Comparison of the Diversity of the Vaginal Microbiota in HIV‐Infected and HIV‐Uninfected Women with or without Bacterial Vaginosis

Department of Immunology/Microbiology, Rush University Medical Center, Chicago, Illinois, USA.
The Journal of Infectious Diseases (Impact Factor: 6). 09/2008; 198(8):1131-40. DOI: 10.1086/591942
Source: PubMed

ABSTRACT Whether human immunodeficiency virus (HIV) infection is associated with a change in the diversity of genital microbiota in women was investigated.
Amplicon length heterogeneity polymerase chain reaction (LH-PCR) analysis and pyrosequencing of the 16S ribosomal RNA gene were used to analyze the diversity of the microbiota in HIV-positive (HIV(+)) and HIV-negative (HIV(-)) women with or without bacterial vaginosis (BV).
LH-PCR analysis revealed significantly more microbiota diversity in BV-positive (BV(+)) women than in BV-negative (BV(-)) women, but no significant difference was noted between HIV(+) women and HIV(-) women. Pyrosequencing revealed that Lactobacillus organisms constituted a median of 96% of the bacteria in BV(-) women. BV(+) women had a significantly higher number of taxa found at > or =1% of the total genital microbiota (median, 11 taxa). Common taxa in BV(+) women were Prevotella, Megasphaera, Gardnerella, Coriobacterineae, Lachnospira, and Sneathia. There was a trend (P = .07) toward the presence of a higher number of taxa in HIV(+)BV(+) women than in HIV(-)BV(+) women. Propionibacterineae, Citrobacter, and Anaerococcus were the taxa found only in HIV(+) women (P < .05).
The present study demonstrated that both LH-PCR analysis and pyrosequencing differentiated microbiota in BV(+) women from that in BV(-) women and that pyrosequencing indicated a trend toward increased diversity in BV(+)HIV(+) women, suggesting that HIV infection is associated with changes in the diversity of genital microbiota.

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    • "Prevotella spp. have been found in the majority of patients in culture-based surveys of vaginal microbiomes [44] and are one of the most common operational taxonomic units (OTUs) present in recent molecular studies [45]. Prevotella spp. "
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    ABSTRACT: Bacterial vaginosis (BV) is a common condition, although its aetiology remains unexplained. The aim of this study was to analyse the composition of vaginal microbiota in women from Greenland to provide a quantitative description and improve the understanding of BV. Self-collected vaginal smears and swabs were obtained from 177 women. The vaginal smears were graded for BV according to Nugent's criteria. The vaginal swab samples were analysed by 19 quantitative PCRs (qPCRs) for selected vaginal bacteria and by PCR for four sexually transmitted infections (STIs). STIs were common: Mycoplasma genitalium 12%, Chlamydia trachomatis 7%, Neisseria gonorrhoeae 1%, and Trichomonas vaginalis 0.5%. BV was found in 45% of women, but was not associated with individual STIs. Seven of the 19 vaginal bacteria (Atopobium vaginae, Prevotella spp., Gardnerella vaginalis, BVAB2, Eggerthella-like bacterium, Leptotrichia amnionii, and Megasphaera type 1) had areas under the receiver operating characteristic (ROC) curve > 85%, suggesting they are good predictors of BV according to Nugent. Prevotella spp. had the highest odds ratio for BV (OR 437; 95% CI 82--2779) in univariate analysis considering only specimens with a bacterial load above the threshold determined by ROC curve analysis as positive, as well as the highest adjusted odds ratio in multivariate logistic regression analysis (OR 4.4; 95% CI 1.4-13.5). BV could be subdivided into clusters dominated by a single or a few species together. BV by Nugent score was highly prevalent. Two of seven key species (Prevotella spp. and A. vaginae) remained significantly associated with BV in a multivariate model after adjusting for other bacterial species. G. vaginalis and Prevotella spp. defined the majority of BV clusters.
    BMC Infectious Diseases 10/2013; 13(1):480. DOI:10.1186/1471-2334-13-480 · 2.61 Impact Factor
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    • "Pyrosequencing is a relatively novel technique which may help to decipher complex viral populations in terms of their diversity and structure. To date, it was successfully used in human immunodeficiency virus (HIV) research to identify minor drug resistant variants, analyze variable regions of heavy and light chains of neutralizing antibodies against HIV, as well as to determine HIV tropism, analyze superinfections and assess diversity of genital microbiota in HIV-infected women [27–31]. Ultradeep sequencing strategies also offers a new approach in HCV research. "
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    ABSTRACT: Genetic variability of hepatitis C virus (HCV) determines pathogenesis of infection, including viral persistence and resistance to treatment. The aim of the present study was to characterize HCV genetic heterogeneity within a hypervariable region 1 (HVR1) of a chronically infected patient by ultradeep 454 sequencing strategy. Three independent sequencing error correction methods were applied. First correction method (Method I) implemented cut-off for genetic variants present in less than 1%. In the second method (Method II), a condition to call a variant was bidirectional coverage of sequencing reads. Third method (Method III) used Short Read Assembly into Haplotypes (ShoRAH) program. After the application of these three different algorithms, HVR1 population consisted of 8, 40, and 186 genetic haplotypes. The most sensitive method was ShoRAH, allowing to reconstruct haplotypes constituting as little as 0.013% of the population. The most abundant genetic variant constituted only 10.5%. Seventeen haplotypes were present in a frequency above 1%, and there was wide dispersion of the population into very sparse haplotypes. Our results indicate that HCV HVR1 heterogeneity and quasispecies population structure may be reconstructed by ultradeep sequencing. However, credible analysis requires proper reconstruction methods, which would distinguish sequencing error from real variability in vivo.
    04/2013; 2013(5):626083. DOI:10.1155/2013/626083
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    • "Our data also support previous studies showing that Prevotella spp. was a highly prevalent and abundant microorganism in the vagina [20], [21], [44], [49]. With our qPCR, Prevotella spp. was detected in 62%, 82% and 96% of the healthy control women, intermediate cases and BV patients, respectively. "
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    ABSTRACT: Bacterial vaginosis (BV) is the most common vaginal disorder, characterized by depletion of the normal lactobacillus-dominant microbiota and overgrowth of commensal anaerobic bacteria. This study aimed to investigate the composition of the vaginal microbiota in women of reproductive age (healthy women and women with BV), with the view of developing molecular criteria for BV diagnosis. Vaginal samples from 163 women (79 control, 73 BV and 11 intermediate (Lactobacillary grade II flora) cases) were analyzed using 454 pyrosequencing of the hypervariable regions V3-V4 of the 16S rRNA gene and 16 quantitative bacterial species/genus-specific real-time PCR assays. Sensitivities and specificities of potential BV markers were computed using the Amsel criteria as reference standard for BV. The use of quantitative thresholds for prediction of BV, determined for both relative abundance measured with 454 pyrosequencing and bacterial load measured with qPCR, was evaluated. Relative to the healthy women, the BV patients had in their vaginal microbiota significantly higher prevalence, loads and relative abundances of the majority of BV associated bacteria. However, only Gardnerella vaginalis, Atopobium vaginae, Eggerthella, Prevotella, BVAB2 and Megasphaera type 1 detected at or above optimal thresholds were highly predictable for BV, with the best diagnostic accuracy shown for A. vaginae. The depletion of Lactobacillus species combined with the presence of either G. vaginalis or A. vaginae at diagnostic levels was a highly accurate BV predictor. Quantitative determination of the presence of G. vaginalis, A. vaginae, Eggerthella, Prevotella, BVAB2 and Megasphaera type 1 as well as the depletion of Lactobacillus was highly accurate for BV diagnosis. Measurements of abundance of normal and BV microbiota relative to total bacteria in vaginal fluid may provide more accurate BV diagnosis, and be used for test-of-cure, rather than qualitative detection or absolute counts of BV related microorganisms.
    PLoS ONE 04/2013; 8(4):e60670. DOI:10.1371/journal.pone.0060670 · 3.23 Impact Factor
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