Survey shows Americans souring on COVID-19 response

Americans are not happy with the country's response to the COVID-19 pandemic, according to a new survey from Pew Research Center.

The survey of more than 10,000 US adults, conducted in early May, found that 62% think the country's COVID-19 response has given too little priority to the needs of K-12 students, while significant shares say too little priority has been given to supporting overall quality of life (48%), business and economic activity (46%), and respecting individuals' choices (46%).

The survey also found the proportion of US adults who rated public health officials as doing an excellent/good responding to the pandemic has fallen from 79% in March 2020 to 52%.

While many Americans appear to be moving on from the pandemic—45% of survey respondents said they now consider COVID-19 a minor threat—there are concerns that the highly transmissible and immune-evasive BA. 5 Omicron sub-variant, which now accounts for 53.6% of new US COVID-19 cases, could change the picture. That appears to be what's happening in Europe, where BA.5 and BA.4 are driving a new wave of infections, a European Medicines Agency official said yesterday in an online briefing, according to the Associated Press.

The current 7-day average of new US COVID-19 cases is 105,971, with 303 daily deaths and 37,590 COVID-19 patients in hospitals, according to the Washington Post tracker. But as has been the case for several months, the true number of infections is likely much higher, given that many home tests are going unreported. The Centers for Disease Control and Prevention (CDC) COVID-19 Community Levels Map, which is based on hospital admissions and inpatient bed metrics, shows that nearly 59% of US counties have medium-to-high COVID levels.

Meanwhile, the effort to vaccinate children under 5 has gotten off to a slow start. A senior Biden administration official told ABC News that to date, 300,000 children under 5 have received at least one dose of COVID-19 vaccine—roughly 1.5% of the 19.5 million US children 4 years old and younger.

Overall, 67% of Americans are fully vaccinated against COVID-19, according to the latest CDC update. But booster uptake continues to lag—47.9% of those eligible have received their first booster dose — but only 27.7% of those eligible have received a second booster.
Jul 7 Pew Research Center survey

Wastewater surveillance tool detects SARS-CoV-2 variants earlier, cheaper

Scientists at Scripps Research Institute and the University of California San Diego (UCSD) have developed a wastewater surveillance tool that—with just 2 teaspoons of raw sewage—can identify the SARS-CoV-2 variants circulating in a population and detect new variants of concern up to 2 weeks before clinical sequencing can.

The algorithm, described in a Nature study published yesterday, is a cheaper, faster, and more accurate method of analyzing SARS-CoV-2 RNA deposited in toilets and sinks by COVID-19–infected people to determine case levels in a population, the researchers said. Until now, they added, wastewater surveillance couldn't differentiate between variants.

Developed with the San Diego Epidemiology and Research for COVID Health study, the scalable tool, called "Freyja," was able to detect Omicron in San Diego wastewater 11 days before it surfaced in clinical reports. Many public health labs and communities around the world have since adopted the algorithm.

Co-senior author Kristian Andersen, PhD, of Scripps, said in a Scripps press release that traditional clinical surveillance for new variants is slow and cost-prohibitive. "But with this new tool, you can take one wastewater sample and basically profile the whole city," he said.

The team used 131 autosamplers to collect wastewater from 343 buildings at UCSD and 17 public schools in four San Diego school districts and obtained samples from wastewater treatment plants in the county. They analyzed more than 20,000 wastewater samples, developed better ways to concentrate viral RNA in wastewater, and quantified SARS-CoV-2 variants from sequencing data.

In a UCSD press release, co-senior author Rob Knight, PhD, said that the new method enables detection of new variants in time to take action.

“Before wastewater sequencing, the only way to do this was through clinical testing, which is not feasible at large scale, especially in areas with limited resources, public participation or the capacity to do sufficient testing and sequencing," he said. "We've shown that wastewater sequencing can successfully track regional infection dynamics with fewer limitations and biases than clinical testing to the benefit of almost any community."
Jul 7 Nature study
Jul 7 Scripps press release
Jul 7 UCSD press release

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

New guidelines aim to promote judicious antibiotic use in pets

The American Animal Hospital Association (AAHA) and the American Association of Feline Practitioners (AAFP) yesterday released new joint recommendations for judicious antibiotic use in cats and dogs.

The guidelines, developed by an expert task force, urge companion animal veterinarians to commit to core principles of antimicrobial stewardship as defined by the American Veterinary Medical Association, emphasize preventive care and routine health monitoring, and work with animal owners to ensure that antibiotics are only used when necessary. When the decision is made to use antibiotics, veterinarians should strive to "optimize therapeutic efficacy, minimize resistance to antimicrobials, and protect public and animal health."

The guidelines also recommend that veterinarians teach pet owners about good animal care practices and hygiene, use therapeutic alternatives where appropriate, consider "watchful waiting" to observe whether a condition truly needs antibiotic therapy, and use diagnostic testing to determine whether an infection is bacterial and will be helped by antibiotics.

"This effort is critical to ensure we continue to have drugs that are effective against bacterial infections," Erin Frey, DVM, MPH, DACVPM, co-author and task force chair of the guidelines, said in an AAHA/AAFP press release. "Bacterial pathogens will always find ways to resist antibiotics, but overuse of antibiotics or using them when it’s not necessary expedites this process, ultimately leaving us with bacteria that are impervious to treatment."
Jul 7 AAHA/AAFP Antimicrobial Stewardship Guidelines
Jul 7 AAHA/AAFP press release

Report describes UK outbreak of extensively drug-resistant Shigella

Originally published by CIDRAP News Jul 7

A study yesterday in The Lancet Infectious Diseases describes an ongoing outbreak of sexually transmitted, extensively drug-resistant (XDR) Shigella sonnei in the United Kingdom.

The outbreak began in September 2021 with the identification of an infected patient in England, followed by anecdotal reports of patients hospitalized with severe S sonnei infections in London in November and December, which prompted an investigation led by researchers from the UK Health Security Agency.

Genomic surveillance identified the infections as belonging to S sonnei clade 5. Cases were subsequently reported in Wales, Scotland, and Northern Ireland. Investigators with the Outbreak Control Team conducted whole-genome sequencing on patient isolates and collected demographic, epidemiologic, and clinical data from patients using questionnaires.

A total of 72 confirmed cases (70 of them in men, median age 34 years) were identified in the United Kingdom from Sep 1, 2021, to Feb 9, 2022. All cases were genotypically multidrug-resistant or XDR, exhibiting genotypic antimicrobial resistance determinants for aminoglycosides, sulfonamides, trimethoprim, fluoroquinolones, and macrolides. In addition, 66 of 72 isolates harbored bla_CTX-M-27, a plasmid-mediated gene that confers resistance to ceftriaxone. Of the 33 patients with clinical data, 19 (58%) received antibiotics and 8 (24%) were hospitalized.

Of the 27 patients who filled out an outbreak questionnaire, 25 (93%) were HIV-negative, 21 (78%) were taking HIV pre-exposure prophylaxis (PrEP), and 11 (41%) reported bacterial sexually transmitted infections (STIs) in the past year that required antibiotics. Twenty-two (81%) reported engaging in one or more sequential oral and anal sexual acts in the week before symptom onset. Two of the patients were immunocompromised individuals whose infections were not associated with sexual transmission, which investigators say highlights the threat of wider transmission.

"Previous evidence has shown that sexually transmitted shigellosis can be transmitted sporadically outside sexual networks; enhanced surveillance for this outbreak provided further evidence of this," the investigators wrote. "Sporadic transmission outside sexual networks, leading to severe cases in immunocompromised individuals, highlights the wider public health risk of continued, uncontrolled transmission of XDR shigellosis."

The investigators added that improved surveillance and updated treatment guidelines for drug-resistant Shigella are needed, and suggested that public health messages about the prevention of shigellosis and other enteric STIs should be included in PrEP delivery.
Jul 26 Lancet Infect Dis study

Joint venture aims to develop targeted antibiotics

Originally published by CIDRAP News Jul 6

German biopharmaceutical company Boehringer Ingleheim, German life sciences company Evotec, and French diagnostics maker bioMérieux announced today they are joining forces to develop a "precision medicine" approach to fighting antibiotic-resistant infections.

The companies say their new joint venture, called Aurobac Therapeutics SAS, will focus on combining actionable diagnostics that rapidly identify pathogens and resistance patterns with next-generation antibiotics, supported by new economic models. The goal, they say, is to move away from empiric, unfocused use of broad-spectrum antibiotics to treat bacterial infections to a more targeted approach.

"The grim prospect of a post-antibiotic era has many causes but only one solution: The development of new, targeted, and effective antimicrobial therapies," Evotec CEO Werner Lanthaler said in a press release. "We are excited to launch Aurobac together with our partners at Boehringer Ingelheim and bioMérieux, to combine our complementary strengths." 

The €40 million venture ($40.7 million USD) will be based in Lyons, France.
Jul 6 bioMérieux press release

Study finds low rate of bacterial, fungal co-infections in US COVID patients

Originally published by CIDRAP News Jul 5

A study of US hospital data found that fewer than 10% of COVID-19 patients had bacterial or fungal co-infections, but they had a higher risk of antibiotic-resistant, healthcare-associated infections than flu patients, Centers for Disease Control and Prevention researchers reported late last week in Clinical Infectious Diseases.

Using patient and microbiologic data from the Premier Healthcare Database, researchers analyzed 206,465 inpatients diagnosed with COVID-19 from January 2020 through June 2o21 and 142,246 patients diagnosed with influenza-like illness (ILI) from January through June 2019. The proportion of patients with a bacterial or fungal culture obtained during hospitalization was similar in both groups (56.2% for COVID-19 and 60.4% for ILI). The percentage of discharges with a positive culture defined as community-onset (CO) was lower in COVID-19 patients than those with ILI (7% vs 10.4%), but the percentage of discharges with a positive culture identified as HO was higher (4.1% vs 2.4%).

Multivariable logistic models showed that COVID-19 patients had significantly lower odds than ILI patients of CO methicillin-resistant Staphylococcus aureus (MRSA), carbapenem-resistant Pseudomonas aeruginosa (CRPA), or carbapenem-resistant Acinetobacter baumannii infections, but significantly higher odds of HO MRSA, CRPA, carbapenem-resistant Enterobacterales, and extended-spectrum beta-lactamase infections. Further analysis suggests the increased risk of antibiotic-resistant infections for COVID-19 patients is linked to longer hospital stays, critical care stay, receipt of invasive mechanical ventilation, and high rates of antibiotic exposure.

"Hospitals should continue to focus on infection control and antibiotic stewardship measures for patients with COVID-19 to prevent healthcare-associated infections, including antibiotic resistant pathogens," the study authors concluded.
Jul 2 Clin Infect Dis abstract

UK announces more funding for antibiotic development

Originally published by CIDRAP News Jul 5

The government of the United Kingdom last week announced an investment of more than $5 million to support development of new treatments to combat antimicrobial resistance (AMR).

The investment of £4.5 million ($5.3 million USD) from the UK government's Global AMR Innovation Fund (GAMRIF) will help the Global Antibiotic Research and Development Partnership (GARDP) develop antibiotics for drug-resistant infections that the World Health Organization has identified as the greatest threats to public health, including neonatal sepsis and hospital-acquired bacterial infections.

The funding, which brings the UK's total investment in GARDP to nearly £19 million ($22.6 million), will also support the development of zoliflodacin, a novel antibiotic for gonorrhea infections that GARDP is developing with Entasis Therapeutics.

"I am thrilled that the UK will be working in partnership with GARDP to deliver crucial research as part of GAMRIF's commitment to a One Health approach," Dame Sally Davies, UK Special Envoy on AMR, said in a press release from the UK's Department of Health and Social Care (DHSC). "Together we are leading efforts to combat AMR where the burden of infection is greatest, and we will use this investment to develop new treatments for drug-resistant infections to protect the world's most vulnerable."
Jun 30 DHSC press release

EU members vote to prohibit certain antibiotics from veterinary use

Originally published by CIDRAP News Jul 5

European Union (EU) member states have formally given their support to a list of antibiotics that will be prohibited from being sold for veterinary use.

The list of antibiotic classes, subclasses, and substances to be reserved for humans only is based on recommendations provided to the European Commission in May by the European Medicines Agency, the European Centre for Disease Prevention and Control, and the EU Food Safety Authority.  Antibiotic classes on the list include carbapenems (eg, meropenem), cephalosporin/beta-lactam inhibitor combinations (ceftolozane-tazobactam), siderophore cephalosporins (cefiderocol), monobactams (aztreonam), carboxypenicillins (piperacillin), glycopeptides (vancomycin), lipopeptides (daptomycin), oxazolidinones (linezolid), and glycylcyclines (tigecycline).

EU member states voted on the list yesterday.

"The list voted today, the first of its kind in the EU, and a landmark worldwide, is a major step forward in our One-Health policy approach to curb antimicrobial resistance," Stella Kyriakides, EU Commissioner for Health and Food Safety, said in a European Commission press release. "It is a prime example of how we address human, animal health and plant health together while at the same time also considering the importance of the environment."

The European Commission says it will formally adopt and publish the list in the coming weeks, and the ban will go into effect 6 months after publication.
Jul 4 European Commission press release