February UTI hour 2022 - Shared screen with speaker view
Annie Joseph
The point about asymptomatic bacteriuria is SO important - a total misnomer in 2022 and needs a complete re-haul in context of the urobiome.
Prof Jenny Rohn
Might there be different “helpful” species in different individuals though? Or do we expect to find a signature consensus that can be broadly applied?
Annie Joseph
Linda - which do you think holds the most promise for future of UTI diagnostics 1)sequencing techniques 2) biomarkers 3) enhanced culture/susceptibility techniques?
Dr. Brubaker
@Prof Rohn - absolutely agree - I don’t know yet, but I suspect that there is a spectrum of “vulnerable” urobiomes - probably with fewer or less “helpful” beneficial microbes (or other aspects of the normal resistance to UTI - phage disorders, etc.)
Dr. Brubaker
@Annie Joseph - I think we will end up with faster testing - starting with point of care - so I don’t think the enhanced culture will be mainstay over time.
Sheryl Justice
Reposting from Dr. Brubaker
Sheryl Justice
@Annie Joseph - I think we will end up with faster testing - starting with point of care - so I don’t think the enhanced culture will be mainstay over time.
Naz Siddiqui (she/her/hers)
This is a fascinating discussion; unfortunately I have to run to another meeting. Will participants be able to access the recording later? THANKS to the panel and organizers!
Sheryl Justice
@Dr. Brubaker. With regards to the “coding” problem, is it a symptom of the training of clinicians or is driven by insurance? How do you think that this is best rectified to have better consensus? This seems like an area where UTIGA could facilitate change.
Sheryl Justice
Resending answer from Dr. Brubaker @Annie Joseph - I think we will end up with faster testing - starting with point of care - so I don’t think the enhanced culture will be mainstay over time.
Dr. Brubaker
Changing the coding problem is a BIG LIFT….It isn’t driven by either clinical training or insurance….selection of coding for UTI is no one’s priority…yet these medical codes continue to be used for “epidemiological research” - garbage in - garbage out, unfortunately
Sheryl Justice
There are a lot of hurdles with UTI ;). Thanks for your response and a very interesting presentation!
Hanson, Braden
What proportion of UTIs currently listed as culture negative is likely to contain non-traditional uropathogens such as actinotigrium, Aerococus
Annie Joseph
Dr Wolfe - what species of Staphylococcus were predominant on 16s species? Was S.sapro present?
Prof Jenny Rohn
Alan, do you think that bacteria normally resident on the vulva might still ‘bloom’ and cause problems in the bladder? Or are they bona fide ‘contaminants’?
Manu Bilsen
Dr. Wolfe - would you recommend the routine use of EQUC in clinical practice (when suspecting UTI in a patient)? Would this lead to increased antibiotic prescribing and perhaps resistance?
Dr. Wolfe
I agree. EQUC is not the future. There will be faster easier tests in the future. We use EQUC and sequencing to identify the microbes that should be included in future tests - both the good and the bad.
Jean-Philippe Gourdine
Great Job Alan and Linda. I gotta go teach my Metabolic Biochem classes now. Lisa will update me! ~JP
Michael Neugent
Dr. Wolfe - Very interesting talk! In the 16S FISH biopsies, 1) was a scrabble probe included to observe background signal? 2) have you performed this with multiple Z-axis image stacking and maximal projection to assess the 3D organization?
Dr. Wolfe
@Hanson - depending upon the type of individual and the type of LUTS, the fraction can be anywhere from 5 - 20%. It’s substantial.
Hi, Dr. Wolfe! How do you propose to distinguish good/bad microbes based on EQUC and sequencing to be included in future tests?
Dr. Wolfe
@Annie Joseph - We see a lot of S. epidermidis and several other species, but not a lot of saprophyticus, which surprises me since I’ve been told that it is one of the common causes. We just don’t see a lot of it.
Nicole De Nisco
Optimized methods for bladder 16S rRNA FISH: https://www.jove.com/t/60458/detection-tissue-resident-bacteria-bladder-biopsies-16s-rrna
Dr. Wolfe
@Michael Neugent - We did all the appropriate controls. The signal is real. The Z-stack analysis is being done as we speak. I can’t wait to see the data.
Michael Hsieh
Alan, your S. sapro finding is interesting, it makes me wonder if the biased nature of SUC is selecting for it, and that really a co-pathogen not detected by SUC may also be in play in affected patients
Manjula Meda
@Prof Wolfe, thank you for the interesting talk. Curious to know if you have studied (compared) urinary micribiome in men?
Dr. Wolfe
@catherine - good question. Of course, the usual suspects will be included. Also, the most common species present in individuals that are asymptomatic (think Lactobacillus). But after that it gets complicated. Not all Lactobacillus are created equal. Some of the emerging uropathogens keep cropping up so they’d be included (Aerococcus, e.g.). But then there is everything in between. We’re working hard to learn something of the pathophysiology of many of the more common but understudied microbes.
Dr. Wolfe
@Michael Hsieh - quite likely. I just don’t know which one(s) it is.
Dr. Wolfe
@Manjula - Yes, we have done some work on men. Streptococcus and Staphylococcus are very common. Lacto or Gardnerella are not.
Prof Jenny Rohn
@Lisa, sorry if I missed it, but is there a growing consensus on the best human depletion method for urine (whether that be biochemical or in silico)?
Hanson, Braden
Have there been studies looking at the intersect between the microbiome and other disorders such as bladder cancer or any other urinary tract disorders?
Prof Jenny Rohn
Linda, thanks - but I do sometimes worry that seeing the signal amidst the incredibly diverse noise might be a challenge given how sensitive our genomic tools now are!
Hanson, Braden
Dr. Wolfe- are you interested in looking at other behavioral aspects that may be contributing to the dynamics of microbiota. Differences in monogamous vs. nonmonogamous sexual relations, Internal exams, or any other behavioral changes?
Lisa Karstens
@Prof Jenny - I am not aware of a consensus for human depletion for urine yet
Prof Jenny Rohn
Thanks Linda!
Michael Neugent
Dr. Karstens - Fabulous talk! Do you have a preferred or recommended strategy for sharing metagenomic data with the broader scientific community? Is sharing raw reads on SRA enough?
Lisa Karstens
Thanks Michael! Sharing sequencing data on the SRA or ENA is great. An essential piece is to add comprehensive metadata. Providing more details or code about how the data was processed and the final precessed data tables on public websites such as Github or Gitlab is good as well.
Prof Jenny Rohn
I do wonder if the key to understanding what is virulent is really not down to the identification of the bug, or its amount, but rather might come down to virulence factors (so your E. coli in a healthy person just is not genetically competent to be a good uropathogen). If that’s true we will need routine WGS to sort it out.
Dr. Wolfe
@Hanson - yes, most of our work has been on urgency urinary incontinence and we and there are several studies on other disorders including bladder cancer.
Michael Neugent
In our WGMS, we do pretty deep seq and see about 65% human content
Prof Jenny Rohn
Hi Alan!
Vanessa Hale
In canine urine, WGMS, without host depletion, we had ~88% host reads. (We’re trying host depletions now!)
Michael Neugent
Can def be higher!
Prof Jenny Rohn
Well done Sanchutha!
Eleanor Kashouris
Thank you everyone
Annie Joseph
Thank you, a great session!
Jo Marshall
thank you everyone! So interesting
Michael Neugent
Great session! Thank you for sharing and organizing!