Microbial Diversity of Genital Ulcers of HSV-2 Seropositive Women

Study information

Reviewed Marked as Reviewed by Svetlana up on 2025-4-15

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

29133803

DOI Digital object identifier for electronic documents.

https://doi.org/10.1038/s41598-017-15554-8

URI

https://www.nature.com/articles/s41598-017-15554-8.

Authors

Mehta SD, Pradhan AK, Green SJ, Naqib A, Odoyo-June E, Gaydos CA, Barry S, Landay A, Bailey RC

Journal

Scientific reports

Year

2017

We measured the microbial community structure of genital ulcers in women. Swabs from clinically detected ulcers were tested for HSV-2 and Treponema pallidum by polymerase chain reaction (PCR). HSV-2 and T. pallidum were detected by serum antibody testing. Microbial community structure was characterized by high-throughput 16 s rRNA gene amplicon sequencing. Multiple group testing and Elastic net and Lasso regressions identified taxa associated with differences in factors of interest. Among 49 ulcer specimens from 49 HSV-2 seropositive women, by PCR HSV-2 was recovered from 28 (57%) specimens and T. pallidum from none; one woman showed serologic evidence of syphilis. Overall, 63% of women were HIV-positive and 49% had an uncircumcised male sex partner. By both multiple group testing and regression, Porphyromonas (FDR p-value = 0.02), Prevotella (FDR p-value = 0.03), Anaerococcus (FDR p-value = 0.07), and Dialister (FDR p-value = 0.09) were detected at higher relative abundance in HSV-2 PCR-positive than negative ulcers. The presence of HSV-2 in a lesion was associated with presumed bacterial agents of Bacterial vaginosis. Differences in bacterial communities may contribute to HSV-2 ulcer pathogenesis, severity, or prolonged healing. If these results are confirmed, future studies may consider the influence of BV treatment on women's GUD and HSV-2 incidence and recurrence.

Experiment 1

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Reviewed Marked as Reviewed by Svetlana up on 2025-4-15

Curated date: 2025/04/04

Curator: Ese

Revision editor(s): Ese

Subjects

Location of subjects: Kenya

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: External female genitalia External female genital organ,External genitalia of female reproductive system,Female external genitalia,Organa genitalia feminina externa,External female genitalia,external female genitalia

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: HSV2 virologic severity measurement Herpes simplex virus-2 virologic severity measurement,HSV2 virologic severity measurement,hSV2 virologic severity measurement

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Women with HSV-2 PCR- Negative Ulcers

Group 1 name Corresponds to the case (exposed) group for case-control studies: Women with HSV-2 PCR- Positive Ulcers

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients were classified as having genital ulcers if detected using polymerase chain reaction (PCR)

Group 0 sample size Number of subjects in the control (unexposed) group: 21

Group 1 sample size Number of subjects in the case (exposed) group: 28

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: Kruskall-Wallis

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.1

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: increased

Signature 1

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Curated date: 2025/04/09

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Source: Table 4

Description: Differentially abundant bacterial taxa in women with HSV-2 PCR positive ulcers

Abundance in Group 1: increased abundance in Women with HSV-2 PCR- Positive Ulcers

NCBI	Quality Control	Links
Anaerococcus
Porphyromonas
Prevotella
Dialister

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Experiment 2

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Curated date: 2025/04/04

Curator: Ese

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Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: HIV infection [X]Human immunodeficiency virus disease,[X]Human immunodeficiency virus disease (disorder),[X]Unspecified human immunodeficiency virus [HIV] disease,[X]Unspecified human immunodeficiency virus [HIV] disease (disorder),HIV - Human immunodeficiency virus infection,HIV INFECT,HIV Infection,HIV infection,HIV Infections,HIV infectious disease,HTLV III INFECT,HTLV III Infections,HTLV III LAV INFECT,HTLV III LAV Infections,HTLV WIII INFECTIONS,HTLV WIII LAV INFECTIONS,HTLV-III Infection,HTLV-III Infections,HTLV-III-LAV Infection,HTLV-III-LAV Infections,HUMAN IMMUNO VIRUS DIS,human immunodeficiency virus,Human immunodeficiency virus [HIV] disease,HUMAN IMMUNOdeficiency VIRUS [HIV] INFECTION,Human immunodeficiency virus caused disease or disorder,Human immunodeficiency virus disease,Human immunodeficiency virus disease (disorder),Human immunodeficiency virus disease or disorder,Human immunodeficiency virus infection,Human immunodeficiency virus infection (disorder),Human immunodeficiency virus infection, NOS,Human immunodeficiency virus infectious disease,human immunodeficiency virus infectious disease,Infection, HIV,Infection, HTLV-III,Infection, HTLV-III-LAV,Infections, HIV,Infections, HTLV-III,Infections, HTLV-III-LAV,LYMPHOTROPIC VIRUS TYPE III INFECTIONS HUMAN T,T LYMPHOTROPIC VIRUS TYPE III INFECT HUMAN,T Lymphotropic Virus Type III Infections, Human,T-Lymphotropic Virus Type III Infections, Human,Unspecified human immunodeficiency virus [HIV] disease (disorder),hIV infection

Group 0 name Corresponds to the control (unexposed) group for case-control studies: HIV Negative Women

Group 1 name Corresponds to the case (exposed) group for case-control studies: HIV Positive Women

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients were classified as having HIV after undergoing HIV testing conducted according to Kenyan national guidelines.