[HN Gopher] Metagenomics test saves woman's sight after mystery ...
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Metagenomics test saves woman's sight after mystery infection
Author : neversaydie
Score : 190 points
Date : 2025-04-30 07:56 UTC (4 days ago)
(HTM) web link (www.bbc.co.uk)
(TXT) w3m dump (www.bbc.co.uk)
| dtech wrote:
| What I find most interesting about this story that antibiotics
| weren't given when the patient had persistent inflammation and a
| clear cause couldn't be identified. It seems like such a common
| low risk treatment just to try. Especially curious why auto
| immune was assumed instead.
| ars wrote:
| This surprised me also, till I realized the story was in the
| UK.
|
| From my understanding it's much less common to get antibiotics
| in the UK vs US.
| OJFord wrote:
| There's concern of resistance taken seriously for sure, but
| it's not like people are making out here - I had fluclox
| prescribed after an online consultation in Jan (for probable
| cellulitis) - they don't give it out like candy, but when
| it's indicated...
|
| Maybe they tried something broad spectrum here, and what was
| necessary (and required the sequencing to know what it
| actually was) was something more targeted.
| philjohn wrote:
| Yep - the UK prescribing guidelines from NICE are eminently
| sensible as a way of staving off antibiotic armaggedon.
|
| One example of the guidance: https://elearning.rcgp.org.uk/
| pluginfile.php/199275/mod_book...
| MattPalmer1086 wrote:
| It does feel like they don't hand them out as often as they
| used to.
|
| I've had 4 infections this year, including an ear infection,
| fingernail, chest (that caused pneumonia on my son) and one
| that caused my left eye to swell up.
|
| I received no antibiotics for any of them, just a suggestion
| that if they didn't go away they might prescribe some. They
| all got better without them (except my son, who ended up in
| emergency and was given two different ones which cleared up
| his infection rapidly).
|
| In the past though I'm pretty sure I would have been
| prescribed them immediately.
| swores wrote:
| It's an intentional policy shift that has come not only as
| guidance to medical professionals, but as an awareness
| campaign (posters in pharmacies etc.) to the general public
| that most minor infections don't need antibiotics, and so
| ones that the body should be able to deal with on its own
| will no longer be prescribed antibiotics.
|
| It used to be that they were prescribed much more freely,
| because on the level of an individual case it's unlikely to
| do any harm and might help speed up getting better, and it
| was an easy way for doctors to make patients feel cared for
| to send them off with a prescription. But sensibly that's
| been course corrected now.
| ajb wrote:
| We don't actually know that they didn't try first-line
| antibiotics. My guess is that they did, and it's one of the
| things that didn't work. The UK is a bit cautious about causing
| antibiotic resistance, but my understanding is that that's more
| of an issue with long term use so may not be the determining
| factor here.
| tekla wrote:
| > In 2019, while still at medical school, Ellie began suffering
| from inflammation in her right eye. All tests for infection
| came back negative and it was assumed she had an autoimmune
| condition.
|
| You know how everyone complains about antibiotic resistance?
| Yeah, they're not going to give some random antibiotic if they
| have no idea what something might be.
| londons_explore wrote:
| Antibiotic resistance is a problem for _society_. Infection
| is a problem for the _individual_.
|
| Modern medical ethics requires you always prioritise the
| individual over society, which means one should always give
| antibiotics if the benefits outweigh the downsides for this
| specific patient, even if that means you might cause
| antibiotic resistance for everyone else in the future.
| tekla wrote:
| What is a society if not a collection of individuals?
|
| You don't get to complain about antibiotic resistance if at
| the first sign of an issue you demand a bathing in random
| antibiotics, especially if you don't even know if you have
| a bacterial infection in the first place
| Hnrobert42 wrote:
| As long as the patient completes the course of
| antibiotics properly, taking antibiotics should not
| contribute to antibiotic resistance.
| londons_explore wrote:
| I don't think there is much solid science behind that
| claim.
|
| Antibiotic resistance could just as easily first happen
| in the sewers and other places where there is a lowish
| concentration of antibiotics.
| TaurenHunter wrote:
| You can't claim to protect society from anything without
| protecting individuals primarily. Society is not a herd
| in which you sacrifice an individual to save the rest.
| londons_explore wrote:
| Isn't putting a murderer in prison for life exactly that?
|
| The prisoner would undoubtedly have a better life if not
| imprisoned. But society does better if they are
| imprisoned.
| hkt wrote:
| See also, placing limitations on political and economic
| power.
| tialaramex wrote:
| If you know they've got an infection then I agree that's a
| problem and medical ethics would suggest treating it with
| antibiotics if available. But, they didn't know she had an
| infection.
|
| You're assuming (and indeed US medicine seems to assume
| this everywhere) that since there don't usually seem to be
| major negative side effects from antibiotics they're
| harmless. However we are now confident they're not - lots
| of interesting things live inside us and whether or not
| they can cope with antibiotics varies, we're an ecosystem
| and so this intervention is a massive change to that
| ecosystem, and while it will usually be justifiable _if we
| know there 's an infection_ if we don't know that's now a
| gamble.
| oleggromov wrote:
| > Antibiotic resistance is a problem for society. Infection
| is a problem for the individual.
|
| Unfortunately not necessarily. For many chronic conditions
| an individual may very well develop an antibiotic resistant
| bug. There's even plenty on YouTube about standard
| penicillins and strep bacteria that start growing right
| inside the antibiotics. Look it up, it's fascinating.
| BobbyTables2 wrote:
| Tell that to my urologists who put me through 4 courses of
| different antibiotics while 5 tests for infections were all
| negative...
| jghn wrote:
| antibiotic resistance is such that it is increasingly less
| common to use it as just a "take 2 of these and call me in the
| morning" shot in the dark treatment.
| like_any_other wrote:
| If the symptoms are a sore throat, yes. If they're going
| blind, we can take a chance with antibiotics.
| typingonmyphone wrote:
| Had this been in the US, good chance would have received
| doxycycline as first line treatment and the leptospirosis
| identified by metagenomic sequencing would have resolved
| nsagent wrote:
| Good question. I started having digestive issues a year and a
| half ago. Went to various doctors and according to their lab
| tests was told everything was fine, that maybe this was my "new
| normal." Recently had an infection that necessitated broad
| spectrum antibiotics and magically my digestion issues have
| cleared up...
|
| If not for getting sick recently I'd probably still be dealing
| with whatever gut infection I had that the doctors essentially
| ignored.
| Aurornis wrote:
| > Recently had an infection that necessitated broad spectrum
| antibiotics and magically my digestion issues have cleared
| up...
|
| There are non-absorbable antibiotics designed to target
| intestinal bacterial overgrowth. It's hit or miss, though.
|
| Unfortunately for many people, taking antibiotics can have
| the opposite effect where it creates or worsens gut problems.
| It's not an easy or reliable solution.
| 2Gkashmiri wrote:
| My family has been testing various food items and it was
| found:
|
| .dressed chicken .peanuts .soyabean oil .cumin
|
| And we used to use these food "daily".
|
| The allergy eruptions, digestive issues went from 100 to 5
| starting next day.
|
| This is such a small thing to check but it has saved us as a
| lot of trouble.
| swores wrote:
| Could you clarify what you mean by "dressed chicken"?
|
| And I'm curious, did all of your family find yourselves
| allergic or sensitive to all of those things, or is that
| list a combination that covers everyone while each
| individual was allergic to one or a few of them?
| 2Gkashmiri wrote:
| One member did an allergy test and that found us major
| allergens. Rest of family just stopped eating those same
| things and things got better for everyone.
|
| Dressed chicken, I meant to say broiler chicken. They are
| raised for the sole purpose of meat and the turnaround
| time is in 45 days or less now. They pump these birds
| full of lots of medication, vaccines and stuff. Everyone
| in the family gets sick eating them. OTOH, farm chicken
| that are naturally grown and have no medication is fine
| so its not chicken per se but maybe some medication or
| food given to these broiler chicken
| jchw wrote:
| Sorry for your situation, or I suppose, glad to hear it's
| better. My understanding as a layperson is that antibiotics
| can be a nightmare for the gut: I don't think it's
| particularly likely, but you are a lot _more_ likely to get
| C. diff while taking antibiotics, and I 'm sure that's not
| the only way it can make things worse, alongside the other
| caveats of antibiotics (e.g. people misusing them in ways
| that threatens their effectiveness.) So, I can understand why
| doctors are not always eager to deploy antibiotics when
| they're not convinced they will help.
|
| I've personally had quite some experiences navigating health
| issues, health anxiety, the medical system, etc. Nothing
| terribly _interesting_ , but, still. I'm actually in middle
| of scheduling tests to see if I might, in fact, have an
| autoimmune condition. If they do find evidence of that, then
| it will have taken me around 6 years to figure it out from my
| very first symptoms. Thanks to modern medical science, I have
| little reason to sweat over it, though. (Of course, I'm still
| hoping for a negative, but at least in the case of a positive
| I can have the relief of knowing what the hell was wrong with
| me all this time.)
| soulofmischief wrote:
| Finding out I had gout was a 10 year process. Apparently
| "full test panels" don't include uric acid tests. And
| whenever symptoms are aggravated, it's much harder to test
| for it anyway as the crystals are lodged in your bones and
| not in your blood stream and urine.
|
| Now I have to go through the entire process again to rule
| out everything else before getting a fibromyalgia
| diagnosis.
|
| Anyway antibiotics have unrelatedly literally saved my life
| on several occasions now and I am glad that in a few
| emergencies I was able to access them on the street without
| needing to navigate the healthcare system. Antibiotics are
| too tightly controlled for humans and not enough for
| animals.
|
| That said, I have had to take them enough that I've
| definitely experienced negative gut effects a couple of
| times. Now I reach for probiotics after a regimen.
| genewitch wrote:
| I'm allergic to all cillins and had a spate of issues that
| required antibiotics 15 years ago, 3 treatments in 17
| months.
|
| I'll have to take probiotics the rest of my life. Because
| I'm not doing a fecal transplant, thanks. Those three times
| of antibiotics completely wrecked my intestines.
| meindnoch wrote:
| >Because I'm not doing a fecal transplant, thanks.
|
| Why?
| FitCodIa wrote:
| Previously on Hacker News (I had bookmarked it):
|
| "Antibiotics damage the colonic mucus barrier in a
| microbiota-independent manner"
|
| https://news.ycombinator.com/item?id=41516419
| TZubiri wrote:
| Pretty sure antibiotics can make digestive problems worst as
| a side effect, so it's cool that it worked for you, but
| hindsight is 20 20
| throwaway743 wrote:
| I just went through that exact situation.
|
| 5-6 years ago my buddy and I got violently ill on a trip to
| Japan. Both agreed it's the sickest either of us have ever
| been, and we both lost 15-20lbs each. Shortly after our
| illnesses went away we both developed digestion issues. Went
| through stool samples and colonoscopies. He got diagnosed
| with uc and I got diagnosed with post-infectious ibs-d. Was
| told all tests were fine, but life since was hell. That is up
| until 2 months ago when I went to the ER with an infection.
|
| Was given 2 weeks of doxycycline and voila, I'm no longer
| scared to fart, not running to the bathroom after eating
| anything, not going 7 times a day, and having solid stools.
| Might be tmi but whatever this is something that I'm happy
| and feel incredibly relieved (no pun intended) about.
|
| Only problem is I still have what I went to the ER for, no
| one knows what it is, and I have to get another colonoscopy
| :/
| sushid wrote:
| Not to mention she swam in untreated water in the Amazon!!
| CJefferson wrote:
| I don't know the details of this story, but I had an illness,
| and tried some antibiotics with no success. After a whole bunch
| more tests they decided it was a bacterial infection which had
| buried itself deep in my digestive system somewhere, and
| killing it required Fluoroquinolone --- which causes serious
| tendon damage in many people who take it.
|
| It cleaned up my infection, and I didn't have any side effects
| --- but hard to shift illnesses can require significant amounts
| of antibiotics with significant side effects.
| raincom wrote:
| Crux:
|
| "Metagenomics technology uses cutting-edge genomic sequencing,
| which can identify all bacteria, fungi or parasites present in a
| sample by comparing them against a database of millions of
| pathogens.
|
| [if you] do a separate test for each and every one and if you've
| got an infection with something that's unexpected, rare or not
| previously known, you won't find it."
| bsder wrote:
| Presumably the issue is that "went swimming in the Amazon"
| suddenly puts a _ton_ of rare, difficult to identify diseases on
| the table.
|
| Leptospirosis is _known_ to be both prevalent in tropical areas
| and to be difficult to positively culture and identify.
| pelorat wrote:
| Doctors here in Europe are not really into diagnostic medicine.
| I'm going to compare with Dr. House from the TV series who with
| a team spent days on a single patient. This is not the reality,
| the reality is that your specialist doctor will spend 10
| minutes thinking about your case before moving on to the next
| patient.
| snkzxbs wrote:
| 10 minutes is extremely charitable. Make it more like 2
| minutes. (And we give the government over half our salary for
| this level of attention!)
| IshKebab wrote:
| > And we give the government over half our salary for this
| level of attention!
|
| Well that's factually bullshit.
| williamdclt wrote:
| Both your statements are just plainly false (and I'm pretty
| sure you know it)
| snkzxbs wrote:
| They are both correct.
|
| Primary care physicians do not spend more than two
| minutes diagnosing you in my experience. The diagnosis is
| always shallow and sometimes wrong because of how rushed
| the process is.
|
| You pay a third of your salary in taxes, then you pay VAT
| on everything you buy plus many more taxes for other
| things such as your property. It amounts to more than
| half the money you earn.
| wizzwizz4 wrote:
| If I'm ever paying a third of my salary in taxes, I'm
| positively _rolling_ in money. And, that 's not how VAT
| works.
| snkzxbs wrote:
| Yes, that's how VAT works. You, the end consumer, pay it
| and the government pockets it.
| wizzwizz4 wrote:
| The third sentence of the Wikipedia article begs to
| differ. https://en.wikipedia.org/w/index.php?title=Value-
| added_tax&o...
|
| > A value-added tax (VAT or goods and services tax (GST),
| general consumption tax (GCT)) is a consumption tax that
| is levied on the value added at each stage of a product's
| production and distribution. [...] VAT is an indirect
| tax, because the consumer who ultimately bears the burden
| of the tax is not the entity that pays it.
|
| (Even then, Wikipedia is oversimplifying: "ultimately
| bears the burden" isn't how economies work.)
| snkzxbs wrote:
| What that means is that you don't pay VAT directly to the
| government, the business collects it from you and is
| responsible for giving the money to the government. But
| yes, the burden is on the end consumer.
| kjkjadksj wrote:
| Sounds like the american system only your employer takes it
| out of your check before you even see it
| swores wrote:
| Keep in mind that even in the excellent documentary to which
| you refer, about Dr Hugh "House" Laurie, MD. PhD. McT., the
| premise is that his setup - a dedicated diagnostics team to
| focus on difficult to diagnose cases - is a rare concept, not
| something seen at most US hospitals. There wasn't, for
| example, a similar team in that other great documentary
| "Scrubs".
| squigz wrote:
| I'm pretty sure that's not the reality... anywhere. That's
| TV.
| pton_xd wrote:
| > It is now presumed Ellie picked up the bug swimming in the
| Amazon river in 2018, while on a trip to Ecuador and Colombia.
|
| Don't doctors always ask about international travel when you
| present with an unknown illness? The exact timeline is difficult
| to infer from the article but that seems like pretty important
| detail to overlook.
| w10-1 wrote:
| Leptospirosis is very rare (~100 cases/year in the UK?) and
| typically affects other tissues (She's lucky it seems to have
| only infected one eye), making it more like a unicorn than a
| zebra diagnostically. Effective antibiotics are common, but even
| via IV they might reach not therapeutic levels in the eye.
|
| Metagenomics are particularly good in cases like this where
| tissue samples are small. These spirochete are too small for
| light microscopy - probably why the lab missed them.
| John23832 wrote:
| Given that leptospirosis is treated with doxycycline, you would
| have thought that they would have at least done a resistance
| study on the culture. Even if you don't know it's
| leptospirosis, you can know it's susceptible to tetracyclines
| and treat it.
| uxhacker wrote:
| The BBC article seems to overstate the uniqueness of the service
| at Great Ormond Street Hospital. While it's true that they are
| the first in the UK to offer a UKAS-accredited clinical
| metagenomics service (UKAS being the United Kingdom Accreditation
| Service, which certifies labs to meet medical testing standards
| like ISO 15189), metagenomics itself is already being used in
| several other places across the UK.
|
| For example, the Earlham Institute, the University of Oxford, and
| the UK Health Security Agency are all actively involved in
| metagenomics research and surveillance.
|
| For example: https://www.phgfoundation.org/blog/metagenomic-
| sequencing-in...
|
| https://www.earlham.ac.uk/events/nanopore-metagenomics-sampl...
| sleepyguy wrote:
| I'm curious if they initially diagnosed her with uveitis and
| began treatment based on that. However, I'm surprised there was
| no mention of consulting an infectious disease specialist.
|
| In Canada, when a complex issue like this arises, it's common to
| see several different specialists; the testing is typically very
| thorough, even including some forms of genetic testing. They do
| everything they can to get you off the steroids, knowing it will
| cause issues if taken long-term.
| animal531 wrote:
| I'm currently struggling with my eyes. Over time my near vision
| started degrading as I'm approaching 50, then I hit that wall
| where it suddenly became a lot worse and I got glasses for the
| first time.
|
| But the problem is that it generates a ton of eye strain for some
| reason, so now I'm on eye drops probably every 30 to 45 minutes
| and if I don't take them my eyes become really sore and useless.
|
| At least I'm working for myself so its less of a hassle, but
| taking constant breaks to rest the eyes isn't great for
| productivity.
| OutOfHere wrote:
| I would supplement vitamin A (10K IU), taurine (1g 2x/day),
| lutein (20 mg) (naturally derived), and zeaxanthin (4 mg). As
| for dry eyes, it is often triggered as an autoimmune condition
| in the absence of adequate vitamin D, but punctual
| cauterization can help.
| jml7c5 wrote:
| Have you tried "computer glasses"? (I.e., a glasses
| prescription that sets the focal length at around 60 cm (or
| whatever your normal distance to a monitor is).) It should help
| with eye strain as the ciliary muscle remains relaxed.
| donatj wrote:
| > It was only after Ellie was offered a "last resort" analysis
| called metagenomics, that she was diagnosed with a rare bacterial
| infection which was cured with antibiotics.
|
| After five years they'd never tried a broad-spectrum antibiotic
| treatment? That's the real story here.
| John23832 wrote:
| What's even worse is that leptospirosis is treated with
| doxycycline... the first line to pretty much all bacterial
| infections (with a cell wall).
|
| Even if you don't know what the bacteria is, if you have a
| culture, do a resistance study.
| sigmoid10 wrote:
| The article literally says that all tests for infection came
| back negative. It is not said explicitly, but this heavily
| implies that she had negative cultures (not uncommon for
| leptospirosis) and did not present with things like elevated
| white counts (also not uncommon for this pathogen -
| especially for superficial infections). The article also
| clearly says they (mis-)diagnosed it as autoimmune disease
| and treated with steroids, which is pretty much the worst
| thing you can do in that case. Leptospirosis goes away most
| of the time without any treatment if you have a working
| immune system. So if you really need a contrarian takeaway
| from this editorial, it's that doctors are still sometimes
| more dangerous than diseases (which used to be true in
| general up until about 100 or so years ago).
| John23832 wrote:
| I was skimming precoffee
| phkahler wrote:
| Yeah I came to quote this:
|
| "All tests for infection came back negative and it was assumed
| she had an autoimmune condition."
|
| They never confirmed the autoimmune hypothesis but tried to
| treat it. What about the hypothesis of "it's some other
| infection our tests don't catch"? Antibiotics are a fairly
| simple thing to try. She got cataracts due to that mistake. Now
| that eye doesn't have dynamic focus.
| shepherdjerred wrote:
| That was my takeaway too. Such a simple solution, though I
| understand over-prescribing antibiotics is not ideal
| patrickhogan1 wrote:
| Regular doxycycline treatment is 5-7 days. She used 21 days of
| treatment. Meaning she may have tried antibiotics at some point,
| we are talking about 5+ years of history.
| loremm wrote:
| I think there is a lot of hope because, in a purely research
| setting, this is extremely routine. The field of genomics is vast
| but the protocols are somewhat cheap and well understood. It's
| always hard to do a trial, and the tools are still often aimed at
| scientists (who are willing to spend months doing a single novel
| analysis), not point and click for a clinician. But even some
| relatively low hanging fruit will be extremely effective I think
|
| Not viral/bacterial but human mutations but this is an inspiring
| study --- https://pubmed.ncbi.nlm.nih.gov/31019026/ ,
| https://radygenomics.org/2021/13-hours-rady-childrens-instit...
|
| A child is born with potential rare genetic disease. They
| sequence their DNA _within 13 hours_ and come back with a
| diagonsis in some proportion of cases (they give lots of stats,
| it 's small sample size, maybe 1/4 improved outcomes, maybe 2/3
| have immediate change to their care)
| epmaybe wrote:
| Eye doctor here: some hot takes in this thread about the
| diagnostic abilities of the specialists involved in this
| patient's care. It's easy to be an armchair clinician.
|
| The timeline for delayed immune reaction to a leptospirosis
| infection makes diagnosis incredibly difficult. There was no
| mention of an acute febrile illness preceding this during the
| patient's trip to the tropics, which I assume a uveitis
| specialist would ask.
|
| While empiric treatment with doxycycline wouldn't be a bad idea,
| you have to decide what to empirically treat with, and for how
| long, and what the ramifications of increasing resistance to
| antibiotics are for society. Do I commit a patient to the
| hospital for two weeks of IV penicillin because I "suspect"
| syphilis? of course not.
|
| Better diagnostics for these occult diseases should be applauded.
| But we shouldn't be vilifying the clinicians that are by all
| accounts doing their best.
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