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Valint D, Fiedler TL, Liu C, Srinivasan S, Fredricks DN. Effect of Metronidazole on Concentrations of Vaginal Bacteria Associated with Risk of HIV Acquisition. Res Sq 2024:rs.3.rs-4219764. [PMID: 38659968 PMCID: PMC11042432 DOI: 10.21203/rs.3.rs-4219764/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Several bacterial vaginosis (BV)-associated bacteria have been associated with elevated risk of HIV acquisition, however susceptibility of these bacteria to antibiotics is poorly understood. Vaginal samples were collected from 22 persons daily for two weeks following BV diagnosis. Metronidazole treatment was prescribed for 5-7 days. Changes in bacterial concentrations were measured with taxon-specific 16S rRNA gene quantitative PCR (qPCR) assays. A culture-based antimicrobial assay confirmed presence of antibiotics in vaginal swab samples. Bacterial DNA concentrations decreased during antibiotic administration for all thirteen bacterial taxa tested. Comparison of bacterial DNA concentrations in samples before administration of antibiotics to samples taken on the last day of antimicrobial assay-confirmed antibiotic presence showed a 2.3-4.5 log10-fold decrease across all taxa. Concentrations were frequently reduced to the qPCR assay's limit of detection, suggesting eradication of bacteria. Mean clearance time varied across taxa (1.2-8.6 days), with several bacteria (e.g., Gemella asaccharolytica, Sneathia spp., Eggerthella-like sp.) taking >7 days to suppress. Metronidazole reduces quantities of bacterial taxa associated with increased HIV acquisition risk. Eradication of high-risk vaginal bacteria using metronidazole is one promising avenue for reducing HIV acquisition risk. A 5-7-day treatment course may not be sufficient to suppress all bacteria.
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Affiliation(s)
- D.J. Valint
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Tina L. Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Congzhou Liu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - David N. Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
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Munch MM, Strenk SM, Srinivasan S, Fiedler TL, Proll S, Fredricks DN. Gardnerella Species and their Association with Bacterial Vaginosis. J Infect Dis 2024:jiae026. [PMID: 38268121 DOI: 10.1093/infdis/jiae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 01/10/2024] [Accepted: 01/19/2024] [Indexed: 01/26/2024] Open
Abstract
BACKGROUND Bacterial vaginosis (BV) is a condition marked by high vaginal bacterial diversity. Gardnerella vaginalis has been implicated in BV but is also detected in healthy women. The Gardnerella genus has been expanded to encompass six validly named species and several genomospecies. We hypothesized that particular Gardnerella species may be more associated with BV. METHODS Quantitative PCR assays were developed targeting the cpn60 gene of species groups including G. vaginalis, G. piotii/pickettii, G. swidsinskii/greenwoodii and G. leopoldii. These assays were applied to vaginal swabs from individuals with (n=101) and without BV (n=150) attending a sexual health clinic in Seattle, Washington. Weekly swabs were collected from 42 participants for up to 12 weeks. RESULTS Concentrations and prevalence of each Gardnerella species group were significantly higher in participants with BV. 91.1% of BV positive participants had three or more Gardnerella species groups detected compared to 32.0% of BV negative participants (p<0.0001). BV negative participants with three or more species groups detected were more likely to develop BV within 100 days versus those with fewer (60.5% vs 3.7%, p<0.0001). CONCLUSIONS These results suggest that BV reflects a state of high Gardnerella species diversity. No Gardnerella species group was a specific marker for BV.
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Affiliation(s)
- Matthew M Munch
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Susan M Strenk
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Tina L Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - Sean Proll
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
| | - David N Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, United States
- Department of Medicine, University of Washington, Seattle, WA, United States
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Srinivasan S, Austin MN, Fiedler TL, Strenk SM, Agnew KJ, Gowda GAN, Raftery D, Beamer MA, Achilles SL, Wiesenfeld HC, Fredricks DN, Hillier SL. Amygdalobacter indicium gen. nov., sp. nov., and Amygdalobacter nucleatus sp. nov., gen. nov.: novel bacteria from the family Oscillospiraceae isolated from the female genital tract. Int J Syst Evol Microbiol 2023; 73. [PMID: 37787404 DOI: 10.1099/ijsem.0.006017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023] Open
Abstract
Four obligately anaerobic Gram-positive bacteria representing one novel genus and two novel species were isolated from the female genital tract. Both novel species, designated UPII 610-JT and KA00274T, and an additional isolate of each species were characterized utilizing biochemical, genotypic and phylogenetic analyses. All strains were non-motile and non-spore forming, asaccharolytic, non-cellulolytic and indole-negative coccobacilli. Fatty acid methyl ester analysis for UPII 610-JT and KA00274T and additional isolates revealed C16 : 0, C18 : 0, C18:1ω9c and C18:2ω6,9c to be the major fatty acids for both species. UPII 610-JT had a 16S rRNA gene sequence similarity of 99.4 % to an uncultured clone sequence (AY724740) designated as Bacterial Vaginosis Associated Bacterium 2 (BVAB2). KA00274T had a 16S rRNA gene sequence similarity of 96.5 % to UPII 610-JT. Whole genomic DNA mol% G+C content was 42.2 and 39.3 % for UPII 610-JT and KA00274T, respectively. Phylogenetic analyses indicate these isolates represent a novel genus and two novel species within the Oscillospiraceae family. We propose the names Amygdalobacter indicium gen. nov., sp. nov., for UPII 610-JT representing the type strain of this species (=DSM 112989T, =ATCC TSD-274T) and Amygdalobacter nucleatus gen. nov., sp. nov., for KA00274T representing the type strain of this species (=DSM 112988T, =ATCC TSD-275T).
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Affiliation(s)
- Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | | | - Tina L Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Susan M Strenk
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Kathy J Agnew
- Division of Gynecologic Oncology, Department of Obstetrics & Gynecology, University of Washington Medical Center, Seattle, WA, USA
| | - G A Nagana Gowda
- Northwest Metabolomics Research Center and Mitochondrial and Metabolism Center, Anesthesiology and Pain Medicine, University of Washington Medical Center, Seattle, WA, USA
| | - Daniel Raftery
- Northwest Metabolomics Research Center and Mitochondrial and Metabolism Center, Anesthesiology and Pain Medicine, University of Washington Medical Center, Seattle, WA, USA
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - May A Beamer
- Magee-Womens Research Institute, Pittsburgh, PA, USA
| | - Sharon L Achilles
- Magee-Womens Research Institute, Pittsburgh, PA, USA
- University of Pittsburgh School of Medicine, Department of Obstetrics, Gynecology and Reproductive Sciences, Pittsburgh PA, USA
| | - Harold C Wiesenfeld
- Magee-Womens Research Institute, Pittsburgh, PA, USA
- University of Pittsburgh School of Medicine, Department of Obstetrics, Gynecology and Reproductive Sciences, Pittsburgh PA, USA
| | - David N Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Sharon L Hillier
- Magee-Womens Research Institute, Pittsburgh, PA, USA
- University of Pittsburgh School of Medicine, Department of Obstetrics, Gynecology and Reproductive Sciences, Pittsburgh PA, USA
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Lee EM, Srinivasan S, Purvine SO, Fiedler TL, Leiser OP, Proll SC, Minot SS, Deatherage Kaiser BL, Fredricks DN. Optimizing metaproteomics database construction: lessons from a study of the vaginal microbiome. mSystems 2023; 8:e0067822. [PMID: 37350639 PMCID: PMC10469846 DOI: 10.1128/msystems.00678-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 04/06/2023] [Indexed: 06/24/2023] Open
Abstract
Metaproteomics, a method for untargeted, high-throughput identification of proteins in complex samples, provides functional information about microbial communities and can tie functions to specific taxa. Metaproteomics often generates less data than other omics techniques, but analytical workflows can be improved to increase usable data in metaproteomic outputs. Identification of peptides in the metaproteomic analysis is performed by comparing mass spectra of sample peptides to a reference database of protein sequences. Although these protein databases are an integral part of the metaproteomic analysis, few studies have explored how database composition impacts peptide identification. Here, we used cervicovaginal lavage (CVL) samples from a study of bacterial vaginosis (BV) to compare the performance of databases built using six different strategies. We evaluated broad versus sample-matched databases, as well as databases populated with proteins translated from metagenomic sequencing of the same samples versus sequences from public repositories. Smaller sample-matched databases performed significantly better, driven by the statistical constraints on large databases. Additionally, large databases attributed up to 34% of significant bacterial hits to taxa absent from the sample, as determined orthogonally by 16S rRNA gene sequencing. We also tested a set of hybrid databases which included bacterial proteins from NCBI RefSeq and translated bacterial genes from the samples. These hybrid databases had the best overall performance, identifying 1,068 unique human and 1,418 unique bacterial proteins, ~30% more than a database populated with proteins from typical vaginal bacteria and fungi. Our findings can help guide the optimal identification of proteins while maintaining statistical power for reaching biological conclusions. IMPORTANCE Metaproteomic analysis can provide valuable insights into the functions of microbial and cellular communities by identifying a broad, untargeted set of proteins. The databases used in the analysis of metaproteomic data influence results by defining what proteins can be identified. Moreover, the size of the database impacts the number of identifications after accounting for false discovery rates (FDRs). Few studies have tested the performance of different strategies for building a protein database to identify proteins from metaproteomic data and those that have largely focused on highly diverse microbial communities. We tested a range of databases on CVL samples and found that a hybrid sample-matched approach, using publicly available proteins from organisms present in the samples, as well as proteins translated from metagenomic sequencing of the samples, had the best performance. However, our results also suggest that public sequence databases will continue to improve as more bacterial genomes are published.
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Affiliation(s)
- Elliot M. Lee
- Fred Hutchinson Cancer Research Center, Seattle, Washington, DC, USA
- University of Washington, Seattle, Washington, DC, USA
| | | | - Samuel O. Purvine
- Pacific Northwest National Laboratory, Richland, Washington, DC, USA
| | - Tina L. Fiedler
- Fred Hutchinson Cancer Research Center, Seattle, Washington, DC, USA
| | - Owen P. Leiser
- Pacific Northwest National Laboratory, Richland, Washington, DC, USA
| | - Sean C. Proll
- Fred Hutchinson Cancer Research Center, Seattle, Washington, DC, USA
| | - Samuel S. Minot
- Fred Hutchinson Cancer Research Center, Seattle, Washington, DC, USA
| | | | - David N. Fredricks
- Fred Hutchinson Cancer Research Center, Seattle, Washington, DC, USA
- University of Washington, Seattle, Washington, DC, USA
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5
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Sabo MC, Lokken EM, Srinivasan S, Kinuthia J, Richardson BA, Fiedler TL, Munch M, Proll S, Salano C, John-Stewart G, Jaoko W, Fredricks DN, McClelland RS. Changes in Vaginal Bacteria and Inflammatory Mediators From Periconception Through the Early Postpartum Period in a Cohort of Kenyan Women Without HIV. J Infect Dis 2023; 228:487-499. [PMID: 37207618 PMCID: PMC10428199 DOI: 10.1093/infdis/jiad168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 05/04/2023] [Accepted: 05/18/2023] [Indexed: 05/21/2023] Open
Abstract
BACKGROUND Women's increased risk of HIV acquisition during pregnancy and postpartum may be mediated by changes in vaginal microbiota and/or cytokines. METHODS A cohort of 80 Kenyan women who were HIV-1 seronegative contributed 409 vaginal samples at 6 pregnancy time points: periconception, positive pregnancy test result, first trimester, second trimester, third trimester, and postpartum. Concentrations of vaginal bacteria linked with HIV risk and Lactobacillus spp were measured using quantitative polymerase chain reaction. Cytokines were measured by immunoassay. RESULTS Based on Tobit regression, later pregnancy time points were associated with lower concentrations of Sneathia spp (P = .01), Eggerthella sp type 1 (P = .002), and Parvimonas sp type 2 (P = .02) and higher concentrations of Lactobacillus iners (P < .001), Lactobacillus crispatus (P < .001), Lactobacillus vaginalis (P < .001), interleukin 6 (P < .001), TNF (P = .004), C-X-C motif chemokine ligand 10 (CXCL10; P < .001), C-C motif ligand 3 (P = .009), C-C motif ligand 4 (P < .001), C-C motif ligand 5 (P = .002), interleukin 1β (P = .02), and interleukin 8 (P = .002). Most cervicovaginal cytokines and vaginal bacteria clustered separately in principal component analysis, except for CXCL10, which did not group with either cytokines or bacteria. The shift toward a Lactobacillus-dominated microbiota during pregnancy mediated the relationship between pregnancy time point and CXCL10. CONCLUSIONS Increases in proinflammatory cytokines, but not vaginal bacterial taxa linked with higher HIV risk, could provide an explanation for increased HIV susceptibility during pregnancy and postpartum.
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Affiliation(s)
- Michelle C Sabo
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Erica M Lokken
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - John Kinuthia
- Department of Research and Programs, Kenyatta National Hospital, Nairobi, Kenya
- Institute of Tropical and Infectious Diseases, University of Nairobi, Nairobi, Kenya
| | - Barbra A Richardson
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Tina L Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Matthew Munch
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Sean Proll
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Clayton Salano
- Department of Research and Programs, Kenyatta National Hospital, Nairobi, Kenya
- Institute of Tropical and Infectious Diseases, University of Nairobi, Nairobi, Kenya
| | - Grace John-Stewart
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | - Walter Jaoko
- Department of Medical Microbiology and Immunology, University of Nairobi, Nairobi, Kenya
| | - David N Fredricks
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - R Scott McClelland
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Department of Medical Microbiology and Immunology, University of Nairobi, Nairobi, Kenya
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6
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Koyama M, Hippe DS, Srinivasan S, Proll SC, Miltiadous O, Li N, Zhang P, Ensbey KS, Hoffman NG, Schmidt CR, Yeh AC, Minnie SA, Strenk SM, Fiedler TL, Hattangady N, Kowalsky J, Grady WM, Degli-Esposti MA, Varelias A, Clouston AD, van den Brink MRM, Dey N, Randolph TW, Markey KA, Fredricks DN, Hill GR. Intestinal microbiota controls graft-versus-host disease independent of donor-host genetic disparity. Immunity 2023; 56:1876-1893.e8. [PMID: 37480848 PMCID: PMC10530372 DOI: 10.1016/j.immuni.2023.06.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 04/11/2023] [Accepted: 06/28/2023] [Indexed: 07/24/2023]
Abstract
Acute graft-versus-host disease (aGVHD) remains a major limitation of allogeneic stem cell transplantation (SCT), and severe intestinal manifestation is the major cause of early mortality. Intestinal microbiota control MHC class II (MHC-II) expression by ileal intestinal epithelial cells (IECs) that promote GVHD. Here, we demonstrated that genetically identical mice of differing vendor origins had markedly different intestinal microbiota and ileal MHC-II expression, resulting in discordant GVHD severity. We utilized cohousing and antibiotic treatment to characterize the bacterial taxa positively and negatively associated with MHC-II expression. A large proportion of bacterial MHC-II inducers were vancomycin sensitive, and peri-transplant oral vancomycin administration attenuated CD4+ T cell-mediated GVHD. We identified a similar relationship between pre-transplant microbes, HLA class II expression, and both GVHD and mortality in a large clinical SCT cohort. These data highlight therapeutically tractable mechanisms by which pre-transplant microbial taxa contribute to GVHD independently of genetic disparity.
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Affiliation(s)
- Motoko Koyama
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA.
| | - Daniel S Hippe
- Clinical Research Division, FHCC, Seattle, WA 98109, USA
| | | | - Sean C Proll
- Vaccine and Infectious Disease Division, FHCC, Seattle, WA 98109, USA
| | - Oriana Miltiadous
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Naisi Li
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA
| | - Ping Zhang
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA
| | - Kathleen S Ensbey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA
| | - Noah G Hoffman
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Christine R Schmidt
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA
| | - Albert C Yeh
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Simone A Minnie
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA
| | - Susan M Strenk
- Vaccine and Infectious Disease Division, FHCC, Seattle, WA 98109, USA
| | - Tina L Fiedler
- Vaccine and Infectious Disease Division, FHCC, Seattle, WA 98109, USA
| | - Namita Hattangady
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA
| | - Jacob Kowalsky
- Vaccine and Infectious Disease Division, FHCC, Seattle, WA 98109, USA
| | - Willian M Grady
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Mariapia A Degli-Esposti
- Infection and Immunity Program and Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Centre for Experimental Immunology, Lions Eye Institute, Nedlands, WA 6009, Australia
| | - Antiopi Varelias
- Transplantation Immunology Laboratory, Cancer Research Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia; Faculty of Medicine, University of Queensland, St Lucia, QLD 4067, Australia
| | - Andrew D Clouston
- Molecular and Cellular Pathology, University of Queensland, Brisbane, QLD 4006, Australia
| | - Marcel R M van den Brink
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Medical College, New York, NY 10065, USA; Department of Immunology, Sloan Kettering Institute, New York, NY 10065, USA
| | - Neelendu Dey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Timothy W Randolph
- Clinical Research Division, FHCC, Seattle, WA 98109, USA; Public Health Sciences Division, FHCC, WA 98109, USA
| | - Kate A Markey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA; Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Weill Cornell Medical College, New York, NY 10065, USA
| | - David N Fredricks
- Vaccine and Infectious Disease Division, FHCC, Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA
| | - Geoffrey R Hill
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center (FHCC), Seattle, WA 98109, USA; Department of Medicine, University of Washington, Seattle, WA 98109, USA.
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Sabo MC, Balkus JE, Richardson BA, Srinivasan S, Kimani J, Anzala O, Schwebke J, Fiedler TL, Fredricks DN, McClelland RS. Next generation sequencing to examine associations between vaginal washing and vaginal microbiota: A cohort study. Int J STD AIDS 2023; 34:557-566. [PMID: 36945124 PMCID: PMC11075686 DOI: 10.1177/09564624231160806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
BACKGROUND The association between vaginal washing and HIV risk may be mediated by vaginal washing-associated changes in vaginal microbiota. METHODS Data from a cohort of HIV-negative US and Kenyan women enrolled in the Preventing Vaginal Infections trial were analyzed. Vaginal fluid samples and vaginal washing data were collected every 2 months for 12 months. Bacterial relative abundances were measured by broad-range 16S rRNA gene polymerase chain reaction with next generation sequencing. Generalized estimating equations were used to evaluate the association between vaginal washing and i) the Shannon Diversity Index (SDI); and ii) mean change in percent bacterial relative abundances, with application of a 10% false discovery rate (FDR). RESULTS Participants (N = 111) contributed 93/630 (14.8%) vaginal washing visits. Mean SDI was 0.74 points higher (95% CI 0.35, 1.14; p < 0.001) at washing visits among US participants (N = 26). Vaginal washing was not associated with SDI in Kenyan participants (N = 85). There were no associations between vaginal washing and vaginal bacterial relative abundances after applying the FDR. CONCLUSIONS The discordant results in Kenyan versus US women suggests the link between vaginal washing and sub-optimal vaginal microbiota may be context specific. Vaginal microbial shifts may not fully explain the association between vaginal washing and HIV acquisition.
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Affiliation(s)
- Michelle C. Sabo
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jennifer E. Balkus
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Barbra A. Richardson
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Biostatistics, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Joshua Kimani
- Institute for Tropical and Infectious Diseases, University of Nairobi, Nairobi, Kenya
| | - Omu Anzala
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Jane Schwebke
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tina L. Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David N. Fredricks
- Department of Medicine, University of Washington, Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - R. Scott McClelland
- Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
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8
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Carter KA, Balkus JE, Anzala O, Kimani J, Hoffman NG, Fiedler TL, Mochache V, Fredricks DN, McClelland RS, Srinivasan S. Associations Between Vaginal Bacteria and Bacterial Vaginosis Signs and Symptoms: A Comparative Study of Kenyan and American Women. Front Cell Infect Microbiol 2022; 12:801770. [PMID: 35310847 PMCID: PMC8931342 DOI: 10.3389/fcimb.2022.801770] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/14/2022] [Indexed: 12/30/2022] Open
Abstract
Background Bacterial colonization and associations with bacterial vaginosis (BV) signs and symptoms (Amsel criteria) may vary between populations. We assessed relationships between vaginal bacteria and Amsel criteria among two populations. Methods Kenyan participants from the placebo arm of the Preventing Vaginal Infections (PVI) trial and participants from a Seattle-based cross-sectional BV study were included. Amsel criteria were recorded at study visits, and the vaginal microbiota was characterized using 16S rRNA gene sequencing. Logistic regression models, accounting for repeat visits as appropriate, were fit to evaluate associations between bacterial relative abundance and each Amsel criterion. Results Among 84 PVI participants (496 observations) and 220 Seattle participants, the prevalence of amine odor was 25% and 40%, clue cells 16% and 37%, vaginal discharge 10% and 52%, elevated vaginal pH 69% and 67%, and BV 13% and 44%, respectively. BV-associated bacterium 1 (BVAB1) was positively associated with all Amsel criteria in both populations. Eggerthella type 1, Fannyhessea (Atopobium) vaginae, Gardnerella spp., Sneathia amnii, and Sneathia sanguinegens were positively associated with all Amsel criteria in the Seattle study, and all but discharge in the PVI trial. Conclusions Core vaginal bacteria are consistently associated with BV signs and symptoms across two distinct populations of women.
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Affiliation(s)
- Kayla A. Carter
- Department of Epidemiology, University of Washington, Seattle, WA, United States
| | - Jennifer E. Balkus
- Department of Epidemiology, University of Washington, Seattle, WA, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Omu Anzala
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Joshua Kimani
- Institute for Tropical and Infectious Diseases, University of Nairobi, Nairobi, Kenya
| | - Noah G. Hoffman
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, United States
| | - Tina L. Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
| | - Vernon Mochache
- Centre for Public Health Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - David N. Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
- Department of Medicine, University of Washington, Seattle, WA, United States
| | - Raymond Scott McClelland
- Department of Epidemiology, University of Washington, Seattle, WA, United States
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
- Department of Medicine, University of Washington, Seattle, WA, United States
- Department of Global Health, University of Washington, Seattle, WA, United States
| | - Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States
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9
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Carter KA, Srinivasan S, Fiedler TL, Anzala O, Kimani J, Mochache V, Wallis JM, Fredricks DN, McClelland RS, Balkus JE. Vaginal Bacteria and Risk of Incident and Persistent Infection With High-Risk Subtypes of Human Papillomavirus: A Cohort Study Among Kenyan Women. Sex Transm Dis 2021; 48:499-507. [PMID: 33346587 PMCID: PMC8184569 DOI: 10.1097/olq.0000000000001343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
BACKGROUND Bacterial vaginosis (BV) is associated with an increased risk of high-risk human papillomavirus (hrHPV), whereas Lactobacillus-dominated vaginal microbiotas are associated with reduced burden of hrHPV. Few epidemiologic studies have prospectively investigated the relationships between vaginal bacteria and hrHPV, particularly among women from countries in Africa. METHODS We conducted a prospective cohort study nested within the Preventing Vaginal Infections trial to evaluate associations between vaginal bacteria and hrHPV incidence and persistence. Sexually active, HIV-seronegative women aged 18 to 45 years who had a vaginal infection at screening were eligible to enroll. Analyses were restricted to participants enrolled in Kenya and randomized to placebo. At enrollment and months 2, 4, 6, 8, 10, and 12, hrHPV testing, quantitative polymerase chain reaction (measuring taxon quantity per swab), and 16S rRNA gene amplicon sequencing of the vaginal microbiota were performed. Generalized estimating equations multinomial logistic regression models were fit to evaluate associations between vaginal bacteria and incident and persistent hrHPV. RESULTS Eighty-four participants were included in this analysis. Higher concentrations of Lactobacillus crispatus were inversely associated with persistent hrHPV detection. Specifically, 1 tertile higher L. crispatus concentration was associated with 50% reduced odds of persistent hrHPV detection (odds ratio, 0.50; 95% confidence interval, 0.29-0.85). CONCLUSIONS This study is consistent with reports that vaginal L. crispatus is associated with reduced susceptibility to hrHPV persistence. Evidence from in vitro studies provides insight into potential mechanisms by which L. crispatus may mediate hrHPV risk. Future studies should further explore in vivo mechanisms that may drive this relationship and opportunities for intervention.
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Affiliation(s)
- Kayla A. Carter
- Department of Epidemiology, University of Washington; Seattle, WA, USA
| | - Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center; Seattle, WA, USA
| | - Tina L. Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center; Seattle, WA, USA
| | - Omu Anzala
- Department of Medical Microbiology, University of Nairobi; Nairobi, Kenya
| | - Joshua Kimani
- University of Nairobi Institute for Tropical and Infectious Diseases, University of Nairobi; Nairobi, Kenya
| | - Vernon Mochache
- Department of Epidemiology, University of Washington; Seattle, WA, USA
| | - Jacqueline M. Wallis
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center; Seattle, WA, USA
| | - David N. Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center; Seattle, WA, USA
- Department of Medicine, University of Washington; Seattle, WA, USA
| | - R. Scott McClelland
- Department of Epidemiology, University of Washington; Seattle, WA, USA
- University of Nairobi Institute for Tropical and Infectious Diseases, University of Nairobi; Nairobi, Kenya
- Department of Medicine, University of Washington; Seattle, WA, USA
- Department of Global Health, University of Washington; Seattle, WA, USA
| | - Jennifer E. Balkus
- Department of Epidemiology, University of Washington; Seattle, WA, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center; Seattle, WA, USA
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10
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Sultan JS, Wang T, Hunte R, Srinivasan S, McWalters J, Tharp GK, Bosinger SE, Fiedler TL, Atrio JM, Murphy K, Barnett R, Ray LR, Krows ML, Fredricks DN, Irungu E, Ngure K, Mugo N, Marrazzo J, Keller MJ, Herold BC. Differences in vaginal microbiota, host transcriptome and proteins in women with bacterial vaginosis are associated with metronidazole treatment response. J Infect Dis 2021; 224:2094-2104. [PMID: 34003290 DOI: 10.1093/infdis/jiab266] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/17/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Bacterial vaginosis (BV) treatment failures and recurrences are common. To identify features associated with treatment response, we compared vaginal microbiota and host ectocervical transcriptome before and after oral metronidazole therapy. METHODS Women with BV (Bronx, NY and Thika, Kenya) received 7 days of oral metronidazole at enrollment (Day 0) and underwent genital tract sampling of microbiome (16S rRNA gene sequencing), transcriptome (RNAseq), and immune mediator concentrations on Day 0, 15 and 35. RESULTS Bronx participants were more likely than Thika participants to clinically respond to metronidazole (19/20 vs 10/18, respectively, p=0.0067) and by changes in microbiota composition and diversity. After dichotomizing the cohort into responders and non-responders by change in alpha diversity between Day 35 and Day 0, we identified transcription differences associated with chemokine signaling (q=0.002) and immune system process (q=2.5e-8) that differentiated responders from non-responders were present at enrollment. Responders had significantly lower levels of CXCL9 in cervicovaginal lavage on Day 0 (p< 0.007) and concentrations of CXCL9, CXCL10 and MCP-1 increased significantly between Day 0 and Day 35 in responders versus non-responders. CONCLUSIONS Response to metronidazole is characterized by significant changes in chemokines and related transcripts suggesting that treatments that promote these pathways may prove beneficial.
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Affiliation(s)
- Joyce Serebrenik Sultan
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Tao Wang
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Richard Hunte
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jessica McWalters
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Gregory K Tharp
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, GA, USA
| | - Steven E Bosinger
- Yerkes Genomics Core Laboratory, Yerkes National Primate Research Center, Atlanta, GA, USA.,Emory University School of Medicine, Department of Pathology & Laboratory Medicine, Atlanta, GA, USA.,Emory Vaccine Center, Emory University, Atlanta,GA, USA
| | - Tina L Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Jessica M Atrio
- Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Kerry Murphy
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Rebecca Barnett
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Laurie R Ray
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Meighan L Krows
- Department of Global Health, University of Washington, Seattle WA, USA
| | - David N Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Elizabeth Irungu
- Department of Medicine, Center for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Kenneth Ngure
- Department of Medicine, Center for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Nelly Mugo
- Department of Medicine, Center for Clinical Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Jeanne Marrazzo
- University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
| | - Marla J Keller
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Betsy C Herold
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, USA.,Department of Pediatrics, Albert Einstein College of Medicine, Bronx, NY, USA
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11
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Eastment MC, Balkus JE, Richardson BA, Srinivasan S, Kimani J, Anzala O, Schwebke J, Fiedler TL, Fredricks DN, McClelland RS. Association Between Vaginal Bacterial Microbiota and Vaginal Yeast Colonization. J Infect Dis 2021; 223:914-923. [PMID: 32726445 PMCID: PMC7938175 DOI: 10.1093/infdis/jiaa459] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/21/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Vaginal yeast is frequently found with Lactobacillus-dominant microbiota. The relationship between vaginal yeast and other bacteria has not been well characterized. METHODS These analyses utilized data from the Preventing Vaginal Infections trial. Relative abundance of vaginal bacteria from 16S ribosomal ribonucleic acid gene amplicon sequencing and quantities of 10 vaginal bacteria using taxon-directed polymerase chain reaction assays were compared at visits with and without detection of yeast on microscopy, culture, or both. RESULTS Higher relative abundances of Megasphaera species type 1 (risk ratio [RR], 0.70; 95% confidence interval [CI], 0.52-0.95), Megasphaera species type 2 (RR, 0.81; 95% CI, 0.67-0.98), and Mageeibacillus indolicus (RR, 0.46; 95% CI, 0.25-0.83) were associated with lower risk of detecting yeast. In contrast, higher relative abundances of Bifidobacterium bifidum, Aerococcus christensenii, Lactobacillus mucosae, Streptococcus equinus/infantarius/lutentiensis, Prevotella bivia, Dialister propionicifaciens, and Lactobacillus crispatus/helveticus were associated with yeast detection. Taxon-directed assays confirmed that increasing quantities of both Megasphaera species and M indolicus were associated with lower risk of detecting yeast, whereas increasing quantities of L crispatus were associated with higher risk of detecting yeast. CONCLUSIONS Despite an analysis that examined associations between multiple vaginal bacteria and the presence of yeast, only a small number of vaginal bacteria were strongly and significantly associated with the presence or absence of yeast.
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Affiliation(s)
- McKenna C Eastment
- University of Washington, Department of Medicine, Seattle, Washington, USA
| | - Jennifer E Balkus
- Department of Global Health, Seattle, Washington, USA
- Department of Epidemiology, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, USA
| | - Barbra A Richardson
- Department of Global Health, Seattle, Washington, USA
- Department of Biostatistics, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, USA
| | - Sujatha Srinivasan
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, USA
| | - Joshua Kimani
- University of Nairobi, Institute of Tropical and Infectious Diseases, Nairobi, Kenya
| | - Omu Anzala
- Kenya AIDS Vaccine Initiative (KAVI)-Institute of Clinical Research, Nairobi, Kenya
| | - Jane Schwebke
- University of Alabama at Birmingham, Division of Infectious Diseases, Birmingham, Alabama, USA
| | - Tina L Fiedler
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, USA
| | - David N Fredricks
- University of Washington, Department of Medicine, Seattle, Washington, USA
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, Washington, USA
| | - R Scott McClelland
- University of Washington, Department of Medicine, Seattle, Washington, USA
- Department of Global Health, Seattle, Washington, USA
- Department of Epidemiology, Seattle, Washington, USA
- University of Nairobi, Institute of Tropical and Infectious Diseases, Nairobi, Kenya
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12
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Srinivasan S, Beamer MA, Fiedler TL, Austin MN, Sizova MV, Strenk SM, Agnew KJ, Gowda GAN, Raftery D, Epstein SS, Fredricks DN, Hillier SL. Megasphaera lornae sp. nov., Megasphaera hutchinsoni sp. nov., and Megasphaera vaginalis sp. nov.: novel bacteria isolated from the female genital tract. Int J Syst Evol Microbiol 2021; 71. [PMID: 33616513 DOI: 10.1099/ijsem.0.004702] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Six strictly anaerobic Gram-negative bacteria representing three novel species were isolated from the female reproductive tract. The proposed type strains for each species were designated UPII 199-6T, KA00182T and BV3C16-1T. Phylogenetic analyses based on 16S rRNA gene sequencing indicated that the bacterial isolates were members of the genus Megasphaera. UPII 199-6T and KA00182T had 16S rRNA gene sequence identities of 99.9 % with 16S rRNA clone sequences previously amplified from the human vagina designated as Megasphaera type 1 and Megasphaera type 2, members of the human vaginal microbiota associated with bacterial vaginosis, preterm birth and HIV acquisition. UPII 199-6T exhibited sequence identities ranging from 92.9 to 93.6 % with validly named Megasphaera isolates and KA00182T had 16S rRNA gene sequence identities ranging from 92.6-94.2 %. BV3C16-1T was most closely related to Megasphaera cerevisiae with a 16S rRNA gene sequence identity of 95.4 %. Cells were coccoid or diplococcoid, non-motile and did not form spores. Genital tract isolates metabolized organic acids but were asaccharolytic. The isolates also metabolized amino acids. The DNA G+C content for the genome sequences of UPII 199-6T, KA00182T and BV3C16-1T were 46.4, 38.9 and 49.8 mol%, respectively. Digital DNA-DNA hybridization and average nucleotide identity between the genital tract isolates and other validly named Megasphaera species suggest that each isolate type represents a new species. The major fatty acid methyl esters include the following: C12 : 0, C16 : 0, C16 : 0 dimethyl acetal (DMA) and summed feature 5 (C15 : 0 DMA and/or C14 : 0 3-OH) in UPII 199-6T; C16 : 0 and C16 : 1 cis 9 in KA00182T; C12 : 0; C14 : 0 3-OH; and summed feature 5 in BV3C16-1T. The isolates produced butyrate, isobutyrate, and isovalerate but there were specific differences including production of formate and propionate. Together, these data indicate that UPII 199-6T, KA00182T and BV3C16-1T represent novel species within the genus Megasphaera. We propose the following names: Megasphaera lornae sp. nov. for UPII 199-6T representing the type strain of this species (=DSM 111201T=ATCC TSD-205T), Megasphaera hutchinsoni sp. nov. for KA00182T representing the type strain of this species (=DSM 111202T=ATCC TSD-206T) and Megasphaera vaginalis sp. nov. for BV3C16-1T representing the type strain of this species (=DSM 111203T=ATCC TSD-207T).
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Affiliation(s)
- Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - May A Beamer
- Magee-Womens Research Institute, Pittsburgh, PA, USA
| | - Tina L Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Maria V Sizova
- Present address: Evelo Biosciences, 620 Memorial Drive, Cambridge, MA, USA.,Department of Biology, Northeastern University, Boston, MA, USA
| | - Susan M Strenk
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Kathy J Agnew
- Division of Gynecologic Oncology, Department of Obstetrics & Gynecology, University of Washington Medical Center, Seattle, WA, USA
| | - G A Nagana Gowda
- Northwest Metabolomics Research Center and Mitochondrial and Metabolism Center, Anesthesiology and Pain Medicine, University of Washington Medical Center, Seattle, WA, USA
| | - Daniel Raftery
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA.,Northwest Metabolomics Research Center and Mitochondrial and Metabolism Center, Anesthesiology and Pain Medicine, University of Washington Medical Center, Seattle, WA, USA
| | - Slava S Epstein
- Department of Biology, Northeastern University, Boston, MA, USA
| | - David N Fredricks
- Department of Medicine, University of Washington, Seattle, WA, USA.,Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Sharon L Hillier
- University of Pittsburgh School of Medicine, Department of Obstetrics, Gynecology and Reproductive Sciences, Pittsburgh, PA, USA.,Magee-Womens Research Institute, Pittsburgh, PA, USA
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13
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Mitchell CM, Srinivasan S, Ma N, Reed SD, Wu MC, Hoffman NG, Valint DJ, Proll S, Fiedler TL, Agnew KJ, Guthrie KA, Fredricks DN. Bacterial Communities Associated With Abnormal Nugent Score in Postmenopausal Versus Premenopausal Women. J Infect Dis 2020; 223:2048-2052. [PMID: 33107562 PMCID: PMC8350750 DOI: 10.1093/infdis/jiaa675] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/22/2020] [Indexed: 11/14/2022] Open
Abstract
The Nugent score is the reference standard for bacterial vaginosis (BV) diagnosis but has not been validated in postmenopausal women. We compared relative abundances from 16S ribosomal RNA gene sequencing of vaginal microbiota with Nugent score in cohorts of premenopausal (n = 220) and postmenopausal (n = 144) women. In premenopausal women, 33 taxa were significantly correlated with Nugent score, including the classic BV-associated taxa Gardnerella, Atopobium, Sneathia, Megasphaera, and Prevotella. In postmenopausal women, 11 taxa were significantly associated with Nugent score, including Prevotella but no other BV-associated genera. High Nugent scores should not be used to infer BV in postmenopausal women.
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Affiliation(s)
- Caroline M Mitchell
- Vincent Center for Reproductive Biology, Massachusetts General Hospital, Boston, Massachusetts, USA,Correspondence: Caroline M. Mitchell, Vincent Center for Reproductive Biology, Massachusetts General Hospital, 55 Fruit St, Boston, MA 02114 ()
| | - Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Nanxun Ma
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Susan D Reed
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, USA
| | - Michael C Wu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Noah G Hoffman
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
| | - Daniel J Valint
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Sean Proll
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Tina L Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Kathy J Agnew
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, USA
| | - Katherine A Guthrie
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - David N Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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14
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Fredricks DN, Plantinga A, Srinivasan S, Oot A, Wiser A, Fiedler TL, Proll S, Wu MC, Marrazzo JM. Extra-vaginal Bacterial Colonization and Risk for Incident Bacterial Vaginosis in a Population of Women who Have Sex with Men. J Infect Dis 2020; 225:1261-1265. [PMID: 32379324 PMCID: PMC8974833 DOI: 10.1093/infdis/jiaa233] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 04/29/2020] [Indexed: 12/13/2022] Open
Abstract
Background Bacterial vaginosis (BV) is a common cause of vaginal discharge and associated with vaginal acquisition of BV-associated bacteria (BVAB). Methods We used quantitative polymerase chain reaction assays to determine whether presence or concentrations of BVAB in the mouth, anus, vagina, or labia before BV predict risk of incident BV in 72 women who have sex with men. Results Baseline vaginal and extra-vaginal colonization with Gardnerella spp, Megasphaera spp, Sneathia spp, BVAB-2, Dialister sp type 2, and other BVAB was more common among subjects with incident BV. Conclusions Prior colonization with BVAB is a consistent risk for BV.
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Affiliation(s)
- David N Fredricks
- Fred Hutchinson Cancer Research Center, Seattle, WA.,University of Washington, Seattle, WA
| | | | | | | | - Andrew Wiser
- Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Sean Proll
- Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Michael C Wu
- Fred Hutchinson Cancer Research Center, Seattle, WA
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15
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Golob JL, DeMeules MM, Loeffelholz T, Quinn ZZ, Dame MK, Silvestri S, Wu M, Schmidt T, Fiedler TL, Hoostal M, Mielcarek M, Spence J, Pergam SA, Fredricks D. 2844. Butyrogenic Bacteria After Acute Graft vs. Host Disease Associate with the Development of Steroid Refractory GVHD. Open Forum Infect Dis 2019. [PMCID: PMC6808863 DOI: 10.1093/ofid/ofz359.149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Steroid refractory acute graft- vs. -host-disease (GVHD) after hematopoietic cell transplantation (HCT) is highly morbid with limited treatment options. Murine studies show protection from GVHD with butyrate exposure but direct exposure of stem/progenitor cells to butyrate inhibits colonic stem cell proliferation.
Methods
Stool samples were collected weekly in a cohort of HCT recipients (n = 210) undergoing allogeneic transplant, and underwent 16S rRNA sequencing to determine the number and relative abundance of butyrogens. Dissociated primary human colonoid cell aggregates (200,000 per well) were plated onto collagen IV-coated transwells (0.4 µm pore size, 0.33 cm2, PET) in stem cell medium for 24 hours. From 24 hours onwards, the basal-lateral chamber was switched to differentiation medium; the apical chamber was Hanks Buffered Salt Solution (HBSS), HBSS with 10 mM butyrate sodium salt early (24 hours onwards) or late (72hours onwards). Trans-epithelial electrical resistance was measured daily.
Results
Retrospective chart review identified 27 recipients who developed acute GVHD of the gut, stratified to be either steroid refractory GVHD (failed to respond to 2 mg/kg of methylprednisolone) or responsive. The presence of butyrogens in the gut microbiome after the onset of severe acute GHVD of the gut associated with increased risk of steroid refractory GVHD (Figure 1; P < 0.05). Direct exposure of human colonic stem/progenitor cells to butyrate inhibits the development of trans-epithelial electrical resistance; exposure after differentiation had no inhibition of barrier formation (Figure 2; P < 0.05 by T-test).
Conclusion
Butyrogens may help prevent the development of acute GVHD of the gut, but once severe GVHD has developed may inhibit recovery due to the loss of crypt architecture exposing colonic stem cells to microbe-produced butyrate with impaired differentiation and cell replacement.
Disclosures
All Authors: No reported Disclosures.
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Affiliation(s)
| | | | | | - Z Z Quinn
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Michael K Dame
- University of Michigan Medical School, Ann Arbor, Michigan
| | | | | | | | - Tina L Fiedler
- Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Marco Mielcarek
- Fred Hutchinsson Cancer Research Center, Seattle, Washington
| | | | - Steven A Pergam
- Fred Hutch Cancer Research Center, University of Washington, Seattle, Washington
| | - David Fredricks
- Fred Hutch and University of Washington, Seattle, Washington
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16
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Golob JL, DeMeules MM, Loeffelholz T, Quinn ZZ, Dame MK, Silvestri SS, Wu MC, Schmidt TM, Fiedler TL, Hoostal MJ, Mielcarek M, Spence J, Pergam SA, Fredricks DN. Butyrogenic bacteria after acute graft-versus-host disease (GVHD) are associated with the development of steroid-refractory GVHD. Blood Adv 2019; 3:2866-2869. [PMID: 31585950 PMCID: PMC6784520 DOI: 10.1182/bloodadvances.2019000362] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/02/2019] [Indexed: 01/24/2023] Open
Abstract
The presence of butyrogenic bacteria after the onset of acute GVHD associates with subsequent steroid-refractory GVHD or chronic GVHD. Butyrate inhibits human colonic stem cells from forming an intact epithelial monolayer.
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Affiliation(s)
- Jonathan L Golob
- Division of Infectious Diseases, Department of Medicine, University of Michigan, Ann Arbor, MI
| | - Martha M DeMeules
- Infectious Disease Sciences, Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Tillie Loeffelholz
- Infectious Disease Sciences, Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Z Z Quinn
- Infectious Disease Sciences, Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Michael K Dame
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
| | | | | | - Thomas M Schmidt
- Division of Infectious Diseases, Department of Medicine, University of Michigan, Ann Arbor, MI
| | - Tina L Fiedler
- Infectious Disease Sciences, Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Matthew J Hoostal
- Division of Infectious Diseases, Department of Medicine, University of Michigan, Ann Arbor, MI
| | - Marco Mielcarek
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Division of Medical Oncology, Department of Medicine, University of Washington, Seattle, WA
| | - Jason Spence
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI
- Department of Biomedical Engineering, University of Michigan College of Engineering, Ann Arbor, MI; and
| | - Steven A Pergam
- Infectious Disease Sciences, Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Division of Allergy & Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA
| | - David N Fredricks
- Infectious Disease Sciences, Vaccines and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA
- Division of Allergy & Infectious Diseases, Department of Medicine, University of Washington, Seattle, WA
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17
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Sabo MC, Lehman DA, Wang B, Richardson BA, Srinivasan S, Osborn L, Matemo D, Kinuthia J, Fiedler TL, Munch MM, Drake AL, Fredricks DN, Overbaugh J, John-Stewart G, McClelland RS, Graham SM. Associations between vaginal bacteria implicated in HIV acquisition risk and proinflammatory cytokines and chemokines. Sex Transm Infect 2019; 96:3-9. [PMID: 31197065 DOI: 10.1136/sextrans-2018-053949] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Revised: 05/07/2019] [Accepted: 05/25/2019] [Indexed: 01/09/2023] Open
Abstract
OBJECTIVES Recent studies have identified vaginal bacterial taxa associated with increased HIV risk. A possible mechanism to explain these results is that individual taxa differentially promote cervicovaginal inflammation. This study aimed to explore relationships between concentrations of bacteria previously linked to HIV acquisition and vaginal concentrations of proinflammatory cytokines and chemokines. METHODS In this cross-sectional analysis, concentrations of 17 bacterial taxa and four proinflammatory cytokines (interleukin (IL)-1β, IL-6, IL-10 and tumour necrosis factor alpha (TNFα)) and two proinflammatory chemokines (IL-8 and interferon gamma-induced protein 10) were measured in vaginal swabs collected from 80 HIV-uninfected women. Cytokine and chemokine concentrations were compared between women with bacterial concentrations above or below the lower limit of detection as determined by quantitative PCR for each taxon. Principal component analysis was used to create a summary score for closely correlated bacteria, and linear regression analysis was used to evaluate associations between this score and increasing concentrations of TNFα and IL-1β. RESULTS Detection of Dialister micraerophilus (p=0.01), Eggerthella sp type 1 (p=0.05) or Mycoplasma hominis (p=0.03) was associated with higher TNFα concentrations, and detection of D. micraerophilus (p<0.01), Eggerthella sp type 1 (p=0.04), M. hominis (p=0.02) or Parvimonas sp type 2 (p=0.05) was associated with significantly higher IL-1β concentrations. Seven bacterial taxa (D. micraerophilus, Eggerthella sp type 1, Gemella asaccharolytica, Sneathia sp, Megasphaera sp, M. hominis and Parvimonas sp type 2) were found to be highly correlated by principal component analysis (eigenvalue 5.24, explaining 74.92% of variability). Linear regression analysis demonstrated associations between this principal component and concentrations of TNFα (β=0.55, 95% CI 0.01 to 1.08; p=0.048) and IL-1β (β=0.96, 95% CI 0.19 to 1.74; p=0.016). CONCLUSIONS This study provides evidence that several highly correlated vaginal bacterial taxa may influence vaginal cytokine and chemokine concentrations. These results suggest a mechanism where the presence of specific bacterial taxa could influence HIV susceptibility by increasing vaginal inflammation.
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Affiliation(s)
- Michelle C Sabo
- Department of Internal Medicine, University of Washington, Seattle, Washington, USA
| | - Dara A Lehman
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Bingjie Wang
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Barbra A Richardson
- Department of Global Health, University of Washington, Seattle, Washington, USA.,Department of Epidemiology, University of Washington, Seattle, Washington, USA.,Department of Biostatistics, University of Washington, Seattle, Washington, United States
| | - Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Lusi Osborn
- Department of Research and Programs, Kenyatta National Hospital, Nairobi, Kenya
| | - Daniel Matemo
- Department of Research and Programs, Kenyatta National Hospital, Nairobi, Kenya
| | - John Kinuthia
- Department of Global Health, University of Washington, Seattle, Washington, USA.,Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Tina L Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Matthew M Munch
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Alison L Drake
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - David N Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Grace John-Stewart
- Department of Internal Medicine, University of Washington, Seattle, Washington, USA.,Department of Global Health, University of Washington, Seattle, Washington, USA.,Department of Epidemiology, University of Washington, Seattle, Washington, USA.,Seattle Children's Hospital, Seattle, Washington, USA
| | - R Scott McClelland
- Department of Internal Medicine, University of Washington, Seattle, Washington, USA.,Department of Global Health, University of Washington, Seattle, Washington, USA.,Department of Epidemiology, University of Washington, Seattle, Washington, USA.,Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Susan M Graham
- Department of Internal Medicine, University of Washington, Seattle, Washington, USA.,Department of Global Health, University of Washington, Seattle, Washington, USA.,Department of Epidemiology, University of Washington, Seattle, Washington, USA
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Lokken EM, Manguro GO, Abdallah A, Ngacha C, Shafi J, Kiarie J, Jaoko W, Srinivasan S, Fiedler TL, Munch MM, Fredricks DN, McClelland RS, Balkus JE. Association between vaginal washing and detection of Lactobacillus by culture and quantitative PCR in HIV-seronegative Kenyan women: a cross-sectional analysis. Sex Transm Infect 2019; 95:455-461. [PMID: 30696752 DOI: 10.1136/sextrans-2018-053769] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 12/06/2018] [Accepted: 01/04/2019] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES Vaginal washing has been associated with reductions in cultivable Lactobacillus and an increased risk of both bacterial vaginosis (BV) and HIV infection. The effect of vaginal washing on the quantity of individual Lactobacillus species is not well characterised. This analysis tested the hypothesis that vaginal washing would be associated with a lower likelihood of Lactobacillus spp. detected by both culture and quantitative PCR (qPCR). METHODS We conducted a cross-sectional study of 272 HIV-seronegative women enrolled in an open-cohort study in Mombasa, Kenya. Vaginal washing and sexual risk behaviours were assessed using face-to-face interviews. Vaginal Lactobacillus spp. were detected using cultivation and PCR methods, with L. crispatus, L. jensenii and L. iners concentrations measured using qPCR assays targeting the 16S rRNA gene. Poisson regression with robust SEs was used to assess associations between vaginal washing and Lactobacillus detection by culture and qPCR. RESULTS Eighty percent (n=217) of participants reported vaginal washing in the prior week. One-fifth (n=58) of participants had BV by Nugent score. In unadjusted analysis, vaginal washing was associated with a 45% decreased likelihood of Lactobacillus spp. detection by culture (prevalence ratio (PR): 0.55, 95% CI 0.37 to 0.82). Adjusting for age and condomless sex in the prior week did not change the magnitude of the association (adjusted PR (aPR): 0.56, 95% CI (0.37 to 0.85). Vaginal washing was associated with approximately a 40% reduction in L. crispatus detection (aPR: 0.57, 95% CI 0.36 to 0.92), but was not significantly associated with L. jensenii (aPR: 0.68, 95% CI 0.42 to 1.09) or L. iners detection (aPR: 1.03, 95% CI 0.92 to 1.15). CONCLUSIONS Vaginal washing in the prior week was associated with a significantly reduced likelihood of detecting cultivable Lactobacillus and L. crispatus by qPCR. Given associations between Lactobacillus detection and improved reproductive health outcomes, these results provide motivation for additional study of vaginal washing cessation interventions to improve vaginal health.
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Affiliation(s)
- Erica M Lokken
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | | | - Amina Abdallah
- Institute of Tropical & Infectious Diseases, University of Nairobi, Nairobi, Kenya
| | - Caroline Ngacha
- Institute of Tropical & Infectious Diseases, University of Nairobi, Nairobi, Kenya
| | - Juma Shafi
- Institute of Tropical & Infectious Diseases, University of Nairobi, Nairobi, Kenya
| | - James Kiarie
- Institute of Tropical & Infectious Diseases, University of Nairobi, Nairobi, Kenya
| | - Walter Jaoko
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Sujatha Srinivasan
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Tina L Fiedler
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Matthew M Munch
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - David N Fredricks
- Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Medicine, University of Washington, Seattle, Washington, USA
| | - R Scott McClelland
- Department of Epidemiology, University of Washington, Seattle, Washington, USA.,Institute of Tropical & Infectious Diseases, University of Nairobi, Nairobi, Kenya.,Department of Medicine, University of Washington, Seattle, Washington, USA.,Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Jennifer E Balkus
- Department of Epidemiology, University of Washington, Seattle, Washington, USA.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Global Health, University of Washington, Seattle, Washington, USA
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19
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Golob JL, Pergam SA, Srinivasan S, Fiedler TL, Liu C, Garcia K, Mielcarek M, Ko D, Aker S, Marquis S, Loeffelholz T, Plantinga A, Wu MC, Celustka K, Morrison A, Woodfield M, Fredricks DN. Stool Microbiota at Neutrophil Recovery Is Predictive for Severe Acute Graft vs Host Disease After Hematopoietic Cell Transplantation. Clin Infect Dis 2018; 65:1984-1991. [PMID: 29020185 PMCID: PMC5850019 DOI: 10.1093/cid/cix699] [Citation(s) in RCA: 125] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 08/03/2017] [Indexed: 12/13/2022] Open
Abstract
Background Graft-versus-host disease (GVHD) is common after allogeneic hematopoietic cell transplantation (HCT). Risk for death from GVHD has been associated with low bacterial diversity in the stool microbiota early after transplant; however, the specific species associated with GVHD risk remain poorly defined. Methods We prospectively collected serial weekly stool samples from 66 patients who underwent HCT, starting pre-transplantation and continuing weekly until 100 days post-transplant, a total of 694 observations in HCT recipients. We used 16S rRNA gene polymerase chain reaction with degenerate primers, followed by high-throughput sequencing to assess the relative abundance of sequence reads from bacterial taxa in stool samples over time. Results The gut microbiota was highly dynamic in HCT recipients, with loss and appearance of taxa common on short time scales. As in prior studies, GVHD was associated with lower alpha diversity of the stool microbiota. At neutrophil recovery post-HCT, the presence of oral Actinobacteria and oral Firmicutes in stool was positively correlated with subsequent GVHD; Lachnospiraceae were negatively correlated. A gradient of bacterial species (difference of the sum of the relative abundance of positive correlates minus the sum of the relative abundance of negative correlates) was most predictive (receiver operator characteristic area under the curve of 0.83) of subsequent severe acute GVHD. Conclusions The stool microbiota around the time of neutrophil recovery post-HCT is predictive of subsequent development of severe acute GVHD in this study.
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Affiliation(s)
- Jonathan L Golob
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute.,Division of Allergy and Infectious Diseases, University of Washington
| | - Steven A Pergam
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute.,Division of Allergy and Infectious Diseases, University of Washington
| | - Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute
| | - Tina L Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute
| | - Congzhou Liu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute
| | - Kristina Garcia
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute
| | - Marco Mielcarek
- Clinical Research Division, Fred Hutchinson Cancer Institute.,Medicine
| | - Daisy Ko
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute
| | - Sarah Aker
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute
| | - Sara Marquis
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute
| | - Tillie Loeffelholz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute
| | | | - Michael C Wu
- Public Health Sciences Division, Fred Hutchinson Cancer Institute
| | - Kevin Celustka
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute
| | - Alex Morrison
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute
| | - Maresa Woodfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute
| | - David N Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Institute.,Division of Allergy and Infectious Diseases, University of Washington.,Department of Microbiology, University of Washington, Seattle
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20
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McClelland RS, Lingappa JR, Srinivasan S, Kinuthia J, John-Stewart GC, Jaoko W, Richardson BA, Yuhas K, Fiedler TL, Mandaliya KN, Munch MM, Mugo NR, Cohen CR, Baeten JM, Celum C, Overbaugh J, Fredricks DN. Evaluation of the association between the concentrations of key vaginal bacteria and the increased risk of HIV acquisition in African women from five cohorts: a nested case-control study. Lancet Infect Dis 2018; 18:554-564. [PMID: 29396006 DOI: 10.1016/s1473-3099(18)30058-6] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 11/06/2017] [Accepted: 12/07/2017] [Indexed: 12/15/2022]
Abstract
BACKGROUND Disruptions of vaginal microbiota might increase women's susceptibility to HIV infection. Advances in molecular microbiology have enabled detailed examination of associations between vaginal bacteria and HIV acquisition. Therefore, this study aimed to evaluate the association between the concentrations of specific vaginal bacteria and increased risk of HIV acquisition in African women. METHODS We did a nested case-control study of participants from eastern and southern Africa. Data from five cohorts of African women (female sex workers, pregnant and post-partum women, and women in serodiscordant relationships) were used to form a nested case-control analysis between women who acquired HIV infection versus those who remained seronegative. Deep sequence analysis of broad-range 16S rRNA gene PCR products was applied to a subset of 55 cases and 55 controls. From these data, 20 taxa were selected for bacterium-specific real-time PCR assays, which were examined in the full cohort as a four-category exposure (undetectable, first tertile, second tertile, and third tertile of concentrations). Conditional logistic regression was used to generate odds ratios (ORs) and 95% CIs. Regression models were stratified by cohort, and adjusted ORs (aORs) were generated from a multivariable model controlling for confounding variables. The Shannon Diversity Index was used to measure bacterial diversity. The primary analyses were the associations between bacterial concentrations and risk of HIV acquisition. FINDINGS Between November, 2004, and August, 2014, we identified 87 women who acquired HIV infection (cases) and 262 controls who did not acquire HIV infection. Vaginal bacterial community diversity was higher in women who acquired HIV infection (median 1·3, IQR 0·4-2·3) than in seronegative controls (0·7, 0·1-1·5; p=0·03). Seven of the 20 taxa showed significant concentration-dependent associations with increased odds of HIV acquisition: Parvimonas species type 1 (first tertile aOR 1·67, 95% CI 0·61-4·57; second tertile 3·01, 1·13-7·99; third tertile 4·64, 1·73-12·46; p=0·005) and type 2 (first tertile 3·52, 1·63-7·61; second tertile 0·85, 0·36-2·02; third tertile 2·18, 1·01-4·72; p=0·004), Gemella asaccharolytica (first tertile 2·09, 1·01-4·36; second tertile 2·02, 0·98-4·17; third tertile 3·03, 1·46-6·30; p=0·010), Mycoplasma hominis (first tertile 1·46, 0·69-3·11; second tertile 1·40, 0·66-2·98; third tertile 2·76, 1·36-5·63; p=0·048), Leptotrichia/Sneathia (first tertile 2·04, 1·02-4·10; second tertile 1·45, 0·70-3·00; third tertile 2·59, 1·26-5·34; p=0·046), Eggerthella species type 1 (first tertile 1·79, 0·88-3·64; second tertile 2·62, 1·31-5·22; third tertile 1·53, 0·72-3·28; p=0·041), and vaginal Megasphaera species (first tertile 3·15, 1·45-6·81; second tertile 1·43, 0·65-3·14; third tertile 1·32, 0·57-3·05; p=0·038). INTERPRETATION Differences in the vaginal microbial diversity and concentrations of key bacteria were associated with greater risk of HIV acquisition in women. Defining vaginal bacterial taxa associated with HIV risk could point to mechanisms that influence HIV susceptibility and provide important targets for future prevention research. FUNDING National Institute of Child Health and Human Development.
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Affiliation(s)
- R Scott McClelland
- Department of Medicine, University of Washington, Seattle, WA, USA; Department of Epidemiology, University of Washington, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA; Institute of Tropical and Infectious Diseases, University of Nairobi, Nairobi, Kenya.
| | - Jairam R Lingappa
- Department of Medicine, University of Washington, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Grace C John-Stewart
- Department of Epidemiology, University of Washington, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA
| | - Walter Jaoko
- Department of Medical Microbiology, University of Nairobi, Nairobi, Kenya
| | - Barbra A Richardson
- Department of Biostatistics, University of Washington, Seattle, WA, USA; Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Krista Yuhas
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Tina L Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | | | - Matthew M Munch
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nelly R Mugo
- Kenya Medical Research Institute, Nairobi, Kenya
| | - Craig R Cohen
- Department of Obstetrics, Gynecology & Reproductive Sciences, University of California at San Francisco, San Francisco, CA, USA
| | - Jared M Baeten
- Department of Medicine, University of Washington, Seattle, WA, USA; Department of Epidemiology, University of Washington, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA
| | - Connie Celum
- Department of Medicine, University of Washington, Seattle, WA, USA; Department of Epidemiology, University of Washington, Seattle, WA, USA; Department of Global Health, University of Washington, Seattle, WA, USA
| | - Julie Overbaugh
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA; Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - David N Fredricks
- Department of Medicine, University of Washington, Seattle, WA, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
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21
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Srinivasan S, Munch MM, Sizova MV, Fiedler TL, Kohler CM, Hoffman NG, Liu C, Agnew KJ, Marrazzo JM, Epstein SS, Fredricks DN. More Easily Cultivated Than Identified: Classical Isolation With Molecular Identification of Vaginal Bacteria. J Infect Dis 2016; 214 Suppl 1:S21-8. [PMID: 27449870 PMCID: PMC4957512 DOI: 10.1093/infdis/jiw192] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Women with bacterial vaginosis (BV) have complex communities of anaerobic bacteria. There are no cultivated isolates of several bacteria identified using molecular methods and associated with BV. It is unclear whether this is due to the inability to adequately propagate these bacteria or to correctly identify them in culture. METHODS Vaginal fluid from 15 women was plated on 6 different media using classical cultivation approaches. Individual isolates were identified by 16S ribosomal RNA (rRNA) gene sequencing and compared with validly described species. Bacterial community profiles in vaginal samples were determined using broad-range 16S rRNA gene polymerase chain reaction and pyrosequencing. RESULTS We isolated and identified 101 distinct bacterial strains spanning 6 phyla including (1) novel strains with <98% 16S rRNA sequence identity to validly described species, (2) closely related species within a genus, (3) bacteria previously isolated from body sites other than the vagina, and (4) known bacteria formerly isolated from the vagina. Pyrosequencing showed that novel strains Peptoniphilaceae DNF01163 and Prevotellaceae DNF00733 were prevalent in women with BV. CONCLUSIONS We isolated a diverse set of novel and clinically significant anaerobes from the human vagina using conventional approaches with systematic molecular identification. Several previously "uncultivated" bacteria are amenable to conventional cultivation.
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MESH Headings
- Bacteria, Anaerobic/classification
- Bacteria, Anaerobic/cytology
- Bacteria, Anaerobic/genetics
- Bacteria, Anaerobic/isolation & purification
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Female
- Gardnerella vaginalis/classification
- Gardnerella vaginalis/cytology
- Gardnerella vaginalis/genetics
- Gardnerella vaginalis/isolation & purification
- Humans
- Microbiota
- Polymerase Chain Reaction
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
- Vagina/microbiology
- Vaginosis, Bacterial/microbiology
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Affiliation(s)
- Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
| | - Matthew M Munch
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
| | - Maria V Sizova
- Department of Biology, Northeastern University, Boston, Massachusetts
| | - Tina L Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
| | - Christina M Kohler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
| | | | - Congzhou Liu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center
| | | | | | - Slava S Epstein
- Department of Biology, Northeastern University, Boston, Massachusetts
| | - David N Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center Department of Medicine Department of Microbiology, University of Washington, Seattle
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22
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Mayer BT, Srinivasan S, Fiedler TL, Marrazzo JM, Fredricks DN, Schiffer JT. Rapid and Profound Shifts in the Vaginal Microbiota Following Antibiotic Treatment for Bacterial Vaginosis. J Infect Dis 2015; 212:793-802. [PMID: 25676470 DOI: 10.1093/infdis/jiv079] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 02/04/2015] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Bacterial vaginosis (BV) is a common polymicrobial disease associated with numerous negative reproductive health outcomes, including an increased risk of human immunodeficiency virus acquisition. BV is treatable with antibiotics, but relapse is common. A more detailed understanding of bacterial dynamics during antibiotic therapy for BV could identify conditions that favor establishment, maintenance, and eradication of BV-associated bacterial species, thereby improving treatment outcomes. METHODS We used mathematical models to analyze daily quantitative measurements of 11 key bacterial species during metronidazole treatment for 15 cases of BV. RESULTS We identified complete reorganization of vaginal bacterial composition within a day of initiating therapy. Although baseline bacterial levels predicted a longer time to clearance, all anaerobic species were eliminated rapidly within a median of 3 days. However, reemergence of BV-associated species was common following treatment cessation. Gardnerella vaginalis, a facultative anaerobe, was cleared more slowly than anaerobic BV-associated species, and levels of G. vaginalis often rebounded during treatment. We observed gradual Lactobacillus species growth, indicating that untargeted microbes fill the transient vacuum formed during treatment. CONCLUSIONS Under antibiotic pressure, the human microbiome can undergo rapid shifts on a scale of hours. When treatment is stopped, BV-associated bacteria quickly reemerge, suggesting a possible role for intermittent prophylactic treatment.
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Affiliation(s)
| | | | | | | | - David N Fredricks
- Vaccine and Infectious Disease Division Clinical Research Division, Fred Hutchinson Cancer Research Center Department of Medicine Department of Microbiology, University of Washington, Seattle
| | - Joshua T Schiffer
- Vaccine and Infectious Disease Division Clinical Research Division, Fred Hutchinson Cancer Research Center Department of Medicine
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23
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Srinivasan S, Morgan MT, Liu C, Matsen FA, Hoffman NG, Fiedler TL, Agnew KJ, Marrazzo JM, Fredricks DN. More than meets the eye: associations of vaginal bacteria with gram stain morphotypes using molecular phylogenetic analysis. PLoS One 2013; 8:e78633. [PMID: 24302980 PMCID: PMC3840219 DOI: 10.1371/journal.pone.0078633] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 09/04/2013] [Indexed: 11/25/2022] Open
Abstract
Bacterial vaginosis (BV) is a highly prevalent condition associated with adverse health outcomes. Gram stain analysis of vaginal fluid is the standard for confirming the diagnosis of BV, wherein abundances of key bacterial morphotypes are assessed. These Lactobacillus, Gardnerella, Bacteroides, and Mobiluncus morphotypes were originally linked to particular bacterial species through cultivation studies, but no studies have systematically investigated associations between uncultivated bacteria detected by molecular methods and Gram stain findings. In this study, 16S-rRNA PCR/pyrosequencing was used to examine associations between vaginal bacteria and bacterial morphotypes in 220 women with and without BV. Species-specific quantitative PCR (qPCR) and fluorescence in Situ hybridization (FISH) methods were used to document concentrations of two bacteria with curved rod morphologies: Mobiluncus and the fastidious BV-associated bacterium-1 (BVAB1). Rank abundance of vaginal bacteria in samples with evidence of curved gram-negative rods showed that BVAB1 was dominant (26.1%), while Mobiluncus was rare (0.2% of sequence reads). BVAB1 sequence reads were associated with Mobiluncus morphotypes (p<0.001). Among women with curved rods, mean concentration of BVAB1 DNA was 2 log units greater than Mobiluncus (p<0.001) using species-specific quantitative PCR. FISH analyses revealed that mean number of BVAB1 cells was 2 log units greater than Mobiluncus cells in women with highest Nugent score (p<0.001). Prevotella and Porphyromonas spp. were significantly associated with the “Bacteroides morphotype,” whereas Bacteroides species were rare. Gram-negative rods designated Mobiluncus morphotypes on Gram stain are more likely BVAB1. These findings provide a clearer picture of the bacteria associated with morphotypes on vaginal Gram stain.
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Affiliation(s)
- Sujatha Srinivasan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail: (SS); (DNF)
| | - Martin T. Morgan
- Public Health Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Congzhou Liu
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Frederick A. Matsen
- Public Health Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Noah G. Hoffman
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Tina L. Fiedler
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Kathy J. Agnew
- Department of Obstetrics and Gynecology, University of Washington, Seattle, Washington, United States of America
| | - Jeanne M. Marrazzo
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - David N. Fredricks
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- * E-mail: (SS); (DNF)
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Srinivasan S, Morgan MT, Liu C, Matsen FA, Hoffman NG, Fiedler TL, Agnew KJ, Marrazzo JM, Fredricks DN. O05.3 More Than Meets the Eye: A Molecular Phylogenetic Analysis Reveals Importance of Novel Bacteria in Bacterial Vaginosis (BV). Br J Vener Dis 2013. [DOI: 10.1136/sextrans-2013-051184.0109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Srinivasan S, Hoffman NG, Morgan MT, Matsen FA, Fiedler TL, Hall RW, Ross FJ, McCoy CO, Bumgarner R, Marrazzo JM, Fredricks DN. Bacterial communities in women with bacterial vaginosis: high resolution phylogenetic analyses reveal relationships of microbiota to clinical criteria. PLoS One 2012; 7:e37818. [PMID: 22719852 PMCID: PMC3377712 DOI: 10.1371/journal.pone.0037818] [Citation(s) in RCA: 435] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 04/24/2012] [Indexed: 12/25/2022] Open
Abstract
Background 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. Methodology/Principal Findings 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. Conclusions/Significance 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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Affiliation(s)
- Sujatha Srinivasan
- Vaccine & Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail: (DNF); (SS)
| | - Noah G. Hoffman
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Martin T. Morgan
- Public Health Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Frederick A. Matsen
- Public Health Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Tina L. Fiedler
- Vaccine & Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Robert W. Hall
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Frederick J. Ross
- Public Health Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Connor O. McCoy
- Public Health Science Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Roger Bumgarner
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Jeanne M. Marrazzo
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - David N. Fredricks
- Vaccine & Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- * E-mail: (DNF); (SS)
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Marrazzo JM, Fiedler TL, Srinivasan S, Thomas KK, Liu C, Ko D, Xie H, Saracino M, Fredricks DN. Extravaginal reservoirs of vaginal bacteria as risk factors for incident bacterial vaginosis. J Infect Dis 2012; 205:1580-8. [PMID: 22448002 DOI: 10.1093/infdis/jis242] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Bacterial vaginosis (BV) represents shifts in microbiota from Lactobacillus spp. to diverse anaerobes. Although antibiotics relieve symptoms and temporarily eradicate BV-associated bacteria (BVAB), BV usually recurs. We investigated the role of extravaginal BVAB reservoirs in recurrence. METHODS Risks for BV acquisition over the course of 1 year were defined. DNA in vaginal, anal, and oral swab samples from enrollment was subjected to quantitative polymerase chain reaction assays targeting 16S ribosomal RNA genes of Gardnerella vaginalis, Lactobacillus crispatus, BVAB1, BVAB2, BVAB3, Megasphaera spp., Lactobacillus jensenii, and Leptotrichia/Sneathia spp. A case-control approach analyzed BVAB detection at enrollment for case patients (BV acquisition) versus controls (none). RESULTS Of 239 women enrolled without BV, 199 were seen in follow-up, and 40 experienced BV; 15 had all samples for analysis. Detection of G. vaginalis in oral cavity or anal samples and Leptotrichia/Sneathia spp. in anal samples was more common at enrollment among case patients, who also had higher concentrations of these bacteria and Megasphaera relative to 30 controls at each site. In contrast, L. crispatus was detected more frequently in anal samples among controls. CONCLUSIONS Women who acquire BV are more likely have previous colonization of extravaginal reservoirs with some BVAB, and less likely to have L. crispatus, suggesting that BVAB may be acquired vaginally from extravaginal reservoirs.
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Affiliation(s)
- Jeanne M Marrazzo
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, WA, USA.
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Srinivasan S, Liu C, Mitchell CM, Fiedler TL, Thomas KK, Agnew KJ, Marrazzo JM, Fredricks DN. Temporal variability of human vaginal bacteria and relationship with bacterial vaginosis. PLoS One 2010; 5:e10197. [PMID: 20419168 PMCID: PMC2855365 DOI: 10.1371/journal.pone.0010197] [Citation(s) in RCA: 315] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2010] [Accepted: 03/16/2010] [Indexed: 11/18/2022] Open
Abstract
Background Little is known about short-term bacterial fluctuations in the human vagina. This study used PCR to assess the variability in concentrations of key vaginal bacteria in healthy women and the immediate response to antibiotic treatment in women with bacterial vaginosis (BV). Methodology/Principal Findings Twenty-two women assessed for BV using Amsel's criteria were evaluated daily for 7 or 14 days, then at 2, 3 and 4 weeks, using a panel of 11 bacterium-specific quantitative PCR assays. Participants with BV were treated with 5 days of intravaginal metronidazole. Participants without BV had vaginal biotas dominated by lactobacilli, whose levels fluctuated with menses. With onset of menstruation, quantities of Lactobacillus jensenii and Lactobacillus crispatus decreased and were found to be inversely related to Gardnerella vaginalis concentrations (p<0.001). Women with BV had a variety of fastidious bacteria whose concentrations dropped below detection thresholds 1–5 days after starting metronidazole. Recurrent BV was characterized by initial profound decreases of BV-associated bacteria after treatment followed by subsequent increases at relapse. Conclusions/Significance The microbiota of the human vagina can be highly dynamic. Healthy women are colonized with Lactobacillus species, but levels can change dramatically over a month. Marked increases in G. vaginalis were observed during menses. Participants with BV have diverse communities of fastidious bacteria that are depleted by vaginal metronidazole therapy. Women with recurrent BV initially respond to antibiotic treatment with steep declines in bacterial concentrations, but these bacteria later reemerge, suggesting that antibiotic resistance in these bacteria is not an important factor mediating BV recurrence.
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Affiliation(s)
- Sujatha Srinivasan
- Vaccine & Infectious Disease Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail: (SS); (DNF)
| | - Congzhou Liu
- Vaccine & Infectious Disease Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Caroline M. Mitchell
- Department of Obstetrics & Gynecology, University of Washington, Seattle, Washington, United States of America
| | - Tina L. Fiedler
- Vaccine & Infectious Disease Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Katherine K. Thomas
- Center for AIDS and STDs, University of Washington, Seattle, Washington, United States of America
| | - Kathy J. Agnew
- Department of Obstetrics & Gynecology, University of Washington, Seattle, Washington, United States of America
| | - Jeanne M. Marrazzo
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
| | - David N. Fredricks
- Vaccine & Infectious Disease Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
- * E-mail: (SS); (DNF)
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Marrazzo JM, Thomas KK, Fiedler TL, Ringwood K, Fredricks DN. Relationship of specific vaginal bacteria and bacterial vaginosis treatment failure in women who have sex with women. Ann Intern Med 2008; 149:20-8. [PMID: 18591634 PMCID: PMC2630802 DOI: 10.7326/0003-4819-149-1-200807010-00006] [Citation(s) in RCA: 107] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Bacterial vaginosis frequently persists after treatment. The role of newly defined bacterial vaginosis-associated bacteria (BVAB), which have a specificity for this condition of 97% or greater, has not been assessed. OBJECTIVE To define risks for bacterial vaginosis persistence, including pretreatment detection of specific vaginal bacteria, among women reporting sex with women. DESIGN Observational cohort study. SETTING University-based research clinic. PATIENTS 335 women age 16 to 29 years reporting sex with at least 1 woman in the past year. Participants were recruited through advertisements and provider referral. INTERVENTION Bacterial vaginosis was treated with intravaginal metronidazole gel (0.75%), 37.5 mg nightly for 5 nights. MEASUREMENTS Species-specific 16S recombinant DNA polymerase chain reaction assays targeting 17 bacterial species were applied to vaginal fluid obtained at baseline. Test of cure by clinical criteria and Gram stain analysis and repeated polymerase chain reaction assays of vaginal fluid were performed 1 month after treatment, and interim behaviors were assessed by using computer-assisted self-interview. RESULTS Of 335 women, 24% of whom also reported sex with men within 3 months before enrollment, 131 (39%) had bacterial vaginosis. In the 120 (92%) women who returned for follow-up, the incidence of persistent bacterial vaginosis was 26% and was statistically significantly higher in women with baseline detection of 3 Clostridiales bacteria, designated as BVAB1 (risk ratio, 2.0 [95% CI, 1.1 to 4.0]), BVAB2 (risk ratio, 8.7 [CI, 2.5 to infinity]), or BVAB3 (risk ratio, 3.1 [CI, 1.7 to 5.8]); Peptoniphilus lacrimalis (risk ratio, 3.5 [CI, 1.6 to 15.5]); and Megasphaera phylotype 2 (risk ratio, 3.4 [CI, 1.4 to 5.5]). Persistence was lower with treatment adherence (risk ratio, 0.4 [0.2 to 0.9]). Detection of these bacteria at the test-of-cure visit was associated with persistence, whereas posttreatment sexual activity was not. LIMITATIONS Findings may not be generalizable to women who have sex only with men, or to women whose bacterial vaginosis is treated with oral antibiotics. The study may be too small and may involve a population that is too highly selected to draw definitive conclusions about associations of persistent infection with posttreatment sexual behaviors. CONCLUSION Persistent bacterial vaginosis is associated with several bacteria in the Clostridiales order, Megasphaera phylotype 2, and P. lacrimalis, suggesting that vaginal microbiology at diagnosis may determine risk for antibiotic failure.
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Affiliation(s)
- Jeanne M Marrazzo
- University of Washington and the Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.
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Fredricks DN, Fiedler TL, Thomas KK, Oakley BB, Marrazzo JM. Targeted PCR for detection of vaginal bacteria associated with bacterial vaginosis. J Clin Microbiol 2007; 45:3270-6. [PMID: 17687006 PMCID: PMC2045326 DOI: 10.1128/jcm.01272-07] [Citation(s) in RCA: 254] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Several novel bacterial species have been detected in subjects with bacterial vaginosis (BV) by using broad-range PCR assays, but this approach is insensitive for detecting minority species. We developed a series of taxon-directed 16S rRNA gene PCR assays for more sensitive detection of key vaginal bacteria. We sought to determine the prevalence of each species in the vagina, its association with BV, and the utility of PCR for the microbiological diagnosis of BV. Targeted PCR assays were developed for 17 vaginal bacterial species and applied to 264 vaginal-fluid samples from 81 subjects with and 183 subjects without BV. The results were compared to those of two widely accepted methods for diagnosing BV, the use of clinical findings (Amsel criteria) and the interpretation of vaginal-fluid Gram stains (Nugent criteria). Leptotrichia/Sneathia, Atopobium vaginae, an Eggerthella-like bacterium, Megasphaera species, and three novel bacteria in the order Clostridiales are among the bacterial species significantly associated with BV. PCR detection of either a Megasphaera species or one of the Clostridiales bacteria yielded a sensitivity of 99% and a specificity of 89% for diagnosis of BV compared to the Amsel clinical criteria and a sensitivity of 95.9% and a specificity of 93.7% compared to the Nugent criteria (Gram stain). PCR detection of one or more fastidious bacterial species is a more reliable indicator of BV than detection of bacteria, such as Gardnerella vaginalis, previously linked to BV, highlighting the potential of PCR for the diagnosis of BV.
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Affiliation(s)
- David N Fredricks
- Program in Infectious Diseases, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue, North, D3-100, Box 19024, Seattle, WA 98109-1024, USA.
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Abstract
BACKGROUND Bacterial vaginosis affects millions of women and is associated with several serious health conditions. The cause of bacterial vaginosis remains poorly understood despite numerous studies based on cultures. Bacteria in microbial communities can be identified without cultivation by characterizing their ribosomal DNA (rDNA) sequences. METHODS We identified bacteria in samples of vaginal fluid with a combination of broad-range polymerase-chain-reaction (PCR) amplification of 16S rDNA with clone analysis, bacterium-specific PCR assay of 16S rDNA, and fluorescence in situ hybridization (FISH) performed directly on vaginal fluid from 27 subjects with bacterial vaginosis and 46 without the condition. Twenty-one subjects were studied with the use of broad-range PCR of 16S rDNA, and 73 subjects were studied with the use of bacterium-specific PCR. RESULTS Women without bacterial vaginosis had 1 to 6 vaginal bacterial species (phylotypes) in each sample (mean, 3.3), as detected by broad-range PCR of 16S rDNA, and lactobacillus species were the predominant bacteria noted (83 to 100 percent of clones). Women with bacterial vaginosis had greater bacterial diversity (P<0.001), with 9 to 17 phylotypes (mean, 12.6) detected per sample and newly recognized species present in 32 to 89 percent of clones per sample library (mean, 58 percent). Thirty-five unique bacterial species were detected in the women with bacterial vaginosis, including several species with no close cultivated relatives. Bacterium-specific PCR assays showed that several bacteria that had not been previously described were highly prevalent in subjects with bacterial vaginosis but rare in healthy controls. FISH confirmed that newly recognized bacteria detected by PCR corresponded to specific bacterial morphotypes visible in vaginal fluid. CONCLUSIONS Women with bacterial vaginosis have complex vaginal infections with many newly recognized species, including three bacteria in the Clostridiales order that were highly specific for bacterial vaginosis.
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Affiliation(s)
- David N Fredricks
- Program in Infectious Diseases, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA.
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Valentine LL, Fiedler TL, Hart AN, Petersen CA, Berninghausen HK, Southworth D. Diversity of ectomycorrhizas associated with Quercus garryana in southern Oregon. ACTA ACUST UNITED AC 2004. [DOI: 10.1139/b03-117] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We investigated diversity of ectomycorrhizas associated with Quercus garryana Dougl. ex Hook. (Oregon white oak, or Garry oak) at Whetstone Savanna Preserve in southern Oregon. Based on morphotyping and DNA restriction fragments, we described 39 ectomycorrhizas. The most common five morphotypes were found in 5% or more of 160 soil cores. Cenococcum geophilum, the most abundant morphotype, occurred in 75% of soil cores. Another common morphotype yielded a restriction fragment length polymorphism (RFLP) pattern similar to that of Tuber species. Uncommon morphotypes were responsible for the majority of ectomycorrhizal diversity on Q. garryana. Morphotype diversity of seedlings was more similar to that of their parent tree than to seedlings under other trees. Internal transcribed spacer (ITS) RFLP patterns of ectomycorrhizas found beneath sporocarps did not match those of the sporocarps fruiting above ground. An understanding of the diversity of the ectomycorrhizal community on Q. garryana will enable us to compare ectomycorrhizas on other oak species and habitats; determine seasonality of ectomycorrhizal growth; evaluate treatments such as fire, grazing, invasion by exotic plants, and other anthropogenic disturbances; and aid restoration protocols.Key words: biocomplexity, biodiversity, ectomycorrhizas, hypogeous fungi, morphotypes, Peziza infossa, Tuber.
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