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Phenotype submission - Urinary Tract Infections

Cohort Definition Name : Earliest event of Urinary tract infections (UTI)

Contributor name : Stephen Fortin

Contributor OrcId : 0000-0002-6976-2594’

Logic Description : Earliest event of diagnosis of urinary tract infections, cohort exist is end of observation period.

Recommended study application : target, outcome

Assertion statement : This cohort definition was executed on at least one real person-level observational health data source and resulted in a cohort with at least 1 person.

Target Clinical Description : A urinary tract infection (UTI) is an infection in any part of the urinary system. The urinary system includes the kidneys, ureters, bladder and urethra. Most infections involve the lower urinary tract — the bladder and the urethra

Evaluation conclusion : A total of 2 950 641, 1 831 405, and 2 294 929 patients meeting study criteria were identified in each database. Overall, the code-based algorithm requiring a primary UTI diagnosis code achieved the highest positive predictive values (PPV; >93.8%) but the lowest sensitivities (<12.9%). Algorithms requiring three UTI diagnosis codes achieved similar PPV (>0.899%) and improved sensitivity (<41.6%). Algorithms requiring a single UTI diagnosis code in any position achieved the highest sensitivities (>72.1%) alongside a slight reduction in PPVs (<78.3%). All-time prevalence estimates of UTI ranged from 21.6% to 48.6%. This work has been published here: https://onlinelibrary.wiley.com/doi/full/10.1002/pds.5492

Thanks @stephenfortin and @Azza_Shoaibi for sharing your phenotype for UTI. And a specific shout-out for this submission, because it’s SUPER useful to see all of the evaluation that you’ve done in the published paper. Well done.

(I’ll also note that, had this been in the Phenotype Library earlier, we definitely could/should have used this during our Sisyphus challenge, it would have saved us from reinventing the wheel and coming up with our own UTI definition, which was not the same as the conceptset created here)

I plan to re-use this work as part of the nesting indication for antibiotics cohorts used for the HowOften effort.

A couple notes as I reviewed this:

  1. I see that there are some non-standard concepts in the conceptset. I suspect that’s also an example of ‘vocabulary drift’, in that I presume they were standard whenever this was originally created.
  2. I noted that there is one MedDRA term being used to exclude concepts. Since MedDRA->SNOMED mapping is on the roadmap for enhancement, this is an example where we may expect further ‘vocabulary drift’ in the future.
  3. (reflecting on my mistake when investigating UTI for the SOS Challenge) : this definition includes Cystitis + descendants, which I fully agree should be part of the definition, and notable that there is substantial record count on ‘acute cystitis’, ‘cystitis’, and ‘hematuria co-occurrent and due to acute cystitis’, which do not roll up to ‘Urinary tract infectious disease’.
  4. Since this is an acute event, and can resolve, and then recur again, I would think that we’d want to attempt to model the individual disease episodes (rather than currently modeling 1st occurrence and assuming a person persists in the UTI disease state until their end of observation). Thinking through how to model cohort exit is an interesting problem: do we combine diagnoses with some short era gap window? do we consider the case to continue while antibiotics are on-board?

Imported to the OHDSI Phenotype Library. It may be expected to be found with id = 861 in the next release. Thank you