Characterization of cervico-vaginal microbiota in women developing persistent high-risk Human Papillomavirus infection

Study information

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

study design

prospective cohort

Citation

PMID PubMed identifier for scientific articles.

28860468

DOI Digital object identifier for electronic documents.

10.1038/s41598-017-09842-6

URI

Authors

Di Paola M, Sani C, Clemente AM, Iossa A, Perissi E, Castronovo G, Tanturli M, Rivero D, Cozzolino F, Cavalieri D, Carozzi F, De Filippo C, Torcia MG

Journal

Scientific reports

Year

2017

Changes in cervico-vaginal microbiota with Lactobacillus depletion and increased microbial diversity facilitate human papillomavirus (HPV) infection and might be involved in viral persistence and cancer development. To define the microbial Community State Types (CSTs) associated with high-risk HPV-persistence, we analysed 55 cervico-vaginal samples from HPV positive (HPV+) women out of 1029 screened women and performed pyrosequencing of 16S rDNA. A total of 17 samples from age-matched HPV negative (HPV-) women were used as control. Clearance or Persistence groups were defined by recalling women after one year for HPV screening and genotyping. A CST IV subgroup, with bacterial genera such as Gardnerella, Prevotella, Megasphoera, Atopobium, frequently associated with anaerobic consortium in bacterial vaginosis (BV), was present at baseline sampling in 43% of women in Persistence group, and only in 7.4% of women in Clearance group. Atopobium genus was significantly enriched in Persistence group compared to the other groups. Sialidase-encoding gene from Gardnerella vaginalis, involved in biofilm formation, was significantly more represented in Persistence group compared to the other groups. Based on these data, we consider the CST IV-BV as a risk factor for HPV persistence and we propose Atopobium spp and sialidase gene from G. vaginalis as microbial markers of HPV-persistence.

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): LGeistlinger, WikiWorks, Victoria

Subjects

Location of subjects: Italy

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: Vaginal fluid Vaginal discharge,Vaginal secretion,Vaginal fluid,vaginal fluid

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,Human papilloma virus infection

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

Group 1 name Corresponds to the case (exposed) group for case-control studies: HPV+

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: HPV+ determined through HR-HC2 assay

Group 0 sample size Number of subjects in the control (unexposed) group: 17

Group 1 sample size Number of subjects in the case (exposed) group: 55

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 3 days

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V5

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Roche454

Statistical Analysis

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

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

Matched on Factors on which subjects have been matched on in a case-control study: age

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

Richness Number of species: unchanged

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

Source: figure 6a

Description: Metagenomic biomarker discovery by LEfSe analysis betweeen HPV+ and HPV- women

Abundance in Group 1: increased abundance in HPV+

NCBI	Quality Control	Links
Sneathia
Megasphaera
Pediococcus
Brevibacterium
Pseudomonas

Revision editor(s): WikiWorks

Signature 2

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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

Source: figure 6a

Description: Metagenomic biomarker discovery by LEfSe analysis betweeen HPV+ and HPV- women

Abundance in Group 1: decreased abundance in HPV+

NCBI	Quality Control	Links
Pseudoxanthomonas
Actinomyces
Vampirovibrio
Alkanindiges

Revision editor(s): WikiWorks

Experiment 2

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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): LGeistlinger, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: HPV+ (clearance)

Group 1 name Corresponds to the case (exposed) group for case-control studies: HPV+ (persistance)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: HR-HPV+ persistence confirmed by HPV genotyping after 1 year