1
|
Eickhardt-Dalbøge CS, Nielsen HV, Fuursted K, Stensvold CR, Andersen LOB, Lilje B, Larsen MK, Kjær L, Christensen SF, Knudsen TA, Skov V, Sørensen AL, Ellervik C, Olsen LR, Christensen JJE, Nielsen XC, Hasselbalch HC, Ingham AC. JAK2V617F drives gut microbiota differences in patients with myeloproliferative neoplasms. Eur J Haematol 2024; 112:776-787. [PMID: 38226781 DOI: 10.1111/ejh.14169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/17/2024]
Abstract
BACKGROUND Essential thrombocythemia (ET), polycythemia vera (PV), and primary myelofibrosis (MF) are myeloproliferative neoplasms (MPN). Inflammation is involved in the initiation, progression, and symptomology of the diseases. The gut microbiota impacts the immune system, infection control, and steady-state hematopoiesis. METHODS We analyzed the gut microbiota of 227 MPN patients and healthy controls (HCs) using next-generation sequencing. We expanded our previous results in PV and ET patients with additional PV, pre-MF, and MF patients which allowed us to compare MPN patients collectively, MPN sub-diagnoses, and MPN mutations (separately and combined) vs. HCs (N = 42) and compare within MPN sub-diagnoses and MPN mutation. RESULTS MPN patients had a higher observed richness (median, 245 [range, 49-659]) compared with HCs (191.5 [range, 111-300; p = .003]) and a lower relative abundance of taxa within the Firmicutes phylum; for example, Faecalibacterium (6% vs. 14%, p < .001). The microbiota of CALR-positive patients (N = 30) resembled that of HCs more than that of patients with JAK2V617F (N = 177). In JAK2V617F-positive patients, only minor differences in the gut microbiota were observed between MPN sub-diagnoses, illustrating the importance of this mutation. CONCLUSION The gut microbiota in MPN patients differs from HCs and is driven by JAK2V617F, whereas the gut microbiota in CALR patients resembles HCs more.
Collapse
Affiliation(s)
- Christina Schjellerup Eickhardt-Dalbøge
- The Regional Department of Clinical Microbiology, University Hospital of Region Zealand, Slagelse, Denmark
- Department of Hematology, Zealand University Hospital, Roskilde, Denmark
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Henrik V Nielsen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Kurt Fuursted
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | - Lee O' Brien Andersen
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Berit Lilje
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Morten Kranker Larsen
- Department of Hematology, Zealand University Hospital, Roskilde, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Kjær
- Department of Hematology, Zealand University Hospital, Roskilde, Denmark
| | | | - Trine Alma Knudsen
- Department of Hematology, Zealand University Hospital, Roskilde, Denmark
| | - Vibe Skov
- Department of Hematology, Zealand University Hospital, Roskilde, Denmark
| | | | - Christina Ellervik
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Pathology, Harvard Medical School, Boston, Massachusetts, USA
- Department of Data and Data Support, Region Zealand, Sorø, Denmark
| | - Lars Rønn Olsen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Jens Jørgen Elmer Christensen
- The Regional Department of Clinical Microbiology, University Hospital of Region Zealand, Slagelse, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Xiaohui Chen Nielsen
- The Regional Department of Clinical Microbiology, University Hospital of Region Zealand, Slagelse, Denmark
| | - Hans Carl Hasselbalch
- Department of Hematology, Zealand University Hospital, Roskilde, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anna Cäcilia Ingham
- Department of Bacteria, Parasites & Fungi, Statens Serum Institut, Copenhagen, Denmark
| |
Collapse
|
2
|
Andersson AM, Ingham AC, Edslev SM, Sølberg J, Skov L, Koch A, Ghauharali-van der Vlugt K, Stet FS, Brüggen CM, Jakasa I, Kezic S, Thyssen JP. Ethnic endotypes in paediatric atopic dermatitis depend on immunotype, lipid composition and microbiota of the skin. J Eur Acad Dermatol Venereol 2024; 38:365-374. [PMID: 37822011 DOI: 10.1111/jdv.19565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/21/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND Atopic dermatitis (AD) endotypes differ with ethnicity. We examined the skin microbiota, cytokine and lipid profiles in Greenlandic Inuit and Danish children with AD. METHODS Twenty-five Inuit children with AD and 25 Inuit control children were clinically examined and compared to previously collected data from 25 Danish children with AD. Skin tape strips and skin swabs were collected from lesional and non-lesional skin. Levels of cutaneous immune biomarkers, free sphingoid bases and their (glycosyl)ceramides were analysed. Skin swabs were analysed with 16S rRNA and tuf gene for characterization of bacterial species communities. RESULTS Bacterial β-diversity was significantly different between Inuit and Danish AD skin, in both lesional (p < 0.001) and non-lesional (p < 0.001) AD skin, and there was a higher relative abundance of Staphylococcus aureus in Danish compared to Inuit lesional (53% vs. 8%, p < 0.01) and non-lesional skin (55% vs. 5%, p < 0.001). Danish AD children had a higher α-diversity than Inuit children in non-lesional (p < 0.05) but not in lesional skin. Significantly higher levels of type 2 immunity cytokine interleukin (IL)-4 (p < 0.05) and IL-5 (p < 0.01) were identified in Inuit compared to Danish AD children. In contrast, IL-33 (p < 0.01) was higher in Danish lesional and non-lesional AD skin. Higher levels of long-chain glucosylceramide (GlcCER)[S](d26:1) were found in lesional (p < 0.001) and non-lesional (p < 0.001) Inuit skin compared with Danish AD skin. NMF levels were similar in Inuit and Danish AD skin. CONCLUSION Skin microbiota, cytokine and lipid composition differed significantly between Inuit and Danish children with AD and showed a stronger type 2 immune signature in Inuit children.
Collapse
Affiliation(s)
- A M Andersson
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
- Ilisimatusarfik, University of Greenland, Nuuk, Greenland
- Copenhagen Research Group for Inflammatory Skin (CORGIS), Hellerup, Denmark
| | - A C Ingham
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - S M Edslev
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - J Sølberg
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
| | - L Skov
- Department of Dermatology and Allergy, Herlev and Gentofte Hospital, University of Copenhagen, Hellerup, Denmark
- Copenhagen Research Group for Inflammatory Skin (CORGIS), Hellerup, Denmark
| | - A Koch
- Ilisimatusarfik, University of Greenland, Nuuk, Greenland
- Department of Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
- Department of Infectious Diseases, Rigshospitalet University Hospital, Copenhagen, Denmark
| | - K Ghauharali-van der Vlugt
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - F S Stet
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - C M Brüggen
- Faculty of Medicine, University Zurich, Zurich, Switzerland
- Department of Dermatology, University Hospital Zurich, Zurich, Switzerland
- Christine Kühne-Center for Allergy Research and Education, Davos, Switzerland
| | - I Jakasa
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Laboratory for Analytical Chemistry, Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - S Kezic
- Department of Public and Occupational Health, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - J P Thyssen
- Department of Dermatology, Bispebjerg Hospital, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
3
|
Eickhardt-Dalbøge CS, Ingham AC, Nielsen HV, Fuursted K, Stensvold CR, Andersen LO, Larsen MK, Kjær L, Christensen SF, Knudsen TA, Skov V, Ellervik C, Olsen LR, Hasselbalch HC, Elmer Christensen JJ, Nielsen XC. Pronounced gut microbiota signatures in patients with JAK2V617F-positive essential thrombocythemia. Microbiol Spectr 2023; 11:e0066223. [PMID: 37695126 PMCID: PMC10581245 DOI: 10.1128/spectrum.00662-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/18/2023] [Indexed: 09/12/2023] Open
Abstract
Essential thrombocythemia (ET) is part of the Philadelphia chromosome-negative myeloproliferative neoplasms. It is characterized by an increased risk of thromboembolic events and also to a certain degree hypermetabolic symptoms. The gut microbiota is an important initiator of hematopoiesis and regulation of the immune system, but in patients with ET, where inflammation is a hallmark of the disease, it is vastly unexplored. In this study, we compared the gut microbiota via amplicon-based 16S rRNA gene sequencing of the V3-V4 region in 54 patients with ET according to mutation status Janus-kinase 2 (JAK2V617F)-positive vs JAK2V617F-negative patients with ET, and in 42 healthy controls (HCs). Gut microbiota richness was higher in patients with ET (median-observed richness, 283.5; range, 75-535) compared with HCs (median-observed richness, 191.5; range, 111-300; P < 0.001). Patients with ET had a different overall bacterial composition (beta diversity) than HCs (analysis of similarities [ANOSIM]; R = 0.063, P = 0.004). Patients with ET had a significantly lower relative abundance of taxa within the Firmicutes phylum compared with HCs (51% vs 59%, P = 0.03), and within that phylum, patients with ET also had a lower relative abundance of the genus Faecalibacterium (8% vs 15%, P < 0.001), an important immunoregulative bacterium. The microbiota signatures were more pronounced in patients harboring the JAK2V617F mutation, and highly similar to patients with polycythemia vera as previously described. These findings suggest that patients with ET may have an altered immune regulation; however, whether this dysregulation is induced in part by, or is itself inducing, an altered gut microbiota remains to be investigated. IMPORTANCE Essential thrombocythemia (ET) is a cancer characterized by thrombocyte overproduction. Inflammation has been shown to be vital in both the initiation and progression of other myeloproliferative neoplasms, and it is well known that the gut microbiota is important in the regulation of our immune system. However, the gut microbiota of patients with ET remains uninvestigated. In this study, we characterized the gut microbiota of patients with ET compared with healthy controls and thereby provide new insights into the field. We show that the gut microbiota of patients with ET differs significantly from that of healthy controls and the patients with ET have a lower relative abundance of important immunoregulative bacteria. Furthermore, we demonstrate that patients with JAK2V617F-positive ET have pronounced gut microbiota signatures compared with JAK2V617F-negative patients. Thereby confirming the importance of the underlying mutation, the immune response as well as the composition of the microbiota.
Collapse
Affiliation(s)
- Christina Schjellerup Eickhardt-Dalbøge
- Regional Department of Clinical Microbiology, Zealand University Hospital, Koege, Denmark
- Department of Hematology, Zealand University Hospital, Roskilde, Denmark
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anna Cäcilia Ingham
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Henrik V. Nielsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Kurt Fuursted
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | - Lee O'Brien Andersen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Morten Kranker Larsen
- Department of Hematology, Zealand University Hospital, Roskilde, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Kjær
- Department of Hematology, Zealand University Hospital, Roskilde, Denmark
| | | | - Trine Alma Knudsen
- Department of Hematology, Zealand University Hospital, Roskilde, Denmark
| | - Vibe Skov
- Department of Hematology, Zealand University Hospital, Roskilde, Denmark
| | - Christina Ellervik
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Laboratory Medicine, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Department of Data and Data Support, Region Zealand, Sorø, Denmark
| | - Lars Rønn Olsen
- Department of Health Technology, Technical University of Denmark, Lyngby, Denmark
| | - Hans Carl Hasselbalch
- Department of Hematology, Zealand University Hospital, Roskilde, Denmark
- Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jens Jørgen Elmer Christensen
- Regional Department of Clinical Microbiology, Zealand University Hospital, Koege, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Xiaohui Chen Nielsen
- Regional Department of Clinical Microbiology, Zealand University Hospital, Koege, Denmark
| |
Collapse
|
4
|
Tams KW, Larsen I, Hansen JE, Spiegelhauer H, Strøm-Hansen AD, Rasmussen S, Ingham AC, Kalmar L, Kean IRL, Angen Ø, Holmes MA, Pedersen K, Jelsbak L, Folkesson A, Larsen AR, Strube ML. The effects of antibiotic use on the dynamics of the microbiome and resistome in pigs. Anim Microbiome 2023; 5:39. [PMID: 37605221 PMCID: PMC10440943 DOI: 10.1186/s42523-023-00258-4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 07/25/2023] [Indexed: 08/23/2023] Open
Abstract
Antibiotics are widely used in pig farming across the world which has led to concerns about the potential impact on human health through the selection of antibiotic resistant pathogenic bacteria. This worry has resulted in the development of a production scheme known as pigs Raised Without Antibiotics (RWA), in which pigs are produced in commercial farms, but are ear-tagged as RWA until slaughter unless they receive treatment, thus allowing the farmer to sell the pigs either as premium priced RWA or as conventional meat. Development of antibiotic resistance in pig farming has been studied in national surveys of antibiotic usage and resistance, as well as in experimental studies of groups of pigs, but not in individual pigs followed longitudinally in a commercial pig farm. In this study, a cohort of RWA designated pigs were sampled at 10 time points from birth until slaughter along with pen-mates treated with antibiotics at the same farm. From these samples, the microbiome, determined using 16S sequencing, and the resistome, as determined using qPCR for 82 resistance genes, was investigated, allowing us to examine the difference between RWA pigs and antibiotic treated pigs. We furthermore included 176 additional pigs from six different RWA farms which were sampled at the slaughterhouse as an endpoint to substantiate the cohort as well as for evaluation of intra-farm variability. The results showed a clear effect of age in both the microbiome and resistome composition from early life up until slaughter. As a function of antibiotic treatment, however, we observed a small but significant divergence between treated and untreated animals in their microbiome composition immediately following treatment, which disappeared before 8 weeks of age. The effect on the resistome was evident and an effect of treatment could still be detected at week 8. In animals sampled at the slaughterhouse, we observed no difference in the microbiome or the resistome as a result of treatment status but did see a strong effect of farm origin. Network analysis of co-occurrence of microbiome and resistome data suggested that some resistance genes may be transferred through mobile genetic elements, so we used Hi-C metagenomics on a subset of samples to investigate this. We conclude that antibiotic treatment has a differential effect on the microbiome vs. the resistome and that although resistance gene load is increased by antibiotic treatment load, this effect disappears before slaughter. More studies are needed to elucidate the optimal way to rear pigs without antibiotics.
Collapse
Affiliation(s)
- Katrine Wegener Tams
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Inge Larsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1871, Copenhagen, Denmark
| | - Julie Elvekjær Hansen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Henrik Spiegelhauer
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | | | - Sophia Rasmussen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Anna Cäcilia Ingham
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut (SSI), 2300, Copenhagen, Denmark
| | - Lajos Kalmar
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Øystein Angen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut (SSI), 2300, Copenhagen, Denmark
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Karl Pedersen
- Department of Animal Health and Antimicrobial Strategies, National Veterinary Institute, 751 89, Uppsala, Sweden
| | - Lars Jelsbak
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Anders Folkesson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
| | - Anders Rhod Larsen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut (SSI), 2300, Copenhagen, Denmark
| | - Mikael Lenz Strube
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark.
| |
Collapse
|
5
|
Abstract
Mucosal microbiotas and their role in stem cell transplantation. Patients with hematological disorders such as leukemia often undergo allogeneic hematopoietic stem cell transplantation, and thereby receive stem cells from a donor for curation of disease. This procedure also involves immunosuppressive and antimicrobial treatments that disturb the important interactions between the microbiota and the immune system, especially at mucosal sites. After transplantation, bacterial diversity decreases together with a depletion of Clostridia, and shifts toward predominance of Proteobacteria. Infectious and inflammatory complications, such as graft-versus-host disease, also interfere with patient recovery. This review collects and contextualizes current knowledge of the role of mucosal microbiotas at different body sites in stem cell transplantation, proposes underlying mechanisms, and discusses potential clinical value of bacterial markers for improved treatment strategies.
Collapse
Affiliation(s)
- Anna Cäcilia Ingham
- Research Group for Genomic EpidemiologyTechnical University of DenmarkKongens LyngbyDenmark,Department of Bacteria, Parasites and FungiStatens Serum InstitutCopenhagenDenmark
| | - Sünje Johanna Pamp
- Research Group for Genomic EpidemiologyTechnical University of DenmarkKongens LyngbyDenmark,Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
| |
Collapse
|
6
|
Medeiros MM, Ingham AC, Nanque LM, Correia C, Stegger M, Andersen PS, Fisker AB, Benn CS, Lanaspa M, Silveira H, Abrantes P. Oral polio revaccination is associated with changes in gut and upper respiratory microbiomes of infants. Front Microbiol 2022; 13:1016220. [PMID: 36386704 PMCID: PMC9649904 DOI: 10.3389/fmicb.2022.1016220] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/03/2022] [Indexed: 11/13/2022] Open
Abstract
After the eradication of polio infection, the plan is to phase-out the live-attenuated oral polio vaccine (OPV). Considering the protective non-specific effects (NSE) of OPV on unrelated pathogens, the withdrawal may impact child health negatively. Within a cluster-randomized trial, we carried out 16S rRNA deep sequencing analysis of fecal and nasopharyngeal microbial content of Bissau–Guinean infants aged 4–8 months, before and after 2 months of OPV revaccination (revaccinated infants = 47) vs. no OPV revaccination (control infants = 47). The aim was to address changes in the gut and upper respiratory bacterial microbiotas due to revaccination. Alpha-diversity for both microbiotas increased similarly over time in OPV-revaccinated infants and controls, whereas greater changes over time in the bacterial composition of gut (padjusted < 0.001) and upper respiratory microbiotas (padjusted = 0.018) were observed in the former. Taxonomic analysis of gut bacterial microbiota revealed a decrease over time in the median proportion of Bifidobacterium longum for all infants (25–14.3%, p = 0.0006 in OPV-revaccinated infants and 25.3–11.6%, p = 0.01 in controls), compatible with the reported weaning. Also, it showed a restricted increase in the median proportion of Prevotella_9 genus in controls (1.4–7.1%, p = 0.02), whereas in OPV revaccinated infants an increase over time in Prevotellaceae family (7.2–17.4%, p = 0.005) together with a reduction in median proportion of potentially pathogenic/opportunistic genera such as Escherichia/Shigella (5.8–3.4%, p = 0.01) were observed. Taxonomic analysis of upper respiratory bacterial microbiota revealed an increase over time in median proportions of potentially pathogenic/opportunistic genera in controls, such as Streptococcus (2.9–11.8%, p = 0.001 and Hemophilus (11.3–20.5%, p = 0.03), not observed in OPV revaccinated infants. In conclusion, OPV revaccination was associated with a healthier microbiome composition 2 months after revaccination, based on a more abundant and diversified bacterial community of Prevotellaceae and fewer pathogenic/opportunistic organisms. Further information on species-level differentiation and functional analysis of microbiome content are warranted to elucidate the impact of OPV-associated changes in bacterial microbiota on child health.
Collapse
Affiliation(s)
- Márcia Melo Medeiros
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Lisboa, Portugal
- *Correspondence: Márcia Melo Medeiros,
| | - Anna Cäcilia Ingham
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Line Møller Nanque
- Bandim Health Project, Bissau, Guinea-Bissau
- Bandim Health Project, Odense Patient Data Explorative Network, Institute of Clinical Research, Odense University Hospital/University of Southern Denmark, Odense, Denmark
| | | | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Paal Skyt Andersen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Ane Baerent Fisker
- Bandim Health Project, Bissau, Guinea-Bissau
- Bandim Health Project, Odense Patient Data Explorative Network, Institute of Clinical Research, Odense University Hospital/University of Southern Denmark, Odense, Denmark
| | - Christine Stabell Benn
- Bandim Health Project, Bissau, Guinea-Bissau
- Bandim Health Project, Odense Patient Data Explorative Network, Institute of Clinical Research, Odense University Hospital/University of Southern Denmark, Odense, Denmark
- Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark
| | - Miguel Lanaspa
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Lisboa, Portugal
| | - Henrique Silveira
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Lisboa, Portugal
| | - Patrícia Abrantes
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade NOVA de Lisboa (UNL), Lisboa, Portugal
| |
Collapse
|
7
|
Ring HC, Thorsen J, Fuursted K, Bjarnsholt T, Bay L, Egeberg A, Ingham AC, Vedel Nielsen H, Frew WJ, Saunte D, Thomsen SF, Jemec GB. Amplicon sequencing demonstrates comparable follicular mycobiomes in patients with hidradenitis suppurativa compared with healthy controls. J Eur Acad Dermatol Venereol 2022; 36:e580-e583. [PMID: 35285081 DOI: 10.1111/jdv.18075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/02/2022] [Indexed: 11/28/2022]
Affiliation(s)
- H C Ring
- Department of Dermato-Venereology & Wound Healing Centre, Bispebjerg Hospital and Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Dermatology, Zealand University Hospital, Roskilde, Denmark
| | - J Thorsen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - K Fuursted
- Department of microbiology and infection control, Statens Serum Institut, Copenhagen, Denmark
| | - T Bjarnsholt
- Costerton Biofilm Center, University of Copenhagen, Denmark.,Department of Clinical Microbiology, Copenhagen University Hospital, Copenhagen, Denmark
| | - L Bay
- Costerton Biofilm Center, University of Copenhagen, Denmark
| | - A Egeberg
- Department of Dermato-Venereology & Wound Healing Centre, Bispebjerg Hospital and Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - A C Ingham
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - H Vedel Nielsen
- Department of microbiology and infection control, Statens Serum Institut, Copenhagen, Denmark.,Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - W J Frew
- Department of Dermatology, Liverpool Hospital, Sydney, Australia
| | - Dml Saunte
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.,Department of Dermatology, Zealand University Hospital, Roskilde, Denmark.,Department of Clinical Medicine, Faculthy of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | - S F Thomsen
- Department of Dermato-Venereology & Wound Healing Centre, Bispebjerg Hospital and Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - G B Jemec
- Department of Dermatology, Zealand University Hospital, Roskilde, Denmark.,Department of Clinical Medicine, Faculthy of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| |
Collapse
|
8
|
Fonager J, Bennedbæk M, Bager P, Wohlfahrt J, Ellegaard KM, Ingham AC, Edslev SM, Stegger M, Sieber RN, Lassauniere R, Fomsgaard A, Lillebaek T, Svarrer CW, Møller FT, Møller CH, Legarth R, Sydenham TV, Steinke K, Paulsen SJ, Castruita JAS, Schneider UV, Schouw CH, Nielsen XC, Overvad M, Nielsen RT, Marvig RL, Pedersen MS, Nielsen L, Nilsson LL, Bybjerg-Grauholm J, Tarpgaard IH, Ebsen TS, Lam JUH, Gunalan V, Rasmussen M. Molecular epidemiology of the SARS-CoV-2 variant Omicron BA.2 sub-lineage in Denmark, 29 November 2021 to 2 January 2022. Euro Surveill 2022; 27. [PMID: 35272746 PMCID: PMC8915403 DOI: 10.2807/1560-7917.es.2022.27.10.2200181] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Following emergence of the SARS-CoV-2 variant Omicron in November 2021, the dominant BA.1 sub-lineage was replaced by the BA.2 sub-lineage in Denmark. We analysed the first 2,623 BA.2 cases from 29 November 2021 to 2 January 2022. No epidemiological or clinical differences were found between individuals infected with BA.1 versus BA.2. Phylogenetic analyses showed a geographic east-to-west transmission of BA.2 from the Capital Region with clusters expanding after the Christmas holidays. Mutational analysis shows distinct differences between BA.1 and BA.2.
Collapse
Affiliation(s)
- Jannik Fonager
- Virus Research and Development Laboratory, Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Bennedbæk
- Virus Research and Development Laboratory, Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Peter Bager
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Jan Wohlfahrt
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | | | - Anna Cäcilia Ingham
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Sofie Marie Edslev
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Raphael Niklaus Sieber
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Ria Lassauniere
- Virus Research and Development Laboratory, Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Fomsgaard
- Virus Research and Development Laboratory, Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Troels Lillebaek
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark.,Global Health Section, University of Copenhagen, Copenhagen, Denmark
| | - Christina Wiid Svarrer
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Frederik Trier Møller
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | | | - Rebecca Legarth
- Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | | | - Kat Steinke
- Department of Clinical Microbiology, Odense University Hospital, Denmark
| | - Sarah Juel Paulsen
- Department of Clinical Microbiology, Copenhagen University Hospital Amager-Hvidovre, Hvidovre, Denmark
| | | | - Uffe Vest Schneider
- Department of Clinical Microbiology, Copenhagen University Hospital Amager-Hvidovre, Hvidovre, Denmark
| | | | | | - Maria Overvad
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Rikke Thoft Nielsen
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Rasmus L Marvig
- Center for Genomic Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Martin Schou Pedersen
- Department of Clinical Microbiology, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Lene Nielsen
- Department of Clinical Microbiology, Copenhagen University Hospital-Herlev and Gentofte, Herlev, Denmark
| | - Line Lynge Nilsson
- Department of Clinical Microbiology, Copenhagen University Hospital-Herlev and Gentofte, Herlev, Denmark
| | | | | | | | - Janni Uyen Hoa Lam
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Vithiagaran Gunalan
- Virus Research and Development Laboratory, Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Morten Rasmussen
- Virus Research and Development Laboratory, Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| |
Collapse
|
9
|
Berbisá MÁF, Nielsen KR, Ingham AC, Midjord J, Hammer T, Patursson P, Vest NMO, Gregersen NO, Burisch J, Vang A. Similar Gut Bacterial Composition Between Patients With Ulcerative Colitis and Healthy Controls in a High Incidence Population: A Cross-sectional Study of the Faroe Islands IBD Cohort. Inflamm Bowel Dis 2022; 28:1081-1089. [PMID: 35138361 PMCID: PMC9247847 DOI: 10.1093/ibd/izab355] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND The Faroe Islands has the world's highest incidence of inflammatory bowel disease (IBD). Epidemiological studies have characterized this unique cohort and a decreased risk of developing IBD with emigration. Therefore, this well-characterized Faroese IBD cohort gives the opportunity to better understand this complex disease. This study represents the first investigation of the gut microbiota for the cohort. METHODS This cross-sectional study consisted of 41 patients with established ulcerative colitis and 144 age- and sex-matched healthy controls recruited through the Faroe Genome project. Participants donated a 1-time fecal sample and completed questionnaires on food frequency, background health, and lifestyle. 16S rRNA amplicon sequencing of the V3-V4 region was performed followed by bioinformatic analysis of taxonomy and diversity metrics. RESULTS The overall bacterial composition in both groups was dominated by Firmicutes and Bacteroidetes. No significant differences were found based on metrics of alpha or beta diversity. However, discriminatory analysis identified differential abundance of several indicator taxa in healthy controls and ulcerative colitis participants, whereas Akkermansia was completely absent from 27% of all study participants. Food frequency questionnaires revealed similar dietary patterns between the 2 groups. CONCLUSION The similarity in bacterial community composition and absence of the beneficial Akkermansia genus in both groups raise further questions concerning the underlying susceptibility toward inflammatory disorders within this high-risk population. Results vary widely by study design and geographic location, which speaks to the need for regionally tuned reference groups and disease-based studies on the Faroe Islands.
Collapse
Affiliation(s)
- Marjun á Fríðirksmørk Berbisá
- Department of Science and Technology, Aarhus University, Aarhus, Denmark,Department of Health Sciences, University of the Faroe Islands, Tórshavn, Faroe Islands
| | - Kári Rubek Nielsen
- Department of Medicine, National Hospital of the Faroe Islands, Tórshavn, Faroe Islands
| | - Anna Cäcilia Ingham
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jóngerð Midjord
- Department of Medicine, National Hospital of the Faroe Islands, Tórshavn, Faroe Islands
| | - Turið Hammer
- Department of Occupational Medicine and Public Health, The Faroese Hospital System, Tórshavn, Faroe Islands
| | - Poula Patursson
- Department of Medicine, National Hospital of the Faroe Islands, Tórshavn, Faroe Islands
| | - Nicolina M O Vest
- Department of Health Sciences, University of the Faroe Islands, Tórshavn, Faroe Islands
| | - Noomi O Gregersen
- FarGen Project, Genetic Biobank of the Faroe Islands, Tórshavn, Faroe Islands
| | | | - Amanda Vang
- Address correspondence to: Amanda Vang, PhD, Hoyvíksvegur 51, 100 Tórshavn, Faroe Islands ()
| |
Collapse
|
10
|
Espenhain L, Funk T, Overvad M, Edslev SM, Fonager J, Ingham AC, Rasmussen M, Madsen SL, Espersen CH, Sieber RN, Stegger M, Gunalan V, Wilkowski B, Larsen NB, Legarth R, Cohen AS, Nielsen F, Lam JUH, Lavik KE, Karakis M, Spiess K, Marving E, Nielsen C, Wiid Svarrer C, Bybjerg-Grauholm J, Olsen SS, Jensen A, Krause TG, Müller L. Epidemiological characterisation of the first 785 SARS-CoV-2 Omicron variant cases in Denmark, December 2021. Euro Surveill 2021; 26. [PMID: 34915977 PMCID: PMC8728489 DOI: 10.2807/1560-7917.es.2021.26.50.2101146] [Citation(s) in RCA: 127] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
By 9 December 2021, 785 SARS-CoV-2 Omicron variant cases have been identified in Denmark. Most cases were fully (76%) or booster-vaccinated (7.1%); 34 (4.3%) had a previous SARS-CoV-2 infection. The majority of cases with available information reported symptoms (509/666; 76%) and most were infected in Denmark (588/644; 91%). One in five cases cannot be linked to previous cases, indicating widespread community transmission. Nine cases have been hospitalised, one required intensive care and no deaths have been registered.
Collapse
Affiliation(s)
- Laura Espenhain
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Tjede Funk
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark.,European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control, (ECDC), Stockholm, Sweden
| | - Maria Overvad
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | - Sofie Marie Edslev
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jannik Fonager
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Anna Cäcilia Ingham
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Morten Rasmussen
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Sarah Leth Madsen
- COVID-19 tracing Unit, Danish Patient Safety Authority, Copenhagen, Denmark
| | | | - Raphael N Sieber
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Vithiagaran Gunalan
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Bartlomiej Wilkowski
- TestCenter Denmark, Statens Serum Institut, Copenhagen, Denmark.,Danish National Biobank, Statens Serum Institut, Copenhagen, Denmark
| | | | - Rebecca Legarth
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| | | | - Finn Nielsen
- The Data integration and Analysis Secretariat, Statens Serum Institut, Copenhagen, Denmark
| | - Janni Uyen Hoa Lam
- The Data integration and Analysis Secretariat, Statens Serum Institut, Copenhagen, Denmark
| | - Kjetil Erdogan Lavik
- The Data integration and Analysis Secretariat, Statens Serum Institut, Copenhagen, Denmark
| | - Marianne Karakis
- The Data integration and Analysis Secretariat, Statens Serum Institut, Copenhagen, Denmark
| | - Katja Spiess
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Ellinor Marving
- Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Christian Nielsen
- TestCenter Denmark, Statens Serum Institut, Copenhagen, Denmark.,Danish National Biobank, Statens Serum Institut, Copenhagen, Denmark
| | - Christina Wiid Svarrer
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | | | - Stefan Schytte Olsen
- The Data integration and Analysis Secretariat, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Jensen
- TestCenter Denmark, Statens Serum Institut, Copenhagen, Denmark.,Danish National Biobank, Statens Serum Institut, Copenhagen, Denmark
| | - Tyra Grove Krause
- Epidemiological Infectious Disease Preparedness, Statens Serum Institut, Copenhagen, Denmark
| | - Luise Müller
- Infectious Disease Epidemiology and Prevention, Statens Serum Institut, Copenhagen, Denmark
| |
Collapse
|
11
|
Nørreslet LB, Lilje B, Ingham AC, Edslev SM, Clausen ML, Plum F, Andersen PS, Agner T. Skin Microbiome in Patients with Hand Eczema and Healthy Controls: A Three-week Prospective Study. Acta Derm Venereol 2021; 102:adv00633. [PMID: 34877605 PMCID: PMC9631265 DOI: 10.2340/actadv.v101.845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The pathogenesis of chronic hand eczema remains unclear. Insights into the skin microbiome in hand eczema and its potential relevance to disease severity may help to elucidate the underlying mechanisms of hand eczema. The aim of this study was to characterize the microbiome in patients with hand eczema and healthy controls. A 5-visit prospective study was conducted over a period of 3 weeks. At each visit, bacterial swabs were taken from the hands of patients with hand eczema and controls. The microbiome was examined using DNA extraction and 16S rRNA amplicon sequencing (V3–V4 regions). Fifty patients with hand eczema and 50 controls were included (follow-up rate=100%). The baseline bacterial α-diversity was reduced on the hands of patients with hand eczema compared with controls (effect size=–0.31; 95% confidence interval (95% CI) –0.50; –0.11; p = 0.003). The dysbiosis on the patients’ hands was stable over the study period, was associated with disease severity, and was characterized by reduced bacterial diversity and different bacterial community compositions.
Collapse
Affiliation(s)
- Line Brok Nørreslet
- Department of Dermatology, University of Copenhagen, Bispebjerg Hospital, Bispebjerg Bakke 23, DK-2400 Copenhagen NV, Denmark.
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Gotfred-Rasmussen H, Stensvold CR, Ingham AC, Johannesen TB, Andersen LO, Röser D, Nielsen HV. Impact of Metronidazole Treatment and Dientamoeba Fragilis Colonization on Gut Microbiota Diversity. J Pediatr Gastroenterol Nutr 2021; 73:23-29. [PMID: 33633081 DOI: 10.1097/mpg.0000000000003096] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
Abstract
OBJECTIVES The intestinal parasite Dientamoeba fragilis is a common colonizer of children in Denmark. Metronidazole has been used to reduce gastrointestinal symptoms in children colonized with D fragilis. We aimed to identify gut microbiota changes associated with D fragilis carrier status and metronidazole treatment of D fragilis-positive children. METHODS The fecal microbiota of 275 fecal samples from children treated with metronidazole (n = 48) or placebo (n = 48) were characterized by ribosomal DNA sequencing. Samples collected before (T1), 2 weeks after (T2), and 8 weeks (T5) after treatment were included. Seventy fecal samples from 70 age-matched parasite-negative children served as controls. RESULTS The abundance of 24 bacterial genera differed significantly according to D fragilis carrier status, with Flavonifractor being remarkably more abundant in children testing negative for D fragilis. Eight bacterial genera changed significantly in abundance in children losing versus keeping D fragilis after metronidazole treatment. Of these, 7 returned to pretreatment (T1) levels at T5. Meanwhile, the abundance of Flavonifractor continued to differ at T5, whereas for Ruminococcus the abundance only remained high in children who were D fragilis-negative at T2 and T5. Increases in Hungatella, Sutterella, and Streptococcus abundances observed at T2 were specific to metronidazole exposure and hence independent of D fragilis colonization. CONCLUSIONS This study revealed that specific bacterial genera were associated with D fragilis colonization. Metronidazole treatment had a short-term impact on the abundance of some bacterial genera, with most of these reverting to pretreatment levels 8 weeks after completed treatment.
Collapse
Affiliation(s)
| | | | - Anna Cäcilia Ingham
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, Copenhagen S
| | - Thor Bech Johannesen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, Copenhagen S
| | | | - Dennis Röser
- Department of Paediatrics, Copenhagen University Hospital Hvidovre, Kettegård Alle 30, Hvidovre, Denmark
| | | |
Collapse
|
13
|
Ingham AC, Kielsen K, Mordhorst H, Ifversen M, Aarestrup FM, Müller KG, Pamp SJ. Microbiota long-term dynamics and prediction of acute graft-versus-host disease in pediatric allogeneic stem cell transplantation. Microbiome 2021; 9:148. [PMID: 34183060 PMCID: PMC8240369 DOI: 10.1186/s40168-021-01100-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/20/2021] [Indexed: 05/11/2023]
Abstract
BACKGROUND Patients undergoing allogeneic hematopoietic stem cell transplantation (HSCT) exhibit changes in their gut microbiota and are experiencing a range of complications, including acute graft-versus-host disease (aGvHD). It is unknown if, when, and under which conditions a re-establishment of microbial and immunological homeostasis occurs. It is also unclear whether microbiota long-term dynamics occur at other body sites than the gut such as the mouth or nose. Moreover, it is not known whether the patients' microbiota prior to HSCT holds clues to whether the patient would suffer from severe complications subsequent to HSCT. Here, we take a holobiont perspective and performed an integrated host-microbiota analysis of the gut, oral, and nasal microbiota in 29 children undergoing allo-HSCT. RESULTS The bacterial diversity decreased in the gut, nose, and mouth during the first month and reconstituted again 1-3 months after allo-HSCT. The microbial community composition traversed three phases over 1 year. Distinct taxa discriminated the microbiota temporally at all three body sides, including Enterococcus spp., Lactobacillus spp., and Blautia spp. in the gut. Of note, certain microbial taxa appeared already changed in the patients prior to allo-HSCT as compared with healthy children. Acute GvHD occurring after allo-HSCT could be predicted from the microbiota composition at all three body sites prior to HSCT. The reconstitution of CD4+ T cells, TH17, and B cells was associated with distinct taxa of the gut, oral, and nasal microbiota. CONCLUSIONS This study reveals for the first time bacteria in the mouth and nose that may predict aGvHD. Monitoring of the microbiota at different body sites in HSCT patients and particularly through involvement of samples prior to transplantation may be of prognostic value and could assist in guiding personalized treatment strategies. The identification of distinct bacteria that have a potential to predict post-transplant aGvHD might provide opportunities for an improved preventive clinical management, including a modulation of microbiomes. The host-microbiota associations shared between several body sites might also support an implementation of more feasible oral and nasal swab sampling-based analyses. Altogether, the findings suggest that the microbiota and host factors together could provide actionable information to guiding precision medicine. Video Abstract.
Collapse
Affiliation(s)
- Anna Cäcilia Ingham
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
- Present address: Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Katrine Kielsen
- Institute for Inflammation Research, Department of Rheumatology and Spine Disease, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Hanne Mordhorst
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Marianne Ifversen
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Klaus Gottlob Müller
- Institute for Inflammation Research, Department of Rheumatology and Spine Disease, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Institute of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Sünje Johanna Pamp
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark.
- Present address: Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
| |
Collapse
|
14
|
Lossius AH, Sundnes O, Ingham AC, Edslev SM, Bjørnholt JV, Lilje B, Bradley M, Asad S, Haraldsen G, Skytt-Andersen P, Holm JØ, Berents TL. Shifts in the Skin Microbiota after UVB Treatment in Adult Atopic Dermatitis. Dermatology 2021; 238:109-120. [PMID: 33887725 DOI: 10.1159/000515236] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/28/2021] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The pathophysiology in atopic dermatitis (AD) is not fully understood, but immune dysfunction, skin barrier defects, and alterations of the skin microbiota are thought to play important roles. AD skin is frequently colonized with Staphylococcus aureus (S. aureus) and microbial diversity on lesional skin (LS) is reduced compared to on healthy skin. Treatment with narrow-band ultraviolet B (nb-UVB) leads to clinical improvement of the eczema and reduced abundance of S. aureus. However, in-depth knowledge of the temporal dynamics of the skin microbiota in AD in response to nb-UVB treatment is lacking and could provide important clues to decipher whether the microbial changes are primary drivers of the disease, or secondary to the inflammatory process. OBJECTIVES To map the temporal shifts in the microbiota of the skin, nose, and throat in adult AD patients after nb-UVB treatment. METHODS Skin swabs were taken from lesional AD skin (n = 16) before and after 3 treatments of nb-UVB, and after 6-8 weeks of full-body treatment. We also obtained samples from non-lesional skin (NLS) and from the nose and throat. All samples were characterized by 16S rRNA gene sequencing. RESULTS We observed shifts towards higher diversity in the microbiota of lesional AD skin after 6-8 weeks of treatment, while the microbiota of NLS and of the nose/throat remained unchanged. After only 3 treatments with nb-UVB, there were no significant changes in the microbiota. CONCLUSION Nb-UVB induces changes in the skin microbiota towards higher diversity, but the microbiota of the nose and throat are not altered.
Collapse
Affiliation(s)
- Astrid Haaskjold Lossius
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Dermatology, Oslo University Hospital, Oslo, Norway.,Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Olav Sundnes
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Dermatology, Oslo University Hospital, Oslo, Norway.,Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Anna Cäcilia Ingham
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Sofie Marie Edslev
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jørgen Vildershøj Bjørnholt
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Berit Lilje
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Maria Bradley
- Division of Dermatology and Venereology, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Samina Asad
- Division of Dermatology and Venereology, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Guttorm Haraldsen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Paal Skytt-Andersen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jan-Øivind Holm
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Department of Dermatology, Oslo University Hospital, Oslo, Norway
| | - Teresa Løvold Berents
- Department of Dermatology, Oslo University Hospital, Oslo, Norway.,Regional Unit of Asthma, Allergy and Hypersensitivity, Oslo University Hospital, Oslo, Norway
| |
Collapse
|
15
|
Edslev SM, Andersen PS, Agner T, Saunte DML, Ingham AC, Johannesen TB, Clausen ML. Identification of cutaneous fungi and mites in adult atopic dermatitis: analysis by targeted 18S rRNA amplicon sequencing. BMC Microbiol 2021; 21:72. [PMID: 33663381 PMCID: PMC7934438 DOI: 10.1186/s12866-021-02139-9] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 02/25/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Atopic dermatitis (AD) patients have an altered skin bacterial community, with an abundance of Staphylococcus aureus associated with flares, highlighting that microbial organisms may be important for disease exacerbation. Despite strong evidence of association between bacterial skin colonisation and AD, very limited knowledge regarding the eukaryotic microbial community, including fungi and ectoparasites, in AD exists. In this study, we compared the skin and nasal eukaryotic microbial community between adult AD patients (n = 55) and non-AD healthy controls (n = 45) using targeted 18S rRNA amplicon sequencing. Analysis was based on the presence or absence of eukaryotic microorganisms. RESULTS The cutaneous composition of the eukaryotic microbial community and the alpha-diversity differed significantly between AD patients and non-AD individuals, with increased species richness on AD skin. Alpha-diversity and beta-diversity were similar on lesional and non-lesional skin of patients. The ectoparasite Demodex folliculorum and the yeast Geotrichum candidum were significantly more prevalent on the skin of AD patients. The prevalence of D. folliculorum on lesional skin was greater among patients recently treated with topical corticosteroid. Malassezia was one of the most frequently detected genera at all sites, with M. globosa and M. restricta being the most prevalent. M. restricta was under represented in the anterior nares of AD patients as compared to the non-AD control population. CONCLUSION Significant differences in the eukaryotic microbial communities were found between AD patients and non-AD individuals, with the most striking finding being the significantly overrepresentation of D. folliculorum on AD skin. Whether D. folliculorum can contribute to skin inflammation in AD needs further investigation.
Collapse
Affiliation(s)
- Sofie Marie Edslev
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark.
| | - Paal Skytt Andersen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark.,Department of Veterinary and Animal Sciences, University of Copenhage, Frederiksberg, Denmark
| | - Tove Agner
- Department of Dermatology, Bispebjerg University Hospital, Copenhagen, Denmark
| | - Ditte Marie Lindhardt Saunte
- Department of Dermatology, Zealand University Hospital, Roskilde, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Anna Cäcilia Ingham
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Thor Bech Johannesen
- Department of Bacteria, Parasites, and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Maja-Lisa Clausen
- Department of Dermatology, Bispebjerg University Hospital, Copenhagen, Denmark
| |
Collapse
|
16
|
Edslev SM, Olesen CM, Nørreslet LB, Ingham AC, Iversen S, Lilje B, Clausen ML, Jensen JS, Stegger M, Agner T, Andersen PS. Staphylococcal Communities on Skin Are Associated with Atopic Dermatitis and Disease Severity. Microorganisms 2021; 9:microorganisms9020432. [PMID: 33669791 PMCID: PMC7921937 DOI: 10.3390/microorganisms9020432] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 12/16/2022] Open
Abstract
The skin microbiota of atopic dermatitis (AD) patients is characterized by increased Staphylococcus aureus colonization, which exacerbates disease symptoms and has been linked to reduced bacterial diversity. Skin bacterial communities in AD patients have mostly been described at family and genus levels, while species-level characterization has been limited. In this study, we investigated the role of the bacteria belonging to the Staphylococcus genus using targeted sequencing of the tuf gene with genus-specific primers. We compared staphylococcal communities on lesional and non-lesional skin of AD patients, as well as AD patients with healthy controls, and determined the absolute abundance of bacteria present at each site. We observed that the staphylococcal community, bacterial alpha diversity, and bacterial densities were similar on lesional and non-lesional skin, whereas AD severity was associated with significant changes in staphylococcal composition. Increased S. aureus, Staphylococcus capitis, and Staphylococcus lugdunensis abundances were correlated with increased severity. Conversely, Staphylococcus hominis abundance was negatively correlated with severity. Furthermore, S. hominis relative abundance was reduced on AD skin compared to healthy skin. In conclusion, various staphylococcal species appear to be important for skin health.
Collapse
Affiliation(s)
- Sofie Marie Edslev
- Bacteria, Parasites, and Fungi, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark; (A.C.I.); (S.I.); (B.L.); (J.S.J.); (M.S.); (P.S.A.)
- Correspondence:
| | - Caroline Meyer Olesen
- Department of Dermatology, Bispebjerg Hospital, Bispebjerg bakke 23, 2400 Copenhagen, Denmark; (C.M.O.); (L.B.N.); (M.-L.C.); (T.A.)
| | - Line Brok Nørreslet
- Department of Dermatology, Bispebjerg Hospital, Bispebjerg bakke 23, 2400 Copenhagen, Denmark; (C.M.O.); (L.B.N.); (M.-L.C.); (T.A.)
| | - Anna Cäcilia Ingham
- Bacteria, Parasites, and Fungi, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark; (A.C.I.); (S.I.); (B.L.); (J.S.J.); (M.S.); (P.S.A.)
| | - Søren Iversen
- Bacteria, Parasites, and Fungi, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark; (A.C.I.); (S.I.); (B.L.); (J.S.J.); (M.S.); (P.S.A.)
| | - Berit Lilje
- Bacteria, Parasites, and Fungi, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark; (A.C.I.); (S.I.); (B.L.); (J.S.J.); (M.S.); (P.S.A.)
| | - Maja-Lisa Clausen
- Department of Dermatology, Bispebjerg Hospital, Bispebjerg bakke 23, 2400 Copenhagen, Denmark; (C.M.O.); (L.B.N.); (M.-L.C.); (T.A.)
| | - Jørgen Skov Jensen
- Bacteria, Parasites, and Fungi, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark; (A.C.I.); (S.I.); (B.L.); (J.S.J.); (M.S.); (P.S.A.)
| | - Marc Stegger
- Bacteria, Parasites, and Fungi, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark; (A.C.I.); (S.I.); (B.L.); (J.S.J.); (M.S.); (P.S.A.)
| | - Tove Agner
- Department of Dermatology, Bispebjerg Hospital, Bispebjerg bakke 23, 2400 Copenhagen, Denmark; (C.M.O.); (L.B.N.); (M.-L.C.); (T.A.)
| | - Paal Skytt Andersen
- Bacteria, Parasites, and Fungi, Statens Serum Institut, Artillerivej 5, 2300 Copenhagen, Denmark; (A.C.I.); (S.I.); (B.L.); (J.S.J.); (M.S.); (P.S.A.)
- Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 15, 1870 Frederiksberg, Denmark
| |
Collapse
|
17
|
Iversen S, Johannesen TB, Ingham AC, Edslev SM, Tevell S, Månsson E, Nilsdotter-Augustinsson Å, Söderquist B, Stegger M, Andersen PS. Alteration of Bacterial Communities in Anterior Nares and Skin Sites of Patients Undergoing Arthroplasty Surgery: Analysis by 16S rRNA and Staphylococcal-Specific tuf Gene Sequencing. Microorganisms 2020; 8:E1977. [PMID: 33322779 PMCID: PMC7763315 DOI: 10.3390/microorganisms8121977] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/07/2020] [Accepted: 12/08/2020] [Indexed: 12/24/2022] Open
Abstract
The aim was to study alterations of bacterial communities in patients undergoing hip or knee arthroplasty to assess the impact of chlorhexidine gluconate soap decolonisation and systemic antibiotic prophylaxis. A Swedish multicentre, prospective collection of samples obtained from elective arthroplasty patients (n = 83) by swabbing anterior nares, skin sites in the groin and the site of planned surgery, before and after arthroplasty surgery, was analysed by 16S rRNA (V3-V4) gene sequencing and a complementary targeted tuf gene sequencing approach to comprehensively characterise alterations in staphylococcal communities. Significant reductions in alpha diversity was detected for both bacterial (p = 0.04) and staphylococcal (p = 0.03) groin communities after arthroplasty surgery with significant reductions in relative Corynebacterium (p = 0.001) abundance and Staphylococcus hominis (p = 0.01) relative staphylococcal abundance. In nares, significant reductions occurred for Staphylococcus hominis (p = 0.02), Staphylococcus haemolyticus (p = 0.02), and Staphylococcus pasteuri (p = 0.003) relative to other staphylococci. Staphylococcus aureus colonised 35% of anterior nares before and 26% after arthroplasty surgery. Staphylococcus epidermidis was the most abundant staphylococcal species at all sampling sites. No bacterial genus or staphylococcal species increased significantly after arthroplasty surgery. Application of a targeted tuf gene sequencing approach provided auxiliary staphylococcal community profiles and allowed species-level characterisation directly from low biomass clinical samples.
Collapse
Affiliation(s)
- Søren Iversen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark; (T.B.J.); (A.C.I.); (S.M.E.); (M.S.); (P.S.A.)
| | - Thor Bech Johannesen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark; (T.B.J.); (A.C.I.); (S.M.E.); (M.S.); (P.S.A.)
| | - Anna Cäcilia Ingham
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark; (T.B.J.); (A.C.I.); (S.M.E.); (M.S.); (P.S.A.)
| | - Sofie Marie Edslev
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark; (T.B.J.); (A.C.I.); (S.M.E.); (M.S.); (P.S.A.)
| | - Staffan Tevell
- Department of Infectious Diseases and Centre for Clinical Research and Education, County Council of Värmland, SE-651 82 Karlstad, Sweden;
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden; (E.M.); (B.S.)
| | - Emeli Månsson
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden; (E.M.); (B.S.)
- Centre for Clinical Research, Hospital Västmanland, Uppsala University, Region Västmanland, SE‐721 89 Västerås, Sweden
| | - Åsa Nilsdotter-Augustinsson
- Department of Infectious Diseases and Department of Clinical and Biomedical Sciences, Linköping University, SE-581 83 Norrköping, Sweden;
| | - Bo Söderquist
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden; (E.M.); (B.S.)
- Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark; (T.B.J.); (A.C.I.); (S.M.E.); (M.S.); (P.S.A.)
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, SE-701 82 Örebro, Sweden; (E.M.); (B.S.)
| | - Paal Skytt Andersen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, 2300 Copenhagen, Denmark; (T.B.J.); (A.C.I.); (S.M.E.); (M.S.); (P.S.A.)
| |
Collapse
|
18
|
Rendboe AK, Johannesen TB, Ingham AC, Månsson E, Iversen S, Baig S, Edslev S, Jensen JS, Söderquist B, Andersen PS, Stegger M. The Epidome - a species-specific approach to assess the population structure and heterogeneity of Staphylococcus epidermidis colonization and infection. BMC Microbiol 2020; 20:362. [PMID: 33243146 PMCID: PMC7691061 DOI: 10.1186/s12866-020-02041-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/09/2020] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Although generally known as a human commensal, Staphylococcus epidermidis is also an opportunistic pathogen that can cause nosocomial infections related to foreign body materials and immunocompromized patients. Infections are often caused by multidrug-resistant (MDR) lineages that are difficult and costly to treat, and can have a major adverse impact on patients' quality of life. Heterogeneity is a common phenomenon in both carriage and infection, but present methodology for detection of this is laborious or expensive. In this study, we present a culture-independent method, labelled Epidome, based on an amplicon sequencing-approach to deliver information beyond species level on primary samples and to elucidate clonality, population structure and temporal stability or niche selection of S. epidermidis communities. RESULTS Based on an assessment of > 800 genes from the S. epidermidis core genome, we identified genes with variable regions, which in combination facilitated the differentiation of phylogenetic clusters observed in silico, and allowed classification down to lineage level. A duplex PCR, combined with an amplicon sequencing protocol, and a downstream analysis pipeline were designed to provide subspecies information from primary samples. Additionally, a probe-based qPCR was designed to provide valuable absolute abundance quantification of S. epidermidis. The approach was validated on isolates representing skin commensals and on genomic mock communities with a sensitivity of < 10 copies/μL. The method was furthermore applied to a sample set of primary skin and nasal samples, revealing a high degree of heterogeneity in the S. epidermidis populations. Additionally, the qPCR showed a high degree of variation in absolute abundance of S. epidermidis. CONCLUSIONS The Epidome method is designed for use on primary samples to obtain important information on S. epidermidis abundance and diversity beyond species-level to answer questions regarding the emergence and dissemination of nosocomial lineages, investigating clonality of S. epidermidis communities, population dynamics, and niche selection. Our targeted-sequencing method allows rapid differentiation and identification of clinically important nosocomial lineages in low-biomass samples such as skin samples.
Collapse
Affiliation(s)
- Amalie Katrine Rendboe
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Thor Bech Johannesen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Anna Cäcilia Ingham
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Emeli Månsson
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Centre for Clinical Research, Hospital of Västmanland, Region Västmanland - Uppsala University, Västerås, Sweden
| | - Søren Iversen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Sharmin Baig
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Sofie Edslev
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Jørgen Skov Jensen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Bo Söderquist
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Paal Skytt Andersen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Stegger
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark.
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.
| |
Collapse
|
19
|
Ingham AC, Kielsen K, Cilieborg MS, Lund O, Holmes S, Aarestrup FM, Müller KG, Pamp SJ. Specific gut microbiome members are associated with distinct immune markers in pediatric allogeneic hematopoietic stem cell transplantation. Microbiome 2019; 7:131. [PMID: 31519210 PMCID: PMC6744702 DOI: 10.1186/s40168-019-0745-z] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 08/29/2019] [Indexed: 05/11/2023]
Abstract
BACKGROUND Increasing evidence reveals the importance of the microbiome in health and disease and inseparable host-microbial dependencies. Host-microbe interactions are highly relevant in patients receiving allogeneic hematopoietic stem cell transplantation (HSCT), i.e., a replacement of the cellular components of the patients' immune system with that of a foreign donor. HSCT is employed as curative immunotherapy for a number of non-malignant and malignant hematologic conditions, including cancers such as acute lymphoblastic leukemia. The procedure can be accompanied by severe side effects such as infections, acute graft-versus-host disease (aGvHD), and death. Here, we performed a longitudinal analysis of immunological markers, immune reconstitution and gut microbiota composition in relation to clinical outcomes in children undergoing HSCT. Such an analysis could reveal biomarkers, e.g., at the time point prior to HSCT, that in the future could be used to predict which patients are of high risk in relation to side effects and clinical outcomes and guide treatment strategies accordingly. RESULTS In two multivariate analyses (sparse partial least squares regression and canonical correspondence analysis), we identified three consistent clusters: (1) high concentrations of the antimicrobial peptide human beta-defensin 2 (hBD2) prior to the transplantation in patients with high abundances of Lactobacillaceae, who later developed moderate or severe aGvHD and exhibited high mortality. (2) Rapid reconstitution of NK and B cells in patients with high abundances of obligate anaerobes such as Ruminococcaceae, who developed no or mild aGvHD and exhibited low mortality. (3) High inflammation, indicated by high levels of C-reactive protein, in patients with high abundances of facultative anaerobic bacteria such as Enterobacteriaceae. Furthermore, we observed that antibiotic treatment influenced the bacterial community state. CONCLUSIONS We identify multivariate associations between specific microbial taxa, host immune markers, immune cell reconstitution, and clinical outcomes in relation to HSCT. Our findings encourage further investigations into establishing longitudinal surveillance of the intestinal microbiome and relevant immune markers, such as hBD2, in HSCT patients. Profiling of the microbiome may prove useful as a prognostic tool that could help identify patients at risk of poor immune reconstitution and adverse outcomes, such as aGvHD and death, upon HSCT, providing actionable information in guiding precision medicine.
Collapse
Affiliation(s)
- Anna Cäcilia Ingham
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Katrine Kielsen
- Institute for Inflammation Research, Department of Rheumatology and Spine Disease, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Malene Skovsted Cilieborg
- Comparative Pediatrics and Nutrition, Department of Clinical Veterinary and Animal Science, University of Copenhagen, Frederiksberg, Denmark
| | - Ole Lund
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Susan Holmes
- Department of Statistics, Stanford University, Stanford, USA
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Klaus Gottlob Müller
- Institute for Inflammation Research, Department of Rheumatology and Spine Disease, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital Rigshospitalet, Copenhagen, Denmark
| | - Sünje Johanna Pamp
- Research Group for Genomic Epidemiology, Technical University of Denmark, Kongens Lyngby, Denmark.
| |
Collapse
|