If you are interested in enterics, we have some of this concordance data on https://wwwn.cdc.gov/narmsnow/
There is also the AMRFinder validation paper from NCBI that does phenotype to genotype correlations https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6811410/
For false negatives, do you mean phenotypically resistant but AMR gene or mutation not identified?
Thanks,
Heather
-----Original Message----- From: Marco van Zwetselaar via Bioinfo List bioinfo-list@seqshare.org Sent: Tuesday, May 14, 2024 5:13 AM To: bioinfo-list@seqshare.org Subject: [Bioinfo-list] Concordance of genotypic AMR prediction and lab AST
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Dear all,
Does anyone have pointers to studies on the concordance of (our) genotypic AMR predictions and actual lab AST results?
When I was at KCRI, we did one such analysis but only for our small collection of Acinetobacters[1]. What I would be interested in is a systematic large scale analysis.
As the SeqAfrica consortium (and with other partners in & outside Africa), we should have plenty of data to do such a study.
My interest in this used to be due to the obvious reason that we need to know how good our predictions are, but there's a much more compelling reason now to gather an extensive collection of *false negatives*. I'll explain later.
Marco
[1] https://academic.oup.com/jac/article/74/6/1484/5370329
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