Srinivasan S, Hoffman NG, Morgan MT, Matsen FA, Fiedler TL, Hall RW et al. Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria. PLoS One 7: e37818

Vaccine & Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America.
PLoS ONE (Impact Factor: 3.23). 06/2012; 7(6):e37818. DOI: 10.1371/journal.pone.0037818
Source: PubMed


Bacterial vaginosis (BV) is a common condition that is associated with numerous adverse health outcomes and is characterized by poorly understood changes in the vaginal microbiota. We sought to describe the composition and diversity of the vaginal bacterial biota in women with BV using deep sequencing of the 16S rRNA gene coupled with species-level taxonomic identification. We investigated the associations between the presence of individual bacterial species and clinical diagnostic characteristics of BV.
Broad-range 16S rRNA gene PCR and pyrosequencing were performed on vaginal swabs from 220 women with and without BV. BV was assessed by Amsel's clinical criteria and confirmed by Gram stain. Taxonomic classification was performed using phylogenetic placement tools that assigned 99% of query sequence reads to the species level. Women with BV had heterogeneous vaginal bacterial communities that were usually not dominated by a single taxon. In the absence of BV, vaginal bacterial communities were dominated by either Lactobacillus crispatus or Lactobacillus iners. Leptotrichia amnionii and Eggerthella sp. were the only two BV-associated bacteria (BVABs) significantly associated with each of the four Amsel's criteria. Co-occurrence analysis revealed the presence of several sub-groups of BVABs suggesting metabolic co-dependencies. Greater abundance of several BVABs was observed in Black women without BV.
The human vaginal bacterial biota is heterogeneous and marked by greater species richness and diversity in women with BV; no species is universally present. Different bacterial species have different associations with the four clinical criteria, which may account for discrepancies often observed between Amsel and Nugent (Gram stain) diagnostic criteria. Several BVABs exhibited race-dependent prevalence when analyzed in separate groups by BV status which may contribute to increased incidence of BV in Black women. Tools developed in this project can be used to study microbial ecology in diverse settings at high resolution.

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    • "In addition to these 16S-based resources, the MicrobesOnline resource (Dehal et al. 2010) offers a very nice interactive tree-based genome browser. On a much smaller scale, there are microbiome body site-specific reference sequence sets (Chen et al. 2010; Griffen et al. 2011; Srinivasan et al. 2012). [14:11 8/12/2014 Sysbio-syu053.tex] "
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    ABSTRACT: The human microbiome is the ensemble of genes in the microbes that live inside and on the surface of humans. Because microbial sequencing information is now much easier to come by than phenotypic information, there has been an explosion of sequencing and genetic analysis of microbiome samples. Much of the analytical work for these sequences involves phylogenetics, at least indirectly, but methodology has developed in a somewhat different direction than for other applications of phylogenetics. In this paper I review the field and its methods from the perspective of a phylogeneticist, as well as describing current challenges for phylogenetics coming from this type of work.
    Systematic Biology 07/2014; 64(1). DOI:10.1093/sysbio/syu053 · 14.39 Impact Factor
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    • "Having examined and dismissed those alternative explanations, we speculate that the BVBlue POC kit was not sensitive in this population because of differences in the composition and diversity of the vaginal bacterial flora among women with BV in our sample. Recent studies using broad-range 16S rRNA gene PCR and pyrosequencing have shown that BV is a highly heterogeneous condition marked by greater species richness and diversity than previously thought, with no single species universally present [34]. Since the BVBlue kit operates on the principle that BV is associated with elevated levels of sialidases, it is possible that the vaginal biota of women with BV in our study population may have sialidase-negative G. vaginalis strains or contain a low number of anaerobic Gram-negative rods such as Prevotella spp. "
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    ABSTRACT: Bacterial vaginosis (BV) is the most common cause of abnormal vaginal discharge in reproductive age women. It is associated with increased susceptibility to HIV/STI and adverse birth outcomes. Diagnosis of BV in resource-poor settings like India is challenging. With little laboratory infrastructure there is a need for objective point-of-care diagnostic tests. Vaginal swabs were collected from women 18 years and older, with a vaginal pH > 4.5 attending a reproductive health clinic. BV was diagnosed with Amsel's criteria, Nugent scores, and the OSOM BVBlue test. Study personnel were blinded to test results. There were 347 participants enrolled between August 2009 and January 2010. BV prevalence was 45.1% (95% confidence interval (CI): 41.5%-52.8%) according to Nugent score. When compared with Nugent score, the sensitivity, specificity, positive predictive value, negative predictive value for Amsel's criteria and BVBlue were 61.9%, 88.3%, 81.5%, 73.7% and 38.1%, 92.7%, 82.1%, 63.9%, respectively. Combined with a "whiff" test, the performance of BVBlue increased sensitivity to 64.4% and negative predictive value to 73.8%. Despite the good specificity, poor sensitivity limits the usefulness of the BVBlue as a screening test in this population. There is a need to examine the usefulness of this test in other Indian populations.
    Infectious Diseases in Obstetrics and Gynecology 01/2014; 2014(9):908313. DOI:10.1155/2014/908313
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    • "mulieris) or Mycoplasma sp. when acute. G. vaginalis sub-dominance in acute BV samples is expected from next-generation sequencing studies; for example, only 53% of 114 acute BV patients analyzed by 16S rRNA gene pyrosequencing had titers above 10% [25]. Future studies may validate that G. vaginalis dominance, as a subtype of BV, is associated with recurrence. "
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    ABSTRACT: Bacterial vaginosis (BV) affects ∼30% of women of reproductive age, has a high rate of recurrence, and is associated with miscarriage, preterm birth, and increased risk of acquiring other sexually transmitted infections, including HIV-1. Little is known of the daily changes in the vaginal bacterial composition as it progresses from treatment to recurrence, or whether any of these might be useful in its prediction or an understanding of its causes. We used phylogenetic branch-inclusive quantitative PCR (PB-qPCR) and Lactobacillus blocked/unblocked qPCR (Lb-qPCR) to characterize longitudinal changes in the vaginal microbiota in sequential vaginal self-swabs from five women with recurrent BV, from diagnosis through remission to recurrence. Both patients with acute BV samples dominated by G. vaginalis recurred during the study with similar profiles, whereas the three patients with acute BV samples dominated by other anaerobes did not recur or recurred to an intermediate Nugent score. L. iners dominated remission phases, with intermittent days of abnormal microbial profiles typically associated with menses. The exception was a newly discovered phenomenon, a sustained period of abnormal profiles, termed conversion, which preceded symptomatic acute BV. Species known to have antagonistic activity towards Lactobacillus were detected in pre-conversion samples, possibly contributing to the decline in Lactobacillus. Lb-qPCR scores define two categories of response in the initial post-treatment visit samples; scores <5 may correspond with poor response to treatment or rapid recurrence, whereas scores >8 may predict delayed or no recurrence. Amsel criteria or Nugent scores did not have this potential predictive capability. Larger studies are warranted to evaluate the prognostic potential of detecting conversion and poor Lb-qPCR scores at the post-treatment visit of recurrent BV patients.
    PLoS ONE 12/2013; 8(12):e82599. DOI:10.1371/journal.pone.0082599 · 3.23 Impact Factor
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