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Table 1 – Specific enteric pathogen primers and probes for TaqMan Array Card used to determine the primary outcome

From: The Safe Start trial to assess the effect of an infant hygiene intervention on enteric infections and diarrhoea in low-income informal neighbourhoods of Kisumu, Kenya: a study protocol for a cluster randomized controlled trial

PATHOGENGENE TARGETFORWARD PRIMERREVERSE PRIMERPROBE SEQUENCERef
BACTERIA
AeromonasAerolysinTYCGYTACCAGTGGGACAAGCCRGCAAACTGGCTCTCGCAGTTCCAGTCCCACCACTT[2]
Campylobacter jejuni/C. colicadFCTGCTAAACCATAGAAATAAAATTTCTCACCTTTGAAGGTAATTTAGATATGGATAATCGCATTTTGACGATTTTTGGCTTGA[2]
Clostridium difficiletcdBGGTATTACCTAATGCTCCAAATAGTTTGTGCCATCATTTTCTAAGCCCTGGTGTCCATCCTGTTTC[2]
Enteroaggregative Escherichia coli (EAEC)aaiCATTGTCCTCAGGCATTTCACACGACACCCCTGATAAACAATAGTGCATACTCATCATTTAAG[2]
Enteroaggregative Escherichia coli (EAEC)aatACTGGCGAAAGACTGTATCATTTTTGCTTCATAAGCCGATAGATGGTTCTCATCTATTACAGACAGC[2]
Enterohemorrhagic E. coli (EHEC) 0157rdbETTTCACACTTATTGGATGGTCTCAACGATGAGTTTATCTGCAAGGTGATCTCTCTTTCCTCTGCGGTCCT[1]
Enteropathogenic
E. coli (EPEC)
eaeCATTGATCAGGATTTTTCTGGTGATACTCATGCGGAAATAGCCGTTAATACTGGCGAGACTATTTCAA[2]
Enteropathogenic
E. coli (EPEC)
bfpATGGTGCTTGCGCTTGCTCGTTGCGCTCATTACTTCTGCAGTCTGCGTCTGATTCCAA[2]
Enterotoxigenic
E. coli (ETEC) LT toxin
ETEC LTTTCCCACCGGATCACCAACAACCTTGTGGTGCATGATGACTTGGAGAGAAGAACCCT[2]
Enterotoxigenic
E. coli (ETEC) ST toxin
STh STpGCTAAACCAGYAGRGTCTTCAAAATGAATCACTTGACTCTTCAAAACCCGGTACARGCAGGATTACAACATGAATCACTTGACTCTTCAAAATGGTCCTGAAAGCATGAATGAACAACACATTTTACTGCT[2]
Salmonella enteritidisttrCTCACCAGGAGATTACAACATGGAGCTCAGACCAAAAGTGACCATCCACCGACGGCGAGACCGACTTT[2]
Shigella spp.virGTCAGAAAGGTAATTGGCATGGAAGAACCGCGCCCAAAGAAGGGCGGAATATT[1]
Vibrio choleraehlyAATCGTCAGTTTGGAGCCAGTTCGATGCGTTAAACACGAAGACCGATGCGATTGCCCAA[2]
PROCESS CONTROL
MS2MS2g1TGGCACTACCCCTCTCCGTATTCACGTACGGGCGACCCCACGATGACCACATCGATAGATCAAGGTGCCTACAAGC[2]
VIRUS
Adenovirus 40–41Fiber GeneAACTTTCTCTCTTAATAGACGCCAGGGGGCTAGAAAACAAAACTGACACGGGCACTCT[2]
Adenovirus broad speciesHexonGCCACGGTGGGGTTTCTAAACTTGCCCCAGTGGTCTTACATGCACATCTGCACCAGACCCGGGCTCAG[1]
Norovirus GIORF 1–2CGYTGGATGCGNTTYCATGACTTAGACGCCATCATCATTYACTGGACAGGAGATCGC[1]
Norovirus GIIORF 1–2CARGARBCNATGTTYAGR TGGATGAGTCGACGCCATCTTCATTCACATGGGAGGGCGATCGCAATCT[2]
RotavirusNSP3ACCATCTWCACRTRACCCTCTATGAGGGTCACATAACGCCCCTATAGCAGTTAAAAGCTAACACTGTCAAA[2]
PROTOZOAN
Giardia duodenalis Assemblage Atriosephosphate isomerase (TPI)TTCCGCCGTACACCTGTCGCGCTGCTATCCTCAACTGATTGCGGCAAACACGTCA[1]
Giardia duodenalis Assemblage Btriosephosphate isomerase (TPI)GATGAACGCAAGGCCAATAACTTTGATTCTCCAATCTCCTTCTTAATATTGCTCAGCTCGAGGC[1]
Cryptosporidium spp.18 s rRNAGGGTTGTATTTATTAGATAAAGAACCAAGGCCAATACCCTACCGTCTTGACATATCATTCAAGTTTCTGAC[2]
C. hominusLIB13TCCTTGAAATGAATATTTGTGACTCGAAATGTGGTAGTTGCGGTTGAAACTTACTTCGTGGCGGCGT[1]
C. parvumLIB13TCCTTGAAATGAATATTTGTGACTCGTTAATGTGGTAGTTGCGGTTGAACTATCTCTTCGTAGCGGCGTA[1]