AMR detection workflows

Escherichia coli

Doi: 10.1099/mgen.0.000531

With this galaxy pipeline you can use Escherichia coli next generation sequencing results to predict bacterial AMR phenotypes and compare the results against gold standard E. coli phenotypic isolates.

This pipeline is based on the work of Sciensano, Belgium.

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Salmonella enterica

Food
Doi: 10.3389/fmicb.2020.00549

With this galaxy pipeline you can use Salmonella sp. next generation sequencing results to predict bacterial AMR phenotypes and compare the results against gold standard Salmonella sp. phenotypes obtained from food.

This pipeline is based on the work of the National Food Agency of Canada.

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Salmonella enterica

Human health
Doi: 10.3390/microorganisms10020292

Correlation between Phenotypic and In Silico Detection of Antimicrobial Resistance in Salmonella enterica in Canada Using Staramr.

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Contributors

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