Table 1. Gene targets, primers and probes used in this study.

a) Initial real-time PCR (qPCR) for STI testing on samples

Trichomonas vaginalis: T. vaginalis specific repeat DNA fragment (amplicon 92 bp) [16]

TV_F: AAAGATGGGTGTTTTAAGCTAGATAAGG

TV_R: TCTGTGCCGTCTTCAAGTATGC

TV_P: [6FAM]AGTTCATGTCCTCTCCAAGCGTAAGT[BHQ1]

Mycoplasma genitalium: MgPa gene (amplicon 78 bp) [17]

MG_F: GAGAAATACCTTGATGGTCAGCAA

MG_R: GTTAATATCATATAAAGCTCTACCGTTGTTATC

MG_P: [6FAM]ACTTTGCAATCAGAAGGT[MGBNFQ]

Chlamydia trachomatis: The cryptic plasmid (amplicon 71 bp) [18]

CT_F: CATGAAAACTCGTTCCGAAATAGAA

CT_R: TCAGAGCTTTACCTAACAACGCATA

CT_P: [6FAM]TCGCATGCAAGATATCGA[MGBNFQ]

Neisseria gonorrhoeae: opa (amplicon 90 bp) [19]

NG_F: TTGAAACACCGCCCGGAA

NG_R: TTTCGGCTCCTTATTCGGTTTGA

NG_P: [6FAM]CCGATATAATCCGCCCTTCAACATCAG[BHQ1]

b) Targeted PCR (tPCR) for nanopore sequencing *

Trichomonas vaginalis: Nitroreductase family protein (ntr6; amplicon 746 bp)

TV_NTR6_BC_F:

5’TTTCTGTTGGTGCTGATATTGCCTTCATTGAATTTATTCGTTCAAAATT

TV_NTR6_BC_R:

5’ACTTGCCTGTCGCTCTATCTTCTTATTCAATGTATGTAACCTTTCTAA

Mycoplasma genitalium: 23S ribosomal RNA (amplicon 688 bp)

Mg 23S_BC_1992F:

5’ TTTCTGTTGGTGCTGATATTGCCCATCTCTTGACTGTCTCGG

Mg 23S_BC_2679R:

5’ ACTTGCCTGTCGCTCTATCTTCTCCTCTCGTACTAGAAGCAAAG

Chlamydia trachomatis: Major outer membrane protein 1 (omp1; amplicon 1060 bp)

CT_OMP1_BC_F:

5’ TTTCTGTTGGTGCTGATATTGCTTTGCCGCTTTGAGTTCTGCT

CT_OMP1_BC_R:

5’ ACTTGCCTGTCGCTCTATCTTCCAATACCGCAAGATTTTCTAGATTTC

Neisseria gonorrhoeae: gyrA (amplicon 1181 bp)

NG_gyrA_BC_F:

5’ TTTCTGTTGGTGCTGATATTGCATCCGCCACGACCACAAATT

NG_gyrA_BC_R:

5’ ACTTGCCTGTCGCTCTATCTTCATATTGGACAGTGCGACGGC

*developed in this study.