TABLE 1.
Primers and PCR cycling parameters for the detection of various potential bacterial pathogens
| Organism | Primer name | Primer sequence (5′–3′) | PCR cycling parameters | Gene (size [bp]) | Reference(s) |
|---|---|---|---|---|---|
| Universal | fDD2 | CCGGATCCGTCGACAGAGTTTGATCITGGCTCAG | 3 min at 94°C; 30 cycles of 94°C for 30 s, 53°C for 30 s, 72°C for 1.5 min | 16S rRNA (1,600) | 29 |
| rPP2 | CCAAGCTTCTAGACGGITACCTTGTTACGACTT | ||||
| Legionella spp. | JFP | AGGGTTGATAGGTTAAGAGC | 5 min at 95°C; 40 cycles of 94°C for 1 min, 57°C for 1.5 min, 72°C for 1 min | Attachment invasion locus gene (386) | 30 |
| JRP | CCAACAGCTAGTTGACATCG | ||||
| Aeromonas spp. | Aero-F | TGTCGGSGATGACATGGAYGTG | 2 min at 95°C; 35 cycles of 94°C for 1 min, 62°C for 1 min, 72°C for 2.5 min | Aerolysin (720) | 31 |
| Aero-R | CCAGTTCCAGTCCCACCACTTCA | ||||
| Shigella spp. | IpaH-F | CCTTGACCGCCTTTCCGATA | 2 min at 95°C; 35 cycles of 94°C for 1 min, 62°C for 1 min, 72°C for 2.5 min | Invasion plasmid antigen H (606) | 31 |
| IpaH-R | CAGCCACCCTCTGAGGTACT | ||||
| Salmonella spp. | IpaB-F | GGACTTTTTAAAAGCGGCGG | 2 min at 95°C; 35 cycles of 94°C for 1 min, 62°C for 1 min, 72°C for 2.5 min | Invasion plasmid antigen B (314) | 31 |
| IpaB-R | GCCTCTCCCAGAGCCGTCTGG | ||||
| Pseudomonas spp. | PA-GS-F | GACGGGTGAGTAATGCCTA | 2 min at 95°C; 25 cycles of 94°C for 20 s, 54°C for 20 s, 72°C for 40 s | 16S rRNA (618) | 32 |
| PA-GS-R | CACTGGTGTTCCTTCCTATA | ||||
| Campylobacter spp. | IC-F | CTAGAGTACAAACTAATAAGTCTC | 3 min at 95°C; 30 cycles of 94°C for 45 s, 52°C for 45 s, 72°C for 45 s | Flanking regions of ITS gene (700) | 33 |
| IC-R | ATTCTAAAACGCATCACTTCCTTG | ||||
| Yersinia spp. | 227Fmod | GTCTGGGCTTTGCTGGTC | 5 min at 95°C; 40 cycles of 94°C for 20 s, 60°C for 20 s, 72°C for 15 s | ompF (428–465) | 34 |
| 669R | GCGTCGTATTTAGCACCAACG | ||||
| Klebsiella spp. | gryA-F | CGCGTACTATACGCCATGAACGTA | 3 min at 95°C; 35 cycles of 94°C for 1 min, 50°C for 30 s, 72°C for 30 s | Gyrase A gene (383) | 35 |
| gyrA-C | ACCGTTGATCACTTCGGTCAGG | ||||
| C. parvum | ExCry1 | GCCAGTAGTCATATGCTTGTCTC | 5 min at 95°C; 10 min at 80°C; 45 cycles of 94°C for 45 s, 53°C for 1 min, 72°C for 45 s | 18S rRNA ribosomal unit (840) | 36 |
| ExCry 2 | ACTGTTAAATAGAAATGCCCCC | ||||
| C. parvum | NesCry3 | GCGAAAAAACTCGACTTTATGGAAGGG | 5 min at 95°C; 10 min at 80°C; 35 cycles of 94°C for 25 s, 65°C for 1 min, 72°C for 25 s | 18S rRNA ribosomal unit (590) | |
| NesCry4 | GGAGTATTCAAGGCATATGCCTGC | ||||
| G. lamblia | Gia2029 | AAGTGTGGTGCAGACGGACTC | 5 min at 94°C; 35 cycles of 94°C for 30s, 65°C for 30 s, 72°C for 1 min | 16S rRNA ribosomal unit (497) | 37, 38 |
| Gia2150c | CTGCTGCCGTCCTTGGATGT | ||||
| G. lamblia | RH11 | CATCCGGTCGATCCTGCC | 5 min at 94°C; 40 cycles of 94°C for 30s, 55°C for 30 s, 72°C for 1 min | 16S rRNA ribosomal unit (292) | |
| RH4 | AGTCGAACCCTGATTCTCCGCCAGG |