Denatonium - 6-6-2024 at 07:00
Hi all,
I know that as a layman, I can get molds identified to the genus level by buying a test kit at Home Depot and paying the $40 for the mail-in
identification service.
Does anyone know of a similar thing except for bacteria and to the species level? To add to the complexity, the organism I have growing might be
pathogenic - possibly BSL-3, but could easily also be an environmental contaminant. The growth medium is Middlebrook 7H10 agar.
unionised - 6-6-2024 at 09:27
OK if they might be BSL 3 pathogens .... Start by autoclaving them.
Then ask your local university to identify what's left, by DNA analysis.
Tsjerk - 7-6-2024 at 09:04
Autoclave and 16S PCR/sequencing. Unless you know what you are doing. But you asking this question tells me you should autoclave first.
Just out of curiosity, what do you think you have growing?
Denatonium - 7-6-2024 at 14:33
I'm suspecting a pathogenic mycobacterium species, but I don't know for certain (this is what I'm trying to find out).
The backstory is that I've been gradually feeling sicker and sicker since the middle of 2022, and since the start of 2023, I've had worsening issues
ranging from fatigue to lower back pain to coughing up blood. Throughout all of this, my doctors have been adamant that my issues must be
psychosomatic. In the first half of 2023, I was tried on amoxicillin and doxycycline and worsened on both. By mid-January of 2024, my lower back pain
and respiratory issues were getting to the point where is was getting difficult to do my job at the local grocery store. My family accused me of being
a deadbeat when I expressed this to them, and out of desperation, I stocked up on fish antibiotics and quickly realized that fluoroquinolones
effectively relieves my symptoms, allowing me to keep going to work and making my family happy.
Since then, everyone in my household has developed symptoms similar to my earliest symptoms. My father, who is in his 70s, has a mild but persistent
cough, and my mother, who is in her late 60s has uveitis. Both have a travel history to Southeast Asia. I have suggested they get tested for TB, but
they have refused, despite me offering to pay. I have tried contacting my state and local health departments, but they just tell me to see my doctors,
who are useless as well as unaffordable. A close friend of mine also has a persistent cough, and she works in a school.
Since everyone in my household already is showing symptoms, I no longer see any danger in attempting to culture the organism in question. I purchased
Middlebrook 7H10 agar base and everything I need to make an approximation of the OADC supplement. My setup isn't sterile, but I did boil the water
beforehand, which hopefully killed off environmental mycobacteria. It's been 8 days, and I'm still waiting for visible growth, but I did do a DIY
at-home AFB smear of a tonsil stone I coughed up and I definitely saw acid fast rods in there.
[Edited on 6/7/2024 by Denatonium]
Metacelsus - 8-6-2024 at 03:43
Yes, for example: https://www.genewiz.com/en/Public/Services/Molecular-Genetic...
bnull - 8-6-2024 at 06:24
It may sound a bit odd (or quite bizarre, as it now seems to me) but, are you friendly with any veterinarian? I mean, is there a veterinarian to which
you take your dog or cat for a check up or treatment or something like that? Perhaps the vet could identify the microbe. The ones where I used to take
my cats to had the necessary to make cultures and test themNote.
By the way, be careful with the antibiotics. Whatever it is that you have, it may well be that the symptoms come from a secondary infection (I guess
that is the correct name). It may be that a virus first decreased your immune response and then something else, susceptible to fluoroquinolones as it
seems, turned your body into a playground.
Note: They used to give me empty rubber-capped flasks (2 to 50 mL, transparent and amber) because of
my interest in chemistry. I even bought some paraformaldehyde from them.
leau - 8-6-2024 at 11:12
More information:
https://www.4shared.com/s/f82Frf93age
can be found in:
The Prokaryotes Third Edition
by Martin Dworkin (Editor-in-Chief), Stanley Falkow, Eugene Rosenberg,
Karl-Heinz Schleifer, Erko Stackebrandt (Editors) et al 
Tsjerk - 9-6-2024 at 01:15
Strange that doctors dont want to test you, maybe go somewhere else? Open TBC is no joke.
But sounds like you have your determination pretty much covered, except for the 16S PCR, which would be conclusive but requires a lab to perform.
Let us know what comes out of your culture test!
Anthracene - 11-6-2024 at 14:19
Instead of a wall of text just a few key points:
There are a couple of options to have bacteria identified and all of them would be extremely pissed if you send them BSL 3 material without proper
procedures.
I don't know where you live but "here" what you are doing would be illegal. Even if you don't have TB on your plates, enriching/isolating anything is
considered BSL 2 if you don't know what you are growing. This of course also applies to sourdough etc but I have not head about someone getting busted
for that...
That something grows on a certain medium and has the right morphology does not mean much.
Sequencing the 16S (or the whole genome, it's 2024) is the gold standard and this is what I would do. However, there are other options, for example,
you could look at the fatty acid profile. Since you are thinking about actinomycetes the mycolic acids would be even more interesting.
The idea "I have TB already so I can culture TB" is flawed. The media we use for heterotrophic bacteria are extremely rich. My microbiology professor
referred to them as Nutella and beer soup. A tiny colony on a plate is already madeuptillions of cells. If a droplet of saliva mafe airborne by
coughing is enough to make you sick, a bit of a dense bacterial culture can easily overwhelm your immune system.
Did you know that some labs working BSL 3 disinfect their labs by gassing them with formaldehyde? Not a suggestion, just a fun fact I thought some
might find interesting.
I work with actinomycetes (BSL 1 and 2 only) and I'd rather make CNBr at home than cultivate those fuckers.
It was funny somehow, my initial reaction to your post was "this is completely irresponsible to do outside of a professional setting" but then I
figured isn't that the same for our chemistry experiments? Seriously though, TB is no joke and you should not fuck with it.
Here are some tests that could potentially be done at home to narrow down what bacteria you have: https://www.vetbact.org/index.php?biochemtest=1
I am not a medical doctor so I can't comment on your ailment, I wish you a speedy recovery though!
Tsjerk - 25-6-2024 at 11:13
Thank you very much Anthracene... All the points you make were already nullified by Denatonium when you posted. The guy and his family already caught
whatever he is cultivating; who cares from that point on. I was harsh when I first posted, which turned out to be unfair. Sorry.
I just came here to post a YouTube video I cake across
https://youtu.be/GFLb5h2O2Ww?si=izmRo8Bujpg35BuE
Btw; your reasoning for his reasoning being flawed is flawed. If one is not infected with TB, you can't culture TB. Catching TB from thin air is
possible, but you also make it sound like you can catch it from a plate. Which is not true.
Don't worry, I also worked in bsl 2 labs, with actual mycobacteria.
They really, really like to stick together. They need some strong coughing to get aerosolized.
[Edited on 25-6-2024 by Tsjerk]
Anthracene - 6-7-2024 at 14:33
I do value your opinion Tsjerk but I disagree. There is no way of knowing what is growing on the plates is what is causing the illness. There is a
chance, of course, but it could be anything.
You are right about aerosolyzing bacteria being difficult, but I was not thinking about bacteria getting airborne from a colony on solid media. I was
more thinking about "smear infection", a miniscule amount sticking to a gloved finger can transfer millions of bacteria while rubbing your eyes or so.
I tried to phrase carefully but maybe I did not get across what I wanted to. Growing bacteria on a medium that is favorable to some nasty pathogens is
a dangerous business and some caution is advised.
About the really like to stick together thing, do you by any change have any advice on how to discourage that? It seems like the mycolic acids in the
cell envelope just make them more attracted to the glass of the bottle than to the water of the medium.