Primers used for PCR and sequence and fragment analyses for <i>hmbR</i> and <i>hpuA</i>.

aPurpose; conditions bCharacterisation of homopolymeric tract and closely flanking regions; PCR - [MgCl2] = 2.5 mM, 25 (up to 45 for direct non-culture fragment analysis) cycles of (95°C – 30 seconds, 53°C – 30 seconds, 72°C – 60 seconds). Sequence analysis annealing temperature = 53°C. For fragment analysis, primers hmbR-RF3 and hpuA350Rev were FAM-labeled. c‘Round 1’ nested PCR for non-culture characterization of homopolymeric tract and closely flanking regions; [MgCl2] = 3 mM, 45 cycles of (95°C – 30 seconds, 56°C – 30 seconds, 72°C – 60 seconds). d‘Round 2’ nested PCR for non-culture characterization of homopolymeric tract and closely flanking regions; [MgCl2] = 3 mM, 25 cycles of (95°C – 30 seconds, 56°C – 30 seconds, 72°C – 60 seconds). eConfirmation of presence of exl3 (that replaces hmbR); [MgCl2] = 3 mM, 35 cycles of (95°C for 30 seconds, 56°C for 30 seconds, 72°C for 60 seconds). f’Round 1’ nested PCR for non-culture characterization of homopolymeric tract and closely flanking regions; [MgCl2] = 3 mM, 45 cycles of (95°C – 30 seconds, 57°C – 30 seconds, 72°C – 150 seconds). g‘Round 2’ nested PCR for non-culture characterization of homopolymeric tract and closely flanking regions; [MgCl2] = 3 mM, 25 cycles of (95°C – 30 seconds, 59°C – 30 seconds, 72°C – 60 seconds). hConfirmation of absence of hpuA; [MgCl2] = 3 mM, 35 cycles (95°C – 30 seconds, 53°C – 30 seconds, 72°C – 180 seconds). Seq = sequence analysis Frag = fragment analysis