TRiCit: A High-Throughput Approach to Detect <i>Trichomonas vaginalis</i> from ITS1 Amplicon Sequencing
Trichomoniasis, caused by <i>Trichomonas vaginalis</i> (TV), is the most common non-viral sexually transmitted infection (STI) worldwide, affecting over 174 million people annually and is frequently associated with reproductive co-morbidities. However, its detection can be time-consuming...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-07-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/14/11839 |
| _version_ | 1797588985933987840 |
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| author | Mykhaylo Usyk Nicolas F. Schlecht Shankar Viswanathan Ana Gradissimo Negin Valizadegan Christopher C. Sollecito Anne Nucci-Sack Angela Diaz Robert D. Burk |
| author_facet | Mykhaylo Usyk Nicolas F. Schlecht Shankar Viswanathan Ana Gradissimo Negin Valizadegan Christopher C. Sollecito Anne Nucci-Sack Angela Diaz Robert D. Burk |
| author_sort | Mykhaylo Usyk |
| collection | DOAJ |
| description | Trichomoniasis, caused by <i>Trichomonas vaginalis</i> (TV), is the most common non-viral sexually transmitted infection (STI) worldwide, affecting over 174 million people annually and is frequently associated with reproductive co-morbidities. However, its detection can be time-consuming, subjective, and expensive for large cohort studies. This case–control study, conducted at the Mount Sinai Adolescent Health Center in New York City, involved 36 women with prevalent TV infections and 36 controls. The objective was to examine Internal Transcribed Spacer region-1 (ITS1) amplicon-derived communities for the detection of prevalent TV infections with the same precision as clinical microscopy and the independent amplification of the TV-specific TVK3/7 gene. DNA was isolated from clinician-collected cervicovaginal samples and amplified using ITS1 primers in a research laboratory. Results were compared to microscopic wet-mount TV detection of concurrently collected cervicovaginal samples and confirmed against TV-specific TVK3/7 gene PCR. The area under the receiver operating characteristics curve (AUC) for diagnosing TV using ITS1 communities was 0.92. ITS1 amplicons displayed an intra-class correlation coefficient (ICC) of 0.96 (95% CI: 0.93–0.98) compared to TVK3/7 PCR fragment testing. TV cases showed an increased risk of bacterial vaginosis (BV) compared to the TV-negative controls (OR = 8.67, 95% CI: 2.24–48.54, <i>p</i>-value = 0.0011), with no significant differences regarding genital yeast or chlamydia infections. This study presents a bioinformatics approach to ITS1 amplicon next-generation sequencing that is capable of detecting prevalent TV infections. This approach enables high-throughput testing for TV in stored DNA from large-scale epidemiological studies. |
| first_indexed | 2024-03-11T00:59:50Z |
| format | Article |
| id | doaj.art-90036482bc9e49178071fb85dfeb1b52 |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-11T00:59:50Z |
| publishDate | 2023-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-90036482bc9e49178071fb85dfeb1b522023-11-18T19:45:50ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-07-0124141183910.3390/ijms241411839TRiCit: A High-Throughput Approach to Detect <i>Trichomonas vaginalis</i> from ITS1 Amplicon SequencingMykhaylo Usyk0Nicolas F. Schlecht1Shankar Viswanathan2Ana Gradissimo3Negin Valizadegan4Christopher C. Sollecito5Anne Nucci-Sack6Angela Diaz7Robert D. Burk8Department of Pediatrics (Genetic Medicine), Albert Einstein College of Medicine, Bronx, NY 10461, USADepartment of Cancer Prevention & Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY 14263, USADepartment of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USADepartment of Pediatrics (Genetic Medicine), Albert Einstein College of Medicine, Bronx, NY 10461, USADepartment of Pediatrics (Genetic Medicine), Albert Einstein College of Medicine, Bronx, NY 10461, USADepartment of Pediatrics (Genetic Medicine), Albert Einstein College of Medicine, Bronx, NY 10461, USADepartment of Pediatrics, Mount Sinai Adolescent Health Center, Icahn School of Medicine at Mount Sinai, Manhattan, NY 10029, USADepartment of Pediatrics, Mount Sinai Adolescent Health Center, Icahn School of Medicine at Mount Sinai, Manhattan, NY 10029, USADepartment of Pediatrics (Genetic Medicine), Albert Einstein College of Medicine, Bronx, NY 10461, USATrichomoniasis, caused by <i>Trichomonas vaginalis</i> (TV), is the most common non-viral sexually transmitted infection (STI) worldwide, affecting over 174 million people annually and is frequently associated with reproductive co-morbidities. However, its detection can be time-consuming, subjective, and expensive for large cohort studies. This case–control study, conducted at the Mount Sinai Adolescent Health Center in New York City, involved 36 women with prevalent TV infections and 36 controls. The objective was to examine Internal Transcribed Spacer region-1 (ITS1) amplicon-derived communities for the detection of prevalent TV infections with the same precision as clinical microscopy and the independent amplification of the TV-specific TVK3/7 gene. DNA was isolated from clinician-collected cervicovaginal samples and amplified using ITS1 primers in a research laboratory. Results were compared to microscopic wet-mount TV detection of concurrently collected cervicovaginal samples and confirmed against TV-specific TVK3/7 gene PCR. The area under the receiver operating characteristics curve (AUC) for diagnosing TV using ITS1 communities was 0.92. ITS1 amplicons displayed an intra-class correlation coefficient (ICC) of 0.96 (95% CI: 0.93–0.98) compared to TVK3/7 PCR fragment testing. TV cases showed an increased risk of bacterial vaginosis (BV) compared to the TV-negative controls (OR = 8.67, 95% CI: 2.24–48.54, <i>p</i>-value = 0.0011), with no significant differences regarding genital yeast or chlamydia infections. This study presents a bioinformatics approach to ITS1 amplicon next-generation sequencing that is capable of detecting prevalent TV infections. This approach enables high-throughput testing for TV in stored DNA from large-scale epidemiological studies.https://www.mdpi.com/1422-0067/24/14/11839<i>Trichomonas vaginalis</i>ITSmycobiomeamplicon<i>molBV</i>molecular diagnosis |
| spellingShingle | Mykhaylo Usyk Nicolas F. Schlecht Shankar Viswanathan Ana Gradissimo Negin Valizadegan Christopher C. Sollecito Anne Nucci-Sack Angela Diaz Robert D. Burk TRiCit: A High-Throughput Approach to Detect <i>Trichomonas vaginalis</i> from ITS1 Amplicon Sequencing International Journal of Molecular Sciences <i>Trichomonas vaginalis</i> ITS mycobiome amplicon <i>molBV</i> molecular diagnosis |
| title | TRiCit: A High-Throughput Approach to Detect <i>Trichomonas vaginalis</i> from ITS1 Amplicon Sequencing |
| title_full | TRiCit: A High-Throughput Approach to Detect <i>Trichomonas vaginalis</i> from ITS1 Amplicon Sequencing |
| title_fullStr | TRiCit: A High-Throughput Approach to Detect <i>Trichomonas vaginalis</i> from ITS1 Amplicon Sequencing |
| title_full_unstemmed | TRiCit: A High-Throughput Approach to Detect <i>Trichomonas vaginalis</i> from ITS1 Amplicon Sequencing |
| title_short | TRiCit: A High-Throughput Approach to Detect <i>Trichomonas vaginalis</i> from ITS1 Amplicon Sequencing |
| title_sort | tricit a high throughput approach to detect i trichomonas vaginalis i from its1 amplicon sequencing |
| topic | <i>Trichomonas vaginalis</i> ITS mycobiome amplicon <i>molBV</i> molecular diagnosis |
| url | https://www.mdpi.com/1422-0067/24/14/11839 |
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