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)

BLAST E-value: basic local alignment search tool expected value