Prevalent high-risk HPV infection and vaginal microbiota in Nigerian women

Study information

Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

26062721

DOI Digital object identifier for electronic documents.

10.1017/S0950268815000965

URI

Authors

Dareng EO, Ma B, Famooto AO, Adebamowo SN, Offiong RA, Olaniyan O, Dakum PS, Wheeler CM, Fadrosh D, Yang H, Gajer P, Brotman RM, Ravel J, Adebamowo CA

Journal

Epidemiology and infection

Year

2016

Keywords:

HIV/AIDS, human papilloma virus (HPV), public health

In this study, we evaluated the association between high-risk human papillomavirus (hrHPV) and the vaginal microbiome. Participants were recruited in Nigeria between April and August 2012. Vaginal bacterial composition was characterized by deep sequencing of barcoded 16S rRNA gene fragments (V4) on Illumina MiSeq and HPV was identified using the Roche Linear Array® HPV genotyping test. We used exact logistic regression models to evaluate the association between community state types (CSTs) of vaginal microbiota and hrHPV infection, weighted UniFrac distances to compare the vaginal microbiota of individuals with prevalent hrHPV to those without prevalent hrHPV infection, and the Linear Discriminant Analysis effect size (LEfSe) algorithm to characterize bacteria associated with prevalent hrHPV infection. We observed four CSTs: CST IV-B with a low relative abundance of Lactobacillus spp. in 50% of participants; CST III (dominated by L. iners) in 39·2%; CST I (dominated by L. crispatus) in 7·9%; and CST VI (dominated by proteobacteria) in 2·9% of participants. LEfSe analysis suggested an association between prevalent hrHPV infection and a decreased abundance of Lactobacillus sp. with increased abundance of anaerobes particularly of the genera Prevotella and Leptotrichia in HIV-negative women (P < 0·05). These results are hypothesis generating and further studies are required.

Experiment 1

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Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

Subjects

Location of subjects: Nigeria

Host species Species from which microbiome was sampled (if applicable): Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Vagina Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: human papilloma virus infection HPV,Human Papilloma Virus Infection,Human papilloma Virus infection,human papilloma virus infection,Human papillomavirus caused disease or disorder,Human papillomavirus disease or disorder,Human Papillomavirus Infection,Human Papillomavirus infection,Human papillomavirus infectious disease

Group 0 name Corresponds to the control (unexposed) group for case-control studies: HPV-/HIV-
Group 1 name Corresponds to the case (exposed) group for case-control studies: HPV+/HIV-
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: HR-HPV+ confirmed by medical records and HPV genotyping test
Group 0 sample size Number of subjects in the control (unexposed) group: 99
Group 1 sample size Number of subjects in the case (exposed) group: 12

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

Statistical test: LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Signature 1

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Reviewed Marked as Reviewed by Fatima Zohra on 2021/02/09

Curated date: 2021/01/10

Curator: Cynthia Anderson

Revision editor(s): WikiWorks, Atrayees

Source: Fig. 4b

Description: Identiﬁed phylotype biomarkers ranked by effect size in HIV–women

Abundance in Group 1: increased abundance in HPV+/HIV-

NCBI	Quality Control	Links
Anaerococcus sp.
Arcanobacterium
Arcanobacterium sp.
Bacteroidales
Bacteroidia
Bacteroidota
Clostridiaceae
Dialister
Dialister micraerophilus
Fusobacteriales
Fusobacteriota
Leptotrichiaceae
Megasphaera
Megasphaera sp.
Peptoniphilus
Peptoniphilus asaccharolyticus
Peptoniphilus sp.
Peptostreptococcaceae
Peptostreptococcus
Peptostreptococcus anaerobius
Prevotella
Prevotella sp.
Prevotellaceae
Sneathia
Sneathia sp.