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Anderson AC, von Ohle C, Frese C, Boutin S, Bridson C, Schoilew K, Peikert SA, Hellwig E, Pelz K, Wittmer A, Wolff D, Al-Ahmad A. The oral microbiota is a reservoir for antimicrobial resistance: resistome and phenotypic resistance characteristics of oral biofilm in health, caries, and periodontitis. Ann Clin Microbiol Antimicrob 2023; 22:37. [PMID: 37179329 PMCID: PMC10183135 DOI: 10.1186/s12941-023-00585-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 04/13/2023] [Indexed: 05/15/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is an ever-growing threat to modern medicine and, according to the latest reports, it causes nearly twice as many deaths globally as AIDS or malaria. Elucidating reservoirs and dissemination routes of antimicrobial resistance genes (ARGs) are essential in fighting AMR. Human commensals represent an important reservoir, which is underexplored for the oral microbiota. Here, we set out to investigate the resistome and phenotypic resistance of oral biofilm microbiota from 179 orally healthy (H), caries active (C), and periodontally diseased (P) individuals (TRN: DRKS00013119, Registration date: 22.10.2022). The samples were analysed using shotgun metagenomic sequencing combined, for the first time, with culture technique. A selection of 997 isolates was tested for resistance to relevant antibiotics. RESULTS The shotgun metagenomics sequencing resulted in 2,069,295,923 reads classified into 4856 species-level OTUs. PERMANOVA analysis of beta-diversity revealed significant differences between the groups regarding their microbiota composition and their ARG profile. The samples were clustered into three ecotypes based on their microbial composition. The bacterial composition of H and C samples greatly overlapped and was based on ecotypes 1 and 2 whereas ecotype 3 was only detected in periodontitis. We found 64 ARGs conveying resistance to 36 antibiotics, particularly to tetracycline, macrolide-lincosamide-streptogramin, and beta-lactam antibiotics, and a correspondingly high prevalence of phenotypic resistance. Based on the microbiota composition, these ARGs cluster in different resistotypes, and a higher prevalence is found in healthy and caries active than in periodontally diseased individuals. There was a significant association between the resistotypes and the ecotypes. Although numerous associations were found between specific antibiotic resistance and bacterial taxa, only a few taxa showed matching associations with both genotypic and phenotypic analyses. CONCLUSIONS Our findings show the importance of the oral microbiota from different niches within the oral cavity as a reservoir for antibiotic resistance. Additionally, the present study showed the need for using more than one method to reveal antibiotic resistance within the total oral biofilm, as a clear mismatch between the shotgun metagenomics method and the phenotypic resistance characterization was shown.
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Affiliation(s)
- A C Anderson
- Department of Operative Dentistry and Periodontology, Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Straße 55, 79106, Freiburg, Germany
| | - C von Ohle
- Department of Conservative Dentistry, Periodontology and Endodontology, University Centre of Dentistry, Oral Medicine and Maxillofacial Surgery, University Hospital Tübingen, Tübingen, Germany
| | - C Frese
- Department of Conservative Dentistry, Clinic for Oral, Dental and Maxillofacial Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - S Boutin
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - C Bridson
- Department of Infectious Diseases, Medical Microbiology and Hygiene, Heidelberg University Hospital, Heidelberg, Germany
- Translational Lung Research Center Heidelberg (TLRC), German Center for Lung Research (DZL), Heidelberg, Germany
| | - K Schoilew
- Department of Conservative Dentistry, Clinic for Oral, Dental and Maxillofacial Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - S A Peikert
- Department of Operative Dentistry and Periodontology, Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Straße 55, 79106, Freiburg, Germany
| | - E Hellwig
- Department of Operative Dentistry and Periodontology, Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Straße 55, 79106, Freiburg, Germany
| | - K Pelz
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - A Wittmer
- Institute of Medical Microbiology and Hygiene, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - D Wolff
- Department of Conservative Dentistry, Clinic for Oral, Dental and Maxillofacial Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - A Al-Ahmad
- Department of Operative Dentistry and Periodontology, Medical Center, Faculty of Medicine, University of Freiburg, Hugstetter Straße 55, 79106, Freiburg, Germany.
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Bridson C, Vellaniparambil L, Antwis RE, Müller W, Gilman RT, Rowntree JK. Genetic diversity of honeybee colonies predicts gut bacterial diversity of individual colony members. Environ Microbiol 2022; 24:5643-5653. [PMID: 35920034 PMCID: PMC10087737 DOI: 10.1111/1462-2920.16150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 07/18/2022] [Accepted: 07/22/2022] [Indexed: 01/13/2023]
Abstract
The gut microbiota of social bees is relatively simple and dominated by a set of core taxa found consistently in individuals around the world. Yet, variation remains and can affect host health. We characterized individual- and regional-scale variation in honeybee (Apis mellifera) gut microbiota from 64 colonies in North-West England by sequencing the V4 region of the 16S rRNA gene and asked whether microbiota were influenced by host genotype and landscape composition. We also characterized the genotypes of individual bees and the land cover surrounding each colony. The literature-defined core taxa dominated across the region despite the varied environments. However, there was variation in the relative abundance of core taxa, and colony membership explained much of this variation. Individuals from more genetically diverse colonies had more diverse microbiotas, but individual genetic diversity did not influence gut microbial diversity. There were weak trends for colonies in more similar landscapes to have more similar microbiota, and for bees from more urban landscapes to have less diverse microbiota. To our knowledge, this is the first report for any species that the gut bacterial communities of individuals are influenced by the genotypes of others in the population.
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Affiliation(s)
- Calum Bridson
- Faculty of Science and Engineering, University of Manchester, Manchester, UK.,Faculty of Biology Medicine and Health, Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK.,Department of Infectious Diseases, Medical Microbiology and Hygiene, University of Heidelberg, Heidelberg, Germany.,Translational Lung Research Centre (TLRC), Heidelberg, Germany
| | - Latha Vellaniparambil
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK
| | - Rachel E Antwis
- School of Science, Engineering and Environment, University of Salford, Salford, UK
| | - Werner Müller
- Faculty of Biology Medicine and Health, Lydia Becker Institute of Immunology and Inflammation, University of Manchester, Manchester, UK.,Miltenyi Biotec, Bergisch Gladbach, Germany
| | - R Tucker Gilman
- Faculty of Science and Engineering, University of Manchester, Manchester, UK
| | - Jennifer K Rowntree
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, Manchester, UK.,School of Biological and Marine Sciences, University of Plymouth, Plymouth, UK
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Frey DL, Bridson C, Dittrich S, Graeber SY, Stahl M, Wege S, Herth F, Sommerburg O, Schultz C, Dalpke A, Mall MA, Boutin S. Changes in Microbiome Dominance Are Associated With Declining Lung Function and Fluctuating Inflammation in People With Cystic Fibrosis. Front Microbiol 2022; 13:885822. [PMID: 35633718 PMCID: PMC9136159 DOI: 10.3389/fmicb.2022.885822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/26/2022] [Indexed: 11/30/2022] Open
Abstract
Airway inflammation and microbiome dysbiosis are hallmarks of cystic fibrosis (CF) lung disease. However, longitudinal studies are needed to decipher which factors contribute to the long-term evolution of these key features of CF. We therefore evaluated the relationship between fluctuation in microbiome and inflammatory parameters in a longitudinal study including a short- (1-year) and a long-term (3+ years) period. We collected 118 sputum samples from 26 CF adult patients and analyzed them by 16S rRNA gene sequencing. We measured the levels of inflammatory cytokines, neutrophil elastase, and anti-proteinases; lung function (FEV1% predicted); and BMI. The longitudinal evolution was analyzed based on (i) the rates of changes; (ii) the intra-patient stability of the variables; and (iii) the dependency of the rates of changes on the baseline values. We observed that the diversity of the microbiome was highly variable over a 1-year period, while the inflammatory markers showed a slower evolution, with significant changes only observed in the 3+ year cohort. Further, the degree of fluctuation of the biomass and the dominance of the microbiome were associated with changes in inflammatory markers, especially IL-1β and IL-8. This longitudinal study demonstrates for the first time that the long-term establishment and periodical variation of the abundance of a dominant pathogen is associated with a more severe increase in inflammation. This result indicates that a single time point or 1-year study might fail to reveal the correlation between microbial evolution and clinical degradation in cystic fibrosis.
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Affiliation(s)
- Dario L. Frey
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany
| | - Calum Bridson
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University of Heidelberg, Heidelberg, Germany
| | - Susanne Dittrich
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany
- Department of Pneumology and Critical Care Medicine, Thoraxklinik at the University Hospital Heidelberg, Heidelberg, Germany
| | - Simon Y. Graeber
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany
- Division of Pediatric Pulmonology and Allergology and Cystic Fibrosis Center, Department of Pediatrics, University of Heidelberg, Heidelberg, Germany
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany
| | - Mirjam Stahl
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Translational Pulmonology, University of Heidelberg, Heidelberg, Germany
- Division of Pediatric Pulmonology and Allergology and Cystic Fibrosis Center, Department of Pediatrics, University of Heidelberg, Heidelberg, Germany
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany
| | - Sabine Wege
- Department of Pneumology and Critical Care Medicine, Thoraxklinik at the University Hospital Heidelberg, Heidelberg, Germany
| | - Felix Herth
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Pneumology and Critical Care Medicine, Thoraxklinik at the University Hospital Heidelberg, Heidelberg, Germany
| | - Olaf Sommerburg
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Division of Pediatric Pulmonology and Allergology and Cystic Fibrosis Center, Department of Pediatrics, University of Heidelberg, Heidelberg, Germany
| | - Carsten Schultz
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Chemical Physiology and Biochemistry, Oregon Health & Science University, Portland, OR, United States
| | - Alexander Dalpke
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University of Heidelberg, Heidelberg, Germany
- Institute of Medical Microbiology and Virology, Technische Universität Dresden, Dresden, Germany
| | - Marcus A. Mall
- Department of Pediatric Respiratory Medicine, Immunology and Critical Care Medicine and Cystic Fibrosis Center, Charité-Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
- German Center for Lung Research (DZL), Associated Partner Site, Berlin, Germany
| | - Sébastien Boutin
- Translational Lung Research Center (TLRC), Member of the German Center for Lung Research (DZL), Heidelberg, Germany
- Department of Infectious Diseases, Medical Microbiology and Hygiene, University of Heidelberg, Heidelberg, Germany
- *Correspondence: Sébastien Boutin,
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Harrison XA, McDevitt AD, Dunn JC, Griffiths SM, Benvenuto C, Birtles R, Boubli JP, Bown K, Bridson C, Brooks DR, Browett SS, Carden RF, Chantrey J, Clever F, Coscia I, Edwards KL, Ferry N, Goodhead I, Highlands A, Hopper J, Jackson J, Jehle R, da Cruz Kaizer M, King T, Lea JMD, Lenka JL, McCubbin A, McKenzie J, de Moraes BLC, O'Meara DB, Pescod P, Preziosi RF, Rowntree JK, Shultz S, Silk MJ, Stockdale JE, Symondson WOC, de la Pena MV, Walker SL, Wood MD, Antwis RE. Fungal microbiomes are determined by host phylogeny and exhibit widespread associations with the bacterial microbiome. Proc Biol Sci 2021; 288:20210552. [PMID: 34403636 PMCID: PMC8370808 DOI: 10.1098/rspb.2021.0552] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/14/2021] [Indexed: 12/30/2022] Open
Abstract
Interactions between hosts and their resident microbial communities are a fundamental component of fitness for both agents. Though recent research has highlighted the importance of interactions between animals and their bacterial communities, comparative evidence for fungi is lacking, especially in natural populations. Using data from 49 species, we present novel evidence of strong covariation between fungal and bacterial communities across the host phylogeny, indicative of recruitment by hosts for specific suites of microbes. Using co-occurrence networks, we demonstrate marked variation across host taxonomy in patterns of covariation between bacterial and fungal abundances. Host phylogeny drives differences in the overall richness of bacterial and fungal communities, but the effect of diet on richness was only evident in the mammalian gut microbiome. Sample type, tissue storage and DNA extraction method also affected bacterial and fungal community composition, and future studies would benefit from standardized approaches to sample processing. Collectively these data indicate fungal microbiomes may play a key role in host fitness and suggest an urgent need to study multiple agents of the animal microbiome to accurately determine the strength and ecological significance of host-microbe interactions.
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Affiliation(s)
| | - Allan D. McDevitt
- School of Science, Engineering and Environment, University of Salford, UK
| | - Jenny C. Dunn
- School of Life Sciences, Joseph Banks Laboratories, University of Lincoln, UK
| | - Sarah M. Griffiths
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
| | - Chiara Benvenuto
- School of Science, Engineering and Environment, University of Salford, UK
| | - Richard Birtles
- School of Science, Engineering and Environment, University of Salford, UK
| | - Jean P. Boubli
- School of Science, Engineering and Environment, University of Salford, UK
| | - Kevin Bown
- School of Science, Engineering and Environment, University of Salford, UK
| | - Calum Bridson
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
- Department of Earth and Environmental Sciences, University of Manchester, UK
| | - Darren R. Brooks
- School of Science, Engineering and Environment, University of Salford, UK
| | - Samuel S. Browett
- School of Science, Engineering and Environment, University of Salford, UK
| | - Ruth F. Carden
- School of Archaeology, University College Dublin, Ireland
- Wildlife Ecological and Osteological Consultancy, Wicklow, Ireland
| | - Julian Chantrey
- Institute of Veterinary Science, University of Liverpool, UK
| | - Friederike Clever
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
- Smithsonian Tropical Research Institute, Ancon, Republic of Panama
| | - Ilaria Coscia
- School of Science, Engineering and Environment, University of Salford, UK
| | - Katie L. Edwards
- North of England Zoological Society, Chester Zoo, Upton-by-Chester, UK
| | - Natalie Ferry
- School of Science, Engineering and Environment, University of Salford, UK
| | - Ian Goodhead
- School of Science, Engineering and Environment, University of Salford, UK
| | - Andrew Highlands
- School of Science, Engineering and Environment, University of Salford, UK
| | - Jane Hopper
- The Aspinall Foundation, Port Lympne Reserve, Hythe, Kent, UK
| | - Joseph Jackson
- School of Science, Engineering and Environment, University of Salford, UK
| | - Robert Jehle
- School of Science, Engineering and Environment, University of Salford, UK
| | | | - Tony King
- The Aspinall Foundation, Port Lympne Reserve, Hythe, Kent, UK
- School of Anthropology and Conservation, University of Kent, UK
| | - Jessica M. D. Lea
- Department of Earth and Environmental Sciences, University of Manchester, UK
| | - Jessica L. Lenka
- School of Science, Engineering and Environment, University of Salford, UK
| | | | - Jack McKenzie
- School of Science, Engineering and Environment, University of Salford, UK
| | | | - Denise B. O'Meara
- School of Science and Computing, Waterford Institute of Technology, Ireland
| | - Poppy Pescod
- School of Science, Engineering and Environment, University of Salford, UK
| | - Richard F. Preziosi
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
| | - Jennifer K. Rowntree
- Ecology and Environment Research Centre, Department of Natural Sciences, Manchester Metropolitan University, UK
| | - Susanne Shultz
- Department of Earth and Environmental Sciences, University of Manchester, UK
| | | | - Jennifer E. Stockdale
- School of Biosciences, University of Cardiff, UK
- School of Life Sciences, University of Nottingham, UK
| | | | | | - Susan L. Walker
- North of England Zoological Society, Chester Zoo, Upton-by-Chester, UK
| | - Michael D. Wood
- School of Science, Engineering and Environment, University of Salford, UK
| | - Rachael E. Antwis
- School of Science, Engineering and Environment, University of Salford, UK
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5
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Cogni R, Cao C, Day JP, Bridson C, Jiggins FM. The genetic architecture of resistance to virus infection in Drosophila. Mol Ecol 2016; 25:5228-5241. [PMID: 27460507 PMCID: PMC5082504 DOI: 10.1111/mec.13769] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Revised: 07/03/2016] [Accepted: 07/05/2016] [Indexed: 12/18/2022]
Abstract
Variation in susceptibility to infection has a substantial genetic component in natural populations, and it has been argued that selection by pathogens may result in it having a simpler genetic architecture than many other quantitative traits. This is important as models of host-pathogen co-evolution typically assume resistance is controlled by a small number of genes. Using the Drosophila melanogaster multiparent advanced intercross, we investigated the genetic architecture of resistance to two naturally occurring viruses, the sigma virus and DCV (Drosophila C virus). We found extensive genetic variation in resistance to both viruses. For DCV resistance, this variation is largely caused by two major-effect loci. Sigma virus resistance involves more genes - we mapped five loci, and together these explained less than half the genetic variance. Nonetheless, several of these had a large effect on resistance. Models of co-evolution typically assume strong epistatic interactions between polymorphisms controlling resistance, but we were only able to detect one locus that altered the effect of the main effect loci we had mapped. Most of the loci we mapped were probably at an intermediate frequency in natural populations. Overall, our results are consistent with major-effect genes commonly affecting susceptibility to infectious diseases, with DCV resistance being a near-Mendelian trait.
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Affiliation(s)
- Rodrigo Cogni
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK.
- Department of Ecology, University of São Paulo, São Paulo, 05508-900, Brazil.
| | - Chuan Cao
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Jonathan P Day
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Calum Bridson
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
| | - Francis M Jiggins
- Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK
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