Table 3 Nucleotide primers used in multiplex PCR and m-FISH probes
Bacterial gene target | nPCR primers | Multiplex PCR primers | m-FISH probe |
|---|---|---|---|
Mycobacterium avium subspecies paratuberculosis (MAP) IS900 | P90: 5′-GTTCGGGGCCGTCGCTTAGG-3′ (BLAST E-value: 2e−04) P91: 5′-GAGGTCGATCGCCCACGTGA-3′ (BLAST E-value: 2e−04) AV1: 5′-ATGTGGTTGCTGTGTTGGATGG-3′ (BLAST E-value: 1e−05) AV2: 5′-CCGCCGCAATCAACTCCAG-3′ (BLAST E-value: 5e−04) | AV1: 5′-ATGTGGTTGCTGTGTTGGATGG-3′ (BLAST E-value: 1e−05) AV2: 5′-CCGCCGCAATCAACTCCAG-3′ (BLAST E-value: 5e−04) | AV1: 5′-AF488 ATGTGGTTGCTGTGTTGGATGG-3′ (BLAST E-value: 1e−05) |
Mycobacterium avium complex (MAC) IS1311 | NA | Forward: 5′-AAACGACCAAGGATCACTACCGAG-3′ (BLAST E-value: 1e−06) Reverse: 5′-GTCGAGGAACACATACGGGAAGT-3′ (BLAST E-value: 4e−06) | NA |
Non-pathogenic E. coli strain K-12 18s | NA | Forward: 5′-CCGCATAACGTCGCAAGACC-3′ (BLAST E-value: 6e−04) Reverse: 5′-CGTAGGAGTCTGGACCGTGTC-3′ (BLAST E-value: 2e−04) | 5′-AF647 GGTCTTGCGACGTTATGCGG-3′ (BLAST E-value: 6e−04) |
AIEC strain LF82 gipA | NA | Forward: 5′-GCTGTGTGCGCTTCGTCTAC-3′ (BLAST E-value: 4e−08) Reverse: 5′-GATGGTAATTCTCGACTCCAGCGA-3′ (BLAST E-value: 2e−07) | 5′-AF568 GTAGACGAAGCGCACACAGC-3′ (BLAST E-value: 4e−08) |
K. pneumoniae 23 s | NA | Forward: 5′-TGGCAGTCAGAGGCGATGAAG-3′ (BLAST E-value: 1e−04) Reverse: 5′-CTTTCCCTCACGGTACTGGTTCA-3′ (BLAST E-value: 0.002) | 5′-AF546 CTTCATCGCCTCTGACTGCCA-3′ (BLAST E-value: 0.001) |