Simultaneous profiling of sexually transmitted bacterial pathogens, microbiome, and concordant host response in cervical samples using whole transcriptome sequencing analysis
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ABSTRACT:
PROVIDER: PRJNA491928 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR7878540_1.fastq.gz | Fastqsanger.gz | |||
| SRR7878540_2.fastq.gz | Fastqsanger.gz | |||
| SRR7878550_1.fastq.gz | Fastqsanger.gz | |||
| SRR7878550_2.fastq.gz | Fastqsanger.gz | |||
| SRR7878541_1.fastq.gz | Fastqsanger.gz |
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Project description:We examined the potential for characterization of host, pathogen and microbiome interactions at a molecular level and identification of novel, outcome-relevant biomarkers in a single, easily obtained, clinical specimen using total RNA-seq.
2019-03-19 | GSE120192 | GEO
Project description:Pelvic inflammatory disease (PID) is a female upper genital tract inflammatory disorder that arises after sexually transmitted bacterial infections (STI). Factors modulating risk for reproductive sequelae include co-infection, microbiota, host genetics and physiology. In a pilot study of cervical samples obtained from women at high risk for STIs, we examined the potential for unbiased characterization of host, pathogen and microbiome interactions using whole transcriptome sequencing analysis of ribosomal RNA-depleted total RNAs (Total RNA-Seq). Only samples from women with STI infection contained pathogen-specific sequences (3 to 38% transcriptome coverage). Simultaneously, we identified and quantified their active microbial communities. After integration with host-derived reads from the same data, we detected clustering of host transcriptional profiles that reflected microbiome differences and STI infection. Together, our study suggests that total RNA profiling will advance understanding of the interplay of pathogen, host and microbiota during natural infection and may reveal novel, outcome-relevant biomarkers.
| S-EPMC6402362 | biostudies-literature
Project description:BackgroundSome sexually transmitted infectious agents, such as Chlamydia trachomatis and Herpes simplex, cause local inflammation, and could contribute to Human Papillomavirus (HPV) and cervical lesion progression. Thus, the aim of this study was to determine any association between the presence of microorganisms of gynecological importance, sexual behavior, clinical and demographical variables to the development and progress of cervical lesions.MethodsOne hundred and thirty-two women between 14 and 78 years and living at Vitória da Conquista, Bahia, Brazil, were included (62 individuals with cervical lesions and 70 without lesions). They answered a questionnaire to provide data for a socioeconomic and sexual activity profile. Samples of cervical swabs were collected and analyzed by PCR to detect genital microorganisms and HPV. Quantitative PCR was used to detect and quantify Ureaplasma urealyticum and Ureaplasma parvum. Univariate and multiple logistic regression were performed to measure the association with the cervical lesions, and an odds ratio (OR) with 95% confidence intervals (95%CI) were calculated. The Mann-Whitney U test was also used to compare the microorganism load in the case and control groups. The significance level was 5% in all hypotheses tested.ResultsCervical lesions were associated with: women in a stable sexual relationship (OR = 14.21, 95%CI = 3.67-55.018), positive PCR for HPV (OR = 16.81, 95%CI = 4.19-67.42), Trichomonas vaginalis (OR = 8.566, 95%CI = 2.04-35.94) and Gardnerella vaginalis (OR = 6.13, 95%CI = 1.53-24.61), adjusted by age and qPCR for U. parvum. U. parvum load showed a statistical difference between the case and control groups (p-value = 0.002).ConclusionVariables such as stable relationship, HPV, T. vaginalis, G. vaginalis were associated with cervical lesions in epidemiological studies. U. parvum load was higher in woman with cervical lesions compared with women without lesions. Additional studies are needed to better understand the role of these factors in cervical lesion development.
| S-EPMC5732421 | biostudies-literature
Project description:The pleuromutilin antibiotic lefamulin demonstrated in vitro activity against the most relevant bacterial pathogens causing sexually transmitted infections (STI), including Chlamydia trachomatis (MIC50/90, 0.02/0.04 mg/liter; n = 15), susceptible and multidrug-resistant Mycoplasma genitalium (MIC range, 0.002 to 0.063 mg/liter; n = 6), and susceptible and resistant Neisseria gonorrhoeae (MIC50/90, 0.12/0.5 mg/liter; n = 25). The results suggest that lefamulin could be a promising first-line antibiotic for the treatment of STI, particularly in populations with high rates of resistance to standard-of-care antibiotics.
| S-EPMC5923106 | biostudies-literature
Project description:This study established a multiplex PCR-based microarray to detect simultaneously a diverse panel of 17 sexually transmitted diseases (STDs)-associated pathogens including Neisseria gonorrhoeae, Chlamydia trachomatis, Mycoplasma genitalium, Mycoplasma hominis, Ureaplasma, Herpes simplex virus (HSV) types 1 and 2, and Human papillomavirus (HPV) types 6, 11, 16, 18, 31, 33, 35, 39, 54 and 58. The target genes are 16S rRNA gene for N. gonorrhoeae, M. genitalium, M. hominism, and Ureaplasma, the major outer membrane protein gene (ompA) for C. trachomatis, the glycoprotein B gene (gB) for HSV; and the L1 gene for HPV. A total of 34 probes were selected for the microarray including 31 specific probes, one as positive control, one as negative control, and one as positional control probe for printing reference. The microarray is specific as the commensal and pathogenic microbes (and closely related organisms) in the genitourinary tract did not cross-react with the microarray probes. The microarray is 10 times more sensitive than that of the multiplex PCR. Among the 158 suspected HPV specimens examined, the microarray showed that 49 samples contained HPV, 21 samples contained Ureaplasma, 15 contained M. hominis, four contained C. trachomatis, and one contained N. gonorrhoeae. This work reports the development of the first high through-put detection system that identifies common pathogens associated with STDs from clinical samples, and paves the way for establishing a time-saving, accurate and high-throughput diagnostic tool for STDs.
| S-EPMC4514671 | biostudies-literature
Project description:ObjectiveThis study investigated the prevalence of infections with human papillomavirus, Chlamydia trachomatis, Ureaplasma urealyticum, Mycoplasma hominis, and Mycoplasma genitalium in the semen of Korean infertile couples and their associations with sperm quality.MethodsSemen specimens were collected from 400 men who underwent a fertility evaluation. Infection with above five pathogens was assessed in each specimen. Sperm quality was compared in the pathogen-infected group and the non-infected group.ResultsThe infection rates of human papillomavirus, C. trachomatis, U. urealyticum, M. hominis, and M. genitalium in the study subjects were 1.57%, 0.79%, 16.80%, 4.46%, and 1.31%, respectively. The rate of morphological normality in the U. urealyticum-infected group was significantly lower than in those not infected with U. urealyticum. In a subgroup analysis of normozoospermic samples, the semen volume and the total sperm count in the pathogen-infected group were significantly lower than in the non-infected group.ConclusionOur results suggest that infection with U. urealyticum alone and any of the five sexually transmitted infections are likely to affect sperm morphology and semen volume, respectively.
| S-EPMC5783918 | biostudies-literature
Project description:Women living with HIV infection are at higher risk for cervical cancer, an AIDS-defining diagnosis. We examined the prevalence of cervical cancer and sexually transmitted disease (STD) screening among human immunodeficiency virus (HIV)-infected women and factors associated with the receipt of Papanicolaou (Pap) tests.We did a cross-sectional analysis of weighted data from a sample of HIV-infected adults receiving outpatient medical care. We used matched interview (report of Pap test) and medical record data (STD screenings) from HIV-infected women. We performed logistic regression to compute adjusted prevalence ratios and 95% confidence intervals for the association between demographic, behavioral, and clinical factors and receipt of Pap tests among HIV-infected women.Data were available for 2,270 women, who represent 112,894 HIV-infected women; 62% were African American, 17% were Hispanic/Latina, and 18% were white. Most (78%) reported having a Pap test in the past year. Among sexually active women (n = 1234), 20% reported sex without condoms, 27% were screened for gonorrhea, and 29% were screened for chlamydia. Being screened for STDs was less likely among women who did not have a Pap test in the past year (adjusted prevalence ratios 0.82, 95% confidence interval 0.77-0.87). Women who were ≥50 years of age and reported income above federal poverty level, no sexual activity, depression, no HIV care from an obstetrician/gynecologist, and no documented STD tests, were less likely to report a Pap test (p < 0.05).Screening for cervical cancer and STDs among HIV-infected women is suboptimal. Clinical visits for Pap tests are an important opportunity for HIV-infected sexually active women to also receive STD screenings and counseling regarding condoms.
| S-EPMC5564184 | biostudies-other
Project description:There are many different sexually transmitted infections that can cause proctitis. Recognition of the common symptoms with anoscopic examination is crucial in accurate diagnosis of the pathogen. Clinicians should have a high index of suspicion of more than one inciting pathogen. Treatment should be prompt and extended to sexual partners who have been exposed to the disease. Effective treatment can alleviate the discomfort and potentially serious complications associated with sexually transmitted proctitides. This article illustrates and discusses the clinical presentations, diagnostic pearls, and treatments of sexually transmitted proctitides.
| S-EPMC4442722 | biostudies-other
Project description:Background: Sexually transmitted diseases (STD) are a major cause of infertility, long-term disability, ectopic pregnancy, and premature birth. Therefore, the development of fast and low-cost laboratory STD diagnostic screening methods will contribute to reducing STD-induced reproductive tract damage and improve women's health worldwide. In this study, we evaluated a novel multiplex real-time PCR melting curve assay method for the simultaneous detection of 9 STD pathogens, including Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma genitalium, Trichomonas vaginalis, Mycoplasma hominis, Ureaplasma urealyticum, Ureaplasma parvum, and herpes simplex virus. Methods: The analytical performance of the method, including its limit of detection (LOD), specificity, repeatability, and effect on different DNA extraction kits were evaluated. Additionally, we obtained 1,328 clinical specimens from 3 hospitals to detect the 9 STD pathogens using multiplex real-time PCR melting curve and Sanger sequencing, to evaluate the sensitivity, specificity, and consistency of the assay method. Results: The results showed that the analytical sensitivity of the novel multiplex real-time PCR melting curve assay is very excellent, with LOD of DNA corresponding to <200 copies/μL for the DNA of the 9 STDs and 1.00 × 104 color change unit /ml for those of UU and UP. Additionally, this assay demonstrated excellent analytical specificity, excellent repeatability, and its results had no effect of different DNA extraction kits. The performance, in terms of sensitivity (91.06-100%) and specificity (99.14-100%), was remarkable, since the consistency between it and Sanger sequencing was more than 0.85 in the clinic. Conclusion: The novel multiplex real-time PCR melting curve assay method has high sensitivity and specificity, relatively low cost, and simple to use for the simultaneous detection of 9 STD pathogens in genitourinary secretions.
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