Hi Marco, and everyone.
I don’t know if this will be helpful - but please check the attached pre-print: https://papers.ssrn.com/sol3/papers.cfm?abstract_id=4652526 We compared 3104 AMR genomic results with phenotypic AST results and got the attached table (please do not distribute - work is under review)
Useful studies for penicillin resistance comparison between phenotypic and genomic results are attached below for S. pneumoniae - as an example (the papers are related). The findings of these papers are incorporated in the S. pneumoniae pipeline that we use and similar definitions are adapted in the above pre-print.
https://pubmed.ncbi.nlm.nih.gov/27302760/ - Penicillin-binding protein transpeptidase signatures for tracking and predicting β-lactam resistance levels in Streptococcus pneumoniae https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4017-7 - Validation of β-lactam minimum inhibitory concentration predictions for pneumococcal isolates with newly encountered penicillin binding protein (PBP) sequences
I'm happy to chat more about this.
Best, Cebile
On 14/05/2024, 11:14, "Marco van Zwetselaar via Bioinfo List" <bioinfo-list@seqshare.org mailto:bioinfo-list@seqshare.org> wrote:
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 https://academic.oup.com/jac/article/74/6/1484/5370329
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