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Qin H, Liu Y, Zhai Z, Xiao B. Biofilm-Forming Capacity and Drug Resistance of Different Gardnerella Subgroups Associated with Bacterial Vaginosis. Microorganisms 2023; 11:2186. [PMID: 37764030 PMCID: PMC10534620 DOI: 10.3390/microorganisms11092186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 08/10/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Bacterial vaginosis (BV) is the most common infection of the lower reproductive tract among women of reproductive age. Recurrent infections and antibiotic resistance associated with biofilms remain significant challenges for BV treatment. Gardnerella species are commonly found in women with and without BV, indicating that genetic differences among Gardnerella isolates may distinguish pathogenic from commensal subgroups. This study isolated 11 Gardnerella strains from vaginal samples obtained from women with BV before or after treatment. The biofilm formation ability of each strain was examined by crystal violet staining. Eight strains were selected using phylogenetic analysis of the cpn60 sequences and classified as subgroups A (6/8), B (1/8), and D (1/8). The biofilm formation ability and antibiotic resistance profile of these strains was compared among the subgroups. Subgroup D had the strongest biofilm formation ability. Six of the planktonic strains exhibited resistance to the first-line BV drug, metronidazole, and one to clindamycin. Moreover, biofilm formation in vitro increased strain resistance to clindamycin. Two strains with strong biofilm ability, S20 and S23, and two with weak biofilm ability, S24 and S25, were selected for comparative genomic analysis. S20 and S23 were found to contain four key genes associated with biofilm formation and more genes involved in carbohydrate synthesis and metabolism than S24 and S25. Identifying differences in the expression of virulence factors between Gardnerella subgroups could inform the development of novel treatments for BV.
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Affiliation(s)
- Hanyu Qin
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing 100034, China
| | - Yun Liu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China (Z.Z.)
| | - Zhengyuan Zhai
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China (Z.Z.)
| | - Bingbing Xiao
- Department of Obstetrics and Gynecology, Peking University First Hospital, Beijing 100034, China
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Tuddenham S, Shafiq M, Mathad JS, Alexander M, Naik S, Kulkarni V, Deshpande P, Humphrys MS, Holm JB, Khan N, Yadana S, Cheedalla A, Bhosale R, Ghanem KG, Wang T, Wang S, Ma B, Ravel J, Gupta A, Shivakoti R. Association of Pregnancy and HIV Status With Molecular-Bacterial Vaginosis in Indian Women. J Acquir Immune Defic Syndr 2023; 93:422-430. [PMID: 37155962 PMCID: PMC10524256 DOI: 10.1097/qai.0000000000003215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 04/17/2023] [Indexed: 05/10/2023]
Abstract
BACKGROUND Bacterial vaginosis (BV) is a highly prevalent disorder of the cervicovaginal microbiota. Molecular-BV may put women at increased risk for adverse reproductive and obstetric outcomes. We investigated the association of HIV and pregnancy on the vaginal microbiota and associations with molecular-BV in women of reproductive age from Pune, India. SETTING We studied vaginal samples from N = 170 women, including N = 44 nonpregnant HIV seronegative, N = 56 pregnant seronegative, N = 47 nonpregnant women with HIV (WWH), and N = 23 pregnant WWH, and collected data on clinical, behavioral, and demographic factors. METHODS We used 16S rRNA gene amplicon sequencing to characterize the composition of the vaginal microbiota. We classified the vaginal microbiota of these women into community state types based on bacterial composition and relative abundance and further categorized them into molecular-BV versus Lactobacillus -dominated states. To determine associations between pregnancy and HIV status with outcome of molecular-BV, logistic regression models were used. RESULTS There was a high prevalence of molecular-BV (30%) in this cohort. We found that pregnancy was associated with decreased odds of molecular-BV (adjusted OR = 0.35, 95% CI: 0.14 to 0.87), while HIV was associated with increased odds of molecular-BV (adjusted OR = 2.76, 95% CI: 1.33 to 5.73), even when controlling for multiple relevant factors such as age, number of sexual partners, condom use, and douching. CONCLUSION Larger and longitudinal studies are needed to further characterize molecular-BV and the vaginal microbiota in pregnant women and WWH and relate these factors to infectious, reproductive, and obstetric outcomes. In the long term, these studies may lead to novel microbiota-based therapeutics to improve women's reproductive and obstetric health.
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Affiliation(s)
- Susan Tuddenham
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Mehr Shafiq
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, USA
| | - Jyoti S. Mathad
- Department of Medicine, Weill Cornell Medical College, New York, USA
| | - Mallika Alexander
- Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, India
| | - Shilpa Naik
- Department of Obstetrics and Gynecology, Byramjee Jeejeebhoy Government Medical College, Pune, India
| | - Vandana Kulkarni
- Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, India
| | - Prasad Deshpande
- Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, India
| | - Mike S. Humphrys
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Johanna B. Holm
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Nawshaba Khan
- Byramjee Jeejeebhoy Government Medical College-Johns Hopkins University Clinical Research Site, Pune, India
| | - Su Yadana
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, USA
| | | | - Ramesh Bhosale
- Department of Obstetrics and Gynecology, Byramjee Jeejeebhoy Government Medical College, Pune, India
| | - Khalil G. Ghanem
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Tian Wang
- Department of Biostatistics, Columbia University Mailman School of Public Health, New York, USA
| | - Shuang Wang
- Department of Biostatistics, Columbia University Mailman School of Public Health, New York, USA
| | - Bing Ma
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Jacques Ravel
- Institute for Genome Sciences and Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, USA
| | - Amita Gupta
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Rupak Shivakoti
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, USA
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Santacroce L, Palmirotta R, Bottalico L, Charitos IA, Colella M, Topi S, Jirillo E. Crosstalk between the Resident Microbiota and the Immune Cells Regulates Female Genital Tract Health. Life (Basel) 2023; 13:1531. [PMID: 37511906 PMCID: PMC10381428 DOI: 10.3390/life13071531] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
The female genital tract (FGT) performs several functions related to reproduction, but due to its direct exposure to the external environment, it may suffer microbial infections. Both the upper (uterus and cervix) and lower (vagina) FGT are covered by an epithelium, and contain immune cells (macrophages, dendritic cells, T and B lymphocytes) that afford a robust protection to the host. Its upper and the lower part differ in terms of Lactobacillus spp., which are dominant in the vagina. An alteration of the physiological equilibrium between the local microbiota and immune cells leads to a condition of dysbiosis which, in turn, may account for the outcome of FGT infection. Aerobic vaginitis, bacterial vaginosis, and Chlamydia trachomatis are the most frequent infections, and can lead to severe complications in reproduction and pregnancy. The use of natural products, such as probiotics, polyphenols, and lactoferrin in the course of FGT infections is an issue of current investigation. In spite of positive results, more research is needed to define the most appropriate administration, according to the type of patient.
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Affiliation(s)
- Luigi Santacroce
- Microbiology and Virology Section, Interdisciplinary Department of Medicine, School of Medicine, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Raffaele Palmirotta
- Microbiology and Virology Section, Interdisciplinary Department of Medicine, School of Medicine, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Lucrezia Bottalico
- Department of Clinical Disciplines, School of Technical Medical Sciences, "Alexander Xhuvani" University of Elbasan, 3001 Elbasan, Albania
| | | | - Marica Colella
- Microbiology and Virology Section, Interdisciplinary Department of Medicine, School of Medicine, University of Bari "Aldo Moro", 70124 Bari, Italy
| | - Skender Topi
- Department of Clinical Disciplines, School of Technical Medical Sciences, "Alexander Xhuvani" University of Elbasan, 3001 Elbasan, Albania
| | - Emilio Jirillo
- Microbiology and Virology Section, Interdisciplinary Department of Medicine, School of Medicine, University of Bari "Aldo Moro", 70124 Bari, Italy
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ÖNER SZ, KALELİ İ, KALELİ B. Vajinal Mikrobiyal Türlerin Bakteriyel Vajinozis ve Human Papillomavirus ile İlişkisinin Araştırılması. KOCAELI ÜNIVERSITESI SAĞLIK BILIMLERI DERGISI 2022. [DOI: 10.30934/kusbed.1132919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Objective: This study was aim to investigate the relationship of vaginal bacterial species with High-Risk Human Papillomavirus (HR-HPV) and bacterial vaginosis (BV).Methods: One hundred and twenty-one women were included in the study. Gram stain was performed for the diagnosis of BV and evaluated according to the Nugent score. HR-HPV diagnosis was made by real-time PCR . Detection of vaginal microbial species and Gardnerella vaginalis subtypes were also performed by real-time PCR.Results: The prevalence of BV was found as 38.8%. The mean number of species was found significantly higher in BV-positive samples compared to BV-intermediate and BV-negative samples (p=0.001). Lactobacillus iners (p=0.036), BVAB2 (p=0.043), Provetella spp. (p=0.015), Leptotrichia/Sneathia (p=0.001), Megaspheara (p=0.048) were found to be associated with bacterial vaginosis. Gardnerella vaginalis subtypes were evaluated in 50 randomly selected samples. The most common strain that was found was “clade 4”. The prevalence of HR-HPV was 9.9%. HPV 16 was the most common HR-HPV type (58.3%). There was no significant difference between the mean value of Lactobacillus sp. HR-HPV-positive and negative samples (p=0.23). No association was found between the specified species and HR-HPV-positive samples (p=0.436).Conclusion: Bacterial diversity was greater in BV-positive patients and BV was significantly associated with Lactobacillus iners, Megaspheara, BVAB2, Provetella spp. and Leptotrichia / Sneathia.
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Mollin A, Katta M, Sobel JD, Akins RA. Association of key species of vaginal bacteria of recurrent bacterial vaginosis patients before and after oral metronidazole therapy with short- and long-term clinical outcomes. PLoS One 2022; 17:e0272012. [PMID: 35901180 PMCID: PMC9333308 DOI: 10.1371/journal.pone.0272012] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/11/2022] [Indexed: 11/23/2022] Open
Abstract
Bacterial vaginosis (BV) is associated with a state of vaginal dysbiosis typically involving depletion of otherwise dominant populations of Lactobacillus. The causes of this microbial succession are not known; there may be multiple causes. Standard treatment includes oral metronidazole, which typically restores Lactobacillus species to dominance. However, recurrence rates are high; recurrent BV patients recur 3–4 times annually and are often refractory to treatment. Our previous qPCR-based study of recurrent BV patients pointed to putatively more virulent species of Gardnerella that were associated with refractory responses to oral metronidazole, and less robust recovery of Lactobacillus species associated with recurrence after an initial period of remission. However, these associations did not account for outcomes in all patients, suggesting that other bacterial species were involved. In this follow-up study, we sequenced the V4 domain of 16S rRNA sequences of 41of these same patients pre- and posttreatment. Overall compositions among pretreatment clinical outcome groups were not different, although alpha diversity significantly decreased: refractory > recurrent > remission. Combinations of key species were associated with and prognostic for outcome. Higher pretreatment abundance of Megasphaera lornae together with lower abundance of Gardnerella Gsp07 and Finegoldia magna predicted long term remission after oral metronidazole. Furthermore, a subset of refractory patients that did not have high levels of Gardnerella Gsp07, instead had elevated levels of alternative species including Atopobium vaginae, Mageeibacillus indolicus (BVAB3), and Prevotella timonensis. Patients who recurred after transient remission had elevated abundance of species including Atopobium vaginae, Gardnerella, and Aerococcus christensenii, compared to long-term remission patients. Core bacterial species among refractory patients did not change in abundance after metronidazole, suggesting resistance or tolerance, in contrast to the loss in abundance of the same species among recurrent or remission patients. These findings have potential prognostic and therapeutic implications.
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Affiliation(s)
- Ashomathi Mollin
- Department of Biochemistry, Microbiology, & Immunology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Mounika Katta
- Department of Biochemistry, Microbiology, & Immunology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Jack D. Sobel
- Division of Infectious Diseases, Wayne State University School of Medicine, Detroit, Michigan, United States of America
| | - Robert A. Akins
- Department of Biochemistry, Microbiology, & Immunology, Wayne State University School of Medicine, Detroit, Michigan, United States of America
- * E-mail:
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Qin H, Xiao B. Research Progress on the Correlation Between Gardnerella Typing and Bacterial Vaginosis. Front Cell Infect Microbiol 2022; 12:858155. [PMID: 35402309 PMCID: PMC8990036 DOI: 10.3389/fcimb.2022.858155] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/01/2022] [Indexed: 11/17/2022] Open
Abstract
Bacterial vaginosis (BV) is the most common infectious disease of the reproductive tract in women of childbearing age. It often manifests as an imbalance in the vaginal microbiome, including a decrease in Lactobacillus and an increase in anaerobic bacteria. While Gardnerella spp. are considered a major cause of BV, they are also detected in the vaginal microbiome of healthy women. G. vaginalis was the only recognized species of Gardnerella until a recent study characterized three new species, G. leopoldii, G. piotii, and G. swidsinskii. This review describes the different types and genetic diversity of Gardnerella, as well as new findings on the correlation between different Gardnerella spp. and BV.
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7
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Protease activities of vaginal Porphyromonas species disrupt coagulation and extracellular matrix in the cervicovaginal niche. NPJ Biofilms Microbiomes 2022; 8:8. [PMID: 35190575 PMCID: PMC8861167 DOI: 10.1038/s41522-022-00270-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 01/14/2022] [Indexed: 12/14/2022] Open
Abstract
Porphyromonas asaccharolytica and Porphyromonas uenonis are common inhabitants of the vaginal microbiome, but their presence has been linked to adverse health outcomes for women, including bacterial vaginosis and preterm birth. However, little is known about the pathogenesis mechanisms of these bacteria. The related oral opportunistic pathogen, Porphyromonas gingivalis, is comparatively well-studied and known to secrete numerous extracellular matrix-targeting proteases. Among these are the gingipain family of cysteine proteases that drive periodontal disease progression and hematogenic transmission to the placenta. In this study, we demonstrate that vaginal Porphyromonas species secrete broad-acting proteases capable of freely diffusing within the cervicovaginal niche. These proteases degrade collagens that are enriched within the cervix (type I) and chorioamniotic membranes (type IV), as well as fibrinogen, which inhibits clot formation. Bioinformatic queries confirmed the absence of gingipain orthologs and identified five serine, cysteine, and metalloprotease candidates in each species. Inhibition assays revealed that each species’ proteolytic activity can be partially attributed to a secreted metalloprotease with broad substrate specificity that is distantly related to the P. gingivalis endopeptidase PepO. This characterization of virulence activities in vaginal Porphyromonas species highlights their potential to alter the homeostasis of reproductive tissues and harm human pregnancy through clotting disruption, fetal membrane weakening, and premature cervical remodeling.
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8
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Plesniarski A, Siddik AB, Su RC. The Microbiome as a Key Regulator of Female Genital Tract Barrier Function. Front Cell Infect Microbiol 2022; 11:790627. [PMID: 34976864 PMCID: PMC8719631 DOI: 10.3389/fcimb.2021.790627] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 11/30/2021] [Indexed: 12/12/2022] Open
Abstract
The microbiome, the collection of microbial species at a site or compartment, has been an underappreciated realm of human health up until the last decade. Mounting evidence suggests the microbiome has a critical role in regulating the female genital tract (FGT) mucosa's function as a barrier against sexually transmitted infections (STIs) and pathogens. In this review, we provide the most recent experimental systems and studies for analyzing the interplay between the microbiome and host cells and soluble factors with an influence on barrier function. Key components, such as microbial diversity, soluble factors secreted by host and microbe, as well as host immune system, all contribute to both the physical and immunologic aspects of the FGT mucosal barrier. Current gaps in what is known about the effects of the microbiome on FGT mucosal barrier function are compared and contrasted with the literature of the gut and respiratory mucosa. This review article presents evidence supporting that the vaginal microbiome, directly and indirectly, contributes to how well the FGT protects against infection.
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Affiliation(s)
- Andrew Plesniarski
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, MB, Canada.,Department of Medical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Abu Bakar Siddik
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, MB, Canada.,Department of Medical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Ruey-Chyi Su
- JC Wilt Infectious Diseases Research Centre, National Microbiology Laboratories, Public Health Agency of Canada, Winnipeg, MB, Canada.,Department of Medical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
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9
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Allali I, Abotsi RE, Tow LA, Thabane L, Zar HJ, Mulder NM, Nicol MP. Human microbiota research in Africa: a systematic review reveals gaps and priorities for future research. MICROBIOME 2021; 9:241. [PMID: 34911583 PMCID: PMC8672519 DOI: 10.1186/s40168-021-01195-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/14/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND The role of the human microbiome in health and disease is an emerging and important area of research; however, there is a concern that African populations are under-represented in human microbiome studies. We, therefore, conducted a systematic survey of African human microbiome studies to provide an overview and identify research gaps. Our secondary objectives were: (i) to determine the number of peer-reviewed publications; (ii) to identify the extent to which the researches focused on diseases identified by the World Health Organization [WHO] State of Health in the African Region Report as being the leading causes of morbidity and mortality in 2018; (iii) to describe the extent and pattern of collaborations between researchers in Africa and the rest of the world; and (iv) to identify leadership and funders of the studies. METHODOLOGY We systematically searched Medline via PubMed, Scopus, CINAHL, Academic Search Premier, Africa-Wide Information through EBSCOhost, and Web of Science from inception through to 1st April 2020. We included studies that characterized samples from African populations using next-generation sequencing approaches. Two reviewers independently conducted the literature search, title and abstract, and full-text screening, as well as data extraction. RESULTS We included 168 studies out of 5515 records retrieved. Most studies were published in PLoS One (13%; 22/168), and samples were collected from 33 of the 54 African countries. The country where most studies were conducted was South Africa (27/168), followed by Kenya (23/168) and Uganda (18/168). 26.8% (45/168) focused on diseases of significant public health concern in Africa. Collaboration between scientists from the United States of America and Africa was most common (96/168). The first and/or last authors of 79.8% of studies were not affiliated with institutions in Africa. Major funders were the United States of America National Institutes of Health (45.2%; 76/168), Bill and Melinda Gates Foundation (17.8%; 30/168), and the European Union (11.9%; 20/168). CONCLUSIONS There are significant gaps in microbiome research in Africa, especially those focusing on diseases of public health importance. There is a need for local leadership, capacity building, intra-continental collaboration, and national government investment in microbiome research within Africa. Video Abstract.
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Affiliation(s)
- Imane Allali
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, and Genomic Centre of Human Pathologies, Faculty of Medicine and Pharmacy, Mohammed V University in Rabat, Rabat, Morocco
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Regina E Abotsi
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Molecular and Cell Biology, Faculty of Science, University of Cape Town, Cape Town, South Africa
- Department of Pharmaceutical Microbiology, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
| | - Lemese Ah Tow
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Lehana Thabane
- Department of Health Research Methods, Evidence and Impact, McMaster University, Hamilton, Ontario, Canada
- Biostatistics Unit, Father Sean O'Sullivan Research Centre, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Departments of Paediatrics and Anaesthesia, McMaster University, Hamilton, Ontario, Canada
- Centre for Evaluation of Medicine, St Joseph's Healthcare, Hamilton, Ontario, Canada
- Population Health Research Institute, Hamilton Health Sciences, Hamilton, Ontario, Canada
- Centre for Evidence-based Health Care, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa
- Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Heather J Zar
- Department of Paediatrics and Child Health, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
- MRC Unit on Child & Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Nicola M Mulder
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Mark P Nicol
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.
- School of Biomedical Sciences, University of Western Australia, M504, Perth, WA, 6009, Australia.
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Deciphering the Role of Mucosal Immune Responses and the Cervicovaginal Microbiome in Resistance to HIV Infection in HIV-Exposed Seronegative (HESN) Women. Microbiol Spectr 2021; 9:e0047021. [PMID: 34704803 PMCID: PMC8549735 DOI: 10.1128/spectrum.00470-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The female genital tract (FGT) is an important site of human immunodeficiency virus (HIV) infection. Discerning the nature of HIV-specific local immune responses is crucial for identifying correlates of protection in HIV-exposed seronegative (HESN) individuals. The present study involved a comprehensive analysis of soluble immune mediators, secretory immunoglobulins (sIg), natural killer (NK) cells, CXCR5+ CD8+ T cells, T follicular helper (Tfh) cells, and T regulatory cells (Tregs) in the vaginal mucosa as well as the nature and composition of the cervicovaginal microbiome in HESN women. We found significantly elevated antiviral cytokines, soluble immunoglobulins, and increased frequencies of activated NK cells, CXCR5+ CD8+ T cells, and Tfh cells in HESN females compared to HIV-unexposed healthy (UH) women. Analysis of the genital microbiome of HESN women revealed a greater bacterial diversity and increased abundance of Gardnerella spp. in the mucosa. The findings suggest that the female genital tract of HESN females represents a microenvironment equipped with innate immune factors, antiviral mediators, and critical T cell subsets that protect against HIV infection. IMPORTANCE The vast majority of human immunodeficiency virus (HIV) infections across the world occur via the sexual route. The genital tract mucosa is thus the primary site of HIV replication, and discerning the nature of HIV-specific immune responses in this compartment is crucial. The role of the innate immune system at the mucosal level in exposed seronegative individuals and other HIV controllers remains largely unexplored. This understanding can provide valuable insights to improve vaccine design. We investigated mucosal T follicular helper (Tfh) cells, CXCR5+ CD8+ T cells, natural killer (NK) cells subsets, soluble immune markers, and microbiome diversity in HIV-exposed seronegative (HESN) women. We found a significantly higher level of mucosal CXCR5+ CD8+ T cells, CD4+ Tfh cells, activated NK cell subsets, and antiviral immune cell mediators in HESN women. We also found a higher abundance of Gardnerella spp., microbiome dysbiosis, and decreased levels of inflammatory markers to be associated with reduced susceptibility to HIV infection. Our findings indicate that increased distribution of mucosal NK cells, CXCR5+ CD8+ T cells, Tfh cells, and soluble markers in HIV controllers with a highly diverse cervicovaginal microbiome could contribute effectively to protection against HIV infection. Overall, our findings imply that future vaccine design should emphasize inducing these highly functional cell types at the mucosal sites.
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HIV-Exposed Seronegative Sex Workers Express Low T-Cell Activation and an Intact Ectocervical Tissue Microenvironment. Vaccines (Basel) 2021; 9:vaccines9030217. [PMID: 33806390 PMCID: PMC7998094 DOI: 10.3390/vaccines9030217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/26/2021] [Accepted: 02/26/2021] [Indexed: 02/07/2023] Open
Abstract
Immunological correlates of natural resistance to HIV have been identified in HIV-exposed seronegative (HESN) individuals and include a low-inflammatory genital mucosal status. The cervicovaginal epithelium has not been studied for such correlates despite constituting an important barrier against sexual HIV transmission. To fill this gap in knowledge, we collected samples of blood, cervical mononuclear cells, cervicovaginal lavage, and ectocervical tissue from Kenyan HESN sex workers (n = 29) and controls (n = 33). The samples were analyzed by flow cytometry, protein profiling, 16S rRNA gene sequencing, in situ image analysis, and tissue-based RNA sequencing. A significantly higher relative proportion of regulatory T cells in blood (B7+CD25hiFoxP3+CD127loCD4+ and B7+Helios+FoxP3+CD4+), and a significantly lower proportion of activated cervical T cells (CCR5+CD69+CD4+ and CCR5+CD69+CD8+), were found in the HESN group compared with the controls. In contrast, there were no statistically significant differences between the study groups in cervicovaginal protein and microbiome compositions, ectocervical epithelial thickness, E-cadherin expression, HIV receptor expression, and tissue RNA transcriptional profiles. The identification of an intact ectocervical microenvironment in HESN individuals add new data to current knowledge about natural resistance to sexual transmission of HIV.
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Prevalence of Genotypes and Subtypes of Gardnerella vaginalis in South African Pregnant Women. Infect Dis Obstet Gynecol 2020; 2020:3176407. [PMID: 32694908 PMCID: PMC7352148 DOI: 10.1155/2020/3176407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/15/2020] [Accepted: 06/01/2020] [Indexed: 01/22/2023] Open
Abstract
Background Gardnerella vaginalis, a microorganism highly linked to bacterial vaginosis (BV), is understudied in terms of genotypic heterogeneity in South African populations. This study investigated the prevalence of G. vaginalis genotypes in BV-positive, BV-intermediate, and BV-negative South African pregnant women. Methods The study population included n = 354 pregnant women recruited from a public hospital in Durban, South Africa. The women provided self-collected vaginal swabs for BV diagnosis by Nugent scoring. For the genotyping assays, the 16S rRNA and sialidase A genes from BV-negative, BV-intermediate, and BV-positive samples were amplified with G. vaginalis-specific primers. The16S rRNA amplicon was digested with TaqI to generate genotyping profiles, and subtypes were determined by correlating BamHI and HindIII digestion profiles. Phylogenetic analysis was performed on the 16S rRNA and sialidase A sequences. The data analysis was performed with R Statistical Computing software, version 3.6.2. Results Two different genotypes, GT1 and GT2, were detected. The most prevalent genotype was GT1. Four subtypes (1, 2B, 2AB, and 2C) were shown to be present. The most prevalent subtype was 2B, followed by subtypes 1, 2C, and 2AB. The phylogenetic analysis of the 16S rRNA showed the presence of 5 clusters. The tree displayed clusters which contained sequences from the same BV group with different genotypes and subtypes. Clusters with sequences from across the BV groups carrying the same genotype and subtype were present. Diversity of the sialidase A across BV groups and genotypes was observed. Finally, the study did not find a significant association (p > 0.05) between reported symptoms of abnormal vaginal discharge and genotype harboured. Conclusion This study provided the first report on the diversity of G. vaginalis in South African pregnant women. Diversity assessments of G. vaginalis with respect to genotypes and virulence factors may aid in a greater understanding of the pathogenesis of this microorganism.
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Castro J, Jefferson KK, Cerca N. Genetic Heterogeneity and Taxonomic Diversity among Gardnerella Species. Trends Microbiol 2020; 28:202-211. [DOI: 10.1016/j.tim.2019.10.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 09/27/2019] [Accepted: 10/08/2019] [Indexed: 12/17/2022]
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14
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Resolution and Cooccurrence Patterns of Gardnerella leopoldii, G. swidsinskii, G. piotii, and G. vaginalis within the Vaginal Microbiome. Infect Immun 2019; 87:IAI.00532-19. [PMID: 31527125 DOI: 10.1128/iai.00532-19] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/09/2019] [Indexed: 12/30/2022] Open
Abstract
Gardnerella vaginalis is a hallmark of vaginal dysbiosis, but it is found in the microbiomes of women with and without vaginal symptoms and those who do not have microbiologically defined dysbiosis. G. vaginalis encompasses diverse taxa differing in attributes that are potentially important for virulence, and there is evidence that clades or subgroups within the species are differentially associated with clinical outcomes. The G. vaginalis species description was recently emended, and three new species within the genus were defined (G. leopoldii, G. swidsinskii, and G. piotii). 16S rRNA sequences for the four Gardnerella species are all >98.5% identical, and no signature sequences differentiate them. We demonstrated that Gardnerella species can be resolved using partial chaperonin 60 (cpn60) sequences, with pairwise percent identities of 87.1 to 97.8% among the type strains. Pairwise cooccurrence patterns of Gardnerella spp. in the vaginal microbiomes of 413 reproductive aged Canadian women were investigated, and several significant cooccurrences of species were identified. Abundance of G. vaginalis and G. swidsinskii was associated with vaginal symptoms of abnormal odor and discharge. cpn60 barcode sequencing can provide a rapid assessment of the relative abundance of Gardnerella spp. in microbiome samples, providing a powerful method of elucidating associations between these diverse organisms and clinical outcomes. Researchers should consider using cpn60 instead of 16S RNA for better resolution of these important organisms.
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Farcasanu M, Kwon DS. The Influence of Cervicovaginal Microbiota on Mucosal Immunity and Prophylaxis in the Battle against HIV. Curr HIV/AIDS Rep 2019. [PMID: 29516267 DOI: 10.1007/s11904-018-0380-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
PURPOSE OF REVIEW Young women in sub-Saharan Africa bear a disproportionate burden of the global HIV epidemic. In this review, we examine how cervicovaginal microbiota modulate structural and immune defenses in the female genital tract and influence HIV susceptibility. RECENT FINDINGS Highly diverse, anaerobic cervicovaginal microbiota prevalent in sub-Saharan African women increase HIV acquisition risk by over fourfold. These bacteria weaken the barrier properties of the vaginal mucosa and increase local inflammation and HIV target cell recruitment, creating an environment permissive to HIV. These communities also diminish the prophylactic efficacy of topical tenofovir and therefore may modulate both biological susceptibility to HIV and the effectiveness of pre-exposure prophylaxis (PrEP). Cervicovaginal bacteria influence multiple reproductive health outcomes, including HIV acquisition. High-diversity, low Lactobacillus abundance cervicovaginal communities prevalent in many regions with high HIV incidence are associated with increased HIV susceptibility. A better understanding of the host-microbial interactions mediating this risk is important to reduce HIV infections, particularly among women living in sub-Saharan Africa.
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Affiliation(s)
- Mara Farcasanu
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, 400 Technology Square, Cambridge, MA, 02139, USA.,Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, 02115, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Douglas S Kwon
- Ragon Institute of MGH, MIT, and Harvard, Massachusetts General Hospital, 400 Technology Square, Cambridge, MA, 02139, USA. .,Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, 02115, USA. .,Harvard Medical School, Boston, MA, 02115, USA.
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Gonzalez SM, Aguilar-Jimenez W, Su RC, Rugeles MT. Mucosa: Key Interactions Determining Sexual Transmission of the HIV Infection. Front Immunol 2019; 10:144. [PMID: 30787929 PMCID: PMC6373783 DOI: 10.3389/fimmu.2019.00144] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2018] [Accepted: 01/17/2019] [Indexed: 12/26/2022] Open
Abstract
In the context of HIV sexual transmission at the genital mucosa, initial interactions between the virus and the mucosal immunity determine the outcome of the exposure. Hence, these interactions have been deeply explored in attempts to undercover potential targets for developing preventative strategies. The knowledge gained has led to propose a hypothetical model for mucosal HIV transmission. Subsequent research studies on this topic further revealed new mechanisms and identified new host-HIV interactions. This review aims at integrating these findings to inform better and update the current model of HIV transmission. At the earliest stage of virus exposure, the epithelial integrity and the presence of antiviral factors are critical in preventing viral entry to the submucosa. However, the virus has been shown to enter to the submucosa in the presence of physical abrasion or via epithelial transmigration using paracellular passage or transcytosis mechanisms. The efficiency of these processes is greater with cell-associated viral inoculums and can be influenced by the presence of viral and immune factors, and by the structure of the exposed epithelium. Once the virus reaches the submucosa, dendritic cells and fibroblasts, as recently described, have been shown in vitro of being capable of facilitating the transfer of viral particles to susceptible cells, leading to viral dissemination, most likely in a trans-infection manner. The presence of activated CD4+ T cells in submucosa increases the probability of infection, where the predominant microbiota could be implicated through the modulation of an inflammatory microenvironment. Other factors such as genital fluids and hormones could also play an essential role in HIV transmission. Here, we review the most recent evidence described for mucosal HIV-transmission contributing with the understanding of this phenomenon.
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Affiliation(s)
- Sandra M Gonzalez
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia.,National HIV and Retrovirology Laboratory, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada
| | | | - Ruey-Chyi Su
- National HIV and Retrovirology Laboratory, JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB, Canada.,Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
| | - Maria T Rugeles
- Grupo Inmunovirología, Facultad de Medicina, Universidad de Antioquia, Medellín, Colombia
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17
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Torcia MG. Interplay among Vaginal Microbiome, Immune Response and Sexually Transmitted Viral Infections. Int J Mol Sci 2019; 20:ijms20020266. [PMID: 30641869 PMCID: PMC6359169 DOI: 10.3390/ijms20020266] [Citation(s) in RCA: 105] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 01/07/2019] [Accepted: 01/08/2019] [Indexed: 12/20/2022] Open
Abstract
The vaginal ecosystem is important for women's health and for a successful reproductive life, and an optimal host-microbial interaction is required for the maintenance of eubiosis. The vaginal microbiota is dominated by Lactobacillus species in the majority of women. Loss of Lactobacillus dominance promotes the colonization by anaerobic bacterial species with an increase in microbial diversity. Vaginal dysbiosis is a very frequent condition which affects the immune homeostasis, inducing a rupture in the epithelial barrier and favoring infection by sexually transmitted pathogens. In this review, we describe the known interactions among immune cells and microbial commensals which govern health or disease status. Particular attention is given to microbiota compositions which, through interplay with immune cells, facilitate the establishment of viral infections, such as Human Immunodeficiency Virus (HIV), Human Papilloma Virus (HPV), Herpes Simplex Virus 2 (HSV2).
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Affiliation(s)
- Maria Gabriella Torcia
- Department of Clinical and Experimental Medicine, University of Firenze, 50139 Firenze, Italy.
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18
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Adebamowo SN, Dareng EO, Famooto AO, Offiong R, Olaniyan O, Obende K, Adebayo A, Ologun S, Alabi B, Achara P, Bakare RA, Odutola M, Olawande O, Okuma J, Odonye G, Adebiyi R, Dakum P, Adebamowo CA. Cohort Profile: African Collaborative Center for Microbiome and Genomics Research's (ACCME's) Human Papillomavirus (HPV) and Cervical Cancer Study. Int J Epidemiol 2018; 46:1745-1745j. [PMID: 28419249 PMCID: PMC5837640 DOI: 10.1093/ije/dyx050] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/06/2017] [Indexed: 11/13/2022] Open
Affiliation(s)
- Sally N Adebamowo
- Department of Epidemiology and Public Health.,Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA.,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Eileen O Dareng
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Ayotunde O Famooto
- Office of Strategic Information and Research, Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Richard Offiong
- Department of Obstetrics and Gynecology, University of Abuja Teaching Hospital
| | | | - Kayode Obende
- Department of Obstetrics and Gynecology, Garki Hospital Abuja
| | - Amos Adebayo
- Department of Obstetrics and Gynecology, Asokoro District Hospital
| | - Sanni Ologun
- Department of Obstetrics and Gynecology, Kubwa General Hospital Abuja
| | - Bunmi Alabi
- Department of Obstetrics and Gynecology, Wuse General Hospital, Abuja, Nigeria
| | - Peter Achara
- Department of Obstetrics and Gynecology, Federal Medical Center, Keffi, Nigeria
| | - Rasheed A Bakare
- Department of Microbiology, University College Hospital, University of Ibadan, Ibadan, Nigeria
| | - Michael Odutola
- Office of Strategic Information and Research, Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Oluwatoyosi Olawande
- Office of Strategic Information and Research, Institute of Human Virology Nigeria, Abuja, Nigeria
| | - James Okuma
- Office of Strategic Information and Research, Institute of Human Virology Nigeria, Abuja, Nigeria
| | - George Odonye
- Office of Strategic Information and Research, Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Ruxton Adebiyi
- Office of Strategic Information and Research, Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Patrick Dakum
- Office of the Chief Executive Officer, Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Clement A Adebamowo
- Department of Epidemiology and Public Health.,Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD, USA.,Department of Nutrition, Harvard T. H. Chan School of Public Health, Boston, MA, USA.,Office of Strategic Information and Research, Institute of Human Virology Nigeria, Abuja, Nigeria.,Institute of Human Virology, University of Maryland, Baltimore, MD, USA
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19
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Freitas AC, Bocking A, Hill JE, Money DM. Increased richness and diversity of the vaginal microbiota and spontaneous preterm birth. MICROBIOME 2018; 6:117. [PMID: 29954448 PMCID: PMC6022438 DOI: 10.1186/s40168-018-0502-8] [Citation(s) in RCA: 109] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 05/18/2018] [Indexed: 05/15/2023]
Abstract
BACKGROUND The bacterial community present in the female lower genital tract plays an important role in maternal and neonatal health. Imbalances in this microbiota have been associated with negative reproductive outcomes, such as spontaneous preterm birth (sPTB), but the mechanisms underlying the association between a disturbed microbiota and sPTB remain poorly understood. An intrauterine infection ascending from the vagina is thought to be an important contributor to the onset of preterm labour. Our objective was to characterize the vaginal microbiota of pregnant women who had sPTB (n = 46) and compare to those of pregnant women who delivered at term (n = 170). Vaginal swabs were collected from women at 11-16 weeks of gestational age. Microbiota profiles were created by PCR amplification and pyrosequencing of the cpn60 universal target region. RESULTS Profiles clustered into seven community state types: I (Lactobacillus crispatus dominated), II (Lactobacillus gasseri dominated), III (Lactobacillus iners dominated), IVA (Gardnerella vaginalis subgroup B or mix of species), IVC (G. vaginalis subgroup A dominated), IVD (G. vaginalis subgroup C dominated) and V (Lactobacillus jensenii dominated). The microbiota of women who experienced preterm birth (< 37 weeks gestation) had higher richness and diversity and higher Mollicutes prevalence when compared to those of women who delivered at term. The two groups did not cluster according to CST, likely because CST assignment is driven in most cases by the dominance of one particular species, overwhelming the contributions of more rare taxa. In conclusion, we did not identify a specific microbial community structure that predicts sPTB, but differences in microbiota richness, diversity and Mollicutes prevalence were observed between groups. CONCLUSIONS Although a causal relationship remains to be determined, our results confirm previous reports of an association between Mollicutes and sPTB and further suggest that a more diverse microbiome may be important in the pathogenesis of some cases.
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Affiliation(s)
- Aline C. Freitas
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5B4 Canada
| | - Alan Bocking
- Departments of Obstetrics and Gynaecology and Physiology, University of Toronto, Toronto, ON M5G 1L4 Canada
- Lunenfeld-Tanenbaum Research Institute, M5T1X5, Toronto, ON Canada
| | - Janet E. Hill
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, SK S7N 5B4 Canada
| | - Deborah M. Money
- Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC V6T 1Z4 Canada
- Women’s Health Research Institute, BC Women’s Hospital & Health Centre, Vancouver, BC V6H 3N1 Canada
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Vibrio Ecology in the Neuse River Estuary, North Carolina, Characterized by Next-Generation Amplicon Sequencing of the Gene Encoding Heat Shock Protein 60 ( hsp60). Appl Environ Microbiol 2018; 84:AEM.00333-18. [PMID: 29678912 DOI: 10.1128/aem.00333-18] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/10/2018] [Indexed: 12/17/2022] Open
Abstract
Of marine eubacteria, the genus Vibrio is intriguing because member species are relevant to both marine ecology and human health. Many studies have touted the relationships of Vibrio to environmental factors, especially temperature and salinity, to predict total Vibrio abundance but lacked the taxonomic resolution to identify the relationships among species and the key drivers of Vibrio dynamics. To improve next-generation sequencing (NGS) surveys of Vibrio, we have conducted both 16S small subunit rRNA and heat shock protein 60 (hsp60) amplicon sequencing of water samples collected at two well-studied locations in the Neuse River Estuary, NC. Samples were collected between May and December 2016 with enhanced sampling efforts in response to two named storms. Using hsp60 sequences, 21 Vibrio species were identified, including the potential human pathogens V. cholerae, V. parahaemolyticus, and V. vulnificus Changes in the Vibrio community mirrored seasonal and storm-related changes in the water column, especially in response to an influx of nutrient-rich freshwater to the estuary after Hurricane Matthew, which initiated dramatic changes in the overall Vibrio community. Individual species dynamics were wide ranging, indicating that individual Vibrio taxa have unique ecologies and that total Vibrio abundance predictors are insufficient for risk assessments of potentially pathogenic species. Positive relationships between Vibrio, dinoflagellates, and Cyanobacteria were identified, as were intraspecies associations, which further illuminated the interactions of cooccurring Vibrio taxa along environmental gradients.IMPORTANCE The objectives of this research were to utilize a novel approach to improve sequence-based surveys of Vibrio communities and to demonstrate the usefulness of this approach by presenting an analysis of Vibrio dynamics in the context of environmental conditions, with a particular focus on species that cause disease in humans and on storm effects. The methods presented here enabled the analysis of Vibrio dynamics with excellent taxonomic resolution and could be incorporated into future ecological studies and risk prediction strategies for potentially pathogenic species. Next-generation sequencing of hsp60 and other innovative sequence-based approaches are valuable tools and show great promise for studying Vibrio ecology and associated public health risks.
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21
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A Lactobacillus-Deficient Vaginal Microbiota Dominates Postpartum Women in Rural Malawi. Appl Environ Microbiol 2018; 84:AEM.02150-17. [PMID: 29305501 PMCID: PMC5835753 DOI: 10.1128/aem.02150-17] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/29/2017] [Indexed: 01/09/2023] Open
Abstract
The bacterial community found in the vagina is an important determinant of a woman's health and disease status. A healthy vaginal microbiota is associated with low species richness and a high proportion of one of a number of different Lactobacillus spp. When disrupted, the resulting abnormal vaginal microbiota is associated with a number of disease states and poor pregnancy outcomes. Studies up until now have concentrated on relatively small numbers of American and European populations that may not capture the full complexity of the community or adequately predict what constitutes a healthy microbiota in all populations. In this study, we sampled and characterized the vaginal microbiota found on vaginal swabs taken postpartum from a cohort of 1,107 women in rural Malawi. We found a population dominated by Gardnerella vaginalis and devoid of the most common vaginal Lactobacillus species, even if the vagina was sampled over a year postpartum. This Lactobacillus-deficient anaerobic community, commonly labeled community state type (CST) 4, could be subdivided into four further communities. A Lactobacillus iners-dominated vaginal microbiota became more common the longer after delivery the vagina was sampled, but G. vaginalis remained the dominant organism. These results outline the difficulty in all-encompassing definitions of what a healthy or abnormal postpartum vaginal microbiota is. Previous identification of community state types and associations among bacterial species, bacterial vaginosis, and adverse birth outcomes may not represent the complex heterogeneity of the microbiota present. (This study has been registered at ClinicalTrials.gov as NCT01239693.) IMPORTANCE A bacterial community in the vaginal tract is dominated by a small number of Lactobacillus species, and when not present there is an increased incidence of inflammatory conditions and adverse birth outcomes. A switch to a vaginal bacterial community lacking in Lactobacillus species is common after pregnancy. In this study, we characterized the postpartum vaginal bacterial community of a large group of women from a resource-poor, undersampled population in rural Malawi. The majority of women were found to have a Lactobacillus-deficient community, and even when sampled a year after delivery the majority of women still did not have Lactobacillus present in their vaginal microbiota. The effect of becoming pregnant again for those who do not revert to a Lactobacillus-dominant community is unknown, and this could suggest that not all Lactobacillus-deficient community structures are adverse. A better understanding of this complex community state type is needed.
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Association of high-risk sexual behaviour with diversity of the vaginal microbiota and abundance of Lactobacillus. PLoS One 2017; 12:e0187612. [PMID: 29095928 PMCID: PMC5667760 DOI: 10.1371/journal.pone.0187612] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 10/23/2017] [Indexed: 02/01/2023] Open
Abstract
Objective To compare the vaginal microbiota of women engaged in high-risk sexual behaviour (sex work) with women who are not engaged in high-risk sexual behaviour. Diverse vaginal microbiota, low in Lactobacillus species, like those in bacterial vaginosis (BV), are associated with increased prevalence of sexually transmitted infections (STIs) and human immunodeficiency virus (HIV) acquisition. Although high-risk sexual behaviour increases risk for STIs, the vaginal microbiota of sex workers is understudied. Methods A retrospective cross-sectional study was conducted comparing vaginal microbiota of women who are not engaged in sex work (non-sex worker controls, NSW, N = 19) and women engaged in sex work (female sex workers, FSW, N = 48), using Illumina sequencing (16S rRNA, V3 region). Results Bacterial richness and diversity were significantly less in controls, than FSW. Controls were more likely to have Lactobacillus as the most abundant genus (58% vs. 17%; P = 0.002) and composition of their vaginal microbiota differed from FSW (PERMANOVA, P = 0.001). Six microbiota clusters were detected, including a high diversity cluster with three sub-clusters, and 55% of women with low Nugent Scores fell within this cluster. High diversity was observed by 16S sequencing in FSW, regardless of Nugent Scores, suggesting that Nugent Score may not be capable of capturing the diversity present in the FSW vaginal microbiota. Conclusions High-risk sexual behaviour is associated with diversity of the vaginal microbiota and lack of Lactobacillus. These factors could contribute to increased risk of STIs and HIV in women engaged in high-risk sexual behaviour.
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Role of HIV exposure and infection in relation to neonatal GBS disease and rectovaginal GBS carriage: a systematic review and meta-analysis. Sci Rep 2017; 7:13820. [PMID: 29062060 PMCID: PMC5653843 DOI: 10.1038/s41598-017-13218-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 09/20/2017] [Indexed: 12/31/2022] Open
Abstract
Streptococcus agalactiae (GBS) is the leading cause worldwide of neonatal sepsis. We sought to assess to which extent HIV exposure of neonates is associated with GBS neonatal disease. Furthermore, we assessed to which extent HIV infection in women is associated with maternal rectovaginal GBS carriage, the single most important risk factor for GBS neonatal disease. We searched Pubmed, Embase, and Web of Science for studies assessing the association between neonatal GBS disease and HIV-status of the mother and studies that assessed the association between rectovaginal GBS colonization and HIV status in women. HIV-exposed uninfected neonates were more than twice as likely to have neonatal GBS disease compared to unexposed neonates. HIV-exposed neonates were not at increased risk for early-onset neonatal disease, but were 4.43 times more likely to have late-onset neonatal GBS disease. There was no significant association between HIV infection status and rectovaginal GBS carriage. Public health interventions preventing neonatal GBS disease are urgently needed for the increasing group of HIV-exposed neonates. A framework integrating and explaining our findings highlights opportunities for the clinical practice and global health policy to prevent disease. Well-designed studies should clarify the relation between HIV-status and GBS carriage.
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The vaginal microbiome of pregnant women is less rich and diverse, with lower prevalence of Mollicutes, compared to non-pregnant women. Sci Rep 2017; 7:9212. [PMID: 28835692 PMCID: PMC5569030 DOI: 10.1038/s41598-017-07790-9] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 07/04/2017] [Indexed: 01/02/2023] Open
Abstract
The vaginal microbiome plays an important role in maternal and neonatal health. Imbalances in this microbiota (dysbiosis) during pregnancy are associated with negative reproductive outcomes, such as pregnancy loss and preterm birth, but the underlying mechanisms remain poorly understood. Consequently a comprehensive understanding of the baseline microbiome in healthy pregnancy is needed. We characterized the vaginal microbiomes of healthy pregnant women at 11–16 weeks of gestational age (n = 182) and compared them to those of non-pregnant women (n = 310). Profiles were created by pyrosequencing of the cpn60 universal target region. Microbiome profiles of pregnant women clustered into six Community State Types: I, II, III, IVC, IVD and V. Overall microbiome profiles could not be distinguished based on pregnancy status. However, the vaginal microbiomes of women with healthy ongoing pregnancies had lower richness and diversity, lower prevalence of Mycoplasma and Ureaplasma and higher bacterial load when compared to non-pregnant women. Lactobacillus abundance was also greater in the microbiomes of pregnant women with Lactobacillus-dominated CSTs in comparison with non-pregnant women. This study provides further information regarding characteristics of the vaginal microbiome of low-risk pregnant women, providing a baseline for forthcoming studies investigating the diagnostic potential of the microbiome for prediction of adverse pregnancy outcomes.
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25
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Schellenberg JJ, Oh AY, Hill JE. Microbial profiling of cpn60 universal target sequences in artificial mixtures of vaginal bacteria sampled by nylon swabs or self-sampling devices under different storage conditions. J Microbiol Methods 2017; 136:57-64. [DOI: 10.1016/j.mimet.2017.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 03/05/2017] [Accepted: 03/06/2017] [Indexed: 01/08/2023]
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Gardnerella vaginalis diversity and ecology in relation to vaginal symptoms. Res Microbiol 2017; 168:837-844. [PMID: 28341009 DOI: 10.1016/j.resmic.2017.02.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 02/27/2017] [Accepted: 02/28/2017] [Indexed: 11/22/2022]
Abstract
Gardnerella vaginalis was first described in 1953, and subsequently identified as the causative agent of a cluster of vaginal symptoms currently known as vaginosis. Research has so far failed to confirm whether and by which mechanism G. vaginalis initiates vaginosis, with, consequently, poor diagnostics and treatment outcomes. Recent molecular analyses of protein-coding genes demonstrate that the taxon G. vaginalis consists of at least four distinct species. This development may represent a critical turning point in clarifying ecological interactions and virulence factors contributing to symptoms and/or sequelae of vaginosis.
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27
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Cools P. The role of Escherichia coli in reproductive health: state of the art. Res Microbiol 2017; 168:892-901. [PMID: 28242352 DOI: 10.1016/j.resmic.2017.02.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 02/09/2017] [Accepted: 02/13/2017] [Indexed: 01/27/2023]
Abstract
Escherichia coli is a well-known commensal of the normal intestinal microbiome that can also colonize the vaginal microbiome, usually without symptoms. However, E. coli can also be a highly virulent and frequently deadly pathogen. In this review, I will discuss the role E. coli has in reproductive health and disease.
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Affiliation(s)
- Piet Cools
- Laboratory Bacteriology Research, Department of Clinical Chemistry, Microbiology and Immunology, Faculty of Medicine and Health Sciences, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium.
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Hong KH, Hong SK, Cho SI, Ra E, Han KH, Kang SB, Kim EC, Park SS, Seong MW. Analysis of the Vaginal Microbiome by Next-Generation Sequencing and Evaluation of its Performance as a Clinical Diagnostic Tool in Vaginitis. Ann Lab Med 2017; 36:441-9. [PMID: 27374709 PMCID: PMC4940487 DOI: 10.3343/alm.2016.36.5.441] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Revised: 04/03/2016] [Accepted: 05/30/2016] [Indexed: 01/30/2023] Open
Abstract
Background Next-generation sequencing (NGS) can detect many more microorganisms of a microbiome than traditional methods. This study aimed to analyze the vaginal microbiomes of Korean women by using NGS that included bacteria and other microorganisms. The NGS results were compared with the results of other assays, and NGS was evaluated for its feasibility for predicting vaginitis. Methods In total, 89 vaginal swab specimens were collected. Microscopic examinations of Gram staining and microbiological cultures were conducted on 67 specimens. NGS was performed with GS junior system on all of the vaginal specimens for the 16S rRNA, internal transcribed spacer (ITS), and Tvk genes to detect bacteria, fungi, and Trichomonas vaginalis. In addition, DNA probe assays of the Candida spp., Gardnerella vaginalis, and Trichomonas vaginalis were performed. Various predictors of diversity that were obtained from the NGS data were analyzed to predict vaginitis. Results ITS sequences were obtained in most of the specimens (56.2%). The compositions of the intermediate and vaginitis Nugent score groups were similar to each other but differed from the composition of the normal score group. The fraction of the Lactobacillus spp. showed the highest area under the curve value (0.8559) in ROC curve analysis. The NGS and DNA probe assay results showed good agreement (range, 86.2-89.7%). Conclusions Fungi as well as bacteria should be considered for the investigation of vaginal microbiome. The intermediate and vaginitis Nugent score groups were indistinguishable in NGS. NGS is a promising diagnostic tool of the vaginal microbiome and vaginitis, although some problems need to be resolved.
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Affiliation(s)
- Ki Ho Hong
- Department of Laboratory Medicine, Seoul Medical Center, Seoul, Korea.,Department of Laboratory Medicine, College of Medicine, Seoul National University, Seoul, Korea
| | - Sung Kuk Hong
- Department of Laboratory Medicine, College of Medicine, Seoul National University, Seoul, Korea.,Department of Laboratory Medicine, Sheikh Khalifa Specialty Hospital, Ras Al Khaimah, United Arab Emirates
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Eunkyung Ra
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Kyung Hee Han
- Department of Obstetrics & Gynecology, Seoul National University Hospital Healthcare System Gangnam Center, Seoul, Korea
| | - Soon Beom Kang
- Department of Obstetrics & Gynecology, Konkuk University Medical Center, Seoul, Korea
| | - Eui Chong Kim
- Department of Laboratory Medicine, Sheikh Khalifa Specialty Hospital, Ras Al Khaimah, United Arab Emirates.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Sheikh Khalifa Specialty Hospital, Ras Al Khaimah, United Arab Emirates.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea
| | - Moon Woo Seong
- Department of Laboratory Medicine, Sheikh Khalifa Specialty Hospital, Ras Al Khaimah, United Arab Emirates.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul, Korea.
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The Application of Molecular Methods Towards an Understanding of the Role of the Vaginal Microbiome in Health and Disease. METHODS IN MICROBIOLOGY 2017. [DOI: 10.1016/bs.mim.2017.08.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Gill C, van de Wijgert JHHM, Blow F, Darby AC. Evaluation of Lysis Methods for the Extraction of Bacterial DNA for Analysis of the Vaginal Microbiota. PLoS One 2016; 11:e0163148. [PMID: 27643503 PMCID: PMC5028042 DOI: 10.1371/journal.pone.0163148] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 09/02/2016] [Indexed: 12/12/2022] Open
Abstract
Background Recent studies on the vaginal microbiota have employed molecular techniques such as 16S rRNA gene sequencing to describe the bacterial community as a whole. These techniques require the lysis of bacterial cells to release DNA before purification and PCR amplification of the 16S rRNA gene. Currently, methods for the lysis of bacterial cells are not standardised and there is potential for introducing bias into the results if some bacterial species are lysed less efficiently than others. This study aimed to compare the results of vaginal microbiota profiling using four different pretreatment methods for the lysis of bacterial samples (30 min of lysis with lysozyme, 16 hours of lysis with lysozyme, 60 min of lysis with a mixture of lysozyme, mutanolysin and lysostaphin and 30 min of lysis with lysozyme followed by bead beating) prior to chemical and enzyme-based DNA extraction with a commercial kit. Results After extraction, DNA yield did not significantly differ between methods with the exception of lysis with lysozyme combined with bead beating which produced significantly lower yields when compared to lysis with the enzyme cocktail or 30 min lysis with lysozyme only. However, this did not result in a statistically significant difference in the observed alpha diversity of samples. The beta diversity (Bray-Curtis dissimilarity) between different lysis methods was statistically significantly different, but this difference was small compared to differences between samples, and did not affect the grouping of samples with similar vaginal bacterial community structure by hierarchical clustering. Conclusions An understanding of how laboratory methods affect the results of microbiota studies is vital in order to accurately interpret the results and make valid comparisons between studies. Our results indicate that the choice of lysis method does not prevent the detection of effects relating to the type of vaginal bacterial community one of the main outcome measures of epidemiological studies. However, we recommend that the same method is used on all samples within a particular study.
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Affiliation(s)
- Christina Gill
- Institute of Infection & Global Health, University of Liverpool, 8 West Derby Street, Liverpool, Merseyside, L69 7BE, United Kingdom
| | - Janneke H. H. M. van de Wijgert
- Institute of Infection & Global Health, University of Liverpool, 8 West Derby Street, Liverpool, Merseyside, L69 7BE, United Kingdom
- * E-mail:
| | - Frances Blow
- Institute of Integrative Biology and the Centre for Genomic Research, University of Liverpool, Biosciences Building, Crown Street, Liverpool, Merseyside, L69 7ZB, United Kingdom
| | - Alistair C. Darby
- Institute of Integrative Biology and the Centre for Genomic Research, University of Liverpool, Biosciences Building, Crown Street, Liverpool, Merseyside, L69 7ZB, United Kingdom
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van de Wijgert JHHM, Borgdorff H, Verhelst R, Crucitti T, Francis S, Verstraelen H, Jespers V. The vaginal microbiota: what have we learned after a decade of molecular characterization? PLoS One 2016. [PMID: 25148517 DOI: 10.1371/joumal.pone.0105998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023] Open
Abstract
We conducted a systematic review of the Medline database (U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, U.S.A) to determine if consistent molecular vaginal microbiota (VMB) composition patterns can be discerned after a decade of molecular testing, and to evaluate demographic, behavioral and clinical determinants of VMB compositions. Studies were eligible when published between 1 January 2008 and 15 November 2013, and if at least one molecular technique (sequencing, PCR, DNA fingerprinting, or DNA hybridization) was used to characterize the VMB. Sixty three eligible studies were identified. These studies have now conclusively shown that lactobacilli-dominated VMB are associated with a healthy vaginal micro-environment and that bacterial vaginosis (BV) is best described as a polybacterial dysbiosis. The extent of dysbiosis correlates well with Nugent score and vaginal pH but not with the other Amsel criteria. Lactobacillus crispatus is more beneficial than L. iners. Longitudinal studies have shown that a L. crispatus-dominated VMB is more likely to shift to a L. iners-dominated or mixed lactobacilli VMB than to full dysbiosis. Data on VMB determinants are scarce and inconsistent, but dysbiosis is consistently associated with HIV, human papillomavirus (HPV), and Trichomonas vaginalis infection. In contrast, vaginal colonization with Candida spp. is more common in women with a lactobacilli-dominated VMB than in women with dysbiosis. Cervicovaginal mucosal immune responses to molecular VMB compositions have not yet been properly characterized. Molecular techniques have now become more affordable, and we make a case for incorporating them into larger epidemiological studies to address knowledge gaps in etiology and pathogenesis of dysbiosis, associations of different dysbiotic states with clinical outcomes, and to evaluate interventions aimed at restoring and maintaining a lactobacilli-dominated VMB.
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Affiliation(s)
| | - Hanneke Borgdorff
- Academic Medical Center and Amsterdam Institute of Global Health and Development, Amsterdam, The Netherlands
| | - Rita Verhelst
- International Centre for Reproductive Health, Ghent University Hospital, Ghent, Belgium
| | - Tania Crucitti
- Prince Leopold Institute of Tropical Medicine, Antwerp, Belgium
| | - Suzanna Francis
- London School for Hygiene and Tropical Medicine, London, United Kingdom
| | - Hans Verstraelen
- Department of Obstetrics and Gynecology, Ghent University Hospital, Ghent, Belgium
| | - Vicky Jespers
- Prince Leopold Institute of Tropical Medicine, Antwerp, Belgium
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A Multi-Country Cross-Sectional Study of Vaginal Carriage of Group B Streptococci (GBS) and Escherichia coli in Resource-Poor Settings: Prevalences and Risk Factors. PLoS One 2016; 11:e0148052. [PMID: 26811897 PMCID: PMC4727807 DOI: 10.1371/journal.pone.0148052] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Accepted: 01/12/2016] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND One million neonates die each year in low- and middle-income countries because of neonatal sepsis; group B Streptococcus (GBS) and Escherichia coli are the leading causes. In sub-Saharan Africa, epidemiological data on vaginal GBS and E. coli carriage, a prerequisite for GBS and E. coli neonatal sepsis, respectively, are scarce but necessary to design and implement prevention strategies. Therefore, we assessed vaginal GBS and E. coli carriage rates and risk factors and the GBS serotype distribution in three sub-Saharan countries. METHODS A total of 430 women from Kenya, Rwanda and South Africa were studied cross-sectionally. Vaginal carriage of GBS and E. coli, and GBS serotype were assessed using molecular techniques. Risk factors for carriage were identified using multivariable logistic regression analysis. RESULTS Vaginal carriage rates in reference groups from Kenya and South Africa were 20.2% (95% CI, 13.7-28.7%) and 23.1% (95% CI, 16.2-31.9%), respectively for GBS; and 25.0% (95% CI, 17.8-33.9%) and 27.1% (95% CI, 19.6-36.2%), respectively for E. coli. GBS serotypes Ia (36.8%), V (26.3%) and III (14.0%) were most prevalent. Factors independently associated with GBS and E. coli carriage were Candida albicans, an intermediate vaginal microbiome, bacterial vaginosis, recent vaginal intercourse, vaginal washing, cervical ectopy and working as a sex worker. GBS and E. coli carriage were positively associated. CONCLUSIONS Reduced vaginal GBS carriage rates might be accomplished by advocating behavioral changes such as abstinence from sexual intercourse and by avoidance of vaginal washing during late pregnancy. It might be advisable to explore the inclusion of vaginal carriage of C. albicans, GBS, E. coli and of the presence of cervical ectopy in a risk- and/or screening-based administration of antibiotic prophylaxis. Current phase II GBS vaccines (a trivalent vaccine targeting serotypes Ia, Ib, and III, and a conjugate vaccine targeting serotype III) would not protect the majority of women against carriage in our study population.
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Schellenberg JJ, Paramel Jayaprakash T, Withana Gamage N, Patterson MH, Vaneechoutte M, Hill JE. Gardnerella vaginalis Subgroups Defined by cpn60 Sequencing and Sialidase Activity in Isolates from Canada, Belgium and Kenya. PLoS One 2016; 11:e0146510. [PMID: 26751374 PMCID: PMC4709144 DOI: 10.1371/journal.pone.0146510] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 12/19/2015] [Indexed: 01/23/2023] Open
Abstract
Increased abundance of Gardnerella vaginalis and sialidase activity in vaginal fluid is associated with bacterial vaginosis (BV), a common but poorly understood clinical entity associated with poor reproductive health outcomes. Since most women are colonized with G. vaginalis, its status as a normal member of the vaginal microbiota or pathogen causing BV remains controversial, and numerous classification schemes have been described. Since 2005, sequencing of the chaperonin-60 universal target (cpn60 UT) has distinguished four subgroups in isolate collections, clone libraries and deep sequencing datasets. To clarify potential clinical and diagnostic significance of cpn60 subgroups, we undertook phenotypic and molecular characterization of 112 G. vaginalis isolates from three continents. A total of 36 subgroup A, 33 B, 35 C and 8 D isolates were identified through phylogenetic analysis of cpn60 sequences as corresponding to four "clades" identified in a recently published study, based on sequencing 473 genes across 17 isolates. cpn60 subgroups were compared with other previously described molecular methods for classification of Gardnerella subgroups, including amplified ribosomal DNA restriction analysis (ARDRA) and real-time PCR assays designed to quantify subgroups in vaginal samples. Although two ARDRA patterns were observed in isolates, each was observed in three cpn60 subgroups (A/B/D and B/C/D). Real-time PCR assays corroborated cpn60 subgroups overall, but 13 isolates from subgroups A, B and D were negative in all assays. A putative sialidase gene was detected in all subgroup B, C and D isolates, but only in a single subgroup A isolate. In contrast, sialidase activity was observed in all subgroup B isolates, 3 (9%) subgroup C isolates and no subgroup A or D isolates. These observations suggest distinct roles for G. vaginalis subgroups in BV pathogenesis. We conclude that cpn60 UT sequencing is a robust approach for defining G. vaginalis subgroups within the vaginal microbiome.
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Affiliation(s)
- John J. Schellenberg
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Canada
| | | | | | - Mo H. Patterson
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Canada
| | | | - Janet E. Hill
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Canada
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34
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The Vaginal Microbiome. Mol Microbiol 2016. [DOI: 10.1128/9781555819071.ch12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Reducing IRF-1 to Levels Observed in HESN Subjects Limits HIV Replication, But Not the Extent of Host Immune Activation. MOLECULAR THERAPY-NUCLEIC ACIDS 2015; 4:e259. [PMID: 26506037 PMCID: PMC4881757 DOI: 10.1038/mtna.2015.29] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/19/2015] [Indexed: 12/14/2022]
Abstract
Cells from women who are epidemiologically deemed resistant to HIV infection exhibit a 40-60% reduction in endogenous IRF-1 (interferon regulatory factor-1), an essential regulator of host antiviral immunity and the early HIV replication. This study examined the functional consequences of reducing endogenous IRF-1 on HIV-1 replication and immune response to HIV in natural HIV target cells. IRF-1 knockdown was achieved in ex vivo CD4(+) T cells and monocytes with siRNA. IRF-1 level was assessed using flow cytometry, prior to infection with HIV-Bal, HIV-IIIB, or HIV-VSV-G. Transactivation of HIV long terminal repeats was assessed by p24 secretion (ELISA) and Gag expression (reverse transcription-polymerase chain reaction (RT-PCR)). The expression of IRF-1-regulated antiviral genes was quantitated with RT-PCR. A modest 20-40% reduction in endogenous IRF-1 was achieved in >87% of ex vivo-derived peripheral CD4(+) T cells and monocytes, resulted in >90% reduction in the transactivation of the HIV-1 genes (Gag, p24) and, hence, HIV replication. Curiously, these HIV-resistant women demonstrated normal immune responses, nor an increased susceptibility to other infection. Similarly, modest IRF-1 knockdown had limited impact on the magnitude of HIV-1-elicited activation of IRF-1-regulated host immunologic genes but resulted in lessened duration of these responses. These data suggest that early expression of HIV-1 genes requires a higher IRF-1 level, compared to the host antiviral genes. Together, these provide one key mechanism underlying the natural resistance against HIV infection and further suggest that modest IRF-1 reduction could effectively limit productive HIV infection yet remain sufficient to activate a robust but transient immune response.
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A Study of the Vaginal Microbiome in Healthy Canadian Women Utilizing cpn60-Based Molecular Profiling Reveals Distinct Gardnerella Subgroup Community State Types. PLoS One 2015; 10:e0135620. [PMID: 26266808 PMCID: PMC4534464 DOI: 10.1371/journal.pone.0135620] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/24/2015] [Indexed: 12/14/2022] Open
Abstract
The vaginal microbiota is important in women’s reproductive and overall health. However, the relationships between the structure, function and dynamics of this complex microbial community and health outcomes remain elusive. The objective of this study was to determine the phylogenetic range and abundance of prokaryotes in the vaginal microbiota of healthy, non-pregnant, ethnically diverse, reproductive-aged Canadian women. Socio-demographic, behavioural and clinical data were collected and vaginal swabs were analyzed from 310 women. Detailed profiles of their vaginal microbiomes were generated by pyrosequencing of the chaperonin-60 universal target. Six community state types (CST) were delineated by hierarchical clustering, including three Lactobacillus-dominated CST (L. crispatus, L. iners, L. jensenii), two Gardnerella-dominated (subgroups A and C) and an “intermediate” CST which included a small number of women with microbiomes dominated by seven other species or with no dominant species but minority populations of Streptococcus, Staphylococcus, Peptoniphilus, E. coli and various Proteobacteria in co-dominant communities. The striking correspondence between Nugent score and deep sequencing CST continues to reinforce the basic premise provided by the simpler Gram stain method, while additional analyses reveal detailed cpn60-based phylogeny and estimated abundance in microbial communities from vaginal samples. Ethnicity was the only demographic or clinical characteristic predicting CST, with differences in Asian and White women (p = 0.05). In conclusion, this study confirms previous work describing four cpn60-based subgroups of Gardnerella, revealing previously undescribed CST. The data describe the range of bacterial communities seen in Canadian women presenting with no specific vaginal health concerns, and provides an important baseline for future investigations of clinically important cohorts.
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Johnson LA, Chaban B, Harding JCS, Hill JE. Optimizing a PCR protocol for cpn60-based microbiome profiling of samples variously contaminated with host genomic DNA. BMC Res Notes 2015; 8:253. [PMID: 26092180 PMCID: PMC4475309 DOI: 10.1186/s13104-015-1170-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 05/13/2015] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND The current recommended protocol for chaperonin-60 (cpn60) universal target based microbiome profiling includes universal PCR of microbiome samples across an annealing temperature gradient to maximize the diversity of sequences amplified. However, the value of including this gradient approach has not been formally evaluated since the optimization of a modified universal PCR primer cocktail for cpn60 PCR. PCR conditions that maximize representation of the microbiome while minimizing PCR-associated distortion of the community structure, especially in samples containing large amounts of host genomic DNA are critical. The goal of this study was to measure the effects of PCR annealing temperature and the ratio of host to bacterial DNA on the outcome of microbiota analysis, using pig microbiota as a model environment. FINDINGS Six samples were chosen with an anticipated range of ratios of pig to bacterial genomic DNA, and universal cpn60 PCR amplification with an annealing temperature gradient was used to create libraries for pyrosequencing, resulting in 426,477 sequences from the six samples. The sequences obtained were classified as target (cpn60) or non-target based on the percent identity of their closest match to the cpnDB reference database, and target sequences were further processed to create microbiome profiles for each sample at each annealing temperature. Annealing temperature affected the amount of PCR product generated, with more product generated at higher temperatures. Samples containing proportionally more host genomic DNA yielded more non-target reads, especially at lower annealing temperatures. However, microbiome composition for each sample across the annealing temperature gradient remained consistent at both the phylum and operational taxonomic unit levels. Although some microbial sequences were detected at only one annealing temperature, these sequences accounted for a minority of the total microbiome. CONCLUSIONS These results indicate that PCR annealing temperature does have an affect on cpn60 based microbiome profiles, but that most of the differences are due to differences in detection of low abundance sequences. Higher annealing temperatures resulted in larger amounts of PCR product and lower amounts of non-target sequence amplification, especially in samples containing proportionally large amounts of host DNA. Taken together these results provide important information to guide decisions about experimental design for cpn60 based microbiome studies.
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Affiliation(s)
- Lisa A Johnson
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada.
| | - Bonnie Chaban
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada. .,Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
| | - John C S Harding
- Department of Large Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada.
| | - Janet E Hill
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, S7N 5B4, Canada.
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Jespers V, van de Wijgert J, Cools P, Verhelst R, Verstraelen H, Delany-Moretlwe S, Mwaura M, Ndayisaba GF, Mandaliya K, Menten J, Hardy L, Crucitti T. The significance of Lactobacillus crispatus and L. vaginalis for vaginal health and the negative effect of recent sex: a cross-sectional descriptive study across groups of African women. BMC Infect Dis 2015; 15:115. [PMID: 25879811 PMCID: PMC4351943 DOI: 10.1186/s12879-015-0825-z] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Accepted: 02/10/2015] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Women in sub-Saharan Africa are vulnerable to acquiring HIV infection and reproductive tract infections. Bacterial vaginosis (BV), a disruption of the vaginal microbiota, has been shown to be strongly associated with HIV infection. Risk factors related to potentially protective or harmful microbiota species are not known. METHODS We present cross-sectional quantitative polymerase chain reaction data of the Lactobacillus genus, five Lactobacillus species, and three BV-related bacteria (Gardnerella vaginalis, Atopobium vaginae, and Prevotella bivia) together with Escherichia coli and Candida albicans in 426 African women across different groups at risk for HIV. We selected a reference group of adult HIV-negative women at average risk for HIV acquisition and compared species variations in subgroups of adolescents, HIV-negative pregnant women, women engaging in traditional vaginal practices, sex workers and a group of HIV-positive women on combination antiretroviral therapy. We explored the associations between presence and quantity of the bacteria with BV by Nugent score, in relation to several factors of known or theoretical importance. RESULTS The presence of species across Kenyan, South African and Rwandan women was remarkably similar and few differences were seen between the two groups of reference women in Kenya and South Africa. The Rwandan sex workers and HIV-positive women had the highest G. vaginalis presence (p = 0.006). Pregnant women had a higher Lactobacillus genus mean log (7.01 genome equivalents (geq)/ml) compared to the reference women (6.08 geq/ml). L. vaginalis (43%) was second to L. iners (81.9%) highly present in women with a normal Nugent score. Recent sexual exposure negatively affected the presence of L. crispatus (<0.001), L. vaginalis (p = 0.001), and Lactobacillus genus (p < 0.001). Having more than one sexual partner in the last three months was associated with an increased prevalence of G. vaginalis (p = 0.044) and L. iners (p = 0.001). CONCLUSIONS Although the composition of species across the studied African countries was similar, the presence of protective species i.e. L. crispatus and L. vaginalis in women with a normal Nugent score appeared lower compared to non-African studies. Furthermore, Lactobacillus species were negatively affected by sexual behavioural. Strategies to support protective Lactobacillus species are urgently needed. TRIAL REGISTRATION The study is registered at the Trial Registration at the National Health Research Ethics Council South Africa with the number DOH2709103223.
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Affiliation(s)
- Vicky Jespers
- Department of Public Health, Unit of Epidemiology and Control of HIV/STD, Institute of Tropical Medicine, Nationalestraat 155, B-2000, Antwerp, Belgium.
| | - Janneke van de Wijgert
- Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK.
| | - Piet Cools
- Laboratory Bacteriology Research, University Gent, Ghent, Belgium.
| | - Rita Verhelst
- International Center for Reproductive Health (ICRH), Ghent University, Ghent, Belgium.
| | - Hans Verstraelen
- Department of Obstetrics and Gynaecology, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
| | - Sinead Delany-Moretlwe
- Wits Reproductive Health & HIV Institute, University of Witwatersrand, Johannesburg, South Africa.
| | | | | | | | - Joris Menten
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.
| | - Liselotte Hardy
- Department of Public Health, Unit of Epidemiology and Control of HIV/STD, Institute of Tropical Medicine, Nationalestraat 155, B-2000, Antwerp, Belgium. .,Department of Clinical Sciences, HIV/STI Reference Laboratory, Institute of Tropical Medicine, Antwerp, Belgium.
| | - Tania Crucitti
- Department of Clinical Sciences, HIV/STI Reference Laboratory, Institute of Tropical Medicine, Antwerp, Belgium.
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Mehta SD, Donovan B, Weber KM, Cohen M, Ravel J, Gajer P, Gilbert D, Burgad D, Spear GT. The vaginal microbiota over an 8- to 10-year period in a cohort of HIV-infected and HIV-uninfected women. PLoS One 2015; 10:e0116894. [PMID: 25675346 PMCID: PMC4326357 DOI: 10.1371/journal.pone.0116894] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 12/16/2014] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND We identified predominant vaginal microbiota communities, changes over time, and how this varied by HIV status and other factors in a cohort of 64 women. METHODS Bacterial DNA was extracted from reposited cervicovaginal lavage samples collected annually over an 8-10 year period from Chicago Women's Interagency HIV Study participants: 22 HIV-negative, 22 HIV-positive with stable infection, 20 HIV-positive with progressive infection. The vaginal microbiota was defined by pyrosequencing of the V1/V2 region of the 16S rRNA gene. Scheduled visits included Bacterial vaginsosis (BV) screening; clinically detected cases were referred for treatment. Hierarchical clustering identified bacterial community state types (CST). Multinomial mixed effects modeling determined trends over time in CST, by HIV status and other factors. RESULTS The median follow-up time was 8.1 years (range 5.5-15.3). Six CSTs were identified. The mean relative abundance (RA) of Lactobacillus spp. by CST (with median number of bacterial taxa) was: CST-1-25.7% (10), CST-2-27.1% (11), CST-3-34.6% (9), CST-4-46.8% (9), CST-5-57.9% (4), CST-6-69.4% (2). The two CSTs representing the highest RA of Lactobacillus and lowest diversity increased with each additional year of follow-up (CST-5, adjusted odds ratio (aOR) = 1.62 [95% CI: 1.34-1.94]; CST-6, aOR = 1.57 [95 CI: 1.31-1.89]), while the two CSTs representing lowest RA of Lactobacillus and higher diversity decreased with each additional year (CST-1, aOR = 0.89 [95% CI: 0.80-1.00]; CST-2, aOR = 0.86 [95% CI: 0.75-0.99]). There was no association between HIV status and CST at baseline or over time. CSTs representing lower RA of Lactobacillus were associated with current cigarette smoking. CONCLUSIONS The vaginal microbial community significantly improved over time in this cohort of women with HIV and at high risk for HIV who had regular detection and treatment referral for BV.
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Affiliation(s)
- Supriya D. Mehta
- Division of Epidemiology and Biostatistics, University of Illinois at Chicago, School of Public Health, Chicago, Illinois, United States of America
- * E-mail:
| | - Brock Donovan
- Department of Bioengineering, University of Illinois at Chicago, College of Medicine, Chicago, Illinois, United States of America
| | - Kathleen M. Weber
- The Core Center at Cook County Health and Hospital System, Chicago, Illinois, United States of America
| | - Mardge Cohen
- The Core Center at Cook County Health and Hospital System, Chicago, Illinois, United States of America
| | - Jacques Ravel
- Institute for Genome Sciences, University of Maryland, and Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Pawel Gajer
- Institute for Genome Sciences, University of Maryland, and Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Maryland, United States of America
| | - Douglas Gilbert
- Department of Immunology & Microbiology, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Derick Burgad
- Department of Immunology & Microbiology, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Greg T. Spear
- Department of Immunology & Microbiology, Rush University Medical Center, Chicago, Illinois, United States of America
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van de Wijgert JHHM, Borgdorff H, Verhelst R, Crucitti T, Francis S, Verstraelen H, Jespers V. The vaginal microbiota: what have we learned after a decade of molecular characterization? PLoS One 2014; 9:e105998. [PMID: 25148517 PMCID: PMC4141851 DOI: 10.1371/journal.pone.0105998] [Citation(s) in RCA: 301] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Accepted: 07/25/2014] [Indexed: 11/19/2022] Open
Abstract
We conducted a systematic review of the Medline database (U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, U.S.A) to determine if consistent molecular vaginal microbiota (VMB) composition patterns can be discerned after a decade of molecular testing, and to evaluate demographic, behavioral and clinical determinants of VMB compositions. Studies were eligible when published between 1 January 2008 and 15 November 2013, and if at least one molecular technique (sequencing, PCR, DNA fingerprinting, or DNA hybridization) was used to characterize the VMB. Sixty three eligible studies were identified. These studies have now conclusively shown that lactobacilli-dominated VMB are associated with a healthy vaginal micro-environment and that bacterial vaginosis (BV) is best described as a polybacterial dysbiosis. The extent of dysbiosis correlates well with Nugent score and vaginal pH but not with the other Amsel criteria. Lactobacillus crispatus is more beneficial than L. iners. Longitudinal studies have shown that a L. crispatus-dominated VMB is more likely to shift to a L. iners-dominated or mixed lactobacilli VMB than to full dysbiosis. Data on VMB determinants are scarce and inconsistent, but dysbiosis is consistently associated with HIV, human papillomavirus (HPV), and Trichomonas vaginalis infection. In contrast, vaginal colonization with Candida spp. is more common in women with a lactobacilli-dominated VMB than in women with dysbiosis. Cervicovaginal mucosal immune responses to molecular VMB compositions have not yet been properly characterized. Molecular techniques have now become more affordable, and we make a case for incorporating them into larger epidemiological studies to address knowledge gaps in etiology and pathogenesis of dysbiosis, associations of different dysbiotic states with clinical outcomes, and to evaluate interventions aimed at restoring and maintaining a lactobacilli-dominated VMB.
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Affiliation(s)
| | - Hanneke Borgdorff
- Academic Medical Center and Amsterdam Institute of Global Health and Development, Amsterdam, The Netherlands
| | - Rita Verhelst
- International Centre for Reproductive Health, Ghent University Hospital, Ghent, Belgium
| | - Tania Crucitti
- Prince Leopold Institute of Tropical Medicine, Antwerp, Belgium
| | - Suzanna Francis
- London School for Hygiene and Tropical Medicine, London, United Kingdom
| | - Hans Verstraelen
- Department of Obstetrics and Gynecology, Ghent University Hospital, Ghent, Belgium
| | - Vicky Jespers
- Prince Leopold Institute of Tropical Medicine, Antwerp, Belgium
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Sharma PK, Fu J, Zhang X, Fristensky B, Sparling R, Levin DB. Genome features of Pseudomonas putida LS46, a novel polyhydroxyalkanoate producer and its comparison with other P. putida strains. AMB Express 2014; 4:37. [PMID: 25401060 PMCID: PMC4230813 DOI: 10.1186/s13568-014-0037-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2014] [Accepted: 03/16/2014] [Indexed: 12/13/2022] Open
Abstract
A novel strain of Pseudomonas putida LS46 was isolated from wastewater on the basis of its ability to synthesize medium chain-length polyhydroxyalkanoates (mcl-PHAs). P.putida LS46 was differentiated from other P.putida strains on the basis of cpn60 (UT). The complete genome of P.putida LS46 was sequenced and annotated. Its chromosome is 5,86,2556 bp in size with GC ratio of 61.69. It is encoding 5316 genes, including 7 rRNA genes and 76 tRNA genes. Nucleotide sequence data of the complete P. putida LS46 genome was compared with nine other P. putida strains (KT2440, F1, BIRD-1, S16, ND6, DOT-T1E, UW4, W619 and GB-1) identified either as biocontrol agents or as bioremediation agents and isolated from different geographical region and different environment. BLASTn analysis of whole genome sequences of the ten P. putida strains revealed nucleotide sequence identities of 86.54 to 97.52%. P.putida genome arrangement was LS46 highly similar to P.putida BIRD1 and P.putida ND6 but was markedly different than P.putida DOT-T1E, P.putida UW4 and P.putida W619. Fatty acid biosynthesis (fab), fatty acid degradation (fad) and PHA synthesis genes were highly conserved among biocontrol and bioremediation P.putida strains. Six genes in pha operon of P. putida LS46 showed >98% homology at gene and proteins level. It appears that polyhydroxyalkanoate (PHA) synthesis is an intrinsic property of P. putida and was not affected by its geographic origin. However, all strains, including P. putida LS46, were different from one another on the basis of house keeping genes, and presence of plasmid, prophages, insertion sequence elements and genomic islands. While P. putida LS46 was not selected for plant growth promotion or bioremediation capacity, its genome also encoded genes for root colonization, pyoverdine synthesis, oxidative stress (present in other soil isolates), degradation of aromatic compounds, heavy metal resistance and nicotinic acid degradation, manganese (Mn II) oxidation. Genes for toluene or naphthalene degradation found in the genomes of P. putida F1, DOT-T1E, and ND6 were absent in the P. putida LS46 genome. Heavy metal resistant genes encoded by the P. putida W619 genome were also not present in the P. putida LS46 genome. Despite the overall similarity among genome of P.putida strains isolated for different applications and from different geographical location a number of differences were observed in genome arrangement, occurrence of transposon, genomic islands and prophage. It appears that P.putida strains had a common ancestor and by acquiring some specific genes by horizontal gene transfer it differed from other related strains.
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Borgdorff H, Tsivtsivadze E, Verhelst R, Marzorati M, Jurriaans S, Ndayisaba GF, Schuren FH, van de Wijgert JHHM. Lactobacillus-dominated cervicovaginal microbiota associated with reduced HIV/STI prevalence and genital HIV viral load in African women. ISME JOURNAL 2014; 8:1781-93. [PMID: 24599071 DOI: 10.1038/ismej.2014.26] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 12/04/2013] [Accepted: 01/20/2014] [Indexed: 01/28/2023]
Abstract
Cervicovaginal microbiota not dominated by lactobacilli may facilitate transmission of HIV and other sexually transmitted infections (STIs), as well as miscarriages, preterm births and sepsis in pregnant women. However, little is known about the exact nature of the microbiological changes that cause these adverse outcomes. In this study, cervical samples of 174 Rwandan female sex workers were analyzed cross-sectionally using a phylogenetic microarray. Furthermore, HIV-1 RNA concentrations were measured in cervicovaginal lavages of 58 HIV-positive women among them. We identified six microbiome clusters, representing a gradient from low semi-quantitative abundance and diversity dominated by Lactobacillus crispatus (cluster R-I, with R denoting 'Rwanda') and L. iners (R-II) to intermediate (R-V) and high abundance and diversity (R-III, R-IV and R-VI) dominated by a mixture of anaerobes, including Gardnerella, Atopobium and Prevotella species. Women in cluster R-I were less likely to have HIV (P=0.03), herpes simplex virus type 2 (HSV-2; P<0.01), and high-risk human papillomavirus (HPV; P<0.01) and had no bacterial STIs (P=0.15). Statistically significant trends in prevalence of viral STIs were found from low prevalence in cluster R-I, to higher prevalence in clusters R-II and R-V, and highest prevalence in clusters R-III/R-IV/R-VI. Furthermore, only 10% of HIV-positive women in clusters R-I/R-II, compared with 40% in cluster R-V, and 42% in clusters R-III/R-IV/R-VI had detectable cervicovaginal HIV-1 RNA (Ptrend=0.03). We conclude that L. crispatus-dominated, and to a lesser extent L. iners-dominated, cervicovaginal microbiota are associated with a lower prevalence of HIV/STIs and a lower likelihood of genital HIV-1 RNA shedding.
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Affiliation(s)
- Hanneke Borgdorff
- Amsterdam Institute for Global Health and Development (AIGHD) and Department of Global Health, Academic Medical Center, Amsterdam, The Netherlands
| | | | - Rita Verhelst
- International Center for Reproductive Health (ICRH), Ghent University, Ghent, Belgium
| | - Massimo Marzorati
- Laboratory of Microbial Ecology and Technology (LabMET), Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Suzanne Jurriaans
- Laboratory of Clinical Virology, Department of Medical Microbiology, Academic Medical Center, Amsterdam, The Netherlands
| | | | - Frank H Schuren
- TNO Microbiology and Systems Biology, Zeist, The Netherlands
| | - Janneke H H M van de Wijgert
- 1] Amsterdam Institute for Global Health and Development (AIGHD) and Department of Global Health, Academic Medical Center, Amsterdam, The Netherlands [2] Department of Clinical Infection, Microbiology and Immunology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
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43
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Shen R, Smith PD. Mucosal correlates of protection in HIV-1-exposed sero-negative persons. Am J Reprod Immunol 2014; 72:219-27. [PMID: 24428610 DOI: 10.1111/aji.12202] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Accepted: 12/17/2013] [Indexed: 01/31/2023] Open
Abstract
Resistance to HIV-1 infection in HIV-1-exposed sero-negative (HESN) persons offers a promising opportunity to identify mechanisms of 'natural' protection. Unique features of the mucosa in particular may contribute to this protection. Here, we highlight several key issues pertaining to the mucosal correlates of protection in HESN persons, including humoral immune responses, mechanisms of mucosal HIV-1 neutralization, immune cell activation, and role of the microbiota in mucosal responses. We also discuss mucosal model systems that can be used to investigate the mechanisms of resistance in HESN subjects. A clear understanding of the mucosal correlates of protection against HIV-1 in HESN persons will provide critical new insights for the development of effective vaccine and microbicide strategies for the prevention of HIV-1 transmission.
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Affiliation(s)
- Ruizhong Shen
- Department of Medicine (Gastroenterology), University of Alabama at Birmingham, Birmingham, AL, USA
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44
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Chaban B, Links MG, Jayaprakash TP, Wagner EC, Bourque DK, Lohn Z, Albert AYK, van Schalkwyk J, Reid G, Hemmingsen SM, Hill JE, Money DM. Characterization of the vaginal microbiota of healthy Canadian women through the menstrual cycle. MICROBIOME 2014; 2:23. [PMID: 25053998 PMCID: PMC4106219 DOI: 10.1186/2049-2618-2-23] [Citation(s) in RCA: 145] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Accepted: 03/31/2014] [Indexed: 05/11/2023]
Abstract
BACKGROUND The vaginal microbial community plays a vital role in maintaining women's health. Understanding the precise bacterial composition is challenging because of the diverse and difficult-to-culture nature of many bacterial constituents, necessitating culture-independent methodology. During a natural menstrual cycle, physiological changes could have an impact on bacterial growth, colonization, and community structure. The objective of this study was to assess the stability of the vaginal microbiome of healthy Canadian women throughout a menstrual cycle by using cpn60-based microbiota analysis. Vaginal swabs from 27 naturally cycling reproductive-age women were collected weekly through a single menstrual cycle. Polymerase chain reaction (PCR) was performed to amplify the universal target region of the cpn60 gene and generate amplicons representative of the microbial community. Amplicons were pyrosequenced, assembled into operational taxonomic units, and analyzed. Samples were also assayed for total 16S rRNA gene content and Gardnerella vaginalis by quantitative PCR and screened for the presence of Mollicutes by using family and genus-specific PCR. RESULTS Overall, the vaginal microbiome of most women remained relatively stable throughout the menstrual cycle, with little variation in diversity and only modest fluctuations in species richness. Microbiomes between women were more different than were those collected consecutively from individual women. Clustering of microbial profiles revealed the expected groupings dominated by Lactobacillus crispatus, Lactobacillus iners, and Lactobacillus jensenii. Interestingly, two additional clusters were dominated by either Bifidobacterium breve or a heterogeneous mixture of nonlactobacilli. Direct G. vaginalis quantification correlated strongly with its pyrosequencing-read abundance, and Mollicutes, including Mycoplasma hominis, Ureaplasma parvum, and Ureaplasma urealyticum, were detected in most samples. CONCLUSIONS Our cpn60-based investigation of the vaginal microbiome demonstrated that in healthy women most vaginal microbiomes remained stable through their menstrual cycle. Of interest in these findings was the presence of Bifidobacteriales beyond just Gardnerella species. Bifidobacteriales are frequently underrepresented in 16S rRNA gene-based studies, and their detection by cpn60-based investigation suggests that their significance in the vaginal community may be underappreciated.
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Affiliation(s)
- Bonnie Chaban
- Department of Veterinary Microbiology, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Matthew G Links
- Department of Veterinary Microbiology, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
- Agriculture and AgriFood Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada
| | - Teenus Paramel Jayaprakash
- Department of Veterinary Microbiology, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Emily C Wagner
- Department of Obstetrics and Gynecology, University of British Columbia, 1190 Hornby Street, Vancouver, BC V6Z 2K5, Canada
- Women’s Health Research Institute, 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
| | - Danielle K Bourque
- Women’s Health Research Institute, 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
| | - Zoe Lohn
- Women’s Health Research Institute, 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
| | - Arianne YK Albert
- Women’s Health Research Institute, 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
| | - Julie van Schalkwyk
- Department of Obstetrics and Gynecology, University of British Columbia, 1190 Hornby Street, Vancouver, BC V6Z 2K5, Canada
- Women’s Health Research Institute, 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
| | - Gregor Reid
- Department of Microbiology and Immunology, University of Western Ontario and Lawson Health Research Institute, London, ON, Canada
| | - Sean M Hemmingsen
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Department of Microbiology & Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Janet E Hill
- Department of Veterinary Microbiology, University of Saskatchewan, 52 Campus Drive, Saskatoon, SK S7N 5B4, Canada
| | - Deborah M Money
- Department of Obstetrics and Gynecology, University of British Columbia, 1190 Hornby Street, Vancouver, BC V6Z 2K5, Canada
- Women’s Health Research Institute, 4500 Oak Street, Vancouver, BC V6H 3N1, Canada
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45
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Balashov SV, Mordechai E, Adelson ME, Gygax SE. Identification, quantification and subtyping of Gardnerella vaginalis in noncultured clinical vaginal samples by quantitative PCR. J Med Microbiol 2013; 63:162-175. [PMID: 24200640 DOI: 10.1099/jmm.0.066407-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Gardnerella vaginalis is an important component of the human vaginal microflora. It is proposed to play a key role in the pathogenesis of bacterial vaginosis (BV), the most common vaginal condition. Here we describe the development, validation and comparative analysis of a novel molecular approach capable of G. vaginalis identification, quantification and subtyping in noncultured vaginal specimens. Using two quantitative PCR (qPCR) assays, we analysed G. vaginalis bacterial loads and clade distribution in 60 clinical vaginal-swab samples. A very high pathogen prevalence was revealed by species-specific qPCR not only among BV patients (100 %), but also in healthy women (97 %), although the G. vaginalis concentration was significantly lower in non-BV samples. G. vaginalis clades identified in vaginal specimens by subtyping multiplex qPCR, which targets four clade-specific genetic markers, had frequencies of 53 % for clade 1, 25 % for clade 2, 32 % for clade 3 and 83 % for clade 4. Multiple clades were found in 70 % of samples. Single G. vaginalis clades were represented by clade 1 and clade 4 in 28 % of specimens. A positive association with BV was shown for clade 1 and clade 3, while clade 2 was positively associated with intermediate vaginal microflora, but not with BV. Clade 4 demonstrated no correlation with the disorder. The presence of multiple clades had a high positive association with BV, whereas G. vaginalis identified as a single clade was negatively linked with the condition. Polyclonal G. vaginalis infection may be a risk factor for BV.
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Affiliation(s)
- Sergey V Balashov
- Femeris Women's Health Research Center, Medical Diagnostic Laboratories, L. C., Genesis Biotechnology Group, Hamilton, NJ, USA
| | - Eli Mordechai
- Femeris Women's Health Research Center, Medical Diagnostic Laboratories, L. C., Genesis Biotechnology Group, Hamilton, NJ, USA
| | - Martin E Adelson
- Femeris Women's Health Research Center, Medical Diagnostic Laboratories, L. C., Genesis Biotechnology Group, Hamilton, NJ, USA
| | - Scott E Gygax
- Femeris Women's Health Research Center, Medical Diagnostic Laboratories, L. C., Genesis Biotechnology Group, Hamilton, NJ, USA
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46
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Links MG, Chaban B, Hemmingsen SM, Muirhead K, Hill JE. mPUMA: a computational approach to microbiota analysis by de novo assembly of operational taxonomic units based on protein-coding barcode sequences. MICROBIOME 2013; 1:23. [PMID: 24451012 PMCID: PMC3971603 DOI: 10.1186/2049-2618-1-23] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 08/03/2013] [Indexed: 05/03/2023]
Abstract
BACKGROUND Formation of operational taxonomic units (OTU) is a common approach to data aggregation in microbial ecology studies based on amplification and sequencing of individual gene targets. The de novo assembly of OTU sequences has been recently demonstrated as an alternative to widely used clustering methods, providing robust information from experimental data alone, without any reliance on an external reference database. RESULTS Here we introduce mPUMA (microbial Profiling Using Metagenomic Assembly, http://mpuma.sourceforge.net), a software package for identification and analysis of protein-coding barcode sequence data. It was developed originally for Cpn60 universal target sequences (also known as GroEL or Hsp60). Using an unattended process that is independent of external reference sequences, mPUMA forms OTUs by DNA sequence assembly and is capable of tracking OTU abundance. mPUMA processes microbial profiles both in terms of the direct DNA sequence as well as in the translated amino acid sequence for protein coding barcodes. By forming OTUs and calculating abundance through an assembly approach, mPUMA is capable of generating inputs for several popular microbiota analysis tools. Using SFF data from sequencing of a synthetic community of Cpn60 sequences derived from the human vaginal microbiome, we demonstrate that mPUMA can faithfully reconstruct all expected OTU sequences and produce compositional profiles consistent with actual community structure. CONCLUSIONS mPUMA enables analysis of microbial communities while empowering the discovery of novel organisms through OTU assembly.
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Affiliation(s)
- Matthew G Links
- Agriculture and AgriFood Canada, 107 Science Place, S7N 0X2, Saskatoon, SK, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, 52 Campus Drive, S7N 5B4, Saskatoon, SK, Canada
| | - Bonnie Chaban
- Department of Veterinary Microbiology, University of Saskatchewan, 52 Campus Drive, S7N 5B4, Saskatoon, SK, Canada
| | - Sean M Hemmingsen
- National Research Council Canada, 110 Gymnasium Place, S7N 0W9, Saskatoon, SK, Canada
- Department of Microbiology & Immunology, University of Saskatchewan, 107 Wiggins Road, S7N 5E5, Saskatoon, SK, Canada
| | - Kevin Muirhead
- National Research Council Canada, 110 Gymnasium Place, S7N 0W9, Saskatoon, SK, Canada
| | - Janet E Hill
- Agriculture and AgriFood Canada, 107 Science Place, S7N 0X2, Saskatoon, SK, Canada
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47
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Chaban B, Albert A, Links MG, Gardy J, Tang P, Hill JE. Characterization of the upper respiratory tract microbiomes of patients with pandemic H1N1 influenza. PLoS One 2013; 8:e69559. [PMID: 23844261 PMCID: PMC3699515 DOI: 10.1371/journal.pone.0069559] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 06/10/2013] [Indexed: 01/27/2023] Open
Abstract
The upper respiratory tract microbiome has an important role in respiratory health. Influenza A is a common viral infection that challenges that health, and a well-recognized sequela is bacterial pneumonia. Given this connection, we sought to characterize the upper respiratory tract microbiota of individuals suffering from the pandemic H1N1 influenza A outbreak of 2009 and determine if microbiome profiles could be correlated with patient characteristics. We determined the microbial profiles of 65 samples from H1N1 patients by cpn60 universal target amplification and sequencing. Profiles were examined at the phylum and nearest neighbor “species” levels using the characteristics of patient gender, age, originating health authority, sample type and designation (STAT/non-STAT). At the phylum level, Actinobacteria-, Firmicutes- and Proteobacteria-dominated microbiomes were observed, with none of the patient characteristics showing significant profile composition differences. At the nearest neighbor “species” level, the upper respiratory tract microbiomes were composed of 13-20 “species” and showed a trend towards increasing diversity with patient age. Interestingly, at an individual level, most patients had one to three organisms dominant in their microbiota. A limited number of discrete microbiome profiles were observed, shared among influenza patients regardless of patient status variables. To assess the validity of analyses derived from sequence read abundance, several bacterial species were quantified by quantitative PCR and compared to the abundance of cpn60 sequence read counts obtained in the study. A strong positive correlation between read abundance and absolute bacterial quantification was observed. This study represents the first examination of the upper respiratory tract microbiome using a target other than the 16S rRNA gene and to our knowledge, the first thorough examination of this microbiome during a viral infection.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Bacteria/classification
- Bacteria/genetics
- British Columbia/epidemiology
- Child
- Child, Preschool
- Female
- Fungi/classification
- Fungi/genetics
- Humans
- Infant
- Infant, Newborn
- Influenza A Virus, H1N1 Subtype/genetics
- Influenza A Virus, H1N1 Subtype/physiology
- Influenza, Human/diagnosis
- Influenza, Human/epidemiology
- Influenza, Human/virology
- Male
- Microbiota
- Middle Aged
- Pandemics
- Phylogeny
- RNA, Ribosomal, 16S/genetics
- RNA, Viral/genetics
- Respiratory System/microbiology
- Reverse Transcriptase Polymerase Chain Reaction
- Young Adult
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Affiliation(s)
- Bonnie Chaban
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Arianne Albert
- Women’s Health Research Institute, Vancouver, British Columbia, Canada
| | - Matthew G. Links
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Saskatoon Research Centre, Agriculture and AgriFood Canada, Saskatoon, Saskatchewan, Canada
| | - Jennifer Gardy
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
| | - Patrick Tang
- British Columbia Centre for Disease Control, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Janet E. Hill
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- *
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48
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Gilbert NM, Lewis WG, Lewis AL. Clinical features of bacterial vaginosis in a murine model of vaginal infection with Gardnerella vaginalis. PLoS One 2013; 8:e59539. [PMID: 23527214 PMCID: PMC3602284 DOI: 10.1371/journal.pone.0059539] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 02/15/2013] [Indexed: 02/03/2023] Open
Abstract
Bacterial vaginosis (BV) is a dysbiosis of the vaginal flora characterized by a shift from a Lactobacillus-dominant environment to a polymicrobial mixture including Actinobacteria and Gram-negative bacilli. BV is a common vaginal condition in women and is associated with increased risk of sexually transmitted infection and adverse pregnancy outcomes such as preterm birth. Gardnerella vaginalis is one of the most frequently isolated bacterial species in BV. However, there has been much debate in the literature concerning the contribution of G. vaginalis to the etiology of BV, since it is also present in a significant proportion of healthy women. Here we present a new murine vaginal infection model with a clinical isolate of G. vaginalis. Our data demonstrate that this model displays key features used clinically to diagnose BV, including the presence of sialidase activity and exfoliated epithelial cells with adherent bacteria (reminiscent of clue cells). G. vaginalis was capable of ascending uterine infection, which correlated with the degree of vaginal infection and level of vaginal sialidase activity. The host response to G. vaginalis infection was characterized by robust vaginal epithelial cell exfoliation in the absence of histological inflammation. Our analyses of clinical specimens from women with BV revealed a measureable epithelial exfoliation response compared to women with normal flora, a phenotype that, to our knowledge, is measured here for the first time. The results of this study demonstrate that G. vaginalis is sufficient to cause BV phenotypes and suggest that this organism may contribute to BV etiology and associated complications. This is the first time vaginal infection by a BV associated bacterium in an animal has been shown to parallel the human disease with regard to clinical diagnostic features. Future studies with this model should facilitate investigation of important questions regarding BV etiology, pathogenesis and associated complications.
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Affiliation(s)
- Nicole M. Gilbert
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Warren G. Lewis
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Amanda L. Lewis
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, United States of America
- Department of Obstetrics and Gynecology, Center for Women’s Infectious Disease Research, Washington University School of Medicine, St. Louis, Missouri, United States of America
- * E-mail:
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49
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Abstract
This review outlines information about the Gram-negative, aerobic bacterium Variovorax paradoxus. The genomes of these species have G+C contents of 66.5-69.4 mol%, and the cells form yellow colonies. Some strains of V. paradoxus are facultative lithoautotrophic, others are chemoorganotrophic. Many of them are associated with important catabolic processes including the degradation of toxic and/or complex chemical compounds. The degradation pathways or other skills related to the following compounds, respectively, are described in this review: sulfolane, 3-sulfolene, 2-mercaptosuccinic acid, 3,3'-thiodipropionic acid, aromatic sulfonates, alkanesulfonates, amino acids and other sulfur sources, polychlorinated biphenyls, dimethyl terephthalate, linuron, 2,4-dinitrotoluene, homovanillate, veratraldehyde, 2,4-dichlorophenoxyacetic acid, anthracene, poly(3-hydroxybutyrate), chitin, cellulose, humic acids, metal-EDTA complexes, yttrium, rare earth elements, As(III), trichloroethylene, capsaicin, 3-nitrotyrosine, acyl-homoserine lactones, 1-aminocyclopropane-1-carboxylate, methyl tert-butyl ether, geosmin, and 2-methylisoborneol. Strains of V. paradoxus are also engaged in mutually beneficial interactions with other plant and bacterial species in various ecosystems. This species comprises probably promising strains for bioremediation and other biotechnical applications. Lately, the complete genomes of strains S110 and EPS have been sequenced for further investigations.
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50
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Links MG, Dumonceaux TJ, Hemmingsen SM, Hill JE. The chaperonin-60 universal target is a barcode for bacteria that enables de novo assembly of metagenomic sequence data. PLoS One 2012. [PMID: 23189159 PMCID: PMC3506640 DOI: 10.1371/journal.pone.0049755] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Barcoding with molecular sequences is widely used to catalogue eukaryotic biodiversity. Studies investigating the community dynamics of microbes have relied heavily on gene-centric metagenomic profiling using two genes (16S rRNA and cpn60) to identify and track Bacteria. While there have been criteria formalized for barcoding of eukaryotes, these criteria have not been used to evaluate gene targets for other domains of life. Using the framework of the International Barcode of Life we evaluated DNA barcodes for Bacteria. Candidates from the 16S rRNA gene and the protein coding cpn60 gene were evaluated. Within complete bacterial genomes in the public domain representing 983 species from 21 phyla, the largest difference between median pairwise inter- and intra-specific distances (“barcode gap”) was found from cpn60. Distribution of sequence diversity along the ∼555 bp cpn60 target region was remarkably uniform. The barcode gap of the cpn60 universal target facilitated the faithful de novo assembly of full-length operational taxonomic units from pyrosequencing data from a synthetic microbial community. Analysis supported the recognition of both 16S rRNA and cpn60 as DNA barcodes for Bacteria. The cpn60 universal target was found to have a much larger barcode gap than 16S rRNA suggesting cpn60 as a preferred barcode for Bacteria. A large barcode gap for cpn60 provided a robust target for species-level characterization of data. The assembly of consensus sequences for barcodes was shown to be a reliable method for the identification and tracking of novel microbes in metagenomic studies.
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Affiliation(s)
- Matthew G. Links
- Agriculture and AgriFood Canada, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Tim J. Dumonceaux
- Agriculture and AgriFood Canada, Saskatoon, Saskatchewan, Canada
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sean M. Hemmingsen
- National Research Council Canada, Saskatoon, Saskatchewan, Canada
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Janet E. Hill
- Department of Veterinary Microbiology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- * E-mail:
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