COVID-19 Scan for Feb 26, 2021

News brief

SARS-CoV-2 reinfects 5 in nursing home, causing worse disease, 1 death

Five residents of a skilled nursing facility in Kentucky were likely reinfected with COVID-19, and the disease was worse the second time, with one patient dying, according to today's Morbidity and Mortality Weekly Report (MMWR).

Between the two outbreaks, which were reported in July and October 2020, each resident had at least four negative reverse-transcription polymerase chain reaction (RT-PCR) tests.

From Jul 16 to Aug 11, 2020, 20 of 115 residents (17.4%) and 5 of 143 (3.5%) healthcare personnel (HCP) tested positive for COVID-19 for an attack rate of 9.7% and 5 resident deaths. The outbreak was considered over after more than 2 weeks elapsed after the last identified case, and from Sep 1 to Oct 29, 2020, 928 COVID tests were performed—biweekly for HCP and upon symptom onset for residents—and all were negative.

During the second outbreak, which occurred Oct 30 to Dec 7, 2020, 85 of 114 (74.6%) of residents and 43 of 146 HCP (29.5%) had positive COVID-19 tests, for an attack rate of 49.2%. Fifteen infected residents (17.6%) died.

Twelve residents who were positive in the first outbreak were there during the second, and 5 of them tested positive again. Of these 5, 3 were asymptomatic and 2 had only mild symptoms during the first outbreak. But during the second, all 5 had symptoms, and the 2 with mild symptoms in the first outbreak had more severe symptoms in the second.

Sufficient RT-PCR test results to suggest at least moderate upper respiratory tract viral loads, and those who had previous symptoms had worse outcomes. One resident who was asymptomatic in the first outbreak died after the second infection and a 7-day hospital stay.

The reinfected residents were ages 67 to 99. All had at least three underlying health conditions but were not immune-suppressed. Because test samples weren't kept, the investigators don't know how related the outbreaks' phylogenetic strains were.

"Skilled nursing facilities should use strategies to reduce the risk for SARS-CoV-2 transmission among all residents, including among those who have previously had a COVID-19 diagnosis," the researchers write. "Vaccination of residents and health care personnel in this setting is particularly important to protect residents."
Feb 26 MMWR study


Sharing a home brings a 10% COVID-19 risk after exposure, study says

People who share a household with a member who has COVID-19 have a 10.1% risk of infection, according to a research letter published today in JAMA Network Open.

The retrospective cohort study used electronic records from the Mass General Brigham health system to track 7,262 COVID-19 index cases and their 17,917 household contacts from Mar 4 to May 17, 2021. During the study period, 1,809 household members (10.1%) were diagnosed as having COVID-19 a median of 3 days after the index diagnosis.

Independent risk factors included adult age and comorbidities. Household contacts from 50 to 64 had an adjusted odds ratio (aOR) of 3.66 (95% confidence interval [CI], 2.92 to 3.66; P < 0.001), the highest increased risk across those 19 and above. High blood pressure and liver disease was associated with the highest risk among comorbidities, with aORs of 1.93 (95% CI, 1.58 to 2.44; P < 0.001) and 2.01 (95% CI, 1.32 to 3.07; P = 0.001), respectively.

One of the study's limits was the electronic medical records' ability to identify household members accurately. To mitigate this, the researchers didn't include household members who did not visit the health system in the past 5 years or households with more than 25 residents.

"Although we acknowledge that contact investigations are the standard approach for estimating household transmission risk, we believe that the consistency of our results with these approaches suggests that our approach may provide a more efficient method for risk estimation and household contact identification," they write.

The researchers also note that the short median interval between the index case and subsequent cases may indicate some common exposures instead of transmissions. Cases also may have been undercounted if they did not seek medical attention.

Even so, the authors write, "Our study showed an overall household infection risk of 10.1%, consistent with reported transmission risk based on more traditional contact tracing, including a recent meta-analysis that reported an overall transmission risk of 17.1%, although there was wide variation across studies."
Feb 26 JAMA Netw Open research letter

News Scan for Feb 26, 2021

News brief

WHO experts swap out 2 flu A strains for next Northern Hemisphere vaccine

The World Health Organization (WHO) today announced that its influenza vaccine strain selection committee has made its recommendations for the Northern Hemisphere's 2021-22 flu season, which swaps out the two influenza A strains for both the egg-based and cell-based or recombinant vaccines.

For the egg-based vaccines, they recommend replacing the current 2009 H1N1 vaccine strain (A/Guangdong-Maonan/SWL1536/2019) with A/Victoria/2570/2019 and replacing the current H3N2 component (A/Hong Kong/2671/2019) with A/Cambodia/e0926360/2020.

For cell-based or recombinant versions, they recommend replacing the H1N1 current vaccine strain (A/Hawaii/70/2019) with A/Wisconsin/588/2019 and the current H3N2 component (A/Hong Kong/45/2019) with the same one as the egg-based strain: A/Cambodia/e0826360/2020.

The influenza B strains remain the same for all vaccine types. For trivalent (three-strain) vaccines, the team recommends including the Victoria lineage.

When compared with the Southern Hemisphere recommendation made in September, the H3N2 recommendations differ for the egg and other versions.

The WHO said flu surveillance was disrupted in most countries early in the pandemic, but has since recovered, with some countries testing even more samples than in previous years. However, there were vastly fewer flu detections with fewer viruses available for sharing.
Feb 26 WHO Northern Hemisphere flu vaccine strain report
Feb 26 WHO
Q and A


WHO shares more details about Russia's recent H5N8 avian flu cases

The WHO today shared more details about the seven recent human H5N8 avian flu infections reported in Russia, the first known cases involving the strain.

Russian officials detected the virus when they tested clinical specimens of poultry farm workers who took part in an H5N8 outbreak response operation in Astrakhan oblast in the south. The outbreak at the layer farm occurred from Dec 3 to Dec 11, killing 101,000 of 900,000 chickens. Given the size of the outbreak, the response took several days.

Patient ages range from 29 to 60 years, and five of them are women.

The workers who tested positive remained asymptomatic over several weeks of observation. Follow-up swab testing was negative for the virus, and serology studies suggested recent infections. No related illnesses were found in any family members or close contacts. Further serology studies in contacts are under way.

An analysis of the H5N8 virus from the poultry found that it belonged to clade of H5 viruses, which have been detected in several European nations, including Russia, as well as Egypt and Iraq.

The WHO said more information is needed to fully assess the risk, but for now, the threat of human-to-human transmission from H5N8 remains low.
Feb 26 WHO statement
Feb 22 CIDRAP News story "
Russia reports first human H5N8 avian flu cases"


Six countries report new polio cases, with some noting the first of 2021

According to the weekly update from the Global Polio Eradication Initiative (GPEI), six countries have reported new cases: Afghanistan, Pakistan, the Republic of the Congo, Ethiopia, Guinea, and Mali.

In Afghanistan, officials confirmed six circulating vaccine-derived polio type 2 (cVDPV2) cases, the first of 2021. The country tracked 305 cVDPV2 cases in 2020. Neighboring Pakistan also tracked two cVDPV2 cases bringing its 2021 total to three cases, as well as one case of wild poliovirus type 1 in Balochistan, the first of 2021.

All African nations reporting polio this week confirmed cases of cVDPV2. Congo and Ethiopia each reported one case, and Guinea noted six cases. They bring Congo's 2020 cases to 2, Ethiopia's to 25, and Guinea's to 45.

Finally, GPEI said Mali recorded 2 cases of cVDPV2 in Koulikoro, bringing its totals for last year to 38.
Feb 26 GPEI

ASP Scan (Weekly) for Feb 26, 2021

News brief

Our weekly wrap-up of antimicrobial stewardship & antimicrobial resistance scans

Danish study finds link between community C diff, proton pump inhibitors

Originally published by CIDRAP News Feb 25

A nationwide study in Denmark found an association between the use of proton pump inhibitors (PPIs) and increased risk of community-associated Clostridioides difficile infections (CA-CDI), Danish researcher reported today in Clinical Infectious Diseases.

For the study, researchers from Denmark's Statens Serum Institute used the Danish National Microbiological Database to identify all incident episodes of CA-CDI in Danish adults from February 2010 through December 2013. They obtained data on filled prescriptions for PPIs, which neutralize or reduce the production of gastric acid, from the Danish National Prescription Registry.

The researchers conducted self-controlled case-series analyses to estimate incidence-rate ratios (IRRs) for CA-CDI, comparing periods with and without exposure to PPIs, and adjusted their models to account for confounders such as chronic disease, genetics, hospital stays, and antibiotic and corticosteroid use.

Of the 3,583 CA-CDI episodes identified, 964 occurred during current use of PPIs, 324 occurred 0 to 6 months after treatment cessation, 123 occurred 6 to 12 months after treatment cessation, and 2,172 occurred during periods with no use of PPIs. When the investigators compared the incidence of CA-CDI during current use of PPIs with periods of non-use, the unadjusted IRR was 2.78 (95% confidence interval [CI], 2.40 to 3.22). When adjusted for hospitalization, antibiotic use, and corticosteroid use, the IRR was 2.03 (95% CI, 1.74 to 2.36). The increased risk remained elevated for extended periods: 1.54 (95% CI, 1.31 to 1.80) for 0 to 6 months and 1.24 (95% CI, 1.00 to 1.53) for 6 to 12 months.

The study authors note that while previous observational studies have found varying levels of association between PPI use and CDI, the association has been questioned because of the absence of data from randomized controlled trials and insufficient adjustment for confounding factors.

"This large study with thorough control for confounding significantly adds to the body of evidence that increased risk of CDI, even in the community setting, should be considered when prescribing CDIs, although the underlying biological mechanisms need to be explored," they write.
Feb 25 Clin Infect Dis study


Report examines social science insights on antibiotic use

Originally published by CIDRAP News Feb 25

The London School of Hygiene and Tropical Medicine (LSHTM) yesterday released a new report on antibiotic use in low- and middle-income countries (LMICs) that focuses on social science research and the emerging insights on novel ways to address antimicrobial resistance (AMR).

The report from LHSTM's Fresh Approaches to the Study of Antimicrobials in Society project examines antibiotic use in LMICs through three different lenses: practices, structures, and networks. The idea behind the report, which combines insights gleaned from a growing body of published social science research into AMR and from a series of panel discussions held in 2020, is to formulate ideas of how these insights can be used to develop local interventions for addressing human and animal antibiotic use in a diverse range of settings.

Among the key themes identified in the report is that antibiotic use in many LMICs does not primarily result from a lack of knowledge about AMR but is related to a web of social, economic, political, and historic conditions, and that modifying how people in these countries use antibiotics requires addressing these issues. Another theme is that fractured healthcare systems and lack of access to clean water and sanitation infrastructure have become structural drivers of antibiotic use in many countries, and fixing these structures, rather than focusing on individual antibiotic use, could lead to longer-term solutions.

"In the last few years, there has been a growing acknowledgement of the vital role of social science in understanding and intervening on antibiotic use, a key driver of AMR," author Clare Chandler, PhD, MSc, director of the LSHTM Antimicrobial Resistance Centre, writes in the report. "The growing concern that our off-the-shelf toolkit for addressing antibiotic use is insufficient in the face of rising use across humans, animals and plants, requires that we take a fresh look at the ways we are understanding this problem and possibilities for solutions."
Feb 24 LSHTM report 


CARB-X to fund development of drug to rejuvenate ineffective antibiotics

Originally published by CIDRAP News Feb 23

CARB-X announced today that it is awarding up to $2.2 million to the University of Queensland's Institute for Molecular Bioscience (IMB) to continue developing new compounds designed to boost antibiotics that have become ineffective against drug-resistant bacterial infections.

The award will help fund IMB's octapeptins research program, which is developing octapeptin peptides that can disrupt the protective outer cell membrane of drug-resistant gram-negative bacteria, allowing antibiotics that have lost efficacy to work again. IMB researchers are currently trying to identify which antibiotics octapeptins are best at helping and can be combined with.

"We will harness this latest funding injection to investigate which existing antibiotics can be rejuvenated by combining them with compounds from the octapeptin family," Mark Blaskovich, PhD, director of the IMB Centre for Superbug Solutions, said in a CARB-X (the Combating Antibiotic-Resistant Bacteria Biopharmaceutical Accelerator) press release.

Octapeptins are being designed for use in low- and middle-income countries, where there are high levels of drug-resistant bacteria and many cheap, generic antibiotics have lost efficacy.

This is the second round of funding IMB has received from CARB-X for the Octapeptins project. 
Feb 23 CARB-X press release


WHO details initial Global Leaders Group meeting

Originally published by CIDRAP News Feb 23

The World Health Organization (WHO) today released a report on the inaugural meeting of the One Health Global Leaders Group (GLG) on Antimicrobial Resistance (AMR).

The group, which is co-chaired by Bangladesh Prime Minister Sheikh Hasina Wazed and Barbados Prime Minister Mia Mottley and includes other heads of state, researchers, and key stakeholders, met Jan 26 and 27 to share ideas and discuss visions for their mission. It was the GLG's first meeting since being launched in November 2020 to provide political leadership for global, regional, and national efforts to address AMR and its impact on humans, animals, and the environment.

According to the WHO report, the members agreed that all GLG actions should add value to the global AMR response and should be guided by evidence and accountability, that national AMR action plans should by the bedrock of the global AMR response, and that there is a need to bolster popular and political support for efforts to tackle AMR.      

The group also discussed ideas for a draft action plan to achieve their objectives. Members agreed that the action plan should be ambitious and evidence-based, with a focus on deliverable actions, should focus on the root causes of AMR, and should prioritize efforts to ensure sustained and dedicated funding.

They concluded that the five categories of recommendations created by the Interagency Coordination Group on AMR (accelerating progress in countries; research and development and innovations to secure the future; enhancing civil society and private sector engagement; investments and sustainable financing; and strengthening global governance with accountability) should provide the overall structure for their action plan.

The GLG plans to meet four times a year. 
Feb 23 WHO report


Australia releases One Health action plan for antimicrobial resistance

Originally published by CIDRAP News Feb 22

The Australian government late last week released a One Health Master Action Plan (OHMAP) to support the country's 2o20 AMR strategy.

The plan highlights areas the Australian government and other stakeholders need to focus on to achieve the seven objectives of the 202o AMR strategy, which established a 20-year vision to minimize the development and spread of AMR in humans, animals, and the environment. The objectives include clear governance for AMR initiatives, prevention and control of infections, greater public awareness of AMR, appropriate antibiotic use and stewardship practices, integrated surveillance, and a strong collaborative research agenda across all sectors.

To achieve these goals, the action plan calls for the creation of sustainable funding for AMR initiatives based on evidence of the economic and societal costs of drug-resistant infections, the adoption of evidence-based and nationally consistent standards for infection prevention and control, and the development of coordinated, evidence-based antibiotic prescribing guidelines across all sectors. It also calls for the creation of a One Health communication strategy, a national One Health surveillance system, and a national AMR research and development agenda.

"By implementing a One Health approach with the OHMAP guiding the way, Australia can minimise the development and spread of antimicrobial resistance and ensure the continued availability of effective antimicrobials," the plan states. "This will help achieve a healthier future for Australians."
Feb 19 Australia One Health Master Action Plan 
Mar 13, 2020, Australia's National Antimicrobial Resistance Strategy

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