1
|
Paulshus E, Colque P, Kühn I, Tauhid T, Hu YOO, Zhou Y, Thorell K, Möllby R, Sørum H, Sjöling Å, Joffré E. Escherichia coli ST2797 Is Abundant in Wastewater and Might Be a Novel Emerging Extended-Spectrum Beta-Lactamase E. coli. Microbiol Spectr 2023; 11:e0448622. [PMID: 37260395 PMCID: PMC10434162 DOI: 10.1128/spectrum.04486-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 05/17/2023] [Indexed: 06/02/2023] Open
Abstract
The increasing prevalence of antibiotic-resistant bacteria is an emerging threat to global health. The analysis of antibiotic-resistant enterobacteria in wastewater can indicate the prevalence and spread of certain clonal groups of multiresistant bacteria. In a previous study of Escherichia coli that were isolated from a pump station in Norway over 15 months, we found a recurring E. coli clone that was resistant to trimethoprim, ampicillin, and tetracycline in 201 of 3,123 analyzed isolates (6.1%). 11 representative isolates were subjected to whole-genome sequencing and were found to belong to the MLST ST2797 E. coli clone with plasmids carrying resistance genes, including blaTEM-1B, sul2, dfrA7, and tetB. A phenotypic comparison of the ST2797 isolates with the uropathogenic ST131 and ST648 that were repeatedly identified in the same wastewater samples revealed that the ST2797 isolates exhibited a comparable capacity for temporal survival in wastewater, greater biofilm formation, and similar potential for the colonization of mammalian epithelial cells. ST2797 has been isolated from humans and has been found to carry extended spectrum β-lactamase (ESBL) genes in other studies, suggesting that this clonal type is an emerging ESBL E. coli. Collectively, these findings show that ST2797 was more ubiquitous in the studied wastewater than were the infamous ST131 and ST648 and that ST2797 may have similar abilities to survive in the environment and cause infections in humans. IMPORTANCE The incidence of drug-resistant bacteria found in the environment is increasing together with the levels of antibiotic-resistant bacteria that cause infections. The COVID-19 pandemic has shed new light on the importance of monitoring emerging threats and finding early warning systems. Therefore, to mitigate the antimicrobial resistance burden, the monitoring and early identification of antibiotic-resistant bacteria in hot spots, such as wastewater treatment plants, are required to combat the occurrence and spread of antibiotic-resistant bacteria. Here, we applied a PhenePlate system as a phenotypic screening method for genomic surveillance and discovered a dominant and persistent E. coli clone ST2797 with a multidrug resistance pattern and equivalent phenotypic characteristics to those of the major pandemic lineages, namely, ST131 and ST648, which frequently carry ESBL genes. This study highlights the continuous surveillance and report of multidrug resistant bacteria with the potential to spread in One Health settings.
Collapse
Affiliation(s)
- Erik Paulshus
- Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
- Department of Analysis and Diagnostics, Norwegian Veterinary Institute, Ås, Norway
| | - Patricia Colque
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Inger Kühn
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Tamanna Tauhid
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Yue O. O. Hu
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
- Centre for Translational Microbiome Research (CTMR), Karolinska Institutet, Stockholm, Sweden
| | - Yingshun Zhou
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
- Department of Pathogen Biology, Southwest Medical University, Luzhou, Sichuan, China
| | - Kaisa Thorell
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Roland Möllby
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Henning Sørum
- Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Åsa Sjöling
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Enrique Joffré
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
2
|
Narayanan A, Söder B, Meurman J, Lundmark A, Hu YOO, Neogi U, Yucel-Lindberg T. Composition of subgingival microbiota associated with periodontitis and diagnosis of malignancy-a cross-sectional study. Front Microbiol 2023; 14:1172340. [PMID: 37426027 PMCID: PMC10325785 DOI: 10.3389/fmicb.2023.1172340] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/02/2023] [Indexed: 07/11/2023] Open
Abstract
Periodontitis is one of the world's most prevalent infectious conditions, affecting between 25 and 40% of the adult population. It is a consequence of the complex interactions between periodontal pathogens and their products, which trigger the host inflammatory response, chronic inflammation, and tissue destruction. Chronic systemic low-grade inflammation is involved in numerous diseases, and it is also known that long-lasting inflammation and chronic infections predispose one to cancer. Here, we characterized and compared the subgingival microbiota associated with periodontitis and diagnosis of malignancy in a longitudinal 10-year follow-up study. The study was conducted on 50 patients with periodontitis and 40 periodontally healthy individuals. The recorded clinical oral health parameters were periodontal attachment loss (AL), bleeding on probing (BOP), gingival index (GI), probing depth (PD), and plaque index (PI). Subgingival plaque was collected from each participant, from which DNA was extracted, and 16S rRNA gene amplicon sequencing performed. Cancer diagnoses data were collected between the years 2008-2018 from the Swedish Cancer Registry. The participants were categorized based on having cancer at the time of sample collection (CSC), having developed cancer later (DCL), and controls without any cancer. The most abundant phyla across all 90 samples were Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes, and Fusobacteria. At the genus level, Treponema, Fretibacterium, and Prevotella were significantly more abundant in samples of periodontitis patients compared to non-periodontitis individuals. With regard to samples of cancer patients, Corynebacterium and Streptococcus were more abundant in the CSC group; Prevotella were more abundant in the DCL group; and Rothia, Neisseria, and Capnocytophaga were more abundant in the control group. In the CSC group, we also found that the presence of periodontal inflammation, in terms of BOP, GI, and PLI, significantly correlated with species belonging to the genera Prevotella, Treponema, and Mycoplasma. Our results revealed that several subgingival genera were differentially enriched among the studied groups. These findings underscore the need for further research to fully understand the role that oral pathogens may play in the development of cancer.
Collapse
Affiliation(s)
- Aswathy Narayanan
- Division of Clinical Microbiology, Department of Laboratory Medicine, ANA Futura, Karolinska Institutet, Stockholm, Sweden
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden
| | - Birgitta Söder
- Division of Periodontology, Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Jukka Meurman
- Department of Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Anna Lundmark
- Division of Pediatric Dentistry, Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Yue O. O. Hu
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden
- School of Environmental Science and Engineering, Hubei Polytechnic University, Huangshi, China
| | - Ujjwal Neogi
- The Systems Virology Lab, Division of Clinical Microbiology, Department of Laboratory Medicine, ANA Futura, Karolinska Institutet, Stockholm, Sweden
| | - Tülay Yucel-Lindberg
- Division of Pediatric Dentistry, Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| |
Collapse
|
3
|
Frede A, Czarnewski P, Monasterio G, Tripathi KP, Bejarano DA, Ramirez Flores RO, Sorini C, Larsson L, Luo X, Geerlings L, Novella-Rausell C, Zagami C, Kuiper R, Morales RA, Castillo F, Hunt M, Mariano LL, Hu YOO, Engblom C, Lennon-Duménil AM, Mittenzwei R, Westendorf AM, Hövelmeyer N, Lundeberg J, Saez-Rodriguez J, Schlitzer A, Das S, Villablanca EJ. B cell expansion hinders the stroma-epithelium regenerative cross talk during mucosal healing. Immunity 2022; 55:2336-2351.e12. [PMID: 36462502 DOI: 10.1016/j.immuni.2022.11.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 07/14/2022] [Accepted: 10/26/2022] [Indexed: 12/05/2022]
Abstract
Therapeutic promotion of intestinal regeneration holds great promise, but defining the cellular mechanisms that influence tissue regeneration remains an unmet challenge. To gain insight into the process of mucosal healing, we longitudinally examined the immune cell composition during intestinal damage and regeneration. B cells were the dominant cell type in the healing colon, and single-cell RNA sequencing (scRNA-seq) revealed expansion of an IFN-induced B cell subset during experimental mucosal healing that predominantly located in damaged areas and associated with colitis severity. B cell depletion accelerated recovery upon injury, decreased epithelial ulceration, and enhanced gene expression programs associated with tissue remodeling. scRNA-seq from the epithelial and stromal compartments combined with spatial transcriptomics and multiplex immunostaining showed that B cells decreased interactions between stromal and epithelial cells during mucosal healing. Activated B cells disrupted the epithelial-stromal cross talk required for organoid survival. Thus, B cell expansion during injury impairs epithelial-stromal cell interactions required for mucosal healing, with implications for the treatment of IBD.
Collapse
Affiliation(s)
- Annika Frede
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Paulo Czarnewski
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Gustavo Monasterio
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kumar P Tripathi
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - David A Bejarano
- Quantitative Systems Biology, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | | | - Chiara Sorini
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Ludvig Larsson
- KTH Royal Institute of Technology Stockholm, Science for Life Laboratory, Stockholm, Sweden
| | - Xinxin Luo
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Laura Geerlings
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Claudio Novella-Rausell
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Chiara Zagami
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Raoul Kuiper
- Norwegian Veterinary Institute, Section for Aquatic Biosecurity Research, Elisabeth Stephansens vei 1, 1433 Ås, Norway; Core Facility for Morphologic Phenotype Analysis, Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Rodrigo A Morales
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Francisca Castillo
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Matthew Hunt
- Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden; Department of Physiology and Pharmacology, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | | | - Yue O O Hu
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Camilla Engblom
- Department of Cell and Molecular Biology, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | | | - Romy Mittenzwei
- Institute for Molecular Medicine and Research Center for Immunotherapy (FZI), University Medical Center Mainz, Johannes Gutenberg University of Mainz, 55131 Mainz, Germany
| | - Astrid M Westendorf
- Institute of Medical Microbiology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Nadine Hövelmeyer
- Institute for Molecular Medicine and Research Center for Immunotherapy (FZI), University Medical Center Mainz, Johannes Gutenberg University of Mainz, 55131 Mainz, Germany
| | - Joakim Lundeberg
- KTH Royal Institute of Technology Stockholm, Science for Life Laboratory, Stockholm, Sweden
| | - Julio Saez-Rodriguez
- Institute of Computational Biomedicine, University of Heidelberg, Heidelberg, Germany
| | - Andreas Schlitzer
- Quantitative Systems Biology, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115 Bonn, Germany
| | - Srustidhar Das
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Eduardo J Villablanca
- Division of Immunology and Allergy, Department of Medicine Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden; Center of Molecular Medicine, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
4
|
Guzman-Otazo J, Joffré E, Agramont J, Mamani N, Jutkina J, Boulund F, Hu YOO, Jumilla-Lorenz D, Farewell A, Larsson DGJ, Flach CF, Iñiguez V, Sjöling Å. Conjugative transfer of multi-drug resistance IncN plasmids from environmental waterborne bacteria to Escherichia coli. Front Microbiol 2022; 13:997849. [DOI: 10.3389/fmicb.2022.997849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/10/2022] [Indexed: 11/13/2022] Open
Abstract
Watersheds contaminated with municipal, hospital, and agricultural residues are recognized as reservoirs for bacteria carrying antibiotic resistance genes (ARGs). The objective of this study was to determine the potential of environmental bacterial communities from the highly contaminated La Paz River basin in Bolivia to transfer ARGs to an Escherichia coli lab strain used as the recipient. Additionally, we tested ZnSO4 and CuSO4 at sub-inhibitory concentrations as stressors and analyzed transfer frequencies (TFs), diversity, richness, and acquired resistance profiles. The bacterial communities were collected from surface water in an urban site close to a hospital and near an agricultural area. High transfer potentials of a large set of resistance factors to E. coli were observed at both sites. Whole-genome sequencing revealed that putative plasmids belonging to the incompatibility group N (IncN, IncN2, and IncN3) were predominant among the transconjugants. All IncN variants were verified to be mobile by a second conjugation step. The plasmid backbones were similar to other IncN plasmids isolated worldwide and carried a wide range of ARGs extensively corroborated by phenotypic resistance patterns. Interestingly, all transconjugants also acquired the class 1 integron intl1, which is commonly known as a proxy for anthropogenic pollution. The addition of ZnSO4 and CuSO4 at sub-inhibitory concentrations did not affect the transfer rate. Metal resistance genes were absent from most transconjugants, suggesting a minor role, if any, of metals in the spread of multidrug-resistant plasmids at the investigated sites.
Collapse
|
5
|
Eriksson K, Lundmark A, Delgado LF, Hu YOO, Fei G, Lee L, Fei C, Catrina AI, Jansson L, Andersson AF, Yucel-Lindberg T. Salivary Microbiota and Host-Inflammatory Responses in Periodontitis Affected Individuals With and Without Rheumatoid Arthritis. Front Cell Infect Microbiol 2022; 12:841139. [PMID: 35360114 PMCID: PMC8964114 DOI: 10.3389/fcimb.2022.841139] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/09/2022] [Indexed: 12/24/2022] Open
Abstract
Objectives Periodontitis and rheumatoid arthritis (RA) are two widespread chronic inflammatory diseases with a previously suggested association. The objective of the current study was to compare the oral microbial composition and host´s inflammatory mediator profile of saliva samples obtained from subjects with periodontitis, with and without RA, as well as to predict biomarkers, of bacterial pathogens and/or inflammatory mediators, for classification of samples associated with periodontitis and RA. Methods Salivary samples were obtained from 53 patients with periodontitis and RA and 48 non-RA with chronic periodontitis. The microbial composition was identified using 16S rRNA gene sequencing and compared across periodontitis patients with and without RA. Levels of inflammatory mediators were determined using a multiplex bead assay, compared between the groups and correlated to the microbial profile. The achieved data was analysed using PCoA, DESeq2 and two machine learning algorithms, OPLS-DA and sPLS-DA. Results Differential abundance DESeq2 analyses showed that the four most highly enriched (log2 FC >20) amplicon sequence variants (ASVs) in the non-RA periodontitis group included Alloprevotella sp., Prevotella sp., Haemophilus sp., and Actinomyces sp. whereas Granulicatella sp., Veillonella sp., Megasphaera sp., and Fusobacterium nucleatum were the most highly enriched ASVs (log2 FC >20) in the RA group. OPLS-DA with log2 FC analyses demonstrated that the top ASVs with the highest importance included Vampirovibrio sp. having a positive correlation with non-RA group, and seven ASVs belonging to Sphingomonas insulae, Sphingobium sp., Novosphingobium aromaticivorans, Delftia acidovorans, Aquabacterium spp. and Sphingomonas echinoides with a positive correlation with RA group. Among the detected inflammatory mediators in saliva samples, TWEAK/TNFSF12, IL-35, IFN-α2, pentraxin-3, gp130/sIL6Rb, sIL-6Ra, IL-19 and sTNF-R1 were found to be significantly increased in patients with periodontitis and RA compared to non-RA group with periodontitis. Moreover, correlations between ASVs and inflammatory mediators using sPLS-DA analysis revealed that TWEAK/TNFSF12, pentraxin-3 and IL-19 were positively correlated with the ASVs Sphingobium sp., Acidovorax delafieldii, Novosphingobium sp., and Aquabacterium sp. Conclusion Our results suggest that the combination of microbes and host inflammatory mediators could be more efficient to be used as a predictable biomarker associated with periodontitis and RA, as compared to microbes and inflammatory mediators alone.
Collapse
Affiliation(s)
- Kaja Eriksson
- Department of Dental Medicine, Division of Pediatric Dentistry, Karolinska Institutet, Huddinge, Sweden
- *Correspondence: Kaja Eriksson, ; Tülay Yucel-Lindberg,
| | - Anna Lundmark
- Department of Dental Medicine, Division of Pediatric Dentistry, Karolinska Institutet, Huddinge, Sweden
| | - Luis F. Delgado
- KTH Royal Institute of Technology, Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Stockholm, Sweden
| | - Yue O. O. Hu
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden
| | - Guozhong Fei
- Center for Rheumatology, Academic Specialist Center, Stockholm Health Region, Stockholm, Sweden
| | - Linkiat Lee
- Department of Dental Medicine, Division of Pediatric Dentistry, Karolinska Institutet, Huddinge, Sweden
| | - Carina Fei
- Department of Dental Medicine, Division of Pediatric Dentistry, Karolinska Institutet, Huddinge, Sweden
| | - Anca I. Catrina
- Rheumatology Clinic, Karolinska University Hospital, Stockholm, Sweden
| | - Leif Jansson
- Department of Dental Medicine, Division of Periodontology, Karolinska Institutet, Huddinge, Sweden
- Department of Periodontology, Folktandvården Stockholms län AB, Folktandvården Eastmaninstitutet, Stockholm, Sweden
| | - Anders F. Andersson
- KTH Royal Institute of Technology, Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Stockholm, Sweden
| | - Tülay Yucel-Lindberg
- Department of Dental Medicine, Division of Pediatric Dentistry, Karolinska Institutet, Huddinge, Sweden
- *Correspondence: Kaja Eriksson, ; Tülay Yucel-Lindberg,
| |
Collapse
|
6
|
Shi W, Hu Y, Ning Z, Xia F, Wu M, Hu YOO, Chen C, Prast-Nielsen S, Xu B. Alterations of gut microbiota in patients with active pulmonary tuberculosis in China: a pilot study. Int J Infect Dis 2021; 111:313-321. [PMID: 34481968 DOI: 10.1016/j.ijid.2021.08.064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 08/20/2021] [Accepted: 08/27/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The aim of this study was to identify the differences in diversity, composition, and function of the gut microbiota between tuberculosis (TB) patients and healthy controls (HCs). METHODS A cross-sectional study was conducted in three cities of China. Stool samples from 94 treatment-naive TB patients and 62 HCs were analyzed by 16S rRNA gene sequencing. TB patients were further divided into antibiotic-free and antibiotic-exposure according to their use of non-specific antibiotics before the TB diagnosis. RESULTS Compared with HCs, antibiotic-free TB patients presented a different gut microbial community (P < 0.005) and decreased Shannon diversity (P < 0.005). Among TB patients, the relative abundances of short-chain fatty acid (SCFA)-producing genera such as Lachnospiraceae ND3007 group (log2(FC) = -2.74) were lower, while several conditional pathogen-related genera such as Enterococcus (log2(FC) = 12.05) and Rothia (log2(FC) = 6.322) were at higher levels. In addition, 41% of patients received antibiotics before TB diagnosis. Antibiotic exposure was correlated with an additional reduction in α diversity and depletion of SCFA-producing bacteria. Microbial functional analysis revealed that the biosynthesis capacity of amino acids and fatty acids was lower among TB patients compared to HCs. CONCLUSIONS Significant alterations in gut microbiota composition and metabolic pathways of TB patients were observed. Antibiotic exposure could alter the gut microbiota of TB patients, which should be considered in anti-TB treatment.
Collapse
Affiliation(s)
- Wenpei Shi
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China
| | - Yi Hu
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China
| | - Zhu Ning
- Zigong City Center for Disease Control and Prevention, Zigong City, Sichuan, China
| | - Fan Xia
- Department of Tuberculosis, 905th Hospital of PLA Navy, Shanghai, China
| | - Meiying Wu
- Department of Clinical Laboratory, The Fifth People's Hospital of Suzhou(The Affiliated Infectious Diseases Hospital of Soochow University), Suzhou City, Jiangsu, China
| | - Yue O O Hu
- Center for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Cheng Chen
- Jiangsu Provincial Centre for Disease Control and Prevention, Nanjing, Jiangsu, China
| | - Stefanie Prast-Nielsen
- Center for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Biao Xu
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China; Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
7
|
Parigi SM, Das S, Frede A, Cardoso RF, Tripathi KP, Doñas C, Hu YOO, Antonson P, Engstrand L, Gustafsson JÅ, Villablanca EJ. Liver X receptor regulates Th17 and RORγt + Treg cells by distinct mechanisms. Mucosal Immunol 2021; 14:411-419. [PMID: 32681027 DOI: 10.1038/s41385-020-0323-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 06/24/2020] [Accepted: 06/30/2020] [Indexed: 02/04/2023]
Abstract
The gastrointestinal microenvironment, dominated by dietary compounds and the commensal bacteria, is a major driver of intestinal CD4+ T helper (Th) cell differentiation. Dietary compounds can be sensed by nuclear receptors (NRs) that consequently exert pleiotropic effects including immune modulation. Here, we found that under homeostatic conditions the NR Liver X receptor (LXR), a sensor of cholesterol metabolites, regulates RORγt+ CD4 T cells in the intestine draining mesenteric lymph node (MLN). While LXR activation led to a decrease, LXR-deficiency resulted in an increase in MLN Th17 and RORγt+ Tregs. Mechanistically, LXR signaling in CD11c+ myeloid cells was required to control RORγt+ Treg. By contrast, modulation of MLN Th17 was independent of LXR signaling in either immune or epithelial cells. Of note, horizontal transfer of microbiota between LXRα-/- and WT mice was sufficient to only partially increase MLN Th17 in WT mice. Despite LXRα deficiency resulted in an increased abundance of Ruminococcaceae and Lachnospiraceae bacterial families compared to littermate controls, microbiota ablation (including SFB) was not sufficient to dampen LXRα-mediated expansion of MLN Th17. Altogether, our results suggest that LXR modulates RORγt+ Treg and Th17 cells in the MLN through distinct mechanisms.
Collapse
Affiliation(s)
- Sara M Parigi
- Division of Immunology and Allergy, Department of Medicine, Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden.,Center for Molecular Medicine, 17176, Stockholm, Sweden
| | - Srustidhar Das
- Division of Immunology and Allergy, Department of Medicine, Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden.,Center for Molecular Medicine, 17176, Stockholm, Sweden
| | - Annika Frede
- Division of Immunology and Allergy, Department of Medicine, Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden.,Center for Molecular Medicine, 17176, Stockholm, Sweden
| | - Rebeca F Cardoso
- Division of Immunology and Allergy, Department of Medicine, Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden.,Center for Molecular Medicine, 17176, Stockholm, Sweden
| | - Kumar Parijat Tripathi
- Division of Immunology and Allergy, Department of Medicine, Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden.,Center for Molecular Medicine, 17176, Stockholm, Sweden
| | - Cristian Doñas
- Division of Immunology and Allergy, Department of Medicine, Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden.,Center for Molecular Medicine, 17176, Stockholm, Sweden
| | - Yue O O Hu
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Karolinska Hospital, Stockholm, Sweden.,Science for Life Laboratory (SciLifeLab), Stockholm, Sweden
| | - Per Antonson
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Lars Engstrand
- Centre for Translational Microbiome Research, Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Karolinska Hospital, Stockholm, Sweden.,Science for Life Laboratory (SciLifeLab), Stockholm, Sweden
| | - Jan-Åke Gustafsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.,Center for Nuclear Receptors and Cell Signaling, Department of Biology and Biochemistry, University of Houston, Houston, TX, USA
| | - Eduardo J Villablanca
- Division of Immunology and Allergy, Department of Medicine, Solna, Karolinska Institutet and University Hospital, Stockholm, Sweden. .,Center for Molecular Medicine, 17176, Stockholm, Sweden.
| |
Collapse
|
8
|
Cheng L, Norenhag J, Hu YOO, Brusselaers N, Fransson E, Ährlund-Richter A, Guðnadóttir U, Angelidou P, Zha Y, Hamsten M, Schuppe-Koistinen I, Olovsson M, Engstrand L, Du J. Vaginal microbiota and human papillomavirus infection among young Swedish women. NPJ Biofilms Microbiomes 2020; 6:39. [PMID: 33046723 PMCID: PMC7552401 DOI: 10.1038/s41522-020-00146-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 09/10/2020] [Indexed: 02/06/2023] Open
Abstract
Human papillomavirus (HPV) infection is one of the most common sexually transmitted diseases. To define the HPV-associated microbial community among a high vaccination coverage population, we carried out a cross-sectional study with 345 young Swedish women. The microbial composition and its association with HPV infection, including 27 HPV types, were analyzed. Microbial alpha-diversity was found significantly higher in the HPV-infected group (especially with oncogenic HPV types and multiple HPV types), compared with the HPV negative group. The vaginal microbiota among HPV-infected women was characterized by a larger number of bacterial vaginosis-associated bacteria (BVAB), Sneathia, Prevotella, and Megasphaera. In addition, the correlation analysis demonstrated that twice as many women with non-Lactobacillus-dominant vaginal microbiota were infected with oncogenic HPV types, compared with L. crispatus-dominated vaginal microbiota. The data suggest that HPV infection, especially oncogenic HPV types, is strongly associated with a non-Lactobacillus-dominant vaginal microbiota, regardless of age and vaccination status.
Collapse
Affiliation(s)
- Liqin Cheng
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research (CTMR), Karolinska Institutet, Stockholm, Sweden
| | - Johanna Norenhag
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Yue O O Hu
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research (CTMR), Karolinska Institutet, Stockholm, Sweden
| | - Nele Brusselaers
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research (CTMR), Karolinska Institutet, Stockholm, Sweden
| | - Emma Fransson
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research (CTMR), Karolinska Institutet, Stockholm, Sweden.,Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | | | - Unnur Guðnadóttir
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research (CTMR), Karolinska Institutet, Stockholm, Sweden
| | - Pia Angelidou
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research (CTMR), Karolinska Institutet, Stockholm, Sweden
| | - Yinghua Zha
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research (CTMR), Karolinska Institutet, Stockholm, Sweden
| | - Marica Hamsten
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research (CTMR), Karolinska Institutet, Stockholm, Sweden
| | - Ina Schuppe-Koistinen
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research (CTMR), Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Matts Olovsson
- Department of Women's and Children's Health, Uppsala University, Uppsala, Sweden
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research (CTMR), Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Juan Du
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research (CTMR), Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
9
|
Sundin J, Aziz I, Nordlander S, Polster A, Hu YOO, Hugerth LW, Pennhag AAL, Engstrand L, Törnblom H, Simrén M, Öhman L. Evidence of altered mucosa-associated and fecal microbiota composition in patients with Irritable Bowel Syndrome. Sci Rep 2020; 10:593. [PMID: 31953505 PMCID: PMC6969101 DOI: 10.1038/s41598-020-57468-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 12/30/2019] [Indexed: 12/14/2022] Open
Abstract
Altered bacterial composition and small intestinal bacterial overgrowth (SIBO) may be associated with irritable bowel syndrome (IBS). This study aimed to determine the fecal and mucosa-associated bacterial composition along the gastrointestinal (GI) tract and to assess SIBO in IBS. Bacterial composition of feces, and mucosa of the duodenum and sigmoid colon was determined by 16S rRNA-amplicon-sequencing. SIBO was evaluated by bacterial culture of duodenal aspirate, glucose and lactulose breath tests. Mucosal antibacterial gene expression was assessed by PCR Array. The bacterial profiles of feces and the mucosa of sigmoid colon, but not duodenum, differed between IBS patients (n = 17) and HS (n = 20). The IBS specific bacterial profiles were linked to the colonic antibacterial gene expression. Fecal bacterial profile differed between IBS subtypes, while the mucosa-associated bacterial profile was associated with IBS symptom severity and breath tests results at baseline (H2 and/or CH4 ≥ 15 ppm). The prevalence of SIBO was similar between IBS patients and HS. This study demonstrates that alterations in the bacterial composition of the sigmoid colon of IBS patients were linked to symptoms and immune activation. While breath tests reflected the mucosa-associated bacterial composition, there was no evidence for high prevalence of SIBO or small intestinal bacterial alterations in IBS.
Collapse
Affiliation(s)
- Johanna Sundin
- Inst. of Medicine, University of Gothenburg, Gothenburg, Sweden.,Inst. of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Imran Aziz
- Inst. of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Sofia Nordlander
- Inst. of Medicine, University of Gothenburg, Gothenburg, Sweden.,Inst. of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Annikka Polster
- Inst. of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Yue O O Hu
- Centre for Translational Microbiome Research (CTMR), Micobiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 417164, Solna, Sweden
| | - Luisa W Hugerth
- Centre for Translational Microbiome Research (CTMR), Micobiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 417164, Solna, Sweden
| | - Alexandra A L Pennhag
- Centre for Translational Microbiome Research (CTMR), Micobiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 417164, Solna, Sweden
| | - Lars Engstrand
- Centre for Translational Microbiome Research (CTMR), Micobiology, Tumor and Cell Biology (MTC), Karolinska Institutet, 417164, Solna, Sweden
| | - Hans Törnblom
- Inst. of Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Simrén
- Inst. of Medicine, University of Gothenburg, Gothenburg, Sweden.,Centre for Functional Gastrointestinal and Motility Disorders, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Lena Öhman
- Inst. of Medicine, University of Gothenburg, Gothenburg, Sweden. .,Inst. of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
| |
Collapse
|
10
|
Shi W, Hu Y, Zheng X, Ning Z, Wu M, Xia F, Prast-Nielsen S, Hu YOO, Xu B. Longitudinal profiling of gut microbiome among tuberculosis patients under anti-tuberculosis treatment in China: protocol of a prospective cohort study. BMC Pulm Med 2019; 19:211. [PMID: 31711450 PMCID: PMC6849301 DOI: 10.1186/s12890-019-0981-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 10/31/2019] [Indexed: 02/08/2023] Open
Abstract
Background Anti-tuberculosis therapy requires at least six-month treatment with continuous administration of combined antibiotics, including isoniazid, rifampicin, pyrazinamide, and ethambutol. The long-term exposure to antibiotics could cause consequent changes in gut microbiota, which may alter the gastrointestinal function and drug absorption in patients, thereby affect the outcome of treatment. The study aims to characterize the longitudinal changes of gut microbiota among tuberculosis (TB) patients under standardized first-line treatment and provide an understanding of the association between alterations in gut microbiota composition and unfavorable clinical outcomes. Methods The study is a multicenter, observational prospective cohort study. Three study sites are purposively selected in the western (Sichuan Province) and eastern (Jiangsu Province and Shanghai) parts of China. Three-hundred patients with bacteriologically confirmed pulmonary TB are enrolled. All eligible patients should be investigated using structured questionnaires before treatment initiation; and be followed up during the treatment at Day-14, Month-2, Month-5, the end of treatment and the sixth month after ending therapy. Stool samples are to be collected at each visit, consisting of six stool samples from each patient. Additionally, 60 healthy volunteers from Sichuan province and Shanghai city will be recruited as healthy controls to form the baseline of patient gut microbiota in the Chinese population. The dynamic changes of gut microbiota in terms of alpha diversity, beta diversity, taxonomic composition are to be illustrated individually from the time at diagnosis until the sixth month after therapy is completed. Furthermore, the diversity and component of gut microbiota will be compared between the groups with and without unfavorable treatment outcome in terms of adverse effect and treatment failure. Discussion Studies on the clinical manifestations, adverse reactions, and gut microbiota alterations will provide scientifically-sound evidence on the impact of gut microbiota alterations on TB treatment outcomes. The study is not only useful for guiding personalized TB treatment but also sheds light on the effects of continuous antibiotics administration on gut microbiota. Trial registration Chinese Clinical Trial Registry, trial ID: ChiCTR1900023369, May 24, 2019. Retrospectively registered.
Collapse
Affiliation(s)
- Wenpei Shi
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China
| | - Yi Hu
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China
| | - Xubin Zheng
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China
| | - Zhu Ning
- Zigong Center for Disease Control and Prevention, Zigong City, Sichuan, China
| | - Meiying Wu
- Department of Clinical Laboratory, The Fifth People's Hospital of Suzhou, Infectious Disease Hospital Affiliated to Soochow University, Suzhou City, Jiangsu, China
| | - Fan Xia
- Department of Tuberculosis, The Eighty-Fifth Hospital of Chinese PLA, Shanghai, China
| | - Stefanie Prast-Nielsen
- Center for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Yue O O Hu
- Center for Translational Microbiome Research (CTMR), Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
| | - Biao Xu
- Department of Epidemiology, School of Public Health and Key Laboratory of Public Health Safety (Ministry of Education), Fudan University, Shanghai, China. .,Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden.
| |
Collapse
|
11
|
Lundmark A, Hu YOO, Huss M, Johannsen G, Andersson AF, Yucel-Lindberg T. Identification of Salivary Microbiota and Its Association With Host Inflammatory Mediators in Periodontitis. Front Cell Infect Microbiol 2019; 9:216. [PMID: 31281801 PMCID: PMC6598052 DOI: 10.3389/fcimb.2019.00216] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 06/05/2019] [Indexed: 12/22/2022] Open
Abstract
Periodontitis is a microbial-induced chronic inflammatory disease, which may not only result in tooth loss, but can also contribute to the development of various systemic diseases. The transition from healthy to diseased periodontium depends on microbial dysbiosis and impaired host immune response. Although periodontitis is a common disease as well as associated with various systemic inflammatory conditions, the taxonomic profiling of the salivary microbiota in periodontitis and its association with host immune and inflammatory mediators has not been reported. Therefore, the aim of this study was to identify key pathogens and their potential interaction with the host's inflammatory mediators in saliva samples for periodontitis risk assessment. The microbial 16S rRNA gene sequencing and the levels of inflammatory mediators were performed in saliva samples from patients with chronic periodontitis and periodontally healthy control subjects. The salivary microbial community composition differed significantly between patients with chronic periodontitis and healthy controls. Our analyses identified a number of microbes, including bacteria assigned to Eubacterium saphenum, Tannerella forsythia, Filifactor alocis, Streptococcus mitis/parasanguinis, Parvimonas micra, Prevotella sp., Phocaeicola sp., and Fretibacterium sp. as more abundant in periodontitis, compared to healthy controls. In samples from healthy individuals, we identified Campylobacter concisus, and Veillonella sp. as more abundant. Integrative analysis of the microbiota and inflammatory mediators/cytokines revealed associations that included positive correlations between the pathogens Treponema sp. and Selenomas sp. and the cytokines chitinase 3-like 1, sIL-6Rα, sTNF-R1, and gp130/sIL-6Rβ. In addition, a negative correlation was identified between IL-10 and Filifactor alocis. Our results reveal distinct and disease-specific patterns of salivary microbial composition between patients with periodontitis and healthy controls, as well as significant correlations between microbiota and host-mediated inflammatory cytokines. The positive correlations between the pathogens Treponema sp. and Selenomas sp. and the cytokines chitinase 3-like 1, sIL-6Rα, sTNF-R1, and gp130/sIL-6Rβ might have the future potential to serve as a combined bacteria-host salivary biomarker panel for diagnosis of the chronic infectious disease periodontitis. However, further studies are required to determine the capacity of these microbes and inflammatory mediators as a salivary biomarker panel for periodontitis.
Collapse
Affiliation(s)
- Anna Lundmark
- Division of Periodontology, Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Yue O O Hu
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.,Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research (CTMR), Karolinska Institutet, Stockholm, Sweden
| | - Mikael Huss
- Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Solna, Sweden
| | - Gunnar Johannsen
- Division of Periodontology, Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Anders F Andersson
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Tülay Yucel-Lindberg
- Division of Periodontology, Department of Dental Medicine, Karolinska Institutet, Huddinge, Sweden
| |
Collapse
|
12
|
Ährlund-Richter A, Cheng L, Hu YOO, Svensson M, Pennhag AAL, Ursu RG, Haeggblom L, Grün N, Ramqvist T, Engstrand L, Dalianis T, Du J. Changes in Cervical Human Papillomavirus (HPV) Prevalence at a Youth Clinic in Stockholm, Sweden, a Decade After the Introduction of the HPV Vaccine. Front Cell Infect Microbiol 2019; 9:59. [PMID: 30949454 PMCID: PMC6435486 DOI: 10.3389/fcimb.2019.00059] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 02/26/2019] [Indexed: 12/21/2022] Open
Abstract
Aim: This study aimed to follow the impact of human papillomavirus (HPV) catch-up and vaccination on the very high cervical HPV-prevalence in women at a youth clinic in central Stockholm during the period 2008–2018. Background: 2008–2010, cervical HPV-prevalence (69.5%) and HPV16 prevalence (34.7%) were high in non-vaccinated women at a youth clinic in Stockholm. 2013–2015, after the introduction of the quadrivalent-Gardasil® HPV-vaccine, HPV16 and HPV6 prevalence had decreased. Here, cervical HPV-prevalence was investigated 10 years after primary sampling. Material and Methods: 2017–2018, 178 cervical swabs, from women aged 15–23 years old, were tested for 27 HPV types by a bead-based multiplex method. HPV-prevalence data were then related to vaccination status and age and compared to HPV-prevalence in 615 samples from 2008 to 2010 and 338 samples from 2013 to 2015 from the same clinic, and to HPV types in 143 cervical cancer cases during 2003–2008 in Stockholm. Results: The proportion of vaccinated women increased from 10.7% (2008–2010) to 82.1% (2017–2018). The prevalence of all 27 HPVs, all high-risk HPVs (HR-HPVs) and the combined presence of the quadrivalent-Gardasil® types HPV16, 18, 6, and 11, was lower in vaccinated compared to unvaccinated women (67.4 vs. 93.3%, p = 0.0031, 60.1 vs. 86.7%, p = 0.0057 and 5.8 vs. 26.7%, p = 0.002, respectively). Furthermore, HPV16 prevalence in non-vaccinated women 2017–2018 was lower than that in 2008–2010 (16.7 and 34.7%, respectively, p = 0.0471) and similar trends were observed for HPV18 and 11. In both vaccinated and non-vaccinated women, the most common non-quadrivalent-Gardasil® vaccine HR-HPV types were HPV39, 51, 52, 56, and 59. Together they accounted for around 9.8% of cervical cancer cases in Stockholm during 2003–2008, and their prevalence tended to have increased during 2017–2018 compared to 2008–2010. Conclusion: Quadrivalent-Gardasil® vaccination has decreased HPV-vaccine type prevalence significantly. However, non-vaccine HR-HPV types remain high in potentially high-risk women at a youth clinic in Stockholm.
Collapse
Affiliation(s)
| | - Liqin Cheng
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden
| | - Yue O O Hu
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
| | - Mikaela Svensson
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden
| | - Alexandra A L Pennhag
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
| | - Ramona G Ursu
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden.,Department of Microbiology (Bacteriology, Virology) and Parasitology, Grigore T. Popa University of Medicine and Pharmacy, Iaşi, Romania
| | - Linnea Haeggblom
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Nathalie Grün
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Torbjörn Ramqvist
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology, Stockholm, Sweden
| | - Tina Dalianis
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Juan Du
- Department of Microbiology, Tumor and Cell Biology, Centre for Translational Microbiome Research, Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
13
|
Lindh MV, Sjöstedt J, Ekstam B, Casini M, Lundin D, Hugerth LW, Hu YOO, Andersson AF, Andersson A, Legrand C, Pinhassi J. Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers. Environ Microbiol 2017; 19:1222-1236. [PMID: 28028880 DOI: 10.1111/1462-2920.13650] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 12/10/2016] [Accepted: 12/18/2016] [Indexed: 12/11/2022]
Abstract
Metapopulation theory developed in terrestrial ecology provides applicable frameworks for interpreting the role of local and regional processes in shaping species distribution patterns. Yet, empirical testing of metapopulation models on microbial communities is essentially lacking. We determined regional bacterioplankton dynamics from monthly transect sampling in the Baltic Sea Proper using 16S rRNA gene sequencing. A strong positive trend was found between local relative abundance and occupancy of populations. Notably, the occupancy-frequency distributions were significantly bimodal with a satellite mode of rare endemic populations and a core mode of abundant cosmopolitan populations (e.g. Synechococcus, SAR11 and SAR86 clade members). Temporal changes in population distributions supported several theoretical frameworks. Still, bimodality was found among bacterioplankton communities across the entire Baltic Sea, and was also frequent in globally distributed datasets. Datasets spanning waters with widely different physicochemical characteristics or environmental gradients typically lacked significant bimodal patterns. When such datasets were divided into subsets with coherent environmental conditions, bimodal patterns emerged, highlighting the importance of positive feedbacks between local abundance and occupancy within specific biomes. Thus, metapopulation theory applied to microbial biogeography can provide novel insights into the mechanisms governing shifts in biodiversity resulting from natural or anthropogenically induced changes in the environment.
Collapse
Affiliation(s)
- Markus V Lindh
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Johanna Sjöstedt
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Börje Ekstam
- Department of Biology and Environmental Science, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Michele Casini
- Department of Aquatic Resources, Institute of Marine Research, Swedish University of Agricultural Sciences, Lysekil, SE-45330, Sweden
| | - Daniel Lundin
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Luisa W Hugerth
- Science for Life Laboratory School of Biotechnology, KTH Royal Institute of Technology, Stockholm, SE-10691, Sweden
| | - Yue O O Hu
- Science for Life Laboratory School of Biotechnology, KTH Royal Institute of Technology, Stockholm, SE-10691, Sweden
| | - Anders F Andersson
- Science for Life Laboratory School of Biotechnology, KTH Royal Institute of Technology, Stockholm, SE-10691, Sweden
| | - Agneta Andersson
- Department of Ecology and Environmental Science, Umeå University, Umeå, SE-90187, Sweden
| | - Catherine Legrand
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| | - Jarone Pinhassi
- Centre for Ecology and Evolution in Microbial model Systems - EEMiS, Linnaeus University, Kalmar, SE-39182, Sweden
| |
Collapse
|
14
|
Hu YOO, Karlson B, Charvet S, Andersson AF. Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea. Front Microbiol 2016; 7:679. [PMID: 27242706 PMCID: PMC4864665 DOI: 10.3389/fmicb.2016.00679] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/26/2016] [Indexed: 01/12/2023] Open
Abstract
Microbial plankton form the productive base of both marine and freshwater ecosystems and are key drivers of global biogeochemical cycles of carbon and nutrients. Plankton diversity is immense with representations from all major phyla within the three domains of life. So far, plankton monitoring has mainly been based on microscopic identification, which has limited sensitivity and reproducibility, not least because of the numerical majority of plankton being unidentifiable under the light microscope. High-throughput sequencing of taxonomic marker genes offers a means to identify taxa inaccessible by traditional methods; thus, recent studies have unveiled an extensive previously unknown diversity of plankton. Here, we conducted ultra-deep Illumina sequencing (average 105 sequences/sample) of rRNA gene amplicons of surface water eukaryotic and bacterial plankton communities sampled in summer along a 2000 km transect following the salinity gradient of the Baltic Sea. Community composition was strongly correlated with salinity for both bacterial and eukaryotic plankton assemblages, highlighting the importance of salinity for structuring the biodiversity within this ecosystem. In contrast, no clear trends in alpha-diversity for bacterial or eukaryotic communities could be detected along the transect. The distribution of major planktonic taxa followed expected patterns as observed in monitoring programs, but groups novel to the Baltic Sea were also identified, such as relatives to the coccolithophore Emiliana huxleyi detected in the northern Baltic Sea. This study provides the first ultra-deep sequencing-based survey on eukaryotic and bacterial plankton biogeography in the Baltic Sea.
Collapse
Affiliation(s)
- Yue O O Hu
- Science for Life Laboratory, Division of Gene Technology, School of Biotechnology, KTH Royal Institute of Technology Stockholm, Sweden
| | - Bengt Karlson
- Oceanography, Research & Development, Swedish Meteorological and Hydrological Institute Gothenburg, Sweden
| | - Sophie Charvet
- Leibniz Institute for Baltic Sea Research Warnemünde Rostock, Germany
| | - Anders F Andersson
- Science for Life Laboratory, Division of Gene Technology, School of Biotechnology, KTH Royal Institute of Technology Stockholm, Sweden
| |
Collapse
|
15
|
Hu YOO, Karlson B, Charvet S, Andersson AF. Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea. Front Microbiol 2016; 7:679. [PMID: 27242706 DOI: 10.3389/fmicb.2016.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/26/2016] [Indexed: 05/22/2023] Open
Abstract
Microbial plankton form the productive base of both marine and freshwater ecosystems and are key drivers of global biogeochemical cycles of carbon and nutrients. Plankton diversity is immense with representations from all major phyla within the three domains of life. So far, plankton monitoring has mainly been based on microscopic identification, which has limited sensitivity and reproducibility, not least because of the numerical majority of plankton being unidentifiable under the light microscope. High-throughput sequencing of taxonomic marker genes offers a means to identify taxa inaccessible by traditional methods; thus, recent studies have unveiled an extensive previously unknown diversity of plankton. Here, we conducted ultra-deep Illumina sequencing (average 10(5) sequences/sample) of rRNA gene amplicons of surface water eukaryotic and bacterial plankton communities sampled in summer along a 2000 km transect following the salinity gradient of the Baltic Sea. Community composition was strongly correlated with salinity for both bacterial and eukaryotic plankton assemblages, highlighting the importance of salinity for structuring the biodiversity within this ecosystem. In contrast, no clear trends in alpha-diversity for bacterial or eukaryotic communities could be detected along the transect. The distribution of major planktonic taxa followed expected patterns as observed in monitoring programs, but groups novel to the Baltic Sea were also identified, such as relatives to the coccolithophore Emiliana huxleyi detected in the northern Baltic Sea. This study provides the first ultra-deep sequencing-based survey on eukaryotic and bacterial plankton biogeography in the Baltic Sea.
Collapse
Affiliation(s)
- Yue O O Hu
- Science for Life Laboratory, Division of Gene Technology, School of Biotechnology, KTH Royal Institute of Technology Stockholm, Sweden
| | - Bengt Karlson
- Oceanography, Research & Development, Swedish Meteorological and Hydrological Institute Gothenburg, Sweden
| | - Sophie Charvet
- Leibniz Institute for Baltic Sea Research Warnemünde Rostock, Germany
| | - Anders F Andersson
- Science for Life Laboratory, Division of Gene Technology, School of Biotechnology, KTH Royal Institute of Technology Stockholm, Sweden
| |
Collapse
|
16
|
Hugerth LW, Muller EEL, Hu YOO, Lebrun LAM, Roume H, Lundin D, Wilmes P, Andersson AF. Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia. PLoS One 2014; 9:e95567. [PMID: 24755918 PMCID: PMC3995771 DOI: 10.1371/journal.pone.0095567] [Citation(s) in RCA: 135] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 03/28/2014] [Indexed: 01/22/2023] Open
Abstract
High-throughput sequencing of ribosomal RNA gene (rDNA) amplicons has opened up the door to large-scale comparative studies of microbial community structures. The short reads currently produced by massively parallel sequencing technologies make the choice of sequencing region crucial for accurate phylogenetic assignments. While for 16S rDNA, relevant regions have been well described, no truly systematic design of 18S rDNA primers aimed at resolving eukaryotic diversity has yet been reported. Here we used 31,862 18S rDNA sequences to design a set of broad-taxonomic range degenerate PCR primers. We simulated the phylogenetic information that each candidate primer pair would retrieve using paired- or single-end reads of various lengths, representing different sequencing technologies. Primer pairs targeting the V4 region performed best, allowing discrimination with paired-end reads as short as 150 bp (with 75% accuracy at genus level). The conditions for PCR amplification were optimised for one of these primer pairs and this was used to amplify 18S rDNA sequences from isolates as well as from a range of environmental samples which were then Illumina sequenced and analysed, revealing good concordance between expected and observed results. In summary, the reported primer sets will allow minimally biased assessment of eukaryotic diversity in different microbial ecosystems.
Collapse
Affiliation(s)
- Luisa W. Hugerth
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden
| | - Emilie E. L. Muller
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Yue O. O. Hu
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden
| | - Laura A. M. Lebrun
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Hugo Roume
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Daniel Lundin
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden
| | - Paul Wilmes
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette, Luxembourg
| | - Anders F. Andersson
- KTH Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Division of Gene Technology, Stockholm, Sweden
| |
Collapse
|