I am working in the field of veterinary infectious diseases and antimicrobial resistance (AMR) under a One Health perspective. In surveillance studies, multiplex PCR is widely used to detect specific resistance genes because of its relatively low cost, rapid turnaround, and straightforward analysis. However, with the increasing availability of whole genome sequencing (WGS), which provides a much broader genetic overview (resistome, virulome, phylogeny, plasmid content), there seems to be a shift toward using WGS as the gold standard.

The challenge I see, particularly in low- and middle-income countries, is balancing cost, infrastructure, bioinformatics expertise, and data interpretation against the additional insights WGS provides. For example, PCR is often sufficient for targeted detection of common AMR determinants, but it lacks resolution when novel or less-characterized resistance mechanisms are involved.

My question is, in practical terms for veterinary AMR surveillance (especially in low-resource settings), is multiplex PCR still the method of choice, or has WGS become more cost-effective and feasible considering its data-to-cost ratio?

I would appreciate perspectives from colleagues working in AMR surveillance, particularly those who have transitioned from PCR-based methods to WGS.