[HN Gopher] Mass spectrometry method identifies pathogens within...
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Mass spectrometry method identifies pathogens within minutes
instead of days
Author : pseudolus
Score : 124 points
Date : 2025-05-06 15:13 UTC (2 days ago)
(HTM) web link (phys.org)
(TXT) w3m dump (phys.org)
| timetobuild wrote:
| Super interesting! But mass spectrometry is an old method, why
| just now?
| prox wrote:
| "Our innovative approach is not to look directly for the
| pathogenic bacteria, but only for their metabolic products.
| This allows us to detect them indirectly, but much more
| quickly."
| pbmonster wrote:
| Often, stuff like that is a compliance thing.
|
| Very possible they're doing the research now, because one of
| the mass spectrometer companies has gotten ISO 13485 certified
| and can now offer the spectrometer for diagnostics in humans as
| a medical device manufacturer.
| WJW wrote:
| Checking out the actual article
| (https://www.nature.com/articles/s41467-024-55457-7) the
| authors write that:
|
| "In recent years, matrix-assisted laser desorption/ionisation-
| mass spectrometry (MALDI-MS) has been rapidly adopted in
| clinical practice to identify bacteria based on unique protein
| profiles6,7. However, while the identification process itself
| is faster, MALDI-MS-based analysis suffers from the same time-
| consuming isolation step as traditional approaches. Time,
| however, is a decisive factor in the successful treatment of
| several infection scenarios such as sepsis4,8. Consequently,
| the ideal scenario of microbial diagnosis is to identify
| bacteria directly from the clinical sample. Using MALDI, so far
| only a small number of applications could be implemented due to
| the high protein background in most clinical samples9."
|
| While mass spectrometry is an old(-ish) method, only recently
| has it become good and fast enough for clinical use. They also
| needed to make their own database of bacterial byproduct
| signatures to look for, as that did not exist yet.
|
| As to "why just now": not everything has been invented yet,
| even things that might seem relatively straightforward.
| w10-1 wrote:
| glossing...
|
| Article mentions existing tools e.g., MasSpec Pen, which
| detect signals of interest in samples with minimal processing
| (i.e., avoiding the hard part of processing/cleaning bio
| samples). But those were specific cancer signals that stood
| out from the general protein noise. (See also the cancer
| knife, that burns to cut and analyzes the smoke to see if you
| have enough margin).
|
| Problem with bacteria is (a) wide diversity and (b) previous
| work was mostly on lipids, not small molecules. For small
| molecule metabolites of bacteria, previous article reported a
| medium-size proof of concept (hundreds of target), and this
| is doing more (thousands), where they identify a few hundred
| unique patterns and then demonstrate their detection.
|
| At 90%, it's likely this would be used for pre-screening to
| identify possible candidates, though it might reinforce
| initial clinical suspicion and preliminary antibiotics.
| shakna wrote:
| Old does not really mean widely available. These machines can
| run into the hundreds of millions of dollars.
|
| Having one spare for research is not the norm, any more than
| having one is.
| 0cf8612b2e1e wrote:
| Incredibly capable mass spectrometers can be had for half a
| million. Plenty of undergrad labs have access to one. A
| student quality single quad is <$100k.
| pbmonster wrote:
| Would be interesting how much resolution they need for the
| diagnosis to be reliable.
|
| Because high resolution mass spectrometers cost millions of
| dollars, and "minutes" for a diagnosis can mean that one
| spectrometer can only run 3 samples per hour - or 72 per day.
|
| And while a research university can afford a million dollar
| spectrometer (and the grad students that run it), even a small
| hospital will create 72 bacterial swaps per hour - while
| absolutely not having the money to get 10 spectrometers with the
| corresponding technicians.
|
| And the incumbent/competitor - standard bacterial cultures - is
| cheap!
| californical wrote:
| But couldn't a hospital use it only for the critical cases?
| Where it is immediately important to know what infection
| someone may have, at imminent risk of death?
|
| Who cares if they need to charge $30k per patient to use it if
| that fast knowledge saves the patient's life. It doesn't need
| to fully replace the existing methods, but could be a useful
| supplement when a patient is in critical condition
| Cthulhu_ wrote:
| Sure, but then they'd have a million(s) dollar machine (plus
| the people trained to operate it) waiting for these critical
| cases. It's a cost / benefit tradeoff, just like whether to
| use an MRI or CAT scan vs x-rays or an echo.
| passwordoops wrote:
| Plus high-res mass specs can't just be turned on, they need
| to be kept on standby which isn't cheap when you cost it
| out over a year
| mapt wrote:
| This is a false dichotomy.
|
| It doesn't have to be used for every patient, and it doesn't
| have to be kept around waiting for Doctor House's third act.
| There is nothing stopping you from a middle ground.
| analog31 wrote:
| In the US, this is already handled by prior authorization.
|
| /s
| Ey7NFZ3P0nzAe wrote:
| Soon resident here: not really super critical to know the
| exact pathogen. There are classes of antibiotics and
| depending on many factors we can have a good estimate of what
| will work so the first try usually helps. What's usually done
| (at least in france) is:
|
| 1. Take some blood to send to the labs to grow bacterias
|
| 2. Only then IV of antibiotics
|
| 3. Adjust at day 3 when you get the results.
|
| And what if it looks super severe en urgent? Then 1. we do
| that too because it's often impossible to know what the
| pathogen was once you IVed all the antibiotics. And 2. we
| start by wide spectrum super strong high dose antibiotics.
|
| Example: purpura fulminans: 1g of 3rd gen cephalosporins.
|
| Ymmv in other countries, especially the USA because IIRC you
| have selected tons of emergent pathogens.
| darth_avocado wrote:
| This. Literally last week, I had to go to the ER and they
| ran a PCR test to identify the infection. But they also
| started broad spectrum antibiotics immediately. But since
| it was a Thursday and the lab only works weekdays, I
| couldn't get the results back until Tuesday. They adjusted
| the antibiotics to a more targeted one once the results
| were back.
| Ey7NFZ3P0nzAe wrote:
| Pretty usual stuff I'd say. And I'm willing to bet that
| the 2nd sets of antibiotic had a lower spectrum of action
| than the 1sr because we had some guess about the initial
| strain.
|
| Also because you're still with us so it probably worked.
|
| In any case I'm glad you're better and sorry you had to
| go through this.
| Agingcoder wrote:
| Do you know how cheap culturing bacteria is ( I really have no
| idea )?
|
| At 1 million/year ( worst case ), that's roughly 3k/day so 40
| dollars / analysis using your numbers . Assuming the machine
| lasts a bit longer ( say 5 years ) that's 8 dollars/analysis,
| assuming 20min/sample. Make it a bit faster (5 minutes) and
| you're down to two dollars which doesn't look super expensive
| to me.
| 5123125 wrote:
| Aren't there are also operating cost ? What you said is just
| depreciating cost of the machine.
| aziaziazi wrote:
| That's assuming the machine works 24/7 matching marching
| perfectly the demand. I'm not a doctor but I guess it's a
| seasonal "business" with more demand when cold winter starts,
| back to school September, epidemic episodes...
| mapt wrote:
| I would also wonder whether cultures are compatible with mass
| spec, and what the bottleneck is on measurement.
|
| Culturing for optical microscopy seems like you need 1-10
| DAYS before you get enough of a colony going to identify
| things, assuming you can successfully culture them at all.
| What if you plopped your culture down on the fermenter and
| gave it three hours (very cheap! Parallelizable!), then threw
| it in the mass spec? Would that shorten mass spec measurement
| time?
| davikr wrote:
| It could be very useful for Oncohematology patients. Cultures
| take a long time, relatively, for them, who often are severely
| immunosuppressed due to treatment.
| vondur wrote:
| I wonder if it needs the high resolution models for this
| technique? The models we used in undergrad were far cheaper
| (probably $250k and up).
| stonemetal12 wrote:
| MRI machines cost up to 0.5 million, and take more than minutes
| for a scan. So this is in the upper realm of reasonable. At
| this point it is an engineering problem to get costs down.
| mattkrause wrote:
| A good MRI machine is way more than $500k!
| westurner wrote:
| There are 0.05 Tesla MRI machines that almost work with a
| normal 15A 110V outlet now FWIU;
| https://news.ycombinator.com/item?id=40965068 :
|
| > _" Whole-body magnetic resonance imaging at 0.05 Tesla"
| [1800W] https://www.science.org/doi/10.1126/science.adm7168
| .. https://news.ycombinator.com/item?id=40335170 _
|
| Other emerging developments in __ spectroscopy:
|
| /?hnlog Spectro:
|
| NIRS;
|
| > _Are there implied molecular structures that can be
| inferred from low-cost {NIRS, Light field, [...]} sensor
| data?_
|
| NIRS would be low cost, but the wavelength compared to the
| sample size.
|
| From https://news.ycombinator.com/item?id=38528844 :
|
| > _" Reversible optical data storage below the diffraction
| limit (2023)" [at cryogenic temperatures]
| https://news.ycombinator.com/item?id=38528844 :_
|
| > [...] _have successfully demonstrated that a beam of light
| can not only be confined to a spot that is 50 times smaller
| than its own wavelength but also "in a first of its kind" the
| spot can be moved by minuscule amounts at the point where the
| light is confined._
|
| "Eye-safe laser technology to diagnose traumatic brain injury
| in minutes" https://news.ycombinator.com/item?id=38510092 :
|
| > _" Window into the mind: Advanced handheld spectroscopic
| eye-safe technology for point-of-care neurodiagnostic" (2023)
| https://www.science.org/doi/10.1126/sciadv.adg5431 _
|
| > multiplex resonance Raman spectroscopy
|
| Holotomographic imaging is yet another imaging method that
| could be less costly than MRI;
| https://news.ycombinator.com/item?id=40819864
|
| "Quantum microscopy study makes electrons visible in slow
| motion" https://news.ycombinator.com/item?id=40981054 :
|
| > _" Terahertz spectroscopy of collective charge density wave
| dynamics at the atomic scale" (2024)
| https://www.nature.com/articles/s41567-024-02552-7 _
| 0cf8612b2e1e wrote:
| If they are just looking for a few signature metabolites, you
| can easily do that on a single quadrupole for <$100k.
| Realistically, I would expect something more precise for
| medical purposes. Say a QExactive orbitrap -gives you
| phenomenal performance (<5ppm accuracy) and can be had for
| $500k.
|
| The only mass specs I think of costing multiple millions of
| dollars are accelerator mass spectrometers (AMS) which are
| meant for isotopic analysis.
| rurban wrote:
| Mass spectromity is a bit expensive. My company can detect a
| common plant virus reliable with multi-spectral imaging only.
| Normal hires B/W cameras. 10 days before visible symptoms.
| SpexAI.com
|
| Only vision scales. We did mass spectromity in Formula 1 because
| we had the money and it doesn't need to scale.
| amelius wrote:
| Sounds like this is exploiting a correlation between the virus
| and how the plant reacts to it. That's very specific.
|
| The nice thing about mass-spec is that you can use it as a
| dragnet detection method.
| caseyy wrote:
| Such approaches are cool for plants and maybe animal
| healthcare, where the other reasonably priced alternative is
| nothing.
|
| I don't know how I'd feel about reliable precision tools in
| human healthcare being substituted with B/W cameras and AI. It
| reminds me of a certain car company, where the human lives lost
| aspect wasn't so liked, even if they saved some money.
| ptsneves wrote:
| This is doing correctly what the car company did wrong. They
| start with a system that does not have a fatal incident upon
| failure. Meaning that even 1% or 10% failure rate is totally
| fine and possibly positive in terms of ROI.
|
| On the other hand, even 0.01% is not acceptable when the
| system is responsible for human lives.
|
| I also believe that cameras and visible spectrum are scalable
| and sufficient, and there is evidence it is so. The most
| reliable system driving cars is the homo sapiens and apart
| from a bit of proprioceptive, vehicles are operated based on
| vision sensors(eyes).
|
| To conclude, I find it a clever move to start refining the
| technology in a field where ROI is in dollar terms and not in
| lives saved.
|
| To the found: Good luck, i am jealous.
| sfilmeyer wrote:
| >On the other hand, even 0.01% is not acceptable when the
| system is responsible for human lives.
|
| I've got bad news for you about a whole lot of medical
| tests and interventions if 0.01% is unacceptable for you. I
| get your point that the stakes might be higher with medical
| technology than in some other fields, but you're still
| setting the bar too high.
|
| The first pathogen I saw mentioned by name while skimming
| through the linked article was H. Pylori, where the false-
| positive and false-negative rates for various currently
| used tests are several dozen times worse than that at about
| 0.30-0.90% [0]. Even just being hospitalized in and of
| itself has failure rates. Just eyeballing some of the
| numbers at [1] and elsewhere, I suspect that at least 0.01%
| of hospitalizations result in a death attributable to a
| hospital acquired infection.
|
| [0] https://www.aafp.org/pubs/afp/issues/2019/0701/p16.html
| [1] https://www.cdc.gov/healthcare-associated-
| infections/php/dat...
| cma wrote:
| It could be used for disease control and not necessarily
| personal health care. You could use something like the plant
| thing if it worked for people by photographing an entire
| stadium of people and finding infected people, airport entry
| lines, etc.
| rurban wrote:
| > B/W cameras and AI.
|
| You forgot multi-spectral. That means single hires images for
| a lot of frequency ranges, which is better than a single
| color image, which merges together all frequencies at once.
|
| In the end the accuracy of detections, false-positives,
| false-negatives wins. And this not comparable to this certain
| car company which refuses to use proper sensors. we also do
| infrared, 3d pointclouds to get the angle at each pixel, and
| thermal imaging.
|
| another neighbor of us is doing real-time imaging for face
| detection, which is the industry leader world-wide. They can
| install a lot of cheap cams in football stadiums and give you
| a list of all 80.000 people, when they have access to the
| government passport/driver license photo database. they have.
| but they cannot detect virus infections as we can do. nor
| bacterial infections. only if they do something illegal. who
| threw a bengal fire or started a fight.
| JoshTko wrote:
| This. Mass Spectrometry should portably only be used to
| confirm/train AI vision models. Once a large enough data
| set has been created for a particular pathogen, incremental
| diagnostic cost would be effectively 0.
| caseyy wrote:
| You're right, I didn't notice the multi-spectral part. My
| point still stands, I wouldn't want human diagnostic
| standards to slip but it is exciting technology. Thanks for
| sharing.
| anarticle wrote:
| A reason for bw cam is sensitivity. No bayer filter means you
| capture all the photons. There are cameras that are sensitive
| enough to count photons as well. When I was in the lab we
| used EMCCD cameras (electron multiplier ccd) that we used to
| detect very low signals from cells (we wanted to be nice to
| them, if you hit them with UV light they don't like that).
|
| There are all kinds of really great hacks to eke out an extra
| couple % at this level, if you consider you're counting
| photons. Back thinned, reverse mounting, high bandwidth
| multichannel readouts. Most of those trade offs are a thing
| of the past, but in the 2000s we were hacking the beans off
| those cameras to get them to do stunts for us.
|
| Things are fast good AND cheap now though!
| meindnoch wrote:
| >Normal hires B/W cameras. 10 days before visible symptoms.
|
| *visible to the human eye
| JR1427 wrote:
| You can identify quite a few pathogens with Attenuated Total
| Reflectance Fourier Transform Infrared Spectroscopy. I think the
| machines for that are smaller and cheaper than mass spec
| machines.
|
| see https://pmc.ncbi.nlm.nih.gov/articles/PMC5631018/ , and this
| company that is commercialising it https://microbira.com/
| snalty wrote:
| This is cool, but I still see sequencing and metagenomics as
| being the gold standard going forward.
| davikr wrote:
| Metagenomics can do hard diagnoses. We achieved the first truly
| confirmed diagnosis of neurohistoplasmosis in our region using
| that technique.
| michaelbarton wrote:
| Yes specifically mcfDNA which also has the advantage of only
| needing a blood draw
| Inuit wrote:
| I wonder how much resolution they need for diagnosis...
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