Table 1.

Characteristics of included studies

Author and year (Reference) // Included infections	Review outcome the main focus of the study? // Aim of the study	Tests performed, (acronym for the NAAT)	Specimens/sites (in women) // Comments	PIS definition // Comments on discrepant analysis
Chernesky M et al 27 (2006) CT	No To compare detection thresholds and inhibitor and infection rates from different specimens	APTIMA Combo 2, (TMA AC2) ProbeTec ET, (SDA ProbeTec ET) Amplicor, (PCR AMP)	3 EC, 3 CCVS and FCU divided into three aliquots Each sample was tested as spiked (with added CT) or without added CT; seemingly all the tests were done to all the samples	≥1 site positive by ≥2 different tests or two specimens positive in a single test (≥2 out of 9 specimen-tests done); VS included in PIS No discrepant analysis described
Cherneskey M et al 31 (2014) CT & NG	No To compare the performance of four second-generation NAATs with FCU and VS	APTIMA Combo 2, (TMA AC2) RealTime CT/NG, (PCR RealTime) ProbeTec CT/GC Qx, (SDA ProbeTec CT/GC Qx) Cobas CT/NG, (PCR Cobas CT/NG)	1 FCU and 4 SCVS Each sample was tested as spiked (with added CT) or without added CT; all the tests were done to all the samples	≥2 of the four assays were positive for any specimen type; VS included in PIS No discrepant analysis described
Cosentino LA et al 28 (2003) CT & NG	Yes To compare vaginal swab specimens to endocervical swab specimens for the detection of CT and NG	ProbeTec ET, (SDA ProbeTec ET) Amplicor, (PCR AMP) Thayer-Martin medium and chocolate agar (for NG culture) LCx, (LCR) for discrepant results	3 EC, 2 (presumably clinician-obtained) VS. One EC used for NG culture CT was tested by PCR and SDA; NG (EC) was tested for by culture and SDA	Positive result by two different molecular tests for CT or for NG by culture or by two molecular tests; VS included in PIS Discrepant analysis for discordant results by LCR
Gaydos CA et al 25 (2010) CT & NG	No To compare the performance of the new RealTime CT/NG assay with the Aptima Combo two assay	RealTime CT/NG, (PCR RealTime) – index APTIMA Combo 2, (TMA AC2) – reference ProbeTec ET, (SDA ProbeTec ET) – reference NG culture	4 EC, 1 SCVS, 2 CCVS, three urine Only one NAAT performed on the SCVS (this test was not used to define PIS); results for this are not presented	≥1 positive result by both of the two reference NAATs, additionally for NG if culture positive the subject was defined as infected. Infection absent if ≥1 reference NAAT was negative for all sample types Discrepant analysis: for CT retested discordant results, for NG not done
Hook, E et al 23 (1997) NG	Yes To evaluate patient-obtained vaginal specimens tested with culture and LCR assays for NG compared with clinician-collected specimens	LCx, (LCR) Modified Thayer-Martin medium (for NG culture)	3 SCVS, 3 EC (one sample at each site not part of this study as processed for CT)	Culture positive from either site; or LCR positive and culture negative with a positive confirmatory LCR; VS is included in PIS Discrepant analysis with, alternative TMA with different target site to confirm discordant results
Le Roy C et al 24 (2012) CT & NG*	No, data extracted based on their reporting Determine clinical performance of Bio-Rad CT/NG/MG assay for detection of CT, NG and Mycoplasma genitalium	Dx CT/NG/MG Assay, (qPCR) – index test Cobas TaqMan CT, (qPCR TaqMan) - reference NG culture	Symptomatic: 2 SCVS, 2 EC and 2 FCU. Asymptomatic: 2 SCVS and FCU. More tests done on symptomatic patients, but all samples seem to have been treated the same.	Study definition: At least two positive results from either of the two assays. We determined PIS based on test results for FCU and VS (which were available for all patients, see online supplementary material for further information); all infected patients had ≥2 positive tests and a positive test at both sites; VS is included in PIS Discrepant analysis used for discordant results
Schachter J et al 30 (2005) CT & NG	Yes To evaluate the performance of APTIMA assays on vaginal swabs for CT and NG	APTIMA CT, (TMA ACT) APTIMA GC, (TMA AGC) APTIMA Combo 2, (TMA AC2) ProbeTec ET, (SDA ProbeTec ET)	1 FCU, 1 SCVS, 1 CCVS, 2 EC swabs All samples tested with three TMAs (two for CT and two for NG) FCU and 1x EC swab were also tested with ProbeTec ET)	Infected if either BD or AC2 were positive on FCU or EC. VS not included in PIS No discrepant analysis described
Shipitsyna E et al 26 (2008) CT	No To evaluate the performance of five PCRs and a recently introduced nucleic acid sequence-based amplification (NASBA) assay	Different ‘in-house’ PCRs tested: cPCR-DT, rtPCR-DT, cPCR-Ly, cPCR-Ep, rtPCR-Ep, real-time NASBA assay Reference methods: Amplicor, (PCR AMP) LightMix, (PCR Lightmix)	Used the subsample who had four specimens collected each: 2 EC and 2 VS All sample sites tested using reference NAAT and at least three other NAATs	Several Russian PCRs used on the sample and the sample was considered true positive if a positive result by a Russian PCR was confirmed by the reference tests; VS included in PIS Discrepant analysis for discordant results
Stary A et al 29 (1998) CT	No To compare TMA assay with LCR assay in detection of CT in genital tract with different specimen types	Aptima CT, (TMA ACT) LCx, (LCR) McCoy cell culture Direct-fluorescent antibody assay (DFA) or alternative TMA for confirming discrepant results	3 EC, 3 CCVS, FCU EC and VS tested with LCR, TMA and culture. FCU tested with LCR and TMA	Positive culture at any site or positive result by both NAATs in one site, or one positive NAAT confirmed with discrepant analysis; VS included in PIS. Discrepant analysis with DFA or TMA with different target site to confirm discordant results

Discrepant analysis : We define discrepant analysis to have occurred in situations where sample was positive for only one of the tests used. In these instances another test was done.

*Too few infections with gonorrhoea for analysis.

Tests used:LCR; PCR AMP (PCR Amplicor); PCR Cobas CT/NG (PCR Cobas CT/NG); PCR ‘In house’; PCR RealTime (PCR RealTime); qPCR TaqMan (Quantitative PCR TaqMan); qPCR DxCT/NG/MG (Quantitative PCR DxCT/NG/MG); PCR LightMix, (PCR Lightmix); NASBA; SDA ProbeTec ET; SDA ProbeTec CT/GC Qx; TMA AC2; TMA ACT; TMA AGC; CT; NG; CCVS; EC; FCU; SCVS; VS.

AMP, Amplicor; CCVS, clinician-collected vaginal specimens; CT, Chlamydia trachomatis; EC, endocervical swabs; FCU, first catch urine; LCR, ligase chain reaction; NASBA, nucleic acid sequence-based amplification; NG, Neisseria gonorrhoea; PIS, patient infection status; qPCR, quantitative PCR; SCVS, self-collected vaginal specimens; SDA, strand displacement amplification; TMA AC2, transcription-mediated amplification Aptima Combo-2; TMA ACT, transcription-mediated amplification Aptima CT; TMA AGC, transcription-mediated amplification Aptima GC; VS, vaginal specimen.