I know we have several methods to look for a specific gene but which one is the most accurate when it come to look for bacterial antibiotics resistance gene, and which one will be the cheapest.
Minimal inhibitory concentration (MIC) assessment remains the classical quantitative method. In contrast, the molecular tools, categorized as qualitative, are very accurate for antibiotic resistance gene detection. The attached paper below gives a short review of different molecular methods employed in AMR research.
DNA microarray and DNA chip are the same method, this technique will help you detect more than 100 genes that encode resistance to antibiotics, toxins and biofilm production...etc. However, it's an expensive method, the least expensive method is PCR, with this technique you can target the resistance genes that you're looking for.