https://doi.org/10.17037/DATA.00002340
Studies employing 16S rRNA sequencing to evaluate the cervicovaginal microbiota suggest that high-intensity urinary S. haematobium infection, in the absence of investigation for genital involvement, may alter cervicovaginal microbiota diversity. In addition, studies reporting qPCR-defined FGS have either not investigated or reported STI prevalence or STI prevalence has been correlated with visual FGS findings. In this cross-sectional study we utilized qPCR to detect Schistosoma DNA in the female genital tract and evaluated the association of PCR-defined FGS with the concentration and presence of key markers of the cervicovaginal microbiota, including STI. The cross-sectional bilharzia and HIV (BILHIV) study was nested in HPTN 071 (PopART), a cluster randomized trial to measure the impact of an HIV-1 combination prevention package. In HPTN 071 (PopART), HIV-1 incidence was measured in a Population Cohort at baseline, 12, 24, and 36 months. Between January and August 2018, after the 36-month HPTN 071 (PopART) visit, community workers made home visits to women expressing interest in the BILHIV study. Eligible women were 18-31 years, not pregnant, sexually active, and resident in one of two urban communities that participated in HPTN 071 (PopART) in Livingstone, Zambia.
The cross-sectional bilharzia and HIV (BILHIV) study was nested in HPTN 071 (PopART), a cluster randomized trial to measure the impact of an HIV-1 combination prevention package. The same ethics approvals apply.
The Microbiota dataset contains the following variable.
| Variable name | Variable label | Answer code | Answer label |
| BILID1 | Participant ID number | Integer | |
| definite1 | FGS status. Study generated variable - presence of any genital PCR positive (women with probable FGS excluded) | ||
| 0 | Negative | ||
| 1 | Positive | ||
| Null | 25 women with probable FGS are made missing | ||
| fgscat | FGS status category (study generated variable) | ||
| 0 | negative FGS | ||
| 1 | probable FGS | ||
| 2 | definite FGS | ||
| edu3 | What is your level of education? | ||
| 0 | No schooling/Any primary school | ||
| 1 | Any secondary school | ||
| 2 | Trade/degree/or higher | ||
| crowding1 | Including yourself, how many people are living in your household? | Integer | |
| partners1 | How many sexual partners have you had in your lifetime? | ||
| 0 | 1 lifetime partner | ||
| 1 | 2 lifetime partners | ||
| 2 | 3 lifetime partners | ||
| 3 | 4+ lifetime partners | ||
| ngbinary | STI status: Lab data from the BILHIV study - Neisseria gonorrhoaea status | ||
| 0 | Negative | ||
| 1 | Positive | ||
| tvbinary | STI status: Lab data from the BILHIV study - Trichomonas vaginalis status | ||
| 0 | Negative | ||
| 1 | Positive | ||
| mgbinary | STI status: Lab data from the BILHIV study - Mycoplasma genitalium status | ||
| 0 | Negative | ||
| 1 | Positive | ||
| ctbinary | STI status: Lab data from the BILHIV study - Chlamydia trachomatis status | ||
| 0 | Negative | ||
| 1 | Positive | ||
| district | Is the patient being recruited in community A or Community B | ||
| 1 | Community A | ||
| 2 | Community B | ||
| CONTRACON | Contraceptive use: Do you use condoms for contraception? | ||
| 0 | No | ||
| 1 | Yes | ||
| CONTRAOCP | contraceptive use: Do you use oral contraceptive tablets for contraception? | ||
| 0 | No | ||
| 1 | Yes | ||
| CONTRAINJ | Contraceptive use: Do you use injectable contraceptives for contraception? | ||
| 0 | No | ||
| 1 | Yes | ||
| CONTRAIMP | Contraceptive use: Do you use implants for contraception? | ||
| 0 | No | ||
| 1 | Yes | ||
| micropos | Binary variable for urine microscopy | ||
| 0 | Negative | ||
| 1 | Positive | ||
| CAAbinary | Binary variable for urine CAA | ||
| 0 | Negative | ||
| 1 | Positive | ||
| Null | 2 vials were empty on arrival to Leiden University Med Center | ||
| mhighct1 | FGS status: Study generated variable - subgroup analysis of women with genital PCR positive (definite FGS), but with Schistosoma DNA PCR Ct <35 | ||
| 0 | negative FGS | ||
| 1 | pcr for FGS positive and <35ct | ||
| Null | probable fgs and/or women with positive PCR and ct>35 | ||
| pcr23pos30 | FGS status: Study generated variable - subgroup analysis of women with genital PCR positive (definite FGS), but with 2-3 positive PCR | ||
| 0 | negative FGS | ||
| 1 | pcr for FGS positive and <35ct | ||
| Null | probable fgs and/or women with 1 positive PCR | ||
| active | Binary variable - urine microscopy or urine CAA positive | ||
| 0 | Negative | ||
| 1 | Positive | ||
| Null | 2 vials were empty on arrival to Leiden University Med Center | ||
| marst1 | What is your marital status? | ||
| 1 | Single | ||
| 2 | Married or living as married | ||
| 3 | Divorced/separated/widowed | ||
| anyhc1 | contraceptive use: Study generated variable - use of any of the above contraceptive methods | ||
| 0 | No | ||
| 1 | Yes | ||
| gvbinary | microbiota status: Lab data from the BILHIV study - G. vaginalis status | ||
| 0 | Negative | ||
| 1 | Positive | ||
| avbinary | microbiota status: Lab data from the BILHIV study - A. vaginae status | ||
| 0 | Negative | ||
| 1 | Positive | ||
| lcbinary | microbiota status: Lab data from the BILHIV study - L. crispatus status | ||
| 0 | Negative | ||
| 1 | Positive | ||
| sexdebut | age at sexual debut: How old were you when you first had sex? | ||
| 0 | 8-16 years of age | ||
| 1 | 17-19 years of age | ||
| 2 | 20-24 years of age | ||
| sexin6 | sexual activity status: Have you been sexually active in the last 6 months? | ||
| 0 | No | ||
| 1 | Yes | ||
| Null | 2 people preferred not to answer and were made missing | ||
| hiv1 | Lab data from the HPTN 071 (PopART) study - HIV status | ||
| 0 | Negative | ||
| 1 | Positive | ||
| agegp4 | data reduced age variable. How old are you? | ||
| 1 | age 18-24 | ||
| 2 | age 25-31 | ||
| libinary | microbiota status: Lab data from the BILHIV study - L. iners status | ||
| 0 | Negative | ||
| 1 | Positive | ||
| cabinary | microbiota status: Lab data from the BILHIV study - Candida spp status | ||
| 0 | Negative | ||
| 1 | Positive | ||
| condomuse | Condom used at last sexual encounter: “The last time you had sex, did you/your partner use a male or female condom?” | ||
| 0 | No | ||
| 1 | Yes | ||
| Null | 10 people preferred not to answer and were made missing | ||
| sti | Self-reported STI status: “Have you previously been diagnosed with a sexually transmitted infection?” | ||
| 0 | No | ||
| 1 | Yes | ||
| Null | 1 person preferred not to answer and was made missing | ||
| conclc | Organism concentration: L. crispatus concentration | Integer | |
| concli | Organism concentration: L. iners concentration | Integer | |
| concav | Organism concentration: A. vaginae concentration | Integer | |
| conctv | Organism concentration: T. vaginalis concentration | Integer | |
| concgv | Organism concentration: G. vaginalis concentration | Integer | |
| loglc | Log transformed concentration: Log transformed L. crispatus concentration | Integer | |
| logli | Log transformed concentration: Log transformed L. iners concentration | Integer | |
| loggv | Log transformed concentration: Log transformed G. vaginalis concentration | Integer | |
| logav | Log transformed concentration: Log transformed A. vaginae concentration | Integer | |
| logtv | Log transformed concentration: Log transformed L. crispatus concentration | Integer |