ShortBred AMR data

[Josie Blair]

Good Afternoon, 

I recently ran several nanopore sequencing runs on blood cultures through EDGE with Gene Family Analysis searching for antimicrobial resistances to compare to Phoenix and phenotypic disc-diffusion studies. 

What criteria is used for these identified genes from Shortbred? Some genes such as mecA are alone indicative of MRSA, so hits for this would confer resistances, however, other genes identified such as blaR1, Erm23S, arna, etc need SNPs/mutations in order to confer resistances. 

Does ShortBred identify just the gene or is it also identifying mutations in these genes and counting them as positive hits for drug-resistance? 

Please see example data in question attached. 

Thank you! 

Josie Blair 

[Lo, Chien-Chi]

Hi,

 

According the my understanding, the ShortBRED is a tool to screen a metagenome or metatranscriptome against a given AMR marker set to profile the presence/absence and relative abundance of the AMR proteins. It based on RAPsearch2 software for fast protein similarity search from short reads. EDGE allows user to adjust default identity and length % threshold (see attached screenshot when user click on addition options).  I don’t think ShortBRED will identify mutations in these genes.

 

Thanks,

Chienchi

 

 

 

 

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[Lo, Chien-Chi]

Hi,

 

Just another thoughts on your question. Since your data is from Nanopore sequencing. The quality of the raw reads may not good enough for SNP/mutations detection and it may have many false variants call. EDGE can assemble nanopore reads and use contig-based gene family analysis which uses RGI to search the AMR genes from CARD. The result of RGI does report SNPs.

 

Thanks,

Chienchi

To view this discussion on the web visit https://groups.google.com/d/msgid/edge-users/CF188EF2-74C9-45BE-B71D-EE957C7BC5D0%40lanl.gov.

[Josie Blair]

Thanks so much you’ve been so helpful! 

Sent from my iPhone

On Jan 18, 2023, at 3:36 PM, Lo, Chien-Chi <chie...@lanl.gov> wrote:



Hi,

 

Just another thoughts on your question. Since your data is from Nanopore sequencing. The quality of the raw reads may not good enough for SNP/mutations detection and it may have many false variants call. EDGE can assemble nanopore reads and use contig-based gene family analysis which uses RGI to search the AMR genes from CARD. The result of RGI does report SNPs.

 

Thanks,

Chienchi

 

From: "'Lo, Chien-Chi' via edge-users" <edge-...@googlegroups.com>
Reply-To: Chien-Chi Lo <chie...@lanl.gov>
Date: Tuesday, January 17, 2023 at 2:27 PM
To: Josie Blair <josie...@gmail.com>, edge-users <edge-...@googlegroups.com>
Subject: Re: [EXTERNAL] ShortBred AMR data

 

Hi,

 

According the my understanding, the ShortBRED is a tool to screen a metagenome or metatranscriptome against a given AMR marker set to profile the presence/absence and relative abundance of the AMR proteins. It based on RAPsearch2 software for fast protein similarity search from short reads. EDGE allows user to adjust default identity and length % threshold (see attached screenshot when user click on addition options).  I don’t think ShortBRED will identify mutations in these genes.

 

Thanks,

Chienchi