Fighting antibiotic resistance, one UTI at a time
Volume 10, Issue 2 | July 18, 2024
Also in This Issue
Home COVID/flu tests are ready for virus season
Protein signature helps diagnose neurodegenerative disease
Bird flu update
New and Noteworthy
New for respiratory virus season 2024-25: Home COVID/flu tests
COVID is on the rise once again this summer - see Your Local Epidemiologist for a superb overview of what’s happening, why it’s happening, and what to do about it. Fortunately, it is not yet flu season in the northern hemisphere, at least for the vast majority of humans (bird flu continues to affect dairy cows, poultry, and other birds and mammals). But preparations for seasonal flu’s arrival in the fall are well underway.
This year the testing industry has added a new weapon to our arsenal. As of now, 15 tests that detect flu A, flu B, and COVID all at the same time have been authorized by the FDA. Of those, seven are fully at-home tests where the sample is taken and results in your hands, in your home, in 30 minutes or less. The other eight are point-of-care tests. See list below.
Commentary: A recent roundtable with infectious-disease, public-health, diagnostics and therapeutic experts discussed the opportunities and challenges with broad access and use of home testing for flu and COVID. (Please note that Mara and Liz participated in this event.) One opportunity noted by the group: These tests have the potential to make “test to treat” more real than it was during COVID. Time will tell.
As of July 2024, 15 EUAs for Flu/COVID tests. 7 of these are Home / Self Tests.
EUAs below are organized by date. Home tests are in italics.
SEKISUI Diagnostics, LLC OSOM Flu SARS-CoV-2 Combo Home Test
CorDx TyFast Flu A/B & COVID-19 At Home Multiplex Rapid Test
Watmind USA Speedy Swab Rapid COVID-19 + Flu A&B Antigen Test
Roche cobas liat SARS-CoV-2, Influenza A/B & RSV nucleic acid test
Healgen COVID-19/Flu A&B Ag Combo Rapid Test Cassette (Swab)
Bird flu update: More human cases, respiratory transmission, testing barriers
Five workers who culled poultry at a Colorado farm hit by H5N1 have tested positive for the virus. The workers have both eye and respiratory symptoms, none of which are life-threatening. Extreme heat made it impossible for the workers to use PPE effectively during the culling process.
Experiments have confirmed that cows can be infected with H5N1 by breathing virus particles carried through the air, according to a preprint published on July 13. However, cows infected that way don’t shed much virus through their airways, which indicates that this route probably isn’t a major way the disease is transmitted. Instead, experts currently agree that the virus spreads mostly through contact with infected milk.
On July 12, Oklahoma announced that cows in a dairy herd in the state tested positive for H5N1 - based on a sample collected in April. No official reason for the delay was given, but according to Reuters, the farm sent the sample for testing “after the farm learned it could receive financial assistance for lost milk production from bird flu.”
Commentary: An article in the New York Times highlights the urgent need for significantly wider availability and greater variety of tests for bird flu. (Mara is quoted.) The CDC is processing applications from non-public health labs to use its H5N1 test and has put out a call for such labs to develop their own high-volume tests for the virus. However, the timeline for results on both those initiatives is on the order of months.
Food for Thought
Fighting antibiotic resistance, one UTI at a time
In 2014, Challenge Works announced a Longitude Challenge Prize that would be awarded for the development of a speedy (30 minutes or less) point-of-care device that reduced the overuse of antibiotics. The £8 million ($8.4 million) prize has now been awarded to the Swedish startup Astrego (acquired by Sysmex in 2022). Their benchtop device confirms a bacterial urinary tract infection (UTI) in 15 minutes and evaluates the offending microbe’s resistance to a panel of five antibiotics within 45 minutes.
Astrego’s approach uses microfluidics and optics in a body-mimicking environment to monitor many single bacteria for their relative health. The approach has broader application in infectious disease - hence the prize - but launch costs are quite high: €4,750 (=$5,180) for the device and €29 (=$32) per cartridge.
Commentary: UTIs are a big deal. They are the most common bacterial infection seen in primary care and give rise to 20-30% of potentially fatal sepsis infections. But this prize is about more than just UTIs specifically - it’s about antibiotic resistance in general.
It is easy to forget that for most of human existence, bacterial infection has been a major cause of death. Improved hygiene (starting around 1900) and widespread antibiotic use (starting in the 1950s - see chart from JAMA below) seemed to have conquered the scourge, but overuse and resulting antibiotic resistance threaten that victory.
Physician adoption of strategies to decrease antimicrobial resistance (AMR) has been disappointing (hospitals have been more proactive about it). While this new device is a Good Thing, it’s not clear that it will be a silver bullet. While 45 minutes is certainly less time than the two to three days that microbiology culture requires, it’s still a lot longer than the few minutes it takes to prescribe a broad-spectrum antibiotic in a primary-care setting.
Looking at proteins to diagnose neurodegenerative disease
Figuring out what flavor of degenerative neurologic disease a patient has is one heck of a challenge. Biopsy is rarely an option. Nearly all of the relevant disorders share many early behavioral changes (e.g., confusion, forgetfulness). The diseases also cause a lot of the same protein changes, which often are upregulated inflammatory responses seen in many brain injuries (e.g., tau tangles, amyloid beta plaques, and NfL, NfH, and GFAP).
However, it turns out that one of these diseases is marked by a signature set of protein changes that can be seen in cerebrospinal fluid (CSF). It’s progressive supranuclear palsy (PSP), a disease that until now could only be diagnosed after death. Interestingly, the six proteins most involved in the condition were all down-regulated, according to the paper in Neurology describing the pattern.
The commercial aptamer method used in this paper is becoming the go-to for proteomics (cheaper, quicker, and easier than mass spectrometry). Basically, an aptamer assay is made up of thousands of short, single-stranded bits of DNA or RNA, each of which can stick to a specific protein. Next-generation sequencing is then used to identify which and how many of these aptamers have bound the sample. The test gives you a quantitative result, which is nice, but there’s a catch. For the test to work, you need to have used the right aptamers in the assay, which means you kind of have to know what you are looking for.
Commentary: Our ability to identify the pathways that lead to these brain disorders is both accelerating and becoming far more sophisticated. Part of the equation here is the failure of amyloid beta and tau to adequately distinguish between different root causes (and even to sort out healthy controls). If we want to know what is actually going on in a cell/tissue, we need to know the type and quantity of proteins present there. Baby steps, perhaps, but we hope that we are now on the right pathway.
Quick Hits
In the battle against obesity, the BMI test isn’t everything. A new framework from the European Association for the Study of Obesity (EASO) takes into account the fact that the amount of abdominal fat a person has is a better predictor of disease than their BMI is. According to the guidelines, adults with excessive abdominal fat may qualify as obese even if their BMI is below 30 (the traditional cutoff for the diagnosis).