A comparison of oligonucleotide-based microarray and real-time PCR for the detection of sexually transmitted infections

AbstractObjectivesTo develop a simple DNA sequencing test for simultaneous identification and antimicrobial resistance (AMR) detection of multiple sexually transmitted infections (STIs).MethodsA total of 200 vulvo-vaginal swab samples from 200 female sex workers in Ecuador were initially tested by real-time PCR for Neisseria gonorrhoeae (NG), Chlamydia trachomatis (CT), Mycoplasma genitalium (MG) and Trichomonas vaginalis (TV). Samples positive for these STIs and controls were subjected to single gene targeted PCR MinION-nanopore sequencing by using the smartphone operated MinIT.ResultsAmong 200 vulvo-vaginal swab samples 43 were positive for at least one of the STIs by real-time PCR. Single gene targeted nanopore sequencing generally yielded higher pathogen specific reads in positive samples than negative controls. Of the 26 CT, NG or MG infections identified by real-time PCR, 25 were clearly distinguishable from the negative controls using sequence read count. Discrimination of TV positives from controls was poorer as many had low pathogen loads (cycle threshold > 35) with associated low sequence read counts. AMR analysis workflow indicated that 11% of the classified reads aligned with antibiotic resistance genes, all of which identified fluoroquinolone resistance in NG.ConclusionsSingle gene targeted nanopore sequencing for diagnosing and simultaneously identifying key antimicrobial resistance markers for four common STIs, associated with genital tract discharge in women shows promise. Further work to optimise accuracy, reduce costs and improve speed may allow sustainable approaches for managing STIs and emerging AMR in resource poor and laboratory limited settings.

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Accuracy of Curable Sexually Transmitted Infections and Genital Mycoplasmas Screening by Multiplex Real-Time PCR Using a Self-Collected Veil among Adult Women in Sub-Saharan Africa

Infectious Diseases in Obstetrics and Gynecology ◽

10.1155/2019/8639510 ◽

2019 ◽

Vol 2019 ◽

pp. 1-15

Author(s):

Zita Aleyo Nodjikouambaye ◽

Fabrice Compain ◽

Damtheou Sadjoli ◽

Ralph-Sydney Mboumba Bouassa ◽

Hélène Péré ◽

...

Keyword(s):

Sexually Transmitted Infections ◽

Real Time ◽

Real Time Pcr ◽

Sub Saharan Africa ◽

Molecular Testing ◽

Adult Women ◽

Sampling Device ◽

Sexually Transmitted ◽

Sub Saharan ◽

Genital Mycoplasmas

Background. Sexually transmitted infections (STIs) are highly prevalent in sub-Saharan Africa. Genital self-sampling may facilitate the screening of STIs in hard-to-reach remote populations far from large health care centers and may increase screening rates. The cross-sectional GYNAUTO-STI study was carried out to assess the performance of a novel genital veil (V-Veil-Up Gyn Collection Device, V-Veil-Up Pharma, Ltd., Nicosia, Cyprus) as a genital self-sampling device to collect genital secretions to diagnose STIs by molecular biology as compared to reference clinician-collected genital specimens, in adult African women. Methods. Adult women living in N’Djamena, the capital city of Chad, were recruited from the community and referred to the clinic for women’s sexual health “La Renaissance Plus”. A clinician obtained an endocervical specimen using flocked swab. Genital secretions were also obtained by self-collection using veil. Both clinician- and self-collected specimens were tested for common curable STIs (including Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium, and Trichomonas vaginalis) and genital Mycoplasma spp. by multiplex real-time PCR (Allplex™ STI Essential Assay, Seegene, Seoul, South Korea). Test positivities for both collection methods were compared by assessing methods agreement, sensitivity, and specificity. Results. A total of 251 women (mean age, 35.1 years) were prospectively enrolled. Only seven (2.8%) women were found to be infected with at least one common STIs [C. trachomatis: 3 (1.2%), N. gonorrhoeae: 1 (0.4%), M. genitalium: 4 (1.6%) and T. vaginalis: 1 (0.4%)], while the prevalence of genital mycoplasmas was much higher (54.2%) with a predominance of Ureaplasma parvum (42.6%). Self-collection by veil was non-inferior to clinician-based collection for genital microorganisms DNA molecular testing, with “almost perfect” agreement between both methods, high sensitivity (97.0%; 95%CI: 92.5-99.2%), and specificity (88.0%; 95%CI: 80.7-93.3%). Remarkably, the mean total number of genital microorganisms detected per woman was 1.14-fold higher in self-collected specimens compared to that in clinician-collected specimens. Conclusions. Veil-based self-collection of female genital secretions constitutes a convenient tool to collect in gentle way cervicovaginal secretions for accurate molecular detection of genital bacteria. Such sampling procedure could be easily implemented in STIs clinics in sub-Saharan Africa.

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Usefulness of a novel multiplex real-time PCR assay for the diagnosis of sexually-transmitted infections

Enfermedades Infecciosas y Microbiología Clínica ◽

10.1016/j.eimc.2015.10.014 ◽

2016 ◽

Vol 34 (8) ◽

pp. 471-476 ◽

Cited By ~ 16

Author(s):

Gema Fernández ◽

Elisa Martró ◽

Victoria González ◽

Verónica Saludes ◽

Elisabet Bascuñana ◽

...

Keyword(s):

Sexually Transmitted Infections ◽

Real Time ◽

Real Time Pcr ◽

Pcr Assay ◽

Sexually Transmitted

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Bacterial etiology of sexually transmitted infections at a STI clinic in Ghana; use of multiplex real time PCR

Ghana Medical Journal ◽

10.4314/gmj.v50i3.5 ◽

2016 ◽

Vol 50 (3) ◽

pp. 142-148

Author(s):

Augustina A Sylverken ◽

Ellis Owusu-Dabo ◽

Denis D Yar ◽

Samson P Salifu ◽

Nana Yaa Awua-Boateng ◽

...

Keyword(s):

Sexually Transmitted Infections ◽

Real Time ◽

Real Time Pcr ◽

Pathogen Detection ◽

Clinical Manifestations ◽

Diagnostic Tools ◽

Transmitted Infection ◽

Sexually Transmitted ◽

Asymptomatic Patients ◽

Syndromic Approach

Background: Most sexually transmitted infection (STI) management efforts focus on the syndromic approach to diagnose and treat patients. However, most women with STIs have been shown to be entirely asymptomatic, or if symptoms exist, are often missed when either clinical or conventional bacteriologic diagnostic tools are employed.Methods: We assessed the performance of a multiplex real time PCR assay to describe other potential pathogens that could be missed by conventional bacteriological techniques in 200 women attending a routine STI clinic in Kumasi, Ghana.Results: Although a total 78.00% of the women were asymptomatic, 77.1% of them tested positive for at least one bacterial STI pathogen. Mycoplasma genitalium was the most commonly detectable pathogen present in 67.5% of all women. Of those testing positive, 25.0% had single infections, while 38.0% and 19.5% had double and triple infections respectively. Altogether, 86.54% and 90.91% of the symptomatic and asymptomatic women respectively tested positive for at least one pathogen (p<0.05). There were no significant associations (p<0.05) between the clinical manifestations of the symptomatic women and the pathogens detected in their samples.Conclusions: Our study confirmed the importance of complementing the syndromic approach to STI management with pathogen detection and most importantly recognise that STIs in women are asymptomatic and regular empirical testing even for both symptomatic and asymptomatic patients is critical for complete clinical treatment.Funding: EOD (Ellis Owusu-Dabo Research working group, KCCR)Keywords: Etiology, Syndromic, Sexually Transmitted Infections, Multiplex real time PCR

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