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Dwivedi V, Shivanna V, Gautam S, Delgado J, Hicks A, Argonza M, Meredith R, Turner J, Martinez-Sobrido L, Torrelles JB, Kulkarni V. Age associated susceptibility to SARS-CoV-2 infection in the K18-hACE2 transgenic mouse model. GeroScience 2024; 46:2901-2913. [PMID: 38388916 PMCID: PMC11009211 DOI: 10.1007/s11357-024-01102-6] [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: 08/10/2023] [Accepted: 02/08/2024] [Indexed: 02/24/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still an ongoing global health crisis. Clinical data indicate that the case fatality rate (CFR) is age dependent, with a higher CFR percentage in the elderly population. We compared the pathogenesis of SARS-CoV-2 in young and aged K18-hACE2 transgenic mice. We evaluated morbidity, mortality, viral titers, immune responses, and histopathology in SARS-CoV-2-infected young and old K18-hACE2 transgenic mice. Within the limitation of having a low number of mice per group, our results indicate that SARS-CoV-2 infection resulted in slightly higher morbidity, mortality, and viral replication in the lungs of old mice, which was associated with an impaired IgM response and altered cytokine and chemokine profiles. Results of this study increase our understanding of SARS-CoV-2 infectivity and immuno-pathogenesis in the elderly population.
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Affiliation(s)
- Varun Dwivedi
- Disease Intervention & Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Vinay Shivanna
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Shalini Gautam
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Jennifer Delgado
- Disease Intervention & Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Amberlee Hicks
- Disease Intervention & Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Marco Argonza
- Disease Intervention & Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Reagan Meredith
- Disease Intervention & Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Joanne Turner
- Host Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA.
| | - Luis Martinez-Sobrido
- Disease Intervention & Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA.
| | - Jordi B Torrelles
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA.
- International Center for the Advancement of Research & Education (I•CARE), Texas Biomedical Research Institute, San Antonio, TX, USA.
| | - Viraj Kulkarni
- Disease Intervention & Prevention Program, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA.
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Jimoh AO, Balle C, Brown B, Feng C, Havyarimana E, Konstantinus IN, Gill K, Bekker LG, Passmore JAS, Jaspan HB, Varsani A, Happel AU. Genome Sequences of Anelloviruses, a Genomovirus, Microviruses, Polyomaviruses, and an Unclassified Caudovirus Identified in Vaginal Secretions from South African Adolescents. Microbiol Resour Announc 2023; 12:e0114322. [PMID: 36533922 PMCID: PMC9872636 DOI: 10.1128/mra.01143-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/03/2022] [Indexed: 12/23/2022] Open
Abstract
Other than for papillomaviruses, there is a paucity of whole-genome sequences for bacteriophages and eukaryote-infecting viruses isolated from the female genital tract. Here, we report the genome sequences of 16 microviruses, 3 anelloviruses, 2 polyomaviruses, 1 genomovirus, and 1 caudovirus that were identified in vaginal secretion samples from adolescents in South Africa.
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Affiliation(s)
- Adijat O. Jimoh
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Genetics, Genomics, and Bioinformatics Department, National Biotechnology Development Agency, Abuja, Nigeria
| | - Christina Balle
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Bryan Brown
- Seattle Children’s Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
| | - Colin Feng
- Seattle Children’s Research Institute, Seattle, Washington, USA
| | - Enock Havyarimana
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
| | - Iyaloo N. Konstantinus
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Namibia Institute of Pathology, Windhoek, Namibia
- NRF-DST Centre of Excellence in HIV Prevention, Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | | | - Linda-Gail Bekker
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
| | - Jo-Ann S. Passmore
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Desmond Tutu HIV Centre, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Cape Town, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Heather B. Jaspan
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Seattle Children’s Research Institute, Seattle, Washington, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, USA
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine and School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Structural Biology Research Unit, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Anna-Ursula Happel
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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Salmanov AG, Netskar IP, Kostikov VV, Artyomenko V, Korniyenko SM, Rud VO, Kovalyshyn OA. PREVALENCE OF AEROBIC VAGINITIS AFTER GYNECOLOGICAL SURGERIES AND ASSOCIATED ADVERSE PREGNANCY OUTCOME IN UKRAINE. POLSKI MERKURIUSZ LEKARSKI : ORGAN POLSKIEGO TOWARZYSTWA LEKARSKIEGO 2023; 51:456-463. [PMID: 38069845 DOI: 10.36740/merkur202305103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
OBJECTIVE Aim: To determine prevalence of Aerobic Vaginitis (AV) after gynecologic surgery, risk factors and antimicrobial resistance of responsible pathogens, and adverse pregnancy outcomes in Ukraine. PATIENTS AND METHODS Materials and Methods: Multicenter retrospective cohort study was conducted from January 2020 to December 2022 in fifteen medical clinics from eight regions of Ukraine. Smears were analyzed using Donders' classification method and Dong's modified AV diagnosis for Gram stains. Definitions of HAIs were adapted from the CDC/NHSN. Antibiotic susceptibility testing of bacteria was determined by Kirby-Bauer disc diffusion test according to the protocol of the EUCAST. RESULTS Results: Prevalence of AV among women's undergoing gynecologic surgery in Ukraine was 68.7%. Of the total AV cases, 70.3% were in non-pregnant and 29,7% in pregnant women. The most common pathogen of AV was Escherichia coli, followed by Enterococcus faecalis, Streptococcus agalactiae, Staphylococcus aureus, Enterococcus faecium, Klebsiella pneumoniae, and Pseudomonas aeruginosa. Among the S. aureus strains, 11,6% of MRSA (Methicillin resistant S.aureus) were isolated whereas none of the CoNS were cefoxitin resistant. History of vaginal infection, history of post-operative infection and antibiotic use acted as an important risk factor of AV incidence rate. The presence of AV worsened pregnancy outcomes, by increasing the incidence of preterm birth, the premature rupture of membranes, miscarriage, neonatal jaundice, and neonatal infection. CONCLUSION Conclusions: Aerobic Vaginitis after gynecological surgeries in Ukraine is a common medical problem in women that is associated with significant morbidity, adverse pregnancy outcome, and hence frequent medical visits.
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Affiliation(s)
- Aidyn G Salmanov
- SHUPYK NATIONAL HEALTHCARE UNIVERSITY OF UKRAINE, KYIV, UKRAINE; INSTITUTE OF PEDIATRICS, OBSTETRICS AND GYNECOLOGY OF THE NATIONAL ACADEMY OF MEDICAL SCIENCES OF UKRAINE, KYIV, UKRAINE
| | - Iryna P Netskar
- SHUPYK NATIONAL HEALTHCARE UNIVERSITY OF UKRAINE, KYIV, UKRAINE
| | | | | | | | - Victor O Rud
- NATIONAL PIROGOV MEMORIAL MEDICAL UNIVERSITY, VINNYTSIA, UKRAINE
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Sattar MN, Khurshid M, El-Beltagi HS, Iqbal Z. Identification and estimation of sequence variation dynamics of Tomato Leaf curl Palampur virus and betasatellite complex infecting a new weed host. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2112911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Affiliation(s)
- Muhammad Naeem Sattar
- Central Laboratories, Department of Biotechnology, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Muhammad Khurshid
- School of Biochemistry and Biotechnology, Faculty of Life Sciences, University of the Punjab, Lahore, Pakistan
| | - Hossam S. El-Beltagi
- Department of Biotechnology, College of Agricultural and Food Sciences, King Faisal University, Al-Ahsa, Saudi Arabia
- Biochemistry Department, Faculty of Agriculture, Cairo University, Cairo, Egypt
| | - Zafar Iqbal
- Central Laboratories, Department of Biotechnology, King Faisal University, Al-Ahsa, Saudi Arabia
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Altered vaginal eukaryotic virome is associated with different cervical disease status. Virol Sin 2022; 38:184-197. [PMID: 36565811 PMCID: PMC10176265 DOI: 10.1016/j.virs.2022.12.004] [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: 09/06/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
Viruses are important components of the human body. Growing evidence suggests that they are engaged in the physiology and disease status of the host. Even though the vaginal microbiome is involved in human papillomavirus (HPV) infection and cervical cancer (CC) progression, little is known about the role of the vaginal virome. In this pilot exploratory study, using unbiased viral metagenomics, we aim to investigate the vaginal eukaryotic virome in women with different levels of cervical lesions, and examine their associations with different cervical disease status. An altered eukaryotic virome was observed in women with different levels of lesions and Lactobacillus profiles. Anelloviruses and papillomaviruses are the most commonly detected eukaryotic viruses of the vaginal virome. Higher abundance and richness of anelloviruses and papillomaviruses were associated with low-grade squamous intraepithelial lesion (LSIL) and CC. Besides, higher anellovirus abundance was also associated with lactobacillus-depleted microbiome profiles and bacterial community state (CST) type IV. Furthermore, increased correlations between Anelloviridae and Papillomaviridae occurred in the women with increased cervical disease severity level from LSIL to CC. These data suggest underlying interactions between different microbes as well as the host physiology. Higher abundance and diversity of both anelloviruses and papillomaviruses shared by LSIL and CC suggest that anellovirus may be used as a potential adjunct biomarker to predict the risk of HPV persistent infection and/or CC. Future studies need to focus on the clinical relevance of anellovirus abundance with cervical disease status, and the evaluation of their potential as a new adjunct biomarker for the prediction and prognoses of CC.
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Gwak HJ, Rho M. ViBE: a hierarchical BERT model to identify eukaryotic viruses using metagenome sequencing data. Brief Bioinform 2022; 23:6603436. [PMID: 35667011 DOI: 10.1093/bib/bbac204] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 11/13/2022] Open
Abstract
Viruses are ubiquitous in humans and various environments and continually mutate themselves. Identifying viruses in an environment without cultivation is challenging; however, promoting the screening of novel viruses and expanding the knowledge of viral space is essential. Homology-based methods that identify viruses using known viral genomes rely on sequence alignments, making it difficult to capture remote homologs of the known viruses. To accurately capture viral signals from metagenomic samples, models are needed to understand the patterns encoded in the viral genomes. In this study, we developed a hierarchical BERT model named ViBE to detect eukaryotic viruses from metagenome sequencing data and classify them at the order level. We pre-trained ViBE using read-like sequences generated from the virus reference genomes and derived three fine-tuned models that classify paired-end reads to orders for eukaryotic deoxyribonucleic acid viruses and eukaryotic ribonucleic acid viruses. ViBE achieved higher recall than state-of-the-art alignment-based methods while maintaining comparable precision. ViBE outperformed state-of-the-art alignment-free methods for all test cases. The performance of ViBE was also verified using real sequencing datasets, including the vaginal virome.
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Affiliation(s)
- Ho-Jin Gwak
- Department of Computer Science, Hanyang University, Seoul, Korea
| | - Mina Rho
- Department of Computer Science, Hanyang University, Seoul, Korea.,Department of Biomedical Informatics, Hanyang University, Seoul, Korea
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Kaelin EA, Skidmore PT, Łaniewski P, Holland LA, Chase DM, Herbst-Kralovetz MM, Lim ES. Cervicovaginal DNA Virome Alterations Are Associated with Genital Inflammation and Microbiota Composition. mSystems 2022; 7:e0006422. [PMID: 35343798 PMCID: PMC9040584 DOI: 10.1128/msystems.00064-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 03/09/2022] [Indexed: 12/11/2022] Open
Abstract
While the link between the cervicovaginal bacterial microbiome, human papillomavirus (HPV) infection, and cervical cancer is recognized (P. Łaniewski, D. Barnes, A. Goulder, H. Cui, et al., Sci. Rep. 8:7593, 2018, http://dx.doi.org/10.1038/s41598-018-25879-7; A. Mitra, D. A. MacIntyre, Y. S. Lee, A. Smith, et al., Sci. Rep. 5:16865, 2015, http://dx.doi.org/10.1038/srep16865; A. Mitra, D. A. MacIntyre, J. R. Marchesi, Y. S. Lee, et al., Microbiome 4:58, 2016, http://dx.doi.org/10.1186/s40168-016-0203-0; J. Norenhag, J. Du, M. Olovsson, H. Verstraelen, et al., BJOG, 127:171-180, 2020, http://dx.doi.org/10.1111/1471-0528.15854; E. O. Dareng, B. Ma, A. O. Famooto, S. N. Adebamowo, et al., Epidemiol. Infect. 144:123-137, 2016, http://dx.doi.org/10.1017/S0950268815000965; A. Audirac-Chalifour, K. Torres-Poveda, M. Bahena-Roman, J. Tellez-Sosa et al., PLoS One 11:e0153274, 2016, http://dx.doi.org/10.1371/journal.pone.0153274; M. Di Paola, C. Sani, A. M. Clemente, A. Iossa, et al., Sci. Rep. 7:10200, 2017, http://dx.doi.org/10.1038/s41598-017-09842-6), the role of the cervicovaginal virome remains poorly understood. In this pilot study, we conducted metagenomic next-generation sequencing of cervicovaginal lavage specimens to investigate the relationship between the cervicovaginal DNA virome, bacterial microbiome, genital inflammation, and HPV infection. Specific virome alterations were associated with features of the local microenvironment related to HPV persistence and progression to cervical cancer. Cervicovaginal viromes clustered distinctly by genital inflammation state. Genital inflammation was associated with decreased virome richness and alpha diversity and an increased abundance of Anelloviridae species from the genus Alphatorquevirus. Lactobacillus bacteriophages were closely associated with increased Lactobacillus abundance, consistent with phage-host relationships. Interestingly, bacteria-bacteriophage transkingdom interactions were linked to genital inflammation and showed specific interactions with bacterial vaginosis-associated bacteria, including Gardnerella, Prevotella, and Sneathia. Taken together, our results reveal prominent virome interactions with features of the cervicovaginal microenvironment that are associated with HPV and cervical cancer. These findings expand our understanding of the cervicovaginal host-microbiome interactions in women's health. IMPORTANCE HPV infection is an established risk factor for cervical cancer. However, more broadly, the role of the cervicovaginal virome in cervical cancer progression is not well understood. Here, we identified cervicovaginal DNA virome alterations associated with local microenvironment factors (vaginal microbiota and genital inflammation) that influence HPV persistence and progression to cervical cancer. These findings indicate that the cervicovaginal virome plays an important role in women's health.
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Affiliation(s)
- Emily A. Kaelin
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Peter T. Skidmore
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Paweł Łaniewski
- Department of Basic Medical Sciences, College of Medicine—Phoenix, University of Arizona, Phoenix, Arizona, USA
| | - LaRinda A. Holland
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
| | - Dana M. Chase
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- UA Cancer Center, University of Arizona, Tucson, Arizona, USA
| | - Melissa M. Herbst-Kralovetz
- Department of Basic Medical Sciences, College of Medicine—Phoenix, University of Arizona, Phoenix, Arizona, USA
- Department of Obstetrics and Gynecology, College of Medicine-Phoenix, University of Arizona, Phoenix, Arizona, USA
- UA Cancer Center, University of Arizona, Tucson, Arizona, USA
| | - Efrem S. Lim
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Fundamental and Applied Microbiomics, The Biodesign Institute, Arizona State University, Tempe, Arizona, USA
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Madere FS, Monaco CL. The female reproductive tract virome: understanding the dynamic role of viruses in gynecological health and disease. Curr Opin Virol 2022; 52:15-23. [PMID: 34800892 PMCID: PMC8844092 DOI: 10.1016/j.coviro.2021.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 02/03/2023]
Abstract
The human body is inhabited by a large and complex network of commensal and predatory eukaryotic viruses and bacteriophages collectively termed the virome. Despite being the most abundant and genetically diverse biological entities on the planet, the impact of viruses on human health especially within the female reproductive tract (FRT) remains understudied. To better appreciate current knowledge regarding the dynamic role of viruses in FRT health and disease, in this review we highlight the known constituents of the FRT virome, transkingdom interactions within the FRT and their influence on gynecological disease. A better understanding of the FRT virome may pave the way toward improved outcomes in gynecological, reproductive, and neonatal health.
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Affiliation(s)
- Ferralita S Madere
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, USA
| | - Cynthia L Monaco
- Department of Microbiology and Immunology, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, USA; Department of Internal Medicine, Division of Infectious Diseases, University of Rochester Medical Center, 601 Elmwood Avenue, Rochester, NY, USA.
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Baldewijns S, Sillen M, Palmans I, Vandecruys P, Van Dijck P, Demuyser L. The Role of Fatty Acid Metabolites in Vaginal Health and Disease: Application to Candidiasis. Front Microbiol 2021; 12:705779. [PMID: 34276639 PMCID: PMC8282898 DOI: 10.3389/fmicb.2021.705779] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/31/2021] [Indexed: 12/28/2022] Open
Abstract
Although the vast majority of women encounters at least one vaginal infection during their life, the amount of microbiome-related research performed in this area lags behind compared to alternative niches such as the intestinal tract. As a result, effective means of diagnosis and treatment, especially of recurrent infections, are limited. The role of the metabolome in vaginal health is largely elusive. It has been shown that lactate produced by the numerous lactobacilli present promotes health by limiting the chance of infection. Short chain fatty acids (SCFA) have been mainly linked to dysbiosis, although the causality of this relationship is still under debate. In this review, we aim to bring together information on the role of the vaginal metabolome and microbiome in infections caused by Candida. Vulvovaginal candidiasis affects near to 70% of all women at least once in their life with a significant proportion of women suffering from the recurrent variant. We assess the role of fatty acid metabolites, mainly SCFA and lactate, in onset of infection and virulence of the fungal pathogen. In addition, we pinpoint where lack of research limits our understanding of the molecular processes involved and restricts the possibility of developing novel treatment strategies.
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Affiliation(s)
- Silke Baldewijns
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Mart Sillen
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Ilse Palmans
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Paul Vandecruys
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Patrick Van Dijck
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
| | - Liesbeth Demuyser
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven-Heverlee, Belgium
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
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The correlation between vaginal microecological dysbiosis-related diseases and preterm birth: A review. MEDICINE IN MICROECOLOGY 2021. [DOI: 10.1016/j.medmic.2021.100043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Mormando R, Wolfe AJ, Putonti C. Discriminating between JCPyV and BKPyV in Urinary Virome Data Sets. Viruses 2021; 13:v13061041. [PMID: 34072839 PMCID: PMC8230216 DOI: 10.3390/v13061041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/15/2021] [Accepted: 05/27/2021] [Indexed: 11/21/2022] Open
Abstract
Polyomaviruses are abundant in the human body. The polyomaviruses JC virus (JCPyV) and BK virus (BKPyV) are common viruses in the human urinary tract. Prior studies have estimated that JCPyV infects between 20 and 80% of adults and that BKPyV infects between 65 and 90% of individuals by age 10. However, these two viruses encode for the same six genes and share 75% nucleotide sequence identity across their genomes. While prior urinary virome studies have repeatedly reported the presence of JCPyV, we were interested in seeing how JCPyV prevalence compares to BKPyV. We retrieved all publicly available shotgun metagenomic sequencing reads from urinary microbiome and virome studies (n = 165). While one third of the data sets produced hits to JCPyV, upon further investigation were we able to determine that the majority of these were in fact BKPyV. This distinction was made by specifically mining for JCPyV and BKPyV and considering uniform coverage across the genome. This approach provides confidence in taxon calls, even between closely related viruses with significant sequence similarity.
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Affiliation(s)
- Rita Mormando
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660, USA;
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stitch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA;
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, IL 60660, USA;
- Department of Microbiology and Immunology, Stitch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA;
- Department of Biology, Loyola University Chicago, Chicago, IL 60660, USA
- Correspondence:
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