Reply to 细菌抗生素耐药性分析 on Sat, 11 Jun 2022 06:41:20 GMT

anneng — Sat, 11 Jun 2022 06:41:20 GMT

https://www.illumina.com/products/by-type/informatics-products/basespace-sequence-hub/apps/goseqit-aps-bacterial-analysis-pipeline.html
illumina basespace的耐药基因和毒力的报告

Reply to 细菌抗生素耐药性分析 on Sat, 11 Jun 2022 09:32:01 GMT

anneng — Sat, 11 Jun 2022 09:32:01 GMT

https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000748?crawler=true
ResFinder – an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes
在ResFinder的文献中提到了和CARD的不同 Resfinder的目标是寻找更具临床意义的耐药基因，而且之包括后天基因。
using CARD as a basis we decided to also create our own database for ResFinder. Based on literature searches we manually curated the database, with the attempt to only include ARGs that had been horizontally acquired
文章还提到除了序列的水平转移，突变也会导致耐药。ResFinder使用 PointFinder 来处理突变耐药性。突变耐药性数据库当前是针对每个物种的。 Salmonella, Escherichia coli and Campylobacter jejuni and Campylobacter coli
AMR can be acquired either through horizontal gene transfer or as mutations in already existing genes.

下载代码构建docker
https://bitbucket.org/genomicepidemiology/resfinder/src/master/

git clone https://git@bitbucket.org/genomicepidemiology/resfinder.git
# Go to ResFinder directory
cd path/to/resfinder
# Build docker image with name resfinder
docker build -t resfinder . --network host
//下载和构建数据库
git clone https://git@bitbucket.org/genomicepidemiology/resfinder_db.git db_resfinder
# Go to the database directory
cd path/to/db_resfinder
python3 INSTALL.py

cd path/to/resfinder/
mkdir results

# Run with raw data (this command mounts the results to the local directory "results")
docker run --rm -it -v $(pwd)/db_resfinder/:/usr/src/db_resfinder -v $(pwd)/results/:/usr/src/results resfinder -ifq /usr/src/tests/data/test_isolate_01_1.fq /usr/src/tests/data/test_isolate_01_2.fq -acq -db_res /usr/src/db_resfinder -o /usr/src/results

# Run with assembled data (this command mounts the results to the local directory "results")
docker run --rm -it -v $(pwd)/db_resfinder/:/usr/src/db_resfinder  -v $(pwd)/results/:/usr/src/results resfinder -ifa /usr/src/tests/data/test_isolate_01.fa -acq -db_res /usr/src/db_resfinder -o /usr/src/results

Reply to 细菌抗生素耐药性分析 on Sat, 11 Jun 2022 03:40:39 GMT

anneng — Sat, 11 Jun 2022 03:40:39 GMT

https://www.uspharmacist.com/article/understanding-antimicrobial-resistance
There are two types of bacterial resistance: intrinsic and acquired
细菌耐药性分内生和后天两种。
In intrinsic resistance, the antibiotic never possessed activity against the pathogen
Acquired resistance is achieved through the transfer of genetic material that confers resistance.