Slashdot Mirror
Microscopic "Tuning Forks" Help Determine Effectiveness of Antibiotics
sciencehabit writes "A patient admitted to a hospital with a serious bacterial infection may have only a few hours to live. Figuring out which antibiotic to administer, however, can take days. Doctors must grow the microbes in the presence of the drugs and see whether they reproduce. Rush the process, and they risk prescribing ineffective antibiotics, exposing the patient to unnecessary side effects, and spreading antibiotic resistance. Now, researchers have developed a microscopic 'tuning fork' that detects tiny vibrations in bacteria. The device might one day allow physicians to tell the difference between live and dead microbes—and enable them to recognize effective and ineffective antibiotics within minutes."
From TFA:
"It's a brilliant method," provided subsequent investigations confirm the researchers' interpretation of their data
I can, however, already hear the feet of the major pharmaceutical multinationals stampeding to get to Dublin....
Religous speak to God. Insane are spoken to by God. When all shut up, one can finally hear Shostakovich in peace
Since you're most likely to contract a hard to cure infection....in hospital..
An RNASeq run, either targeted to the ribosome or total (given that rRNA takes the lion's share) is a little bit quicker than culture, as long as the bioinformatics side of it is appropriately set up (e.g. massively parallel mapping, and automated count summarisation).
Sample preparation will take a few hours, and there are sequencers that will get results out in a few hours -- the mythical Oxford nanopore sequencers will speed both of these things up as well.
Ask me about repetitive DNA
Funny, I read it as "Microsoft Turing Fords Kelp Detriment Affection of Antimatter" but I didn't want to bore anyone with my lack of reading ability.
Tic-Tac-Toe, Global Thermonuclear War, and relationships all have the same winning move.
"We made a tiny bar that vibrates when it's surrounded by bacteria! It stopped vibrating when the bacteria were given antibiotics and we think this means the bacteria were dead. We don't know why it vibrates and currently we have no way of telling the difference between different kinds of bacteria."
Cool technology, but keep your pants on. This has very little application for a very long time.
"With patience a ruler may be persuaded, and a soft tongue will break a bone."
That's nice that a new technique is developed to measure/observe bacteria, but what's with all that bullshit about rushed bacterial infection?
PR idiots.
As a clinical (critical care, if you care to know) physician, I too am a bit puzzled by the description.
Patients in septic shock are very sick and the prescription of antibiotics is a delicate subject....antibiotics need to be started within a few hours of diagnosis, and getting it wrong (prescribing an antibiotic to which the bacteria is resistant) and the patient has a 50% increase in mortality. To this end we use the broadest spectrum antibiotics available, and most hospitals develop an "Antibiogram " specific for their institution and their pt population. These antibiotics are so powerful, it is rare, but not unheard of, for organisms to be resistant to them.
The process goes like this:
Pt is admitted to an ICU
Cultures of all likely sources (urine, lung, blood, CSF, abscess fluid) are obtained
Antibiotics are started (sometimes before the cultures are drawn, but ideally after), as well as other therapies
Over the next few days the antibiotics are "De-escalated" as dictated by the cultures (see below)
Hopefully the pt recovers and their care is down-graded and ultimately discharged
The cultures are sent to the lab after being draw and in a process that (time-wise) parallels the above:
The sample is extracted from the specimen container and are plated on a growth medium or placed in a broth
They are allowed to grow for (around) 24 hours
The plates are examined to determine if anything actually grew (may take up to 3 days for blood)
If something grew, two processes happen:
The culture is sent through a variety of tests (gram-stain, etc) to determine the species of bacteria which will dictate the next step.
The specimen is then re-suspended in a culture medium and plated and allowed to grow in the presence of antibiotics thus yielding that particular organisms antibiogram
A you can see, there really isn't anywhere to rush the process. And I would be very interested to see how they can speed this up with their technology....the who purpose of the plating is to amplify the bacteria from the milieu of the body fluids and to find the dominant organism growing.
In addition, some cultures are already "contaminated" with body flora (e.g. upper respiratory and stool) and the purpose of the culture is to amplify pathological bacteria from the benign-normal flora.
Longer video that gives a better front to back description
They should proceed with caution. They could end up quacks at any time. The famous Royal Rife machine used vibrations to kil bacteria. And here it is, all these years later, and it turns out bacteria *does* vibrate:
Doctors destroy health, lawyers destroy justice, universities destroy knowledge, religion destroys spirituality
The process goes like this:
They are allowed to grow for (around) 24 hours
The plates are examined to determine if anything actually grew (may take up to 3 days for blood)
If something grew, two processes happen:
The culture is sent through a variety of tests (gram-stain, etc) to determine the species of bacteria which will dictate the next step.
The specimen is then re-suspended in a culture medium and plated and allowed to grow in the presence of antibiotics thus yielding that particular organisms antibiogram
A you can see, there really isn't anywhere to rush the process.
qPCR, RT-PCR, and/or ELISA tests to determine which bacteria are common and which antibiotic resistance genes are heavily expressed at the infection site or the blood stream. Would only take a few hours from taking the sample to having results, as opposed to 1-3 days to do a culture.
The real usefulness of a technique like this (as I understand from the sepsis researchers that I've interacted with), is improved antibiotic stewardship -- preventing overuse of antibiotics and reducing the time the patient need be treated. These rapid assays can provide a better and more timely means to monitor a patient's response to treatment.
The talk about early diagnosis and saving lives is simply a lot more sexy and easier to sell than antibiotic stewardship. The grandstanding about this particular application aside, though, the technique itself is interesting.
read "Microsoft" the first time when I saw the news in reader and was "Wtf? Microsoft Tuning Fork? Parsing error!" and now after opening the story did the same thing again ;)
It's so good to see Ugol's Law in action! Once I'd realized that I'd misread the title, I wondered if anybody else would be willing to admit that they'd done the same thing. I feel so much better!
Good, inexpensive web hosting
qPCR, RT-PCR, and/or ELISA
Doesn't this assume you know what bacterium you are looking for, that you have the right primers, and that you know where the antibiotic resistance genes are? There seem to be too many variables to test for all of them. And why qPCR instead of regular old PCR? qPCR machines are pricey.
There is already a fast way to tell if bacteria are dead or alive; it's called live/dead staining. Basically, it stains living cells one fluorescent colour and dead cells another. You can then look at the sample under a fluorescent microscope or with a flow cytometer to quantify the amount of killing caused by the antibiotic.
Also PCR and ELISA are much more expensive and time consuming processes than plating or "brothing", and you also have to have a reasonable clue as to the organism that you expect to encounter (see below) - If I knew the bug before hand, I'd treat for it. Those in my position often get surprised by the organism that finally grows. I once had a case of endocarditis in a cardiac transplant patient, the culture came back with an unusual organism....googl-ing that organism yielded 4 hits (granted not the most scientific process) - sorry can't recall the bug, it was that unusual.
But also please reference my statement about amplification of the dominant organism above the ambient noise.
Sorry, just looked down and saw the reply by the.original.drg, basically the same argument, but with some personal experience thrown in
The real usefulness of a technique like this (as I understand from the sepsis researchers that I've interacted with), is improved antibiotic stewardship -- preventing overuse of antibiotics and reducing the time the patient need be treated.
Please see my line about "De-escalated" - that is antibiotic stewardship in action.
These rapid assays can provide a better and more timely means to monitor a patient's response to treatment.
Again, where can this be applied in a "noisy" real world scenario? The researcher took an already cultured (i.e. purified) sample to prove the concept. I am trying illustrate the complexity of translating this into a real world application.
The talk about early diagnosis and saving lives is simply a lot more sexy and easier to sell than antibiotic stewardship.
They are two sides of the same coin....the bug I treat today with the tightest adequate spectrum of coverage is the bug I do not have to treat with the big guns later, or worse, have the big guns fail.....The situation for my patients really descends into the realm of "life sucks" when we're having the discussion "if we try this antibiotic I can treat his/her infection, but we're going to trash his/her {kidneys | lung | liver} in the process."
The grandstanding about this particular application aside, though, the technique itself is interesting.
No doubt that this is interesting, I again question where this is going to be useful....The best I can see is using it in place of the traditional sensitivity step - replacing the Kirby-Bauer test...but this is going to save hours. I guess that's going to be the "big saving"; still every hour I gain is something. Hopefully they can make this test cost-effective so we can actually persuade the bean-counters that it'll be worth it.
However, growth to visible cultures is composed of hundreds of generations, and if you had a more sensitive detector of bacterial reproduction, that didn't have to wait so many generations, you could reach colclusions[sic] a lot faster; limited primarily by the drug uptake rate.
Hmmm....me thinks you should look into your math...:-) (I'm being purely humorous at this point, not meant to be mean, but with real math)
doubling time is about 20 min in ideal circumstances so 100*20 is 2000 min or ~ 33.3 hrs
100 generations == 2^100 bacteria or 1,267,650,600,228,229,401,496,703,205,376
each bacteria weights about 9.5^-13g
so total bio mass is about 13,343,690,528,718,204g or 13,343,690,528,718kg or 1.3e13kg
for reference, the earth weighs...5.9e24 kg, (moon is merely 7.3e22, the USS Iowa battleship is about 5.2e7kg, a supertanker is 1.1e10 kg)
For a gram of bacteria (that's a lot!) only takes about 40 generations under ideal circumstances....now I'm ignoring lag and standing phases and focusing on the log phase just to give you an idea of the order of magnitude.
They claim they can detect bacterial metabolism directly. So for bactericides, at least, they don't even have to wait one generation to detect results.
Well, there's still the lag for them to grow to culture, again its the in vivo milieu that needs to be discarded.
I suspect that bacteria could be classified crudely using some variant of flow cytometry, and then you could test antibiotics against each group.
Looks like its been done. Didn't read too far in, I suspect it is not ost effective tho.
Expense: Yes, those techniques are more labor and/or equipment intensive than culturing. I'm going on the assumption that there are cases where having the answer in 3 hrs instead of 3 days would drastically improve the outcome. How about this: If the only benefit to getting the result 20-70 hrs sooner was that patients ended up spending one less day in an ICU, the technique would save money if it cost less than ~$5k.
Knowing what to look for: You can differentiate A LOT of pathogens using a single set of primers, PCR, and RFLP analysis: combining speciation/strain ID and quantification is another matter, true, but that's why I mentioned qPCR. ELISAs can pick up which toxins and how much of each are actually present in a septic patient.
But I blanked on what would probably work best: array based techniques. Arrays on chips can identify ~100 different bacterial resistance genes, or simultaneously look for all of the most commonly feared biowarfare bactera and viruses. Bead arrays can simultaneously identify species/strain and quantify them. These techniques can also identify strains and viruses that are difficult to culture.