“…In order to determine the presence of penA mosaic XXXIV and other mosaic types with homologous sequences in the target region, which include X, XXVII, XXXVII, XLII, LI, LII, LIII, LIV, LV, and LVIII (determined in silico by performing BLAST [23] against a sequence database of penA mosaic patterns, courtesy of Magnus Unemo), some of which have been associated with reduced susceptibility to ESCs (24, 25), we designed a novel real-time PCR based on an existing TaqMan PCR assay (26). Modifications in primer and probe sequences were made to convert the assay to FRET probe format due to the incompatibility of the TaqMan assay with the previously validated FRET probebased gyrA genotyping assay (16) (see Table S1 in the supplemental material).…”