Metagenomics test saves woman's sight after mystery infection

https://www.bbc.co.uk/news/articles/czx45vze0vyo

by neversaydie • 1 year ago

204 80 1 year ago

bbc.co.uk

dtech• 1 year ago

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• 1 year ago

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• 1 year ago

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.

MattPalmer10862• 1 year ago

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.

ajb• 1 year ago

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.

tekla2• 1 year ago

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_explore3• 1 year ago

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.

BobbyTables2• 1 year ago

Tell that to my urologists who put me through 4 courses of different antibiotics while 5 tests for infections were all negative…

jghn• 1 year ago

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• 1 year ago

If the symptoms are a sore throat, yes. If they're going blind, we can take a chance with antibiotics.

typingonmyphone• 1 year ago

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• 1 year ago

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• 1 year ago

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.

2Gkashmiri2• 1 year ago

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.

jchw• 1 year ago

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.)

TZubiri• 1 year ago

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• 1 year ago

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• 1 year ago

Not to mention she swam in untreated water in the Amazon!!

CJefferson• 1 year ago

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• 1 year ago

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• 1 year ago

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• 1 year ago

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.

snkzxbs5• 1 year ago

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!)

swores3• 1 year ago

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• 1 year ago

I'm pretty sure that's not the reality... anywhere. That's TV.

pton_xd• 1 year ago

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• 1 year ago

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.

John238324• 1 year ago

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.

dillydogg• 1 year ago

I don't know what kind of resistance study you would order if you don't have an isolate growing. I don't know how you could have a culture growing but not know the causative organism is a Leptospira spp. .

uxhacker• 1 year ago

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...

hoseja• 1 year ago

It might be so that the plebs don't start demanding it from the NHS.

sleepyguy• 1 year ago

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.

animal5313• 1 year ago

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• 1 year ago

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.

animal5313• 1 year ago

I've started taking supplements to see if I can help the problem. Basically I'm now adding and removing a bit of everything that can help with or make the problem worse, but I'm only a day or three into that.

I'll check out the ones you mention.

jml7c5• 1 year ago

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.

animal5313• 1 year ago

Yeah I got some reading/computer glasses and today installed a monitor arm so I can more easily control the distance, no luck with it as of yet.

donatj• 1 year ago

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.

John238324• 1 year ago

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• 1 year ago

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).

phkahler• 1 year ago

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• 1 year ago

That was my takeaway too. Such a simple solution, though I understand over-prescribing antibiotics is not ideal

patrickhogan1• 1 year ago

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• 1 year ago

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• 1 year ago

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.

greg• 1 year ago

Not sure how “cutting edge” meta genomics still is, although it’s still not widespread. I worked on a project to provide free metagenomic analysis that was launched in 2017 and still going: https://czid.org/

I always keep metagenomics in mind now for friends and family who have mystery ailments.

Metagenomics test saves woman's sight after mystery infection

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