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Bargheet A, Klingenberg C, Esaiassen E, Hjerde E, Cavanagh JP, Bengtsson-Palme J, Pettersen VK. Development of early life gut resistome and mobilome across gestational ages and microbiota-modifying treatments. EBioMedicine 2023; 92:104613. [PMID: 37187112 DOI: 10.1016/j.ebiom.2023.104613] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/21/2023] [Accepted: 04/27/2023] [Indexed: 05/17/2023] Open
Abstract
BACKGROUND Gestational age (GA) and associated level of gastrointestinal tract maturation are major factors driving the initial gut microbiota composition in preterm infants. Besides, compared to term infants, premature infants often receive antibiotics to treat infections and probiotics to restore optimal gut microbiota. How GA, antibiotics, and probiotics modulate the microbiota's core characteristics, gut resistome and mobilome, remains nascent. METHODS We analysed metagenomic data from a longitudinal observational study in six Norwegian neonatal intensive care units to describe the bacterial microbiota of infants of varying GA and receiving different treatments. The cohort consisted of probiotic-supplemented and antibiotic-exposed extremely preterm infants (n = 29), antibiotic-exposed very preterm (n = 25), antibiotic-unexposed very preterm (n = 8), and antibiotic-unexposed full-term (n = 10) infants. The stool samples were collected on days of life 7, 28, 120, and 365, and DNA extraction was followed by shotgun metagenome sequencing and bioinformatical analysis. FINDINGS The top predictors of microbiota maturation were hospitalisation length and GA. Probiotic administration rendered the gut microbiota and resistome of extremely preterm infants more alike to term infants on day 7 and ameliorated GA-driven loss of microbiota interconnectivity and stability. GA, hospitalisation, and both microbiota-modifying treatments (antibiotics and probiotics) contributed to an elevated carriage of mobile genetic elements in preterm infants compared to term controls. Finally, Escherichia coli was associated with the highest number of antibiotic-resistance genes, followed by Klebsiella pneumoniae and Klebsiella aerogenes. INTERPRETATION Prolonged hospitalisation, antibiotics, and probiotic intervention contribute to dynamic alterations in resistome and mobilome, gut microbiota characteristics relevant to infection risk. FUNDING Odd-Berg Group, Northern Norway Regional Health Authority.
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Affiliation(s)
- Ahmed Bargheet
- Host-Microbe Interaction Research Group, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway; Paediatric Research Group, Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway; Center for New Antibacterial Strategies, UiT The Arctic University of Norway, Tromsø, Norway
| | - Claus Klingenberg
- Paediatric Research Group, Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway; Center for New Antibacterial Strategies, UiT The Arctic University of Norway, Tromsø, Norway; Department of Paediatrics, University Hospital of North Norway, Tromsø, Norway
| | - Eirin Esaiassen
- Paediatric Research Group, Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway; Department of Paediatrics, University Hospital of North Norway, Tromsø, Norway
| | - Erik Hjerde
- Center for New Antibacterial Strategies, UiT The Arctic University of Norway, Tromsø, Norway; Department of Chemistry, Norstruct, UiT The Arctic University of Norway, Tromsø, Norway
| | - Jorunn Pauline Cavanagh
- Paediatric Research Group, Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway; Center for New Antibacterial Strategies, UiT The Arctic University of Norway, Tromsø, Norway
| | - Johan Bengtsson-Palme
- Division of Systems Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, SE-412 96, Sweden; Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10A, Gothenburg, SE-413 46, Sweden; Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Veronika Kuchařová Pettersen
- Host-Microbe Interaction Research Group, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway; Paediatric Research Group, Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway; Center for New Antibacterial Strategies, UiT The Arctic University of Norway, Tromsø, Norway.
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Samara J, Moossavi S, Alshaikh B, Ortega VA, Pettersen VK, Ferdous T, Hoops SL, Soraisham A, Vayalumkal J, Dersch-Mills D, Gerber JS, Mukhopadhyay S, Puopolo K, Tompkins TA, Knights D, Walter J, Amin H, Arrieta MC. Supplementation with a probiotic mixture accelerates gut microbiome maturation and reduces intestinal inflammation in extremely preterm infants. Cell Host Microbe 2022; 30:696-711.e5. [PMID: 35550672 DOI: 10.1016/j.chom.2022.04.005] [Citation(s) in RCA: 63] [Impact Index Per Article: 31.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 02/08/2022] [Accepted: 04/11/2022] [Indexed: 11/19/2022]
Abstract
Probiotics are increasingly administered to premature infants to prevent necrotizing enterocolitis and neonatal sepsis. However, their effects on gut microbiome assembly and immunity are poorly understood. Using a randomized intervention trial in extremely premature infants, we tested the effects of a probiotic product containing four strains of Bifidobacterium species autochthonous to the infant gut and one Lacticaseibacillus strain on the compositional and functional trajectory of microbiome. Daily administration of the mixture accelerated the transition into a mature, term-like microbiome with higher stability and species interconnectivity. Besides infant age, Bifidobacterium strains and stool metabolites were the best predictors of microbiome maturation, and structural equation modeling confirmed probiotics as a major determinant for the trajectory of microbiome assembly. Bifidobacterium-driven microbiome maturation was also linked to an anti-inflammatory intestinal immune milieu. This demonstrates that Bifidobacterium strains are ecosystem engineers that lead to an acceleration of microbiome maturation and immunological consequences in extremely premature infants.
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Affiliation(s)
- Jumana Samara
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada; Health Sciences Centre, Winnipeg, MB, Canada
| | - Shirin Moossavi
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada; Microbiome and Microbial Ecology Interest Group (MMEIG), Universal Scientific Education and Research Network (USERN), Calgary, Canada
| | - Belal Alshaikh
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Calgary Zone Section of Neonatology, Calgary, AB, Canada
| | - Van A Ortega
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada
| | - Veronika Kuchařová Pettersen
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada; Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Tahsin Ferdous
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada
| | - Suzie L Hoops
- Biotechnology Institute and Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Amuchou Soraisham
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Calgary Zone Section of Neonatology, Calgary, AB, Canada
| | - Joseph Vayalumkal
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada
| | - Deonne Dersch-Mills
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Calgary Zone Section of Neonatology, Calgary, AB, Canada
| | - Jeffrey S Gerber
- Division of Infectious Diseases, Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sagori Mukhopadhyay
- Newborn Care at Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Karen Puopolo
- Newborn Care at Children's Hospital of Philadelphia, Philadelphia, PA, USA; Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | | | - Dan Knights
- Biotechnology Institute and Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Jens Walter
- School of Microbiology, Department of Medicine, and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Harish Amin
- Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; Calgary Zone Section of Neonatology, Calgary, AB, Canada
| | - Marie-Claire Arrieta
- Department of Physiology and Pharmacology, Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada; Department of Pediatrics, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB, Canada; International Microbiome Centre, University of Calgary, Calgary, AB, Canada.
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Pettersen VK, Dufour A, Arrieta MC. Metaproteomic profiling of fungal gut colonization in gnotobiotic mice. Anim Microbiome 2022; 4:14. [PMID: 35193703 PMCID: PMC8862486 DOI: 10.1186/s42523-022-00163-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 01/29/2022] [Indexed: 12/03/2022] Open
Abstract
Background Eukaryotic microbes can modulate mammalian host health and disease states, yet the molecular contribution of gut fungi remains nascent. We previously showed that mice exclusively colonised with fungi displayed increased sensitivity to allergic airway inflammation and had fecal metabolite profiles similar to germ-free mice. This marginal effect on the host metabolome suggested that fungi do not primarily use metabolites to modulate the host immune system. Methods To describe functional changes attributed to fungal colonisation, we performed mass spectrometry-based analyses of feces (Label-Free Quantitative; LFQ) and the small intestine (labeling with Tandem Mass Tag; TMT) of gnotobiotic mice colonised with defined consortia of twelve bacterial species, five fungal species, or both. We also evaluated the effect of microbiome perturbances on the metaproteome by analysing feces from mouse pups treated with an antibiotic or antifungal. Results We detected 6675 proteins in the mice feces, of which 3845 had determined LFQ levels. Analysis of variance showed changes in the different gnotobiotic mouse groups; specifically, 46% of 2860 bacterial, 15% of 580 fungal, and 76% of 405 mouse quantified proteins displayed differential levels. The antimicrobial treatments resulted in lasting changes in the bacterial and fungal proteomes, suggesting that the antimicrobials impacted the entire community. Fungal colonisation resulted in changes in host proteins functional in innate immunity as well as metabolism, predicting specific roles of gut fungi on host systems during early developmental stages. Several of the detected fungal proteins (3% of 1492) have been previously reported as part of extracellular vesicles and having immunomodulating properties. Using an isobaric labelling TMT approach for profiling low abundant proteins of the jejunal tissue, we confirmed that the five fungal species differentially impacted the host intestinal proteome compared to the bacterial consortium. The detected changes in mouse jejunal proteins (4% of 1514) were mainly driven by metabolic proteins. Conclusions We used quantitative proteomic profiling of gnotobiotic conditions to show how colonisation with selected fungal species impacts the host gut proteome. Our results suggest that an increased abundance of certain gut fungal species in early life may affect the developing intracellular attributes of epithelial and immune cells. Supplementary Information The online version contains supplementary material available at 10.1186/s42523-022-00163-2.
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Pettersen VK, Antunes LCM, Dufour A, Arrieta MC. Inferring early-life host and microbiome functions by mass spectrometry-based metaproteomics and metabolomics. Comput Struct Biotechnol J 2021; 20:274-286. [PMID: 35024099 PMCID: PMC8718658 DOI: 10.1016/j.csbj.2021.12.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 12/08/2021] [Accepted: 12/08/2021] [Indexed: 12/17/2022] Open
Abstract
Humans have a long-standing coexistence with microorganisms. In particular, the microbial community that populates the human gastrointestinal tract has emerged as a critical player in governing human health and disease. DNA and RNA sequencing techniques that map taxonomical composition and genomic potential of the gut community have become invaluable for microbiome research. However, deriving a biochemical understanding of how activities of the gut microbiome shape host development and physiology requires an expanded experimental design that goes beyond these approaches. In this review, we explore advances in high-throughput techniques based on liquid chromatography-mass spectrometry. These omics methods for the identification of proteins and metabolites have enabled direct characterisation of gut microbiome functions and the crosstalk with the host. We discuss current metaproteomics and metabolomics workflows for producing functional profiles, the existing methodological challenges and limitations, and recent studies utilising these techniques with a special focus on early life gut microbiome.
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Affiliation(s)
- Veronika Kuchařová Pettersen
- Research Group for Host-Microbe Interactions, Department of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
- Pediatric Research Group, Department of Clinical Medicine, UiT The Arctic University of Norway, Tromsø, Norway
- Centre for New Antibacterial Strategies, UiT The Arctic University of Norway, Tromsø, Norway
| | - Luis Caetano Martha Antunes
- Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
- National Institute of Science and Technology of Innovation on Diseases of Neglected Populations, Center for Technological Development in Health, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | - Antoine Dufour
- Department of Physiology & Pharmacology, University of Calgary, Calgary, Canada
| | - Marie-Claire Arrieta
- Department of Physiology & Pharmacology, University of Calgary, Calgary, Canada
- Department of Pediatrics, University of Calgary, Calgary, AB, Canada
- International Microbiome Centre, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
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Ali Mohammed MM, Pettersen VK, Nerland AH, Wiker HG, Bakken V. Label-free quantitative proteomic analysis of the oral bacteria Fusobacterium nucleatum and Porphyromonas gingivalis to identify protein features relevant in biofilm formation. Anaerobe 2021; 72:102449. [PMID: 34543761 DOI: 10.1016/j.anaerobe.2021.102449] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 07/24/2021] [Accepted: 09/14/2021] [Indexed: 11/28/2022]
Abstract
BACKGROUND The opportunistic pathogens Fusobacterium nucleatum and Porphyromonas gingivalis are Gram-negative bacteria associated with oral biofilm and periodontal disease. This study investigated interactions between F. nucleatum and P. gingivalis proteomes with the objective to identify proteins relevant in biofilm formation. METHODS We applied liquid chromatography-tandem mass spectrometry to determine the expressed proteome of F. nucleatum and P. gingivalis cells grown in biofilm or planktonic culture, and as mono- and dual-species models. The detected proteins were classified into functional categories and their label-free quantitative (LFQ) intensities statistically compared. RESULTS The proteomic analyses detected 1,322 F. nucleatum and 966 P. gingivalis proteins, including abundant virulence factors. Using univariate statistics, we identified significant changes between biofilm and planktonic culture (p-value ≤0.05) in 0,4% F. nucleatum, 7% P. gingivalis, and 14% of all proteins in the dual-species model. For both species, proteins involved in vitamin B2 (riboflavin) metabolism had significantly increased levels in biofilm. In both mono- and dual-species biofilms, P. gingivalis increased the production of proteins for translation, oxidation-reduction, and amino acid metabolism compared to planktonic cultures. However, when we compared LFQ intensities between mono- and dual-species, over 90% of the significantly changed P. gingivalis proteins had their levels reduced in biofilm and planktonic settings of the dual-species model. CONCLUSIONS The findings suggest that P. gingivalis reduces the production of multiple proteins because of the F. nucleatum presence. The results highlight the complex interactions of bacteria contributing to oral biofilms, which need to be considered in the design of prevention strategies.
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Affiliation(s)
| | | | - Audun H Nerland
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway.
| | - Harald G Wiker
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway.
| | - Vidar Bakken
- Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway.
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Pettersen VK, Steinsland H, Wiker HG. Front Cover: Distinct Metabolic Features of Pathogenic
Escherichia coli
and
Shigella
spp. Determined by Label‐Free Quantitative Proteomics. Proteomics 2021. [DOI: 10.1002/pmic.202170011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Pettersen VK, Steinsland H, Wiker HG. Distinct Metabolic Features of Pathogenic Escherichia coli and Shigella spp. Determined by Label-Free Quantitative Proteomics. Proteomics 2020; 21:e2000072. [PMID: 33025732 DOI: 10.1002/pmic.202000072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 09/04/2020] [Indexed: 11/07/2022]
Abstract
Escherichia coli and Shigella spp. causing illnesses in humans represent a genotypically and phenotypically diverse group of pathogens. Although E. coli diversity has been studied by comparative genomics, the intra-species variation at the proteome level is currently unknown. The proteomes of 16 pathogenic E. coli, 2 non-pathogenic E. coli, and 5 Shigella strains originating from 18 phylogenetic lineages are investigated. By applying label-free quantitative proteomics on trypsin-digested cell extracts from bacteria grown on blood agar, 4018 proteins are detected, 3285 of which arequantified, and 261 represented virulence factors. Of 753 proteins quantified in all strains, the levels of 153 vary substantially between strains and are functionally associated mostly with stress response and peripheral metabolism. The levels of proteins associated with the central metabolism vary considerably less than the levels of proteins from other metabolic pathways. Hierarchical clustering analysis based on the protein levels results in strains grouping that differ from that obtained by gene-based phylogenetic analysis. Finally, strains of some E. coli pathotypes have more similar protein profiles even when the strains are not genetically closely related. The results suggest that the degree of genetic relatedness may not necessarily be a good predictor of E. coli phenotypic characteristics.
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Affiliation(s)
- Veronika Kuchařová Pettersen
- The Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, Haukeland universitetssykehus, Laboratoriebygget, Bergen, 5020, Norway
| | - Hans Steinsland
- Centre for International Health, Department of Global Public Health and Primary Care, University of Bergen, Alrek helseklynge, blokk D, Årstadveien 17, Bergen, 5020, Norway.,Department of Biomedicine, University of Bergen, Jonas Lies vei 91, Bergen, 5020, Norway
| | - Harald G Wiker
- The Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, Haukeland universitetssykehus, Laboratoriebygget, Bergen, 5020, Norway
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Pettersen VK, Steinsland H, Wiker HG. Comparative Proteomics of Enterotoxigenic Escherichia coli Reveals Differences in Surface Protein Production and Similarities in Metabolism. J Proteome Res 2017; 17:325-336. [DOI: 10.1021/acs.jproteome.7b00593] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Veronika Kuchařová Pettersen
- The Gade Research Group for Infection and Immunity, Department of
Clinical Science, ‡Centre for International Health, Department of Global Public Health
and Primary Care, and §Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
| | - Hans Steinsland
- The Gade Research Group for Infection and Immunity, Department of
Clinical Science, ‡Centre for International Health, Department of Global Public Health
and Primary Care, and §Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
| | - Harald G. Wiker
- The Gade Research Group for Infection and Immunity, Department of
Clinical Science, ‡Centre for International Health, Department of Global Public Health
and Primary Care, and §Department of Biomedicine, University of Bergen, 5021 Bergen, Norway
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Mohammed MMA, Pettersen VK, Nerland AH, Wiker HG, Bakken V. Quantitative proteomic analysis of extracellular matrix extracted from mono- and dual-species biofilms of Fusobacterium nucleatum and Porphyromonas gingivalis. Anaerobe 2017; 44:133-142. [PMID: 28285095 DOI: 10.1016/j.anaerobe.2017.03.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/02/2017] [Accepted: 03/03/2017] [Indexed: 01/08/2023]
Abstract
The Gram-negative bacteria Fusobacterium nucleatum and Porphyromonas gingivalis are members of a complex dental biofilm associated with periodontal disease. In this study, we cultured F. nucleatum and P. gingivalis as mono- and dual-species biofilms, and analyzed the protein composition of the biofilms extracellular polymeric matrix (EPM) by high-resolution liquid chromatography-tandem mass spectrometry. Label-free quantitative proteomic analysis was used for identification of proteins and sequence-based functional characterization for their classification and prediction of possible roles in EPM. We identified 542, 93 and 280 proteins in the matrix of F. nucleatum, P. gingivalis, and the dual-species biofilm, respectively. Nearly 70% of all EPM proteins in the dual-species biofilm originated from F. nucleatum, and a majority of these were cytoplasmic proteins, suggesting an enhanced lysis of F. nucleatum cells. The proteomic analysis also indicated an interaction between the two species: 22 F. nucleatum proteins showed differential levels between the mono and dual-species EPMs, and 11 proteins (8 and 3 from F. nucleatum and P. gingivalis, respectively) were exclusively detected in the dual-species EPM. Oxidoreductases and chaperones were among the most abundant proteins identified in all three EPMs. The biofilm matrices in addition contained several known and hypothetical virulence proteins, which can mediate adhesion to the host cells and disintegration of the periodontal tissues. This study demonstrated that the biofilm matrix of two important periodontal pathogens consists of a multitude of proteins whose amounts and functionalities vary largely. Relatively high levels of several of the detected proteins might facilitate their potential use as targets for the inhibition of biofilm development.
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Affiliation(s)
- Marwan Mansoor Ali Mohammed
- The Gade Research Group for Infection and Immunity, Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway.
| | - Veronika Kuchařová Pettersen
- The Gade Research Group for Infection and Immunity, Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway.
| | - Audun H Nerland
- The Gade Research Group for Infection and Immunity, Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway.
| | - Harald G Wiker
- The Gade Research Group for Infection and Immunity, Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway.
| | - Vidar Bakken
- The Gade Research Group for Infection and Immunity, Department of Clinical Science, Faculty of Medicine and Dentistry, University of Bergen, Bergen, Norway.
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Kittang BR, Pettersen VK, Oppegaard O, Skutlaberg DH, Dale H, Wiker HG, Skrede S. Zoonotic necrotizing myositis caused by Streptococcus equi subsp. zooepidemicus in a farmer. BMC Infect Dis 2017; 17:147. [PMID: 28201995 PMCID: PMC5312586 DOI: 10.1186/s12879-017-2262-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 11/04/2016] [Accepted: 02/10/2017] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Streptococcus equi subsp. zooepidemicus is a beta-hemolytic group C streptococcus mainly causing infections in domesticated animals. Here we describe the first case of zoonotic necrotizing myositis caused by this bacterium. CASE PRESENTATION The patient was a 73-year-old, previously healthy farmer with two asymptomatic Shetland ponies in his stable. After close contact with the ponies while feeding them, he rapidly developed erythema of his left thigh and sepsis with multiple organ failure. The clinical course was severe and complicated, requiring repetitive surgical excision of necrotic muscle, treatment with vasopressors, mechanical ventilation and continuous venovenous hemofiltration, along with adjunctive hyperbaric oxygen therapy. The patient was discharged from hospital at day 30, without obvious sequelae. The streptococcal isolate was identified as Streptococcus equi by MALDI-ToF MS, and was later assigned subspecies identification as S. equi subsp. zooepidemicus. Multilocus sequence typing identified the strain as a novel sequence type (ST 364), closely related to types previously identified in horses and cattle. A focused proteomic analysis revealed that the ST 364 expressed putative virulence factors similar to that of Streptococcus pyogenes, including homologues of the M protein, streptodornases, interleukin 8-protease and proteins involved in the biosynthesis of streptolysin S. CONCLUSION This case illustrates the zoonotic potential of S. equi subsp. zooepidemicus and the importance of early clinical recognition, rapid and radical surgical therapy, appropriate antibiotics and adequate supportive measures when necrotizing soft tissue infection is suspected. The expression of Streptococcus pyogenes-like putative virulence determinants in ST 364 might partially explain the fulminant clinical picture.
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Affiliation(s)
| | - Veronika Kuchařová Pettersen
- The Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Oddvar Oppegaard
- The Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
| | - Dag Harald Skutlaberg
- The Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Håvard Dale
- Department of Orthopaedic Surgery, Haukeland University Hospital, Bergen, Norway
| | - Harald G Wiker
- The Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Microbiology, Haukeland University Hospital, Bergen, Norway
| | - Steinar Skrede
- The Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, Bergen, Norway.,Department of Medicine, Haukeland University Hospital, Bergen, Norway
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Pettersen VK, Mosevoll KA, Lindemann PC, Wiker HG. Coordination of Metabolism and Virulence Factors Expression of Extraintestinal Pathogenic Escherichia coli Purified from Blood Cultures of Patients with Sepsis. Mol Cell Proteomics 2016; 15:2890-907. [PMID: 27364158 PMCID: PMC5013306 DOI: 10.1074/mcp.m116.060582] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Indexed: 02/06/2023] Open
Abstract
One of the trademarks of extraintestinal pathogenic Escherichia coli is adaptation of metabolism and basic physiology to diverse host sites. However, little is known how this common human pathogen adapts to permit survival and growth in blood. We used label-free quantitative proteomics to characterize five E. coli strains purified from clinical blood cultures associated with sepsis and urinary tract infections. Further comparison of proteome profiles of the clinical strains and a reference uropathogenic E. coli strain 536 cultivated in blood culture and on two different solid media distinguished cellular features altered in response to the pathogenically relevant condition. The analysis covered nearly 60% of the strains predicted proteomes, and included quantitative description based on label-free intensity scores for 90% of the detected proteins. Statistical comparison of anaerobic and aerobic blood cultures revealed 32 differentially expressed proteins (1.5% of the shared proteins), mostly associated with acquisition and utilization of metal ions critical for anaerobic or aerobic respiration. Analysis of variance identified significantly altered amounts of 47 proteins shared by the strains (2.7%), including proteins involved in vitamin B6 metabolism and virulence. Although the proteomes derived from blood cultures were fairly similar for the investigated strains, quantitative proteomic comparison to the growth on solid media identified 200 proteins with substantially changed levels (11% of the shared proteins). Blood culture was characterized by up-regulation of anaerobic fermentative metabolism and multiple virulence traits, including cell motility and iron acquisition. In a response to the growth on solid media there were increased levels of proteins functional in aerobic respiration, catabolism of medium-specific carbon sources and protection against oxidative and osmotic stresses. These results demonstrate on the expressed proteome level that expression of extraintestinal virulence factors and overall cellular metabolism closely reflects specific growth conditions. Data are available via ProteomeXchange with identifier PXD002912.
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Affiliation(s)
- Veronika Kuchařová Pettersen
- From the ‡The Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway;
| | | | - Paul Christoffer Lindemann
- From the ‡The Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; ¶Department of Microbiology; Haukeland University Hospital, N-5021 Bergen, Norway
| | - Harald G Wiker
- From the ‡The Gade Research Group for Infection and Immunity, Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway; ¶Department of Microbiology; Haukeland University Hospital, N-5021 Bergen, Norway
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12
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Pettersen VK, Steinsland H, Wiker HG. Improving genome annotation of enterotoxigenicEscherichia coliTW10598 by a label-free quantitative MS/MS approach. Proteomics 2015; 15:3826-34. [DOI: 10.1002/pmic.201500278] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 08/18/2015] [Accepted: 09/04/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Veronika Kuchařová Pettersen
- The Gade Research Group for Infection and Immunity; Department of Clinical Science; University of Bergen; Bergen Norway
| | - Hans Steinsland
- Centre for International Health; Department of Global Public Health and Primary Care; University of Bergen; Bergen Norway
- Department of Biomedicine; University of Bergen; Bergen Norway
| | - Harald G. Wiker
- The Gade Research Group for Infection and Immunity; Department of Clinical Science; University of Bergen; Bergen Norway
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