pulse dosing of vancomycin every 2 or 3 days. Stool samples were collected to measure the concentration of C. difficile during and after treatment, vancomycin concentrations, and growth of vegetative C. difficile during every 3 days dosing. Pulse dosing of vancomycin was not effective in maintaining suppression of C. difficile (P > 0.05 in comparison to saline controls); growth of vegetative C. difficile occurred between pulse doses when vancomycin decreased to undetectable levels. Daily dosing of vancomycin suppressed C. difficile during treatment, but recurrent colonization occurred after treatment in more than 75% of mice, and by post-treatment day 14, there was no significant difference among the control, pulse dosing, and daily dosing groups (P > 0.05). These findings demonstrate that pulse dosing of vancomycin every 2 or 3 days does not facilitate the clearance of C. difficile spores in mice. Studies are needed to examine the impact of vancomycin taper and pulsed regimens in patients.

Efficacy of a far-ultraviolet-C light technology for continuous decontamination of air and surfaces

A wall-mounted, far-ultraviolet-C light technology reduced aerosolized bacteriophage MS2 by >3 log10 plaque-forming units within 30 minutes. Vegetative bacterial pathogens on steel disk carriers in the center of the room were reduced by >3 log10 after 45 minutes of exposure, but Candida auris and Clostridioides difficile spores were not.

Efficacy of 23 commonly used liquid disinfectants against Candida auris isolates from the 4 major clades

We tested the effectiveness of 23 disinfectants used in healthcare facilities against isolates from the 4 major clades of Candida auris. Sporicidal disinfectants were consistently effective, whereas quaternary-ammonium disinfectants had limited activity. Quaternary-ammonium-alcohol and hydrogen-peroxide-based disinfectants varied in effectiveness against C. auris.

Carbon Dioxide Monitoring Demonstrates Variations in the Quality of Ventilation on Public Transportation Buses and University Student Shuttle Vans and Identifies Effective Interventions

Background

There is a risk for transmission of severe acute respiratory syndrome 2 (SARS-CoV-2) and other respiratory viruses in motor vehicles, particularly if ventilation is inadequate.

Methods

We used carbon dioxide monitoring to examine the quality of ventilation in several public transportation buses and in university student shuttle vans in the Cleveland metro area during peak and non-peak travel times. Carbon dioxide levels above 800 parts per million (ppm) were considered an indicator of suboptimal ventilation for the number of people present. In the shuttle vans, we evaluated the impact of an intervention to improve ventilation.

Results

In large articulated buses with 2 ventilation systems, carbon dioxide concentrations never exceeded 800 ppm, whereas in standard buses with 1 ventilation system concentrations rose above 800 ppm during peak travel times and on some trips during non-peak travel times. In shuttle vans, the ventilation system was not turned on during routine operation, and carbon dioxide levels rose above 800 ppm on all trips during peak and non-peak travel times. In the shuttle vans, an intervention involving operation of the existing ventilation system resulted in a significant reduction in carbon dioxide levels (mean concentration, 1,042 no intervention versus 785 with intervention; P < 0.001).

Conclusions

Our findings demonstrate substantial variability in the quality of ventilation in public transportation buses and university shuttle vans. There is a need for efforts to assess and optimize ventilation in motor vehicles used for public transportation to reduce the risk for aerosol-mediated transmission of respiratory viruses. Carbon dioxide monitoring may provide a useful tool to assess and improve ventilation.

High technology and low technology measures to reduce risk of SARS-CoV-2 transmission

During the coronavirus disease 2019 (COVID-19) pandemic, a variety of low technology and high technology measures have been proposed to reduce the risk for transmission. Identifying those measures likely to be useful in reducing viral transmission without undue expense or potential for adverse effects has been a challenge for infection control programs. The challenge has been compounded by the lack of tools that can be used to assess the risk for viral transmission in different settings. This review discusses practical tools that can be used to assess ventilation and airflow and evaluates some of the low technology and high technology measures that have been proposed as control measures for COVID-19. Some typical questions posed to infection control programs during the pandemic are presented to illustrate real-world application of the concepts being discussed.

Disinfection and sterilization: New technologies

BACKGROUND

Adherence to professional guidelines and/or manufacturer's instructions for use regarding proper disinfection and sterilization of medical devices is crucial to preventing cross transmission of pathogens between patients. Emerging pathogens (e.g., Candida auris) and complex medical devices provide new challenges.

METHODS

A search for published English articles on new disinfection and sterilization technologies was conducted by Google, Google scholar and PubMed.

RESULTS

Several new disinfection methods or products (e.g., electrostatic spraying, new sporicides, colorized disinfectants, "no touch" room decontamination, continuous room decontamination) and sterilization technologies (e.g., new sterilization technology for endoscopes) were identified.

CONCLUSIONS

These technologies should reduce patient risk.

Empowering patients to prevent healthcare-associated infections

In recent years there has been increasing interest in the empowerment of patients to serve as partners in efforts to prevent healthcare-associated infections. However, patients often have limited awareness of the risk for acquisition and dissemination of healthcare-associated pathogens and have received limited information on how they might participate in infection prevention efforts. This review highlights some of the areas where patient empowerment initiatives in infection control and antimicrobial stewardship may be useful and reviews available evidence that such initiatives can be beneficial. Although patients are the primary focus of these initiatives, inclusion of family members should be considered in many situations because they often play a major role in healthcare decision-making.

Update on potential interventions to reduce the risk for transmission of health care-associated pathogens from floors and sinks

Health care facility floors and sink drains and other wastewater drainage sites are universally contaminated with potential pathogens and there are plausible mechanisms by which organisms can be disseminated from these sites. However, floors and sink drains are not addressed as potential sources of pathogen transmission in most health care facilities. One factor that has hindered progress in addressing floors and sinks has been the lack of practical and effective measures to reduce the risk for dissemination of organisms from these sites. This article provides an update on some of the potential interventions being used to reduce the risk for transmission of health care-associated pathogens from floors and sinks. Practical approaches to address these sites of contamination are emphasized.

Continuous surface and air decontamination technologies: Current concepts and controversies

Effective and safe continuous surface and air decontamination technologies could be a useful adjunct to routine cleaning and disinfection in health care settings. Continuously active quaternary ammonium disinfectants that provide residual antimicrobial activity on undisturbed surfaces for up to 24.ßhours have been shown to reduce the recovery of clinically important pathogens in some but not all real-world studies. Although quaternary ammonium-based supplemental coatings have been reported to provide prolonged residual efficacy in patient care settings, there is concern that some of these products may be removed by routine cleaning and disinfection. To address this concern, the Environmental Protection Agency has recently issued updated guidance requiring demonstration of efficacy after multiple abrasion and chemical exposures for registration of supplemental residual antimicrobial coatings. Far-ultraviolet-C and direct irradiation below exposure limits are promising technologies for continuous air and surface decontamination in occupied spaces, but additional studies are needed to evaluate their long-term safety and efficacy. Given the increasing use of electronic air cleaning technologies in community and health care settings, there is a need for studies to assess real-world efficacy and safety.

A do-it-yourself test protocol using commercial Bacillus atrophaeus spores to evaluate the effectiveness of ultraviolet-C light room-decontamination devices

We developed a do-it-yourself test protocol using commercial Bacillus atrophaeus spores to assess the efficacy of ultraviolet-C (UV-C) light room-decontamination devices. Overall, 4 UV-C devices reduced B. atrophaeus by ≥3 log10 colony-forming units in 10 minutes, whereas a smaller device required 60 minutes. Of 10 in-use devices, only 1 was ineffective.

Multistep Testing Algorithms for Clostridioides difficile Infection

A 10-year-old girl with spina bifida and neurogenic bowel hospitalized for abdominal pain, dehydration, and more than 20 episodes of diarrhea per day. A stool sample test result was positive for Clostridioides difficile by polymerase chain reaction and an enzyme immunoassay result for C difficile toxin A and B was negative. How do you interpret these test results?

Real-world evaluation of a two-step testing algorithm for Clostridioides difficile infection

During the 4 years after implementation of the 2-step Clostridioides difficile infection (CDI) testing algorithm, 70% to 78% of patients with suspected CDI and a positive nucleic acid amplification test but a negative toxin test (NAAT+/TOX-) received CDI treatment. Overall, 73% of NAAT+/TOX- patients were classified as having probable or possible CDI.

Effectiveness of ultraviolet-C light treatment of shoes in reducing the transfer of pathogens into patient rooms by shoes of healthcare personnel

Contaminated shoes are a potential vector for dissemination of healthcare-associated pathogens. We demonstrated that healthcare personnel walking into patient rooms frequently transferred pathogens from their shoes to the floor. An 8-second treatment of shoes with a UV-C decontamination device significantly reduced the frequency of transfer of vegetative bacterial pathogens.

Polymer Additives to Personal Protective Equipment can Inactivate Pathogens

Face masks have been proven to be medicine's best public health tool for preventing transmission of airborne pathogens. However, in situations with continuous exposure, lower quality and "do-it-yourself" face masks cannot provide adequate protection against pathogens, especially when mishandled. In addition, the use of multiple face masks each day places a strain on personal protective equipment (PPE) supply and is not environmentally sustainable. Therefore, there is a significant clinical and commercial need for a reusable, pathogen-inactivating face mask. Herein, we propose adding quaternary poly(dimethylaminohexadecyl methacrylate), q(PDMAHDM), abbreviated to q(PDM), to existing fabric networks to generate "contact-killing" face masks-effectively turning cotton, polypropylene, and polyester into pathogen resistant materials. It was found that q(PDM)-integrated face masks were able to inactivate both Gram-positive and Gram-negative bacteria in liquid culture and aerosolized droplets. Furthermore, q(PDM) was electrospun into homogeneous polymer fibers, which makes the polymer practical for low-cost, scaled-up production.

Natural history of Clostridioides difficile colonization and infection following new acquisition of carriage in healthcare settings: A prospective cohort study

BACKGROUND

Limited information is available on the natural history of Clostridioides difficile colonization and infection in patients with new acquisition of C. difficile in healthcare settings.

METHODS

In 3 hospitals and affiliated long-term care facilities, we collected serial perirectal cultures from patients with no diarrhea on enrollment to identify new acquisition of toxigenic C. difficile carriage and determined the duration and burden of carriage. Asymptomatic carriage was defined as transient if only 1 culture was positive with negative cultures before and after or persistent if 2 or more cultures were positive. Clearance of carriage was defined as 2 consecutive negative perirectal cultures.

RESULTS

Of 1,432 patients with negative initial cultures and at least 1 follow-up culture, 39 (2.7%) developed CDI without prior detection of carriage and 142 (9.9%) acquired asymptomatic carriage with 19 (13.4%) subsequently diagnosed with CDI. Of 82 patients analyzed for persistence of carriage, 50 (61.0%) had transient carriage and 32 (39.0%) had persistent carriage, with an estimated median of 77 days to clearance of colonization (range, 14 to 133 days). Most persistent carriers had a relatively high burden of carriage and maintained the same ribotype over time, whereas most transient carriers had a low burden of carriage detected only using broth enrichment cultures.

CONCLUSIONS

In 3 healthcare facilities, 9.9% of patients acquired asymptomatic carriage of toxigenic C. difficile, and 13.4% were subsequently diagnosed with CDI. Most carriers had transient rather than persistent carriage and most patients developing CDI did not have prior detection of carriage.

Update on Clostridioides difficile Infection in Older Adults

Clostridioides difficile is a common cause of community-associated and health care-associated infections. Older adults are disproportionately affected, and long-term care facilities (LTCFs) have borne a substantial proportion of the burden of C difficile infection (CDI). Recurrences of CDI are common in older adults and have substantial adverse effects on quality of life. Appropriate diagnostic testing and management is essential for older adults in the community and in LTCFs. This review focuses on current concepts related to the epidemiology, diagnosis, and management of CDI in older adults.

How effective are the alcohol flush and drying cycles of automated endoscope reprocessors? Stripped endoscope model

BACKGROUND

Effective drying of the internal channels of endoscopes is essential to prevent the growth of water-borne pathogens and to assure adequate sterilization with vaporized hydrogen peroxide or ethylene oxide. The aim of this study was to evaluate the dryness of endoscopes after a routine disinfection process in an automated endoscope reprocessor.

METHODS

Stripped endoscopes (SE) that allow for visual inspection of the inside channels were reprocessed per protocol in a large urban medical center, with a 3-minute or 10-minute air flush following reprocessing. SE was hung and observed for any water within the channels after reprocessing and after a week of ambient storage. Ready-for-use endoscopes were also randomly spot-checked for moisture visually and with moisture detection paper.

RESULTS

All SE were grossly wet after HLD with a 3-minute air flush, despite alcohol flush and drying cycle. The 10-minute air flush was effective at drying the biopsy/suction channel, but not the air/water channels. Hanging had limited effect, being most effective in the biopsy/suction channels. Of the 77 ready-for-use respiratory and gastrointestinal endoscopes assessed, 37 (48.1%) showed evidence of retained moisture.

CONCLUSIONS

Air flush cycles commonly used in the final steps of automated endoscope reprocessing may not adequately dry endoscope channels, particularly the narrower diameter air/water channels. An extended 10-minute air flush appears effective at drying the larger biopsy/suction channel, but has limited effect on the air/water channels.

Containment of COVID-19 outbreak at a veterans affairs community living center

Asymptomatic and pre-symptomatic staff and residents likely contribute to widespread transmission of COVID-19 in long-term care settings. Here, we describe the successful containment of a COVID-19 outbreak on one floor of a 163-bed Veterans Affairs (VA) Community Living Center (CLC). Testing using nasopharyngeal swabs with a rapid turn-around-time identified 3 of 28 (11%) residents and 2 of 41 (5%) healthcare personnel (HCP) with COVID-19. Both HCP likely worked on the floor while pre-symptomatic. When one HCP reported a cough to the secondary (employee) screening clinic, she was erroneously advised to work. Protocols to limit the risk for HCP to import COVID-19 were reinforced with Community Living Center staff as well as with personnel in secondary screening. Further, the CLC implemented an expanded screening tool that assessed residents for typical and atypical symptoms of COVID-19. No further cases of COVID-19 were detected on the CLC floor in the subsequent 6 weeks. Swift recognition and response helped contain the outbreak and prevent further COVID-19 infections among other residents and staff.

Can Electronic Clinical Decision Support Systems Improve the Diagnosis of Urinary Tract Infections? A Systematic Review and Meta-Analysis

Background

Urinary tract infection (UTI) is a commonly misdiagnosed infectious syndrome. Diagnostic stewardship interventions can reduce rates of asymptomatic bacteriuria treatment but are often labor intensive, and thus an automated means of reducing unnecessary urine testing is preferred. In this systematic review and meta-analysis, we sought to identify studies describing interventions utilizing clinical decision support (CDS) to optimize UTI diagnosis and to characterize the effectiveness of these interventions.

Methods

We conducted a comprehensive electronic search and manual reference list review for peer-reviewed articles published before July 2, 2021. Publications describing an intervention intending to enhance UTI diagnosis via CDS were included. The primary outcome was urine culture test rate.

Results

The electronic search identified 5013 studies for screening. After screening and full-text review, 9 studies met criteria for inclusion, and a manual reference list review identified 5 additional studies, yielding a total of 14 studies included in the systematic review. The most common CDS intervention was urinalysis with reflex to urine culture based on prespecified urinalysis parameters. All 9 studies that provided statistical comparisons reported a decreased urine culture rate postintervention, 8 of which were statistically significant. A meta-analysis including 4 studies identified a pooled urine culture incidence rate ratio of 0.56 (95% confidence interval, .52-.60) favoring the postintervention versus preintervention group.

Conclusions

In this systematic review and meta-analysis, CDS appeared to be effective in decreasing urine culture rates. Prospective trials are needed to confirm these findings and to evaluate their impact on antimicrobial prescribing, patient-relevant outcomes, and potential adverse effects.

Evaluation of Interventions to Improve Ventilation in Households to Reduce Risk for Transmission of Severe Acute Respiratory Syndrome Coronavirus 2

Background

Inadequate ventilation may contribute to the high risk for household transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

Methods

We evaluated the effectiveness of several interventions recommended to improve ventilation in households. In 7 residential homes, carbon dioxide monitoring was conducted to assess ventilation in occupied open areas such as family rooms and in bedrooms and/or offices. Carbon dioxide levels above 800 parts per million (ppm) were considered an indicator of suboptimal ventilation for the number of people present. In 1 of the 7 homes, various interventions to improve ventilation or to filter air were assessed in a kitchen area by measuring clearance of aerosol particles produced using an aerosol-based spray system and carbon dioxide generated by cooking with a gas stove.

Results

Carbon dioxide levels rose above 800 ppm in bedrooms and offices with 2 occupants when windows and doors were closed and in open areas during gatherings of 5 to 10 people; carbon dioxide levels decreased when windows or doors were opened. Clearance of carbon dioxide and aerosol particles significantly increased with interventions including running fans, operating portable air cleaners, and opening windows, particularly when there was a noticeable breeze or when a window fan was used to blow contaminated air outside.

Conclusion

In households, several measures to improve ventilation or air filtration were effective in reducing carbon dioxide accumulation or enhancing clearance of carbon dioxide and aerosol particles. Studies are needed to determine if interventions to improve ventilation can reduce the risk for airborne transmission of SARS-CoV-2 in households.

Health care staff perceptions of gaps and education needs for patient-led preoperative hygiene using chlorhexidine gluconate skin cleansing products

Through survey-led interviews, health care staff recognizes that patients have different bathing techniques and need more education on chlorhexidine gluconate cleansing. Preliminary findings gathered will be used to develop and test electronic competency-based tools to ensure patients are provided with the same comprehensive instructions before using chlorhexidine gluconate bathing products.

A MUC5B Gene Polymorphism, rs35705950-T, Confers Protective Effects Against COVID-19 Hospitalization but Not Severe Disease or Mortality

Rationale: A common MUC5B gene polymorphism, rs35705950-T, is associated with idiopathic pulmonary fibrosis (IPF), but its role in severe acute respiratory syndrome coronavirus 2 infection and disease severity is unclear. Objectives: To assess whether rs35705950-T confers differential risk for clinical outcomes associated with coronavirus disease (COVID-19) infection among participants in the Million Veteran Program (MVP). Methods: The MUC5B rs35705950-T allele was directly genotyped among MVP participants; clinical events and comorbidities were extracted from the electronic health records. Associations between the incidence or severity of COVID-19 and rs35705950-T were analyzed within each ancestry group in the MVP followed by transancestry meta-analysis. Replication and joint meta-analysis were conducted using summary statistics from the COVID-19 Host Genetics Initiative (HGI). Sensitivity analyses with adjustment for additional covariates (body mass index, Charlson comorbidity index, smoking, asbestosis, rheumatoid arthritis with interstitial lung disease, and IPF) and associations with post-COVID-19 pneumonia were performed in MVP subjects. Measurements and Main Results: The rs35705950-T allele was associated with fewer COVID-19 hospitalizations in transancestry meta-analyses within the MVP (N_cases = 4,325; N_controls = 507,640; OR = 0.89 [0.82-0.97]; P = 6.86 × 10^-3) and joint meta-analyses with the HGI (N_cases = 13,320; N_controls = 1,508,841; OR, 0.90 [0.86-0.95]; P = 8.99 × 10^-5). The rs35705950-T allele was not associated with reduced COVID-19 positivity in transancestry meta-analysis within the MVP (N_cases = 19,168/N_controls = 492,854; OR, 0.98 [0.95-1.01]; P = 0.06) but was nominally significant (P < 0.05) in the joint meta-analysis with the HGI (N_cases = 44,820; N_controls = 1,775,827; OR, 0.97 [0.95-1.00]; P = 0.03). Associations were not observed with severe outcomes or mortality. Among individuals of European ancestry in the MVP, rs35705950-T was associated with fewer post-COVID-19 pneumonia events (OR, 0.82 [0.72-0.93]; P = 0.001). Conclusions: The MUC5B variant rs35705950-T may confer protection in COVID-19 hospitalizations.

Real-World Evidence on the Effectiveness of Plexiglass Barriers in Reducing Aerosol Exposure

Reprinted with permission, Cleveland Clinic Foundation ©2022. All Rights Reserved.

BACKGROUND

Barriers are commonly installed in workplace situations where physical distancing cannot be maintained to reduce the risk for transmission of respiratory viruses. Although some types of barriers have been shown to reduce exposure to aerosols in laboratory-based testing, limited information is available on the efficacy of barriers in real-world settings.

METHODS

In an acute care hospital, we tested the effectiveness of in-use plexiglass barriers in reducing exposure of staff to aerosolized particles. A nebulizer was used to release 5% NaCl aerosol 1 meter from staff members with and without the barrier positioned between the point of aerosol release and the hospital staff. Particle counts on the staff side of the barrier were measured using a 6-channel particle counter. A condensed moisture (fog) generating device was used to visualize the airflow patterns.

RESULTS

Of 13 in-use barriers tested, 6 (46%) significantly reduced aerosol particle counts detected behind the barrier, 6 (46%) reduced particle counts to a modest, non-significant degree, and 1 (8%) significantly increased particle counts behind the barrier. Condensed moisture fog accumulated in the area where staff were seated behind the barrier that increased particle exposure, but not behind the other barriers. After repositioning the ineffective barrier, the condensed moisture fog no longer accumulated behind the barrier and aerosol exposure was reduced.

CONCLUSION

In real-world settings, plexiglass barriers vary widely in effectiveness in reducing staff exposure to aerosols, and some barriers may increase risk for exposure if not positioned correctly. Devices that visualize airflow patterns may be useful as simple tools to assess barriers.

Dissemination of methicillin-resistant Staphylococcus aureus and bacteriophage MS2 from floors in long-term care facility resident rooms

We demonstrated that methicillin-resistant Staphylococcus aureus (MRSA) contamination on floors in the rooms of colonized long-term care facility residents was frequently transferred by shoes to adjacent patient rooms. A benign virus inoculated onto the floor was transferred to floors and high-touch surfaces in adjacent rooms and the nursing station. These results suggest that shoes may serve as a vector for dissemination of healthcare-associated pathogens from rooms of MRSA-colonized patients.

COVID-19 infection and transmission includes complex sequence diversity

SARS-CoV-2 whole genome sequencing has played an important role in documenting the emergence of polymorphisms in the viral genome and its continuing evolution during the COVID-19 pandemic. Here we present data from over 360 patients to characterize the complex sequence diversity of individual infections identified during multiple variant surges (e.g., Alpha and Delta). Across our survey, we observed significantly increasing SARS-CoV-2 sequence diversity during the pandemic and frequent occurrence of multiple biallelic sequence polymorphisms in all infections. This sequence polymorphism shows that SARS-CoV-2 infections are heterogeneous mixtures. Convention for reporting microbial pathogens guides investigators to report a majority consensus sequence. In our study, we found that this approach would under-report sequence variation in all samples tested. As we find that this sequence heterogeneity is efficiently transmitted from donors to recipients, our findings illustrate that infection complexity must be monitored and reported more completely to understand SARS-CoV-2 infection and transmission dynamics. Many of the nucleotide changes that would not be reported in a majority consensus sequence have now been observed as lineage defining SNPs in Omicron BA.1 and/or BA.2 variants. This suggests that minority alleles in earlier SARS-CoV-2 infections may play an important role in the continuing evolution of new variants of concern.

Association of Kidney Comorbidities and Acute Kidney Failure With Unfavorable Outcomes After COVID-19 in Individuals With the Sickle Cell Trait

Importance

Sickle cell trait (SCT), defined as the presence of 1 hemoglobin beta sickle allele (rs334-T) and 1 normal beta allele, is prevalent in millions of people in the US, particularly in individuals of African and Hispanic ancestry. However, the association of SCT with COVID-19 is unclear.

Objective

To assess the association of SCT with the prepandemic health conditions in participants of the Million Veteran Program (MVP) and to assess the severity and sequelae of COVID-19.

Design, Setting, and Participants

COVID-19 clinical data include 2729 persons with SCT, of whom 353 had COVID-19, and 129 848 SCT-negative individuals, of whom 13 488 had COVID-19. Associations between SCT and COVID-19 outcomes were examined using firth regression. Analyses were performed by ancestry and adjusted for sex, age, age squared, and ancestral principal components to account for population stratification. Data for the study were collected between March 2020 and February 2021.

Exposures

The hemoglobin beta S (HbS) allele (rs334-T).

Main Outcomes and Measures

This study evaluated 4 COVID-19 outcomes derived from the World Health Organization severity scale and phenotypes derived from International Classification of Diseases codes in the electronic health records.

Results

Of the 132 577 MVP participants with COVID-19 data, mean (SD) age at the index date was 64.8 (13.1) years. Sickle cell trait was present in 7.8% of individuals of African ancestry and associated with a history of chronic kidney disease, diabetic kidney disease, hypertensive kidney disease, pulmonary embolism, and cerebrovascular disease. Among the 4 clinical outcomes of COVID-19, SCT was associated with an increased COVID-19 mortality in individuals of African ancestry (n = 3749; odds ratio, 1.77; 95% CI, 1.13 to 2.77; P = .01). In the 60 days following COVID-19, SCT was associated with an increased incidence of acute kidney failure. A counterfactual mediation framework estimated that on average, 20.7% (95% CI, -3.8% to 56.0%) of the total effect of SCT on COVID-19 fatalities was due to acute kidney failure.

Conclusions and Relevance

In this genetic association study, SCT was associated with preexisting kidney comorbidities, increased COVID-19 mortality, and kidney morbidity.

Why Does Doxycycline Pose a Relatively Low Risk for Promotion of Clostridioides difficile Infection?

Background:

Clinical studies suggest that doxycycline poses a low risk for promotion of Clostridioides difficile infection, but the microbiologic explanation for this finding is unclear.

Methods:

Mice treated with oral doxycycline, oral azithromycin, subcutaneous ceftriaxone, doxycycline plus ceftriaxone, or azithromycin plus ceftriaxone were challenged with 10⁴ colony-forming units of 2 different C. difficile strains on day 2 of 5 of treatment. The concentration of C. difficile was measured in stool 2 and 5 days after challenge. The impact of the treatments on the microbiota was assessed by sequencing.

Results:

Doxycycline and azithromycin treatment did not promote colonization by either C. difficile strain in comparison to saline controls. Doxycycline treatment significantly reduced ceftriaxone-induced overgrowth of a C. difficile strain with doxycycline minimum-inhibitory concentration (MIC) of 0.06 µg/mL (P<0.01) but not a strain with doxycycline MIC of 48 µg/mL (P>0.05); azithromycin treatment did not reduce ceftriaxone-induced overgrowth of either strain. 16S rRNA amplicon sequencing revealed significantly lower bacterial diversity in the stool of ceftriaxone-treated mice, in comparison to doxycycline-treated and azithromycin-treated mice.

Conclusions:

These findings suggest that doxycycline may have a low propensity to promote C. difficile colonization because it causes relatively limited alteration of the indigenous microbiota that provide colonization resistance and because it provides inhibitory activity against some C. difficile strains.

Houston, We Have a Problem: Reports of Clostridioides difficile Isolates with Reduced Vancomycin Susceptibility

During the past 4 decades, oral vancomycin has been a mainstay of Clostridioides difficile infection (CDI) therapy with no reports of treatment failure due to emergence of vancomycin resistance. However, C. difficile isolates with high-level phenotypic resistance to vancomycin have recently been reported in 3 distinct geographic regions. There is an urgent need for surveillance to determine if strains with reduced vancomycin susceptibility are circulating in other areas. In a Cleveland area hospital, screening of 176 CDI stool specimens yielded no C. difficile isolates with reduced vancomycin susceptibility and highlighted the potential for false-positive results due to contamination with vancomycin-resistant enterococci. Additional studies are needed to clarify whether reduced vancomycin susceptibility is an emerging problem that will alter clinical practice. Clinicians should alert their health department if they observe a substantial increase in the frequency of vancomycin treatment failure in patients diagnosed with CDI with no alternative explanation for diarrhea.

Bacterial urine profile and optimal urine specimen collection timing in asymptomatic chronically catheterized adults with spinal cord injuries and disorders

BACKGROUND

Adults with spinal cord injuries and disorders (SCI/D) require chronic indwelling catheterization which is associated with an increased risk of catheter-associated (CA) adverse events.

METHODS

We studied urine samples (culture and urinalysis) from 2 cohorts of chronically catheterized males with SCI/D. Cohort 1 included 28 participants; 3 samples per patient were collected (before, after, and 7 days after catheter change). Cohort 2 included 21 participants; 7 samples per patient were collected (before, immediately after, 30 minutes, 1 hour, 1 day, 2 days, and 7 days after catheter change).

RESULTS

A statistically significant decrease in the post catheter change percentage of "significant cultures" was found in both our cohorts (P<.05). Additionally, our second cohort demonstrated a significant decrease in the number of organisms growing at 100.000 cfu/mL (median=-1, mean=-1.5, P=.0006) and in urinalysis bacterial numbers (median=-0.5, mean=-1, P=.006) from pre- to 1-hour post catheter removal.

CONCLUSIONS

Although there appears to be an improvement of organism burden seen after catheter change, this is only temporary, and its significance in chronically catheterized patients is still unknown. Our second cohort demonstrated an optimal time for sample collection at the 1-hour post-catheter change sample, but further research is required for the extrapolation of these findings.

Airflow Patterns in Double-Occupancy Patient Rooms May Contribute to Roommate-to-Roommate Transmission of Severe Acute Respiratory Syndrome Coronavirus 2

BACKGROUND

Hospitalized patients are at risk to acquire severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from roommates with unrecognized coronavirus disease 2019 (COVID-19). We hypothesized that airflow patterns might contribute to SARS-CoV-2 transmission in double-occupancy patient rooms.

METHODS

A device emitting condensed moisture was used to identify airflow patterns in double-occupancy patient rooms. Simulations were conducted to assess transfer of fluorescent microspheres, 5% sodium chloride aerosol, and aerosolized bacteriophage MS2 between patient beds 3 meters apart and to assess the effectiveness of privacy curtains and portable air cleaners in reducing transfer.

RESULTS

Air flowed from inlet vents in the center of the room to an outlet vent near the door, resulting in air currents flowing toward the bed adjacent to the outlet vent. Fluorescent microspheres (212-250-µm diameter), 5% sodium chloride aerosol, and aerosolized bacteriophage MS2 released from the inner bed were carried on air currents toward the bed adjacent to the outlet vent. Closing curtains between the patient beds reduced transfer of each of the particles. Operation of a portable air cleaner reduced aerosol transfer to the bed adjacent to the outlet vent but did not offer a benefit over closing the curtains alone, and in some situations, resulted in an increase in aerosol exposure.

CONCLUSIONS

Airflow patterns in double-occupancy patient rooms may contribute to risk for transmission of SARS-CoV-2 between roommates. Keeping curtains closed between beds may be beneficial in reducing risk.

Planes, Trains, and Automobiles: Use of Carbon Dioxide Monitoring to Assess Ventilation During Travel

Background: Travel poses a risk for transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses. Poorly ventilated indoor settings pose a particularly high risk for transmission.   Methods:  We used carbon dioxide measurements to assess adequacy of ventilation during 5 trips that included air travel. During selected parts of each trip that involved indoor settings, we monitored carbon dioxide levels every 1 minute and recorded peak levels and the number of people present. Carbon dioxide readings above 800 parts per million (ppm) were considered an indicator of suboptimal ventilation.      Results: Carbon dioxide levels remained below 800 ppm during train rides to and from the airport and inside airports except in a crowded boarding area with ~300 people present. Carbon dioxide levels exceeded 800 ppm inside the airplanes, but the air was filtered with high efficiency particulate air filters. Carbon dioxide levels remained below 800 ppm in common areas of a hotel but exceeded 800 ppm in a hotel room with 2 to 3 occupants and in a fitness center with 3 people exercising. In restaurants, carbon dioxide levels increased above 800 ppm during crowded conditions with 24 or more people present and 75% or more seat occupancy. Conclusion: Our results suggest that ventilation may be sufficient to minimize the risk for airborne transmission in many situations during travel. However, ventilation may be suboptimal in some areas or under certain conditions such as in hotel rooms or when restaurants, fitness centers, or airplane boarding areas are crowded. There is a need for larger scale studies to assess the quality of ventilation in a wide range of community settings.  

SARS in Cars: Carbon Dioxide Levels Provide a Simple Means to Assess Ventilation in Motor Vehicles

Background:

Poorly ventilated enclosed spaces pose a risk for airborne transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses. Limited information is available on ventilation in motor vehicles under differing driving conditions.

Methods:

We conducted carbon dioxide measurements to assess ventilation in motor vehicles under varying driving conditions with 2 to 3 vehicle occupants. During routine driving, carbon dioxide produced by the breathing of vehicle occupants was measured inside 5 cars and a van under a variety of driving conditions with or without the ventilation fan on and with windows open or closed. Carbon dioxide readings above 800 parts per million (ppm) were considered an indicator of suboptimal ventilation.

Results:

Carbon dioxide levels remained below 800 ppm in all vehicles if the ventilation fan was on and/or the windows were open while parked or during city or highway driving. With the ventilation system set on non-recirculation mode, carbon dioxide levels rose above 800 ppm in all vehicles when the fan was off and the windows were closed while parked and during city driving, and in 2 of the 6 vehicles during highway driving. With the ventilation system set on recirculation mode, carbon dioxide rose above 800 ppm within 10 minutes in all vehicles tested.

Conclusion:

Carbon dioxide measurements could provide a practical and rapid method to assess ventilation in motor vehicles. Simple measures such as opening windows, turning on the fan, and avoiding the recirculation mode greatly improve ventilation.

Use of carbon dioxide measurements to assess ventilation in an acute care hospital

Poorly ventilated indoor spaces pose a risk for airborne transmission of SARS-CoV-2. We measured carbon dioxide levels in a multiple areas in an acute care hospital to assess the adequacy of ventilation. Carbon dioxide levels remained below 800 parts per million in most areas but exceeded this level in a small conference room with 8 occupants, an office with 3 occupants, and a bathroom with 2 occupants. Measuring carbon dioxide levels could provide a simple means for healthcare facilities to assess the adequacy of ventilation.

Coronavirus disease 2019 (COVID-19) research agenda for healthcare epidemiology

This SHEA white paper identifies knowledge gaps and challenges in healthcare epidemiology research related to coronavirus disease 2019 (COVID-19) with a focus on core principles of healthcare epidemiology. These gaps, revealed during the worst phases of the COVID-19 pandemic, are described in 10 sections: epidemiology, outbreak investigation, surveillance, isolation precaution practices, personal protective equipment (PPE), environmental contamination and disinfection, drug and supply shortages, antimicrobial stewardship, healthcare personnel (HCP) occupational safety, and return to work policies. Each section highlights three critical healthcare epidemiology research questions with detailed description provided in supplementary materials. This research agenda calls for translational studies from laboratory-based basic science research to well-designed, large-scale studies and health outcomes research. Research gaps and challenges related to nursing homes and social disparities are included. Collaborations across various disciplines, expertise and across diverse geographic locations will be critical.

Small phenolic and indolic gut-dependent molecules in the primate central nervous system: levels vs. bioactivity

INTRODUCTION

A rapidly growing body of data documents associations between disease of the brain and small molecules generated by gut-microbiota (GMB). While such metabolites can affect brain function through a variety of mechanisms, the most direct action would be on the central nervous system (CNS) itself.

OBJECTIVE

Identify indolic and phenolic GMB-dependent small molecules that reach bioactive concentrations in primate CNS.

METHODS

We conducted a PubMed search for metabolomic studies of the primate CNS [brain tissue or cerebrospinal fluid (CSF)] and then selected for phenolic or indolic metabolites that (i) had been quantified, (ii) were GMB-dependent. For each chemical we then conducted a search for studies of bioactivity conducted in vitro in human cells of any kind or in CNS cells from the mouse or rat.

RESULTS

36 metabolites of interests were identified in primate CNS through targeted metabolomics. Quantification was available for 31/36 and in vitro bioactivity for 23/36. The reported CNS range for 8 metabolites 2-(3-hydroxyphenyl)acetic acid, 2-(4-hydroxyphenyl)acetic acid, 3-(3-hydroxyphenyl)propanoic acid, (E)-3-(3,4-dihydroxyphenyl)prop-2-enoic acid [caffeic acid], 3-hydroxybenzoic acid, 4-hydroxybenzoic acid, 2-acetamido-3-(1H-indol-3-yl)propanoic acid [N-acetyltryptophan], 1H-indol-3-yl hydrogen sulfate [indoxyl-3-sulfate] overlapped with a bioactive concentration. However, the number and quality of relevant studies of CNS neurochemistry as well as of bioactivity were highly limited. Structural isomers, multiple metabolites and potential confounders were inadequately considered.

CONCLUSION

The potential direct bioactivity of GMB-derived indolic and phenolic molecules on primate CNS remains largely unknown. The field requires additional strategies to identify and prioritize screening of the most promising small molecules that enter the CNS.

Effectiveness and real-world materials compatibility of a novel hydrogen peroxide disinfectant cleaner

A novel 4% hydrogen peroxide disinfectant was effective against methicillin-resistant Staphylococcus aureus (MRSA), Clostridioides difficile spores, carbapenem-resistant Escherichia coli, and 2 strains of Candida auris. In laboratory testing, a sodium hypochlorite disinfectant caused fading and loss of pliability of a hospital mattress, but the hydrogen peroxide disinfectant did not. These findings suggest that the hydrogen peroxide-based disinfectant may be a useful addition to the sporicidal disinfectant products available for use in healthcare settings.

Impact of fever thresholds in detection of COVID-19 in Department of Veterans Affairs Community Living Center residents

Background

Among nursing home residents, for whom age and frailty can blunt febrile responses to illness, the temperature used to define fever can influence the clinical recognition of COVID‐19 symptoms. To assess the potential for differences in the definition of fever to characterize nursing home residents with COVID‐19 infections as symptomatic, pre‐symptomatic, or asymptomatic, we conducted a retrospective study on a national cohort of Department of Veterans Affairs (VA) Community Living Center (CLC) residents tested for SARS‐CoV‐2.

Methods

Residents with positive SARS‐CoV‐2 tests were classified as asymptomatic if they did not experience any symptoms, and as symptomatic or pre‐symptomatic if the experienced a fever (>100.4°F) before or following a positive SARS‐CoV‐2 test, respectively. All‐cause 30‐day mortality was assessed as was the influence of a lower temperature threshold (>99.0°F) on classification of residents with positive SARS‐CoV‐2 tests.

Results

From March 2020 through November 2020, VA CLCs tested 11,908 residents for SARS‐CoV‐2 using RT‐PCR, with a positivity of rate of 13% (1557). Among residents with positive tests and using >100.4°F, 321 (21%) were symptomatic, 425 (27%) were pre‐symptomatic, and 811 (52%) were asymptomatic. All‐cause 30‐day mortality among residents with symptomatic and pre‐symptomatic COVID‐19 infections was 24% and 26%, respectively, while those with an asymptomatic infection had mortality rates similar to residents with negative SAR‐CoV‐2 tests (10% and 5%, respectively). Using >99.0°F would have increased the number of residents categorized as symptomatic at the time of testing from 321 to 773.

Conclusions

All‐cause 30‐day mortality was similar among VA CLC residents with symptomatic or pre‐symptomatic COVID‐19 infection, and lower than rates reported in non‐VA nursing homes. A lower temperature threshold would increase the number of residents recognized as having symptomatic infection, potentially leading to earlier detection and more rapid implementation of therapeutic interventions and infection prevention and control measures.