The present invention is concerned with PCR-based detection methods and kits for the identification, differentiation, and quantification of different bacterial strains (e.g., Gram-negative bacterial strains), and also association of two or more PCR-positive genes to a single genome. The methods generally comprise carrying out PCR reactions using at least a first PCR primer set and/or probe for at least one target nucleic acid; and a second PCR primer set and/or probe for at least a second target nucleic acid. Positive PCR reaction products are then detected to determine test samples containing positive PCR reaction products for both the first and second target nucleic acids. This information can be used to calculate the gene association rate to determine whether the sample contains, for example, Shiga toxin-producing E. coli of the O-type serogroup.