Antimicrobial resistance surveillance systems and data generation by whole genome sequencing

The emergence and steady increase in the incidence of antimicrobial resistance (AMR) in bacteria from food animals is a grave threat of public health concern. The World Health Organization (WHO) has called for efforts at global level to map the extent and depth of AMR by launching and intensifying AMR surveillance incorporating One Health initiatives. The call by WHO has been heeded by national governments globally, however, surveillance efforts in different regions are not matched in One Health criteria and many surveillance Systems (SS) are not integrated. The measurement of the extent of AMR prevalence is routinely practiced by sampling, isolation of index bacteria, and subjecting isolates to common phenotypic Antimicrobial Susceptibility Testing (AST) methods. However, the data generated by these methods have their own set of limitations. Although the genomic methods for AMR monitoring have taken rapid strides, still the phenotypic methods of testing are basic tools employed. The European Union (EU) has recently gone ahead with a SS which includes Whole Genome Sequencing (WGS) as one of the futuristic methods for AMR surveillance. WGS is a rapid method with potential to unravel the complete gamut of AMR genes and mutations in the AMR strains. It is thus important to integrate WGS as a method for AMR surveillance.