In 2014, Sharon Peacock, a professor of microbiology at the Unviersity of Cambridge, wrote an important piece in Nature, first page shown below, advocating sequencing as a standard of care to rapidly determine the causative pathogen and direct appropriate therapy—since the sequence can reveal mutations that confer resistance to antibiotics. She wrote: “Microbial sequencing should be done as close to the patient as possible.” To achieve the best outcome, the need for speed to crack the case and initiate the right treatment cannot be emphasized enough.
This is the opening paragraph from Dr Eric Topol's article A Culture of [Blood] Cultures in Ground Truths. erictopol.substack.com/p/a-...
Snips:
In that same year, 2014, we saw the life saved of Joshua Osborne, who had sequencing of his cerebrospinal fluid finally establish (within 48 hours) the elusive diagnosis of leptospirosis after many weeks of an extensive battery of tests, including a brain biopsy, that had failed to establish the cause of his encephalitis. About half of such infections of the brain are left undiagnosed with current approaches which include lab screening for a variety of pathogens and culture of the cerebrospinal fluid.
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Today when a patient presents with possible sepsis we draw multiple blood cultures and wait a few days before the results come back with a possible pathogen and readout for antibiotics that may be useful. The patient is bombarded with “empiric, broad spectrum antibiotics” to cover all the bacteria that are thought to be potentially causal, with implicit acknowledgement that viruses and other pathogens (fungi, parasites) won’t be covered by the antibiotic cocktail. That “blitzkrieg” cocktail, which may not even be directed to the underlying pathogen, has potential toxicity for the kidneys and other vital organs, and is typically continued until the cultures come back. All too often the cultures are negative, not revealing a/the pathogen, or show a contaminant, so, dependent on the patient’s clinical condition, the cocktail is continued for a full course of several days or longer. More potential for adverse effects of potentially misdirected antibiotics.
(This has been my experience several times now when I've been admitted for febrile neutropenia or some unknown infection and I know from other posts, that this is indeed the standard approach as Dr Topol states.)
In contrast, “clinical metagenomics” as the field is known, takes an agnostic approach as to what is the causative pathogen. As shown in this excellent review, sequencing can be performed on any body fluid or tissue and there are several steps required, besides the sequencing, that include library preparation and bioinformatic analysis. There is no assumption about the bug—many cases successfully diagnosed by this technique would have been unthinkable pathogens, like an ameba or tuberculosis. The sequence tells the story in place of a clinician’s intuition for what might be the cause of infection.
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While the opportunities here are extraordinary but the field is unmoved, UCSF, a pioneer in this movement, has already gone on beyond pathogen sequencing. They recently published the integrated use of metagenomics of the pathogen with host gene expression in critically ill patients, which identified 99% of confirmed sepsis cases, and the ability to separate out sepsis from non-sepsis etiologies. (See attached graphic, plus emphasis is mine - Neil)
One big reason we haven’t seen clinical metagenomics take off is our culture, which gets me back to the title of this post. We’ve been doing blood cultures for many decades (7 or more), and using broad-spectrum antibiotics (which have undoubtedly contributed to the crisis of antibiotic resistance) for many decades, and waiting for multiple days per patient for many decades. There’s considerable resistance to change in medicine, despite so many alluring aspects of this technology.
The bottom line: this can be done, but we’re not doing it. There appears to be no drive or incentive to change or adopt this technology for routine medical practice. Meanwhile, sepsis is a leading cause of death—it accounts for 1 of 5 deaths globally—about 11 million deaths in 2017. Patients and their families don’t know about this technology, but if they did, and started clamoring about it, we might begin to see some traction. I keep thinking of how many lives we could save (and could have saved) if only we responded to the charge in Peacock’s 2014 editorial.
I just saw this on Topol's twitter feed and am glad to see it posted here. Maybe it will begin to gain some traction if Eric Topol is talking about it? (Sadly, only 32 retweets so far)
The cost is lower each year, but it's still not cheap. As the article notes:-
Some health systems, after a patient has not had a diagnosis for a protracted period of time, and is unresponsive to antimicrobials, will send out a sample to outside laboratories such as UCSF or commercial entities (ID by DNA, Karius, Hugo Biotechnology, Aperiomics, and others) that will turn around the sample in <48 hours. But there’s a delay imposed by shipping and a significant cost (>$1000) involved. This is often a “last ditch” approach, and even then the success for diagnosis is about 50%, a rate that will continue to increase as more pathogen sequencing is done and data are shared (which isn’t being done across the various companies and labs).
Say it costs as much as $5,000. How does that compare with the cost per day of hospital care for IV antibiotic administration and if you are neutropenic, barrier nursing? Meanwhile, your life hangs in the balance...
My son works in metagenomics, although not human. He often tells me that the technology is getting cheaper and better, so I think it is just a matter of time.
On the question of antibiotics, your article reminds me of my first hospital admission with pneumonia and sepsis. I was hospitalised for 4 weeks very unwell and not at all in the picture regarding what was going on.
I do recall a senior consultant saying to me “we have tried all antibiotics known to mankind on you and now think we have the answer”
Although my infections continued from 2010 upto 2013/14 with further sepsis infections I then became aware that I now had chronic kidney disease.
This one frontiersin.org/articles/10... is more about metagenomics in disease outbreaks and the difficulties middle-to-low income countries face in adopting the technology (it does, however, talk about pathogen detection in clinical settings). The subheading Financial Cost starts with this:
The cost of sequencing has dropped precipitously over the past few decades. In the early 1990's, the Human Genome Project, designed to sequence the entire Homo sapiens genome, cost US$2.7 billion and took over 13 years to complete. By 2010, the complete human genome could be sequenced for US$10,000, and in 2022 the cost has dropped to a mere US$600, equivalent to about US$3 per gigabyte of sequence data.
If cost is the main barrier at present, we shouldn't have to wait many years for pathogen diagnosis by metagenomics to become standard of care in wealthier countries.
one does not need to sequence a complete patients genome to sequence enough of a pathogen’s genome to identify the likely culprit. PCR technologies are relatively cheap and can be used on any fluid from any tissue with superior sensitivity…in the last years we’ve done zillions of PCR tests looking specifically for Covid infections…looking for a whole variety of different pathogens that might be present in fluids would seem trivial in light of the fact we can make PCR reactions to detect completely unknown life forms in sea water . How hard would it be to create PCR reactions against general classes of human pathogenic viruses as well as bacterial and fungal cells known to circulating? Sequencing of PCR fragments could then be used to verify the actual strain?
Neil, you make some very good points but I am concerned about how fast such sequencing could be undertaken, if available.
When I was hospitalized with a high fever, the on-call internist had literally just hours to treat. My only symptoms were shivers and high fever and my organs began shutting down. As I understand it, the physician wasn’t even sure whether it was a viral or bacterial infection so she treated for both. So, the results of such tests would have had to be available in a very short period of time - even if it might be costly, is it practical?
If a hospital has the equipment, it only takes a few hours. The FDA approved at least one device here in the US Nov 2021. There are other companies making PCR devices.
The US California Department of Public Health uses PCR for testing 3 disease states. Hopefully other places will start using this tech in the near future.
It's not just the equipment, but also the genetic tag kits that also cost. Doing one-off sequences on a machine designed to do many samples from different patients is not efficient. Much of the drop in the cost of whole genome sequencing is due to scaling the cost of the reagent kits across hundreds of simultaneous patients.
What we saw with PCR and COVID was a little of both massive scale and single patient testing, and mosy of it paid for by the government.
There are a growing number of PCR diagnostic panels for up to dozens of different pathogens, such as respiratory pathogens. They're called Multiplex Assays. There's a lack of standards for PCR tedtin in general, and multiplex assays perform differently for each pathogen.
Reviews of multiplex panels like BioFire 2.1 which tests for 2 dozen pathogens, can trip poisitive for fairly high PCR cycle counts. The cycle count on my BioFire 2.0 back in June was not reported. All PCR needs the cycle count to be reported to set the proper context for interpretation. I expect that other single stranded viruses. I imagine that bacteria are not a problem.
Comparative Performance Evaluation of FilmArray BioFire 2.1 and MAScIR 2.0 Assays for SARS-CoV-2 Detection
Accirding to this, the BioFire proprietary FilmArray machine costs about US $50K, with supplies costing $130. A single instrument can do about 22 samples a day at roughly 45 minutes per sample, plus needed maintenance.
I'm not familiar at all with the work flow of more general purpose sequencers in a clinical environment. But standards are needed for each pathogen and test platform. I would prefer seeing non-proprietary platforms. The fact tgat BioFire exists means there is a significant market already, usually for emergency departments.
PCR has been used for quite a while. If you've had to rule out strep throat or a urinary tract infection in the US in the past mmm 20+ years, they don't culture anymore for the positive, it's been PCR for decades. They do finish the culture to run antibiotic sensitivity, but the "positive within 24-48 hours" is PCR based. Covid PCR testing is more a problem of "Covid/those tests", not PCR reliability in general.
Using your example, we shouldn't rely on the NGS tests either for uMRD, because the principles are similar. Amplifying what is already there. PCR is actually *used* in NGS technology.
So while I agree there are problems with Covid tests, I disagree about the PCR reliability part. Some of that Covid testing issue, is that the virus is harder to capture accurately. Or that particular test brand isn't optimal/working as intended. Not that the test itself is inherently unreliable.
Didn't happen to me either, but I could have done without having two different types of IV antibiotics for most of each day last admission, because they didn't know what was making me ill (I had a high fever while taking paracetamol and my blood tests showed high CRP, indicating an infection/inflammation). Plus hospitals are very good places to pick up extra infections (there are lots of sick people there ), so good places to have shorter stays than the 5 weeks it took for me to recover!
I too remember gasping for air in the early hours of the morning on more than one occasion, the thought of it happening again fill’s me with absolute terror.
I think they first have to think it might be sepsis. January 23, 2020, I arrived at the hospital via ambulance with what my doctor later described as a raging septic prosthetic joint infection. Unable to walk, in the early stages of delirium, I was still not running a fever, had no redness or swelling of the knee, and my inflammatory markers were normal. All those things would later soar through the roof. It was a master class in how our immune system does not respond properly to infections with CLL. My ER doc decided I had most likely hurt it in an exercise class, and left me in a corner of the ER. The hospitalist came along and saved my life.
Very interesting article - no time to read the discussion ATM.
Two main points seem to emerge regarding the slowness with which this is taking off:
1. inertia - the 'we've always done it this way' approach. You get this in all professions and other jobs too, from a good many people. That will change with time and, maybe, persuasion.
2. cost - ATM, the cost appears high compared to traditional approaches - but maybe even now, only if you consider the upfront cost as opposed to the long-term cost of incorrect diagnosis and treatment... but short-termism, a plague of political systems and bureaucrats everywhere, who rarely see much further than their noses.
(This last I can describe from personal experience - I had a not very large cancer on my nose; delay in diagnosis and treatment led to it growing so large that three ops under general anaesthetic were needed, at hundreds of times the cost of an early intervention.)
So I suppose we'll get there - eventually. How quickly depends on how much fuss people kick up, to get the backing of those with the power to alter the way things are done.
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), so good places to have shorter stays than the 5 weeks it took for me to recover! 
