From 8a971f871e91b309051e0a64d36fbbb1d2d402d5 Mon Sep 17 00:00:00 2001 From: Kat Holt Date: Tue, 17 Sep 2024 07:46:33 +0100 Subject: [PATCH] Update README.md to include carbs --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 5a5c8c6..2140ab2 100644 --- a/README.md +++ b/README.md @@ -52,7 +52,7 @@ The [Mykrobe](https://github.com/Mykrobe-tools/mykrobe) software provides a plat * the *acrB*-R717Q/L mutations associated with azithromycin resistance * plasmid replicons and major subtypes of the IncHI1 plasmid typically associated with multidrug resistance -Drugs for which resistance is typed are: `ampicillin`, `azithromycin`, `ceftriaxone`, `ciprofloxacin`, `chloramphenicol`, `sulfonamides`, `trimethoprim`, `trimethoprim-sulfamethoxazole`, `tetracycline`. The output is presented as an antibiogram, indicating resistant (R) or susceptible (S) predictions for each drug in each genome. +Drugs/classes for which resistance is typed are: `ampicillin`, `azithromycin`, `carbapenems`, `ceftriaxone`, `ciprofloxacin`, `chloramphenicol`, `sulfonamides`, `trimethoprim`, `trimethoprim-sulfamethoxazole`, `tetracycline`. The output is presented as an antibiogram, indicating resistant (R), intermediate (I), or susceptible (S) predictions for each drug in each genome. A full list of AMR/plasmid typing targets is in the file `typhimykrobe/AMR_genes_mutations_plasmids.csv` @@ -179,7 +179,7 @@ python parse_typhi_mykrobe.py --jsons *.json --prefix mykrobe_out * **max support for additional markers**: For any markers detected that are incongruent with the final genotype call, this column reports the percentage of reads supporting the marker allele at the best supported additional marker. * **additional markers**: Lists any markers that are incongruent with the final genotype call. Markers are separated by ';', and the format is identical to column _poorly supported markers_. The highest read support for any such marker is reported in the previous column. * **node support**: A list of all markers in the final genotype call with their Mykrobe quality calls (1, 0.5, or 0) and the read depths at the marker allele / reference allele (as per _poorly supported markers_ and _additional markers_). -* **resistance predictions**: Columns `ampicillin`, `azithromycin`, `ceftriaxone`, `ciprofloxacin`, `chloramphenicol`, `sulfonamides`, `trimethoprim`, `trimethoprim-sulfamethoxazole`, `tetracycline` indicate resistant (R) or susceptible (S) predictions for each genome. For `ciprofloxacin`, low-level resistance (associated with a single mutation or gene) is indicated as intermediate (I) and high-level resistance (multiple determinants) as R. A resistant (I/R) prediction is appended with the genes or mutations giving rise to that prediction. +* **resistance predictions**: Columns `ampicillin`, `azithromycin`, `carbapenems`, `ceftriaxone`, `ciprofloxacin`, `chloramphenicol`, `sulfonamides`, `trimethoprim`, `trimethoprim-sulfamethoxazole`, `tetracycline` indicate resistant (R) or susceptible (S) predictions for each genome. For `ciprofloxacin`, low-level resistance (associated with a single mutation or gene) is indicated as intermediate (I) and high-level resistance (multiple determinants) as R. A resistant (I/R) prediction is appended with the genes or mutations giving rise to that prediction. * **remaining columns** indicate presence (1) or absence (0) of each QRDR or _acrB_ mutation, AMR gene, or plasmid replicon as indicated by the header of the column. For the AMR genes, _specific alleles are **not detected**_ (with the exception of _dfrA_ and blaOXA, where Mykrobe can distinguish between _dfrA1_, _dfrA5_, _dfrA7_, _dfrA14_, _dfrA15_, _dfrA17_ and _dfrA18_; and blaOXA-7 and blaOXA-134). * **num QRDR**: Total number of mutations detected in the quinolone-resistance determining regions (QRDR) of genes _gyrA_, _parC_ and _gyrB_. * **IncHI1_ST6** indicates whether the IncHI1 replicon (from column IncHI1BR27) is pST6 (1) or not (0).