Next Generation Antimicrobial Resistance Profiling Using Whole Genome Sequences

Contributed by Darwin Bandoy, DVM

Antimicrobial resistance is a key issue as pathogens develop resistance due to the misuse of antimicrobials in food animals. While some countries have already banned the use of antibiotics as growth promotants, emerging economies find it difficult to implement due to numerous factors. From a monitoring point of view, large harmonization of standards make it difficult to compare the AMR profile across different countries. Whole-genome sequencing has recently been used to profile antimicrobial resistance and is shown to be robust in detecting the antibiotic resistance genes for the most commonly used antibiotics. One of my favorite tools is Abricate by Torsten Seeman (who also developed the hugely popular Prokka tool). This tool allows me to perform in silico AMR profiling of whole genomes of pathogenic organisms.

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