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Coll F, Blane B, Bellis KL, Matuszewska M, Wonfor T, Jamrozy D, Toleman MS, Geoghegan JA, Parkhill J, Massey RC, Peacock SJ, Harrison EM. The mutational landscape of Staphylococcus aureus during colonisation. Nat Commun 2025; 16:302. [PMID: 39805814 PMCID: PMC11730646 DOI: 10.1038/s41467-024-55186-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Accepted: 12/02/2024] [Indexed: 01/16/2025] Open
Abstract
Staphylococcus aureus is an important human pathogen and a commensal of the human nose and skin. Survival and persistence during colonisation are likely major drivers of S. aureus evolution. Here we applied a genome-wide mutation enrichment approach to a genomic dataset of 3060 S. aureus colonization isolates from 791 individuals. Despite limited within-host genetic diversity, we observed an excess of protein-altering mutations in metabolic genes, in regulators of quorum-sensing (agrA and agrC) and in known antibiotic targets (fusA, pbp2, dfrA and ileS). We demonstrated the phenotypic effect of multiple adaptive mutations in vitro, including changes in haemolytic activity, antibiotic susceptibility, and metabolite utilisation. Nitrogen metabolism showed the strongest evidence of adaptation, with the assimilatory nitrite reductase (nasD) and urease (ureG) showing the highest mutational enrichment. We identified a nasD natural mutant with enhanced growth under urea as the sole nitrogen source. Inclusion of 4090 additional isolate genomes from 731 individuals revealed eight more genes including sasA/sraP, darA/pstA, and rsbU with signals of adaptive variation that warrant further characterisation. Our study provides a comprehensive picture of the heterogeneity of S. aureus adaptive changes during colonisation, and a robust methodological approach applicable to study in host adaptive evolution in other bacterial pathogens.
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Affiliation(s)
- Francesc Coll
- Applied Microbial Genomics Unit, Department of Molecular Basis of Disease, Institute of Biomedicine of Valencia (IBV-CSIC), Valencia, Spain.
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
- Parasites & Microbes Programme, Wellcome Sanger Institute, Hinxton, UK.
| | - Beth Blane
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Katherine L Bellis
- Parasites & Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Marta Matuszewska
- Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Toska Wonfor
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
- Department of Microbes, Infection & Microbiomes, College of Medicine & Health, University of Birmingham, Birmingham, UK
| | - Dorota Jamrozy
- Parasites & Microbes Programme, Wellcome Sanger Institute, Hinxton, UK
| | | | - Joan A Geoghegan
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
- Department of Microbes, Infection & Microbiomes, College of Medicine & Health, University of Birmingham, Birmingham, UK
- Department of Microbiology, Moyne Institute of Preventive Medicine, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Ruth C Massey
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Ewan M Harrison
- Parasites & Microbes Programme, Wellcome Sanger Institute, Hinxton, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
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Reslane I, Watson GF, Handke LD, Fey PD. Regulatory dynamics of arginine metabolism in Staphylococcus aureus. Biochem Soc Trans 2024; 52:2513-2523. [PMID: 39656074 PMCID: PMC11668279 DOI: 10.1042/bst20240710] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2024] [Revised: 11/07/2024] [Accepted: 11/11/2024] [Indexed: 12/20/2024]
Abstract
Staphylococcus aureus is a highly significant pathogen with several well studied and defined virulence factors. However, the metabolic pathways that are required to facilitate infection are not well described. Previous data have documented that S. aureus requires glucose catabolism during initial stages of infection. Therefore, certain nutrients whose biosynthetic pathway is under carbon catabolite repression and CcpA, including arginine, must be acquired from the host. However, even though S. aureus encodes pathways to synthesize arginine, biosynthesis of arginine is repressed even in the absence of glucose. Why is S. aureus a functional arginine auxotroph? This review discusses recently described regulatory mechanisms that are linked to repression of arginine biosynthesis using either proline or glutamate as substrates. In addition, recent studies are discussed that shed insight into the ultimate mechanisms linking arginine auxotrophy and infection persistence.
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Affiliation(s)
- Itidal Reslane
- Department of Pathology, Microbiology, and Immunology, University of Nebraska Medical Center, Omaha, NE 68198, U.S.A
| | - Gabrielle F. Watson
- Department of Pathology, Microbiology, and Immunology, University of Nebraska Medical Center, Omaha, NE 68198, U.S.A
| | - Luke D. Handke
- Department of Pathology, Microbiology, and Immunology, University of Nebraska Medical Center, Omaha, NE 68198, U.S.A
| | - Paul D. Fey
- Department of Pathology, Microbiology, and Immunology, University of Nebraska Medical Center, Omaha, NE 68198, U.S.A
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Wu Y, Shi Y, Liang X. Evolution of two metabolic genes involved in nucleotide and amino acid metabolism in Pseudomonas aeruginosa. PLoS One 2024; 19:e0315931. [PMID: 39689084 DOI: 10.1371/journal.pone.0315931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Accepted: 12/03/2024] [Indexed: 12/19/2024] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen causing various severe infections. Understanding genetic mechanisms of its metabolic versatility aids in developing novel antibacterial drugs and therapeutic strategies to address multidrug-resistant P. aeruginosa infections. The metabolism of nucleotides and amino acids contributes to the cycle of two key biological macromolecules in the genetic central dogma. Guanine deaminase (GuaD) catalyzes the deamination of guanine to produce xanthine to maintain the homeostasis of the nucleotide pool, and transporters specific to BCAAs (termed as BraT) import BCAAs to keep its intracellular availability level. However, little is known about the evolution of GuaD and BraT in P. aeruginosa population. Here, two copies turned out to be widespread in P. aeruginosa population for each of GuaD and BraT. The phylogenic analysis demonstrated that GuaD1 and BraB were inherited from the ancestor of Pseudomonas, while GuaD2 and BraZ were additionally acquired via evolutionary events in the ancestors of P. aeruginosa. The functional divergence of two copies was supported by different distribution patterns of dN/dS ratios, divergent expression levels, differentially co-expressed genes, and their functional enrichment modules with few intersections. Besides, some co-expressed genes with known functions are involved in infecting hosts, forming biofilm and resisting antibiotic treatment. Taken together, functional divergence following copy number increase and differentiation of co-expression networks might confer greater metabolic potential to P. aeruginosa, especially in response to host immune responses and antibiotic treatments in clinical settings.
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Affiliation(s)
- Yutong Wu
- Gansu Provincial Hospital of TCM, Gansu University of Chinese Medicine, Lanzhou, Gansu, China
| | - Yuqi Shi
- The State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China
| | - Xiaohui Liang
- Department of Critical Care Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, Jiangsu, China
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4
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González-García S, Hamdan-Partida A, Pérez-Ramos J, Aguirre-Garrido JF, Bustos-Hamdan A, Bustos-Martínez J. Comparison of the bacterial microbiome in the pharynx and nasal cavity of persistent, intermittent carriers and non-carriers of Staphylococcus aureus. J Med Microbiol 2024; 73:001940. [PMID: 39629792 PMCID: PMC11616445 DOI: 10.1099/jmm.0.001940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Accepted: 11/13/2024] [Indexed: 12/08/2024] Open
Abstract
Introduction. Staphylococcus aureus is a bacterium that colonizes various human sites. The pharynx has been considered as a site of little clinical relevance and little studied. Recently, it has been reported that S. aureus can colonize more the pharynx than the nose. In addition, S. aureus can persist in these sites for prolonged periods of time.Hypothesis. The composition of the pharyngeal and nasal microbiome will differ between persistent, intermittent carriers and non-carriers of S. aureus.Aim. Determine whether the pharyngeal and nasal microbiome is different between carriers and non-carriers of S. aureus.Methodology. S. aureus carriers were monitored by means of pharyngeal and nasal exudates of apparently healthy adult university students for 3 months. Samples from individuals of the same carrier type were pooled, and DNA was extracted and the 16S rRNA was sequenced. The sequences were analysed in MOTHUR v.1.48.0 software, by analysing the percentages of relative abundance in the STAMP 2.1.3 program, in addition to the predictive analysis of metabolic pathways in PICRUSt2.Results. A greater colonization of S. aureus was found in the pharynx than in the nose. The microbiomes of S. aureus carriers and non-carriers do not show significant differences. The main microbiome difference found was between pharyngeal and nasal microbiomes. No significant differences were found in the abundance of the genus Staphylococcus in pharyngeal and nasal S. aureus carriers and non-carriers. The nasal microbiome was found to have more variation compared to the pharyngeal microbiome, which appears to be more stable between individuals and pools. Predictive analysis of metabolic pathways showed a greater presence of Staphylococcus-associated pathways in the nose than in the pharynx.Conclusion. S. aureus can colonize and persist in the pharynx in equal or greater proportion than in the nose. No statistically significant differences were found in the microbiome of the pharyngeal and nasal carriers and non-carriers of S. aureus, but the pharyngeal and nasal microbiomes are different independent of the type of S. aureus carrier or non-carrier. Therefore, the microbiome apparently does not influence the persistence of S. aureus.
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Affiliation(s)
- Samuel González-García
- Doctorado en Ciencias Biológicas y de la Salud, Universidad Autónoma Metropolitana, Mexico City, Mexico
| | - Aida Hamdan-Partida
- Departamento de Atención a la Salud, UAM Xochimilco, Calzada del Hueso 1100, Colonia Villa Quietud, Alcaldía Coyoacán, C.P. 04960, CDMX, Mexico
| | - Julia Pérez-Ramos
- Departamento de Sistemas Biológicos, UAM Xochimilco, Calzada del Hueso 1100, Colonia Villa Quietud, Alcaldía Coyoacán, C.P. 04960, CDMX, Mexico
| | - José Félix Aguirre-Garrido
- Departamento de Ciencias Ambientales, UAM Lerma, Av. de las Garzas 10E, l Panteón 52005, Municipio Lerma de Villada, Estado de México, Mexico
| | - Anaíd Bustos-Hamdan
- Departamento de Atención a la Salud, UAM Xochimilco, Calzada del Hueso 1100, Colonia Villa Quietud, Alcaldía Coyoacán, C.P. 04960, CDMX, Mexico
| | - Jaime Bustos-Martínez
- Departamento de Atención a la Salud, UAM Xochimilco, Calzada del Hueso 1100, Colonia Villa Quietud, Alcaldía Coyoacán, C.P. 04960, CDMX, Mexico
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5
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Wang Y, Shi YN, Xiang H, Shi YM. Exploring nature's battlefield: organismic interactions in the discovery of bioactive natural products. Nat Prod Rep 2024; 41:1630-1651. [PMID: 39316448 DOI: 10.1039/d4np00018h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2024]
Abstract
Covering: up to March 2024.Microbial natural products have historically been a cornerstone for the discovery of therapeutic agents. Advanced (meta)genome sequencing technologies have revealed that microbes harbor far greater biosynthetic capabilities than previously anticipated. However, despite the application of CRISPR/Cas-based gene editing and high-throughput technologies to activate silent biosynthetic gene clusters, the rapid identification of new natural products has not led to a proportional increase in the discovery rate of lead compounds or drugs. A crucial issue in this gap may be insufficient knowledge about the inherent biological and physiological functions of microbial natural products. Addressing this gap necessitates recognizing that the generation of functional natural products is deeply rooted in the interactions between the producing microbes and other (micro)organisms within their ecological contexts, an understanding that is essential for harnessing their potential therapeutic benefits. In this review, we highlight the discovery of functional microbial natural products from diverse niches, including those associated with humans, nematodes, insects, fungi, protozoa, plants, and marine animals. Many of these findings result from an organismic-interaction-guided strategy using multi-omic approaches. The current importance of this topic lies in its potential to advance drug discovery in an era marked by increasing antimicrobial resistance.
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Affiliation(s)
- Yuyang Wang
- Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
| | - Yan-Ni Shi
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Hao Xiang
- Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yi-Ming Shi
- Key Laboratory of Quantitative Synthetic Biology, Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China.
- University of Chinese Academy of Sciences, Beijing 100049, China
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6
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Zelasko S, Swaney MH, Sandstrom S, Davenport TC, Seroogy CM, Gern JE, Kalan LR, Currie CR. Upper respiratory microbial communities of healthy populations are shaped by niche and age. MICROBIOME 2024; 12:206. [PMID: 39425237 PMCID: PMC11490146 DOI: 10.1186/s40168-024-01940-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 09/23/2024] [Indexed: 10/21/2024]
Abstract
BACKGROUND Alterations in upper respiratory microbiomes have been implicated in shaping host health trajectories, including by limiting mucosal pathogen colonization. However, limited comparative studies of respiratory microbiome development and functioning across age groups have been performed. Herein, we perform shotgun metagenomic sequencing paired with pathogen inhibition assays to elucidate differences in nasal and oral microbiome composition and intermicrobial interactions across healthy 24-month-old infant (n = 229) and adult (n = 100) populations. RESULTS We find that beta diversity of nasal and oral microbiomes varies with age, with nasal microbiomes showing greater population-level variation compared to oral microbiomes. Infant microbiome alpha diversity was significantly lower across nasal samples and higher in oral samples, relative to adults. Accordingly, we demonstrate significant differences in genus- and species-level composition of microbiomes between sites and age groups. Antimicrobial resistome patterns likewise varied across body sites, with oral microbiomes showing higher resistance gene abundance compared to nasal microbiomes. Biosynthetic gene clusters encoding specialized metabolite production were found in higher abundance across infant oral microbiomes, relative to adults. Investigation of pathogen inhibition revealed greater inhibition of gram-negative and gram-positive bacteria by oral commensals, while nasal isolates had higher antifungal activity. CONCLUSIONS In summary, we identify significant differences in the microbial communities inhabiting nasal and oral cavities of healthy infants relative to adults. These findings inform our understanding of the interactions impacting respiratory microbiome composition and functions related to colonization resistance, with important implications for host health across the lifespan. Video Abstract.
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Affiliation(s)
- Susan Zelasko
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA.
| | - Mary Hannah Swaney
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Shelby Sandstrom
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
| | - Timothy C Davenport
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
| | - Christine M Seroogy
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - James E Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Lindsay R Kalan
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, ON, Canada
| | - Cameron R Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Biochemistry and Biomedical Sciences, M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, ON, Canada.
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7
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Ju Y, Zhang Z, Liu M, Lin S, Sun Q, Song Z, Liang W, Tong X, Jie Z, Lu H, Cai K, Chen P, Jin X, Zhang W, Xu X, Yang H, Wang J, Hou Y, Xiao L, Jia H, Zhang T, Guo R. Integrated large-scale metagenome assembly and multi-kingdom network analyses identify sex differences in the human nasal microbiome. Genome Biol 2024; 25:257. [PMID: 39380016 PMCID: PMC11463039 DOI: 10.1186/s13059-024-03389-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 09/06/2024] [Indexed: 10/10/2024] Open
Abstract
BACKGROUND Respiratory diseases impose an immense health burden worldwide. Epidemiological studies have revealed extensive disparities in the incidence and severity of respiratory tract infections between men and women. It has been hypothesized that there might also be a nasal microbiome axis contributing to the observed sex disparities. RESULTS Here, we study the nasal microbiome of healthy young adults in the largest cohort to date with 1593 individuals, using shotgun metagenomic sequencing. We compile the most comprehensive reference catalog for the nasal bacterial community containing 4197 metagenome-assembled genomes and integrate the mycobiome, to provide a valuable resource and a more holistic perspective for the understudied human nasal microbiome. We systematically evaluate sex differences and reveal extensive sex-specific features in both taxonomic and functional levels in the nasal microbiome. Through network analyses, we capture markedly higher ecological stability and antagonistic potentials in the female nasal microbiome compared to the male's. The analysis of the keystone bacteria reveals that the sex-dependent evolutionary characteristics might have contributed to these differences. CONCLUSIONS In summary, we construct the most comprehensive catalog of metagenome-assembled-genomes for the nasal bacterial community to provide a valuable resource for the understudied human nasal microbiome. On top of that, comparative analysis in relative abundance and microbial co-occurrence networks identify extensive sex differences in the respiratory tract community, which may help to further our understanding of the observed sex disparities in the respiratory diseases.
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Affiliation(s)
- Yanmei Ju
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhe Zhang
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI Research, Shenzhen, 518083, China
| | - Mingliang Liu
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shutian Lin
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Sun
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI Research, Shenzhen, 518083, China
- Department of Statistical Sciences, University of Toronto, 700 University Ave, Toronto, ON, M5G 1Z5, Canada
| | | | - Weiting Liang
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI Research, Shenzhen, 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xin Tong
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI Research, Shenzhen, 518083, China
| | - Zhuye Jie
- BGI Research, Shenzhen, 518083, China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI Research, Shenzhen, 518083, China
| | - Haorong Lu
- China National Genebank, BGI Research, Shenzhen, 518210, China
| | - Kaiye Cai
- BGI Research, Shenzhen, 518083, China
| | | | - Xin Jin
- BGI Research, Shenzhen, 518083, China
| | | | - Xun Xu
- BGI Research, Shenzhen, 518083, China
| | - Huanming Yang
- BGI Research, Shenzhen, 518083, China
- James D, Watson Institute of Genome Sciences, Hangzhou, 310013, China
| | - Jian Wang
- BGI Research, Shenzhen, 518083, China
| | - Yong Hou
- BGI Research, Shenzhen, 518083, China
| | - Liang Xiao
- BGI Research, Shenzhen, 518083, China
- Shenzhen Engineering Laboratory of Detection and Intervention of Human Intestinal Microbiome, BGI Research, Shenzhen, 518083, China
- Qingdao-Europe Advanced Institute for Life Sciences, BGI Research, Qingdao, 266555, China
| | - Huijue Jia
- School of Life Sciences, Fudan University, Shanghai, 200433, China.
- Greater Bay Area Institute of Precision Medicine, Guangzhou, 511458, China.
| | - Tao Zhang
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI Research, Shenzhen, 518083, China.
- BGI Research, Wuhan, 430074, China.
| | - Ruijin Guo
- BGI Research, Shenzhen, 518083, China.
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI Research, Shenzhen, 518083, China.
- BGI Research, Wuhan, 430074, China.
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Leonidou N, Xia Y, Friedrich L, Schütz MS, Dräger A. Exploring the metabolic profile of A. baumannii for antimicrobial development using genome-scale modeling. PLoS Pathog 2024; 20:e1012528. [PMID: 39312576 PMCID: PMC11463759 DOI: 10.1371/journal.ppat.1012528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 10/09/2024] [Accepted: 08/26/2024] [Indexed: 09/25/2024] Open
Abstract
With the emergence of multidrug-resistant bacteria, the World Health Organization published a catalog of microorganisms urgently needing new antibiotics, with the carbapenem-resistant Acinetobacter baumannii designated as "critical". Such isolates, frequently detected in healthcare settings, pose a global pandemic threat. One way to facilitate a systemic view of bacterial metabolism and allow the development of new therapeutics is to apply constraint-based modeling. Here, we developed a versatile workflow to build high-quality and simulation-ready genome-scale metabolic models. We applied our workflow to create a metabolic model for A. baumannii and validated its predictive capabilities using experimental nutrient utilization and gene essentiality data. Our analysis showed that our model iACB23LX could recapitulate cellular metabolic phenotypes observed during in vitro experiments, while positive biomass production rates were observed and experimentally validated in various growth media. We further defined a minimal set of compounds that increase A. baumannii's cellular biomass and identified putative essential genes with no human counterparts, offering new candidates for future antimicrobial development. Finally, we assembled and curated the first collection of metabolic reconstructions for distinct A. baumannii strains and analyzed their growth characteristics. The presented models are in a standardized and well-curated format, enhancing their usability for multi-strain network reconstruction.
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Affiliation(s)
- Nantia Leonidou
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karl University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard Karl University of Tübingen, Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, Eberhard Karl University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Germany
- Quantitative Biology Center (QBiC), Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Yufan Xia
- Department of Computer Science, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Lea Friedrich
- Interfaculty Institute for Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany
| | - Monika S. Schütz
- German Center for Infection Research (DZIF), partner site Tübingen, Germany
- Interfaculty Institute for Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, University Hospital Tübingen, Tübingen, Germany
| | - Andreas Dräger
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karl University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Germany
- Quantitative Biology Center (QBiC), Eberhard Karl University of Tübingen, Tübingen, Germany
- Data Analytics and Bioinformatics, Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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9
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Tran TH, Escapa IF, Roberts AQ, Gao W, Obawemimo AC, Segre JA, Kong HH, Conlan S, Kelly MS, Lemon KP. Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.05.543719. [PMID: 37333201 PMCID: PMC10274666 DOI: 10.1101/2023.06.05.543719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Corynebacterium species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of Corynebacterium are often positively associated with health. Among the most common human nasal Corynebacterium species are C. propinquum, C. pseudodiphtheriticum, C. accolens, and C. tuberculostearicum. To gain insight into the functions of these four species, we identified genomic, phylogenomic, and pangenomic properties and estimated the metabolic capabilities of 87 distinct human nasal Corynebacterium strain genomes: 31 from Botswana and 56 from the USA. C. pseudodiphtheriticum had geographically distinct clades consistent with localized strain circulation, whereas some strains from the other species had wide geographic distribution spanning Africa and North America. All species had similar genomic and pangenomic structures. Gene clusters assigned to all COG metabolic categories were overrepresented in the persistent versus accessory genome of each species indicating limited strain-level variability in metabolic capacity. Based on prevalence data, at least two Corynebacterium species likely coexist in the nasal microbiota of 82% of adults. So, it was surprising that core metabolic capabilities were highly conserved among the four species indicating limited species-level metabolic variation. Strikingly, strains in the USA clade of C. pseudodiphtheriticum lacked genes for assimilatory sulfate reduction present in most of the strains in the Botswana clade and in the other studied species, indicating a recent, geographically related loss of assimilatory sulfate reduction. Overall, the minimal species and strain variability in metabolic capacity implies coexisting strains might have limited ability to occupy distinct metabolic niches.
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Affiliation(s)
- Tommy H. Tran
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Isabel F. Escapa
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Ari Q. Roberts
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Wei Gao
- The Forsyth Institute (Microbiology), Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
| | - Abiola C. Obawemimo
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Julia A. Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Heidi H. Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sean Conlan
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Matthew S. Kelly
- Division of Pediatric Infectious Diseases, Duke University School of Medicine, Durham, NC, USA
| | - Katherine P. Lemon
- Alkek Center for Metagenomics & Microbiome Research, Department of Molecular Virology & Microbiology, Baylor College of Medicine, Houston, Texas, USA
- Division of Infectious Diseases, Texas Children’s Hospital, Department of Pediatrics, Baylor College of Medicine, Houston, Texas, USA
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10
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Jawad A, Dagman SN, Yaseen MM, Al-Karagoly H. Phylogenetic analysis of Staphylococcus aureus enterotoxin A gene in Iraqi breed cows with bovine mastitis: Implications for disease management. Open Vet J 2024; 14:1644-1657. [PMID: 39175982 PMCID: PMC11338610 DOI: 10.5455/ovj.2024.v14.i7.14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 06/26/2024] [Indexed: 08/24/2024] Open
Abstract
Background Although milk is nutritionally valuable, it also serves as a significant medium for the transmission of pathogens and their toxins. Aim This study aimed to investigate the role of enterotoxin gene A (SEA) in the development of bovine mastitis. We accomplished this by examining milk through polymerase chain reaction (PCR) testing, amino acid substitution analysis, and phylogenetic analysis. Methods A total of fifty milk samples were collected from locally bred dairy cows in Al-Diwaniyah, located in southern Iraq. We employed the VITEK-2 platform to validate the diagnosis of Staphylococcus aureus and confirm the results of routine tests (culturing and biochemical tests). Subsequently, the genetic mutation and phylogeny analysis were achieved utilizing DNA sequencing to 16S rRNA and enterotoxin A genes. Results 66% (33/50) of the milk samples found to be contain S. aureus by the VITEK-2 system. Furthermore, 25/33 of the samples were positive by the PCR test. While 60% (15 out of 25) tested positive for the SEA gene. After genomic analysis, we identified amino acid substitutions of serine, glutamine with arginine, tyrosine with cysteine, and aspartic acid with glycine at positions 9, 101, 119, 187, and 191. The phylogenetic investigation demonstrated a genetic relationship between our isolates (Iraqi isolates) and isolates from Indian and the United States. Conclusion Our study indicated the widespread distribution of the enterotoxin gene A (SEA) of S. aureus among dairy cows. The molecular study revealed significant changes in key amino acids that could play an important role in the bacterium's pathogenesis. The phylogenetic similarities among S. aureus samples from various countries suggest that the bacteria has spread globally.
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Affiliation(s)
- Alaa Jawad
- Department of Microbiology, College of Veterinary Medicine, University of Al-Qadisiyah, Al-Diwaniyah, Iraq
| | - Sabreen Noori Dagman
- Department of Microbiology, College of Veterinary Medicine, University of Al-Qadisiyah, Al-Diwaniyah, Iraq
| | - Mohammed Mahdi Yaseen
- Department of Public Health, College of Veterinary Medicine, University of Al-Qadisiyah, Al-Diwaniyah, Iraq
| | - Hassan Al-Karagoly
- Department of Internal and Preventive Medicine, College of Veterinary Medicine, University of Al-Qadisiyah, Al-Diwaniyah, Iraq
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11
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Connor MG, Hamon MA. Advances in regulation of homeostasis through chromatin modifications by airway commensals. Curr Opin Microbiol 2024; 80:102505. [PMID: 38936013 DOI: 10.1016/j.mib.2024.102505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 06/07/2024] [Accepted: 06/07/2024] [Indexed: 06/29/2024]
Abstract
Commensal bacteria are residents of the human airway where they interact with both colonizing pathogens and host respiratory epithelial cells of this mucosal surface. It is here that commensals exert their influence through host signaling cascades, host transcriptional responses and host immunity, all of which are rooted in chromatin remodeling and histone modifications. Recent studies show that airway commensals impact host chromatin, but compared the what is known for gut commensals, the field remains in its infancy. The mechanisms by which airway commensals regulate respiratory health and homeostasis through chromatin modifications is of increasing interest, specifically since their displacement precedes the increased potential for respiratory disease. Herein we will discuss recent advances and intriguing avenues of future work aimed at deciphering how airway commensals protect and influence respiratory health.
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Affiliation(s)
- Michael G Connor
- Institut Pasteur, Université de Paris Cité, Unité Chromatine et Infection, F-75015 Paris, France.
| | - Melanie A Hamon
- Institut Pasteur, Université de Paris Cité, Unité Chromatine et Infection, F-75015 Paris, France.
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12
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Leonidou N, Ostyn L, Coenye T, Crabbé A, Dräger A. Genome-scale model of Rothia mucilaginosa predicts gene essentialities and reveals metabolic capabilities. Microbiol Spectr 2024; 12:e0400623. [PMID: 38652457 PMCID: PMC11237427 DOI: 10.1128/spectrum.04006-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/20/2024] [Indexed: 04/25/2024] Open
Abstract
Cystic fibrosis (CF), an inherited genetic disorder caused by mutations in the cystic fibrosis transmembrane conductance regulator gene, results in sticky and thick mucosal fluids. This environment facilitates the colonization of various microorganisms, some of which can cause acute and chronic lung infections, while others may positively impact the disease. Rothia mucilaginosa, an oral commensal, is relatively abundant in the lungs of CF patients. Recent studies have unveiled its anti-inflammatory properties using in vitro three-dimensional lung epithelial cell cultures and in vivo mouse models relevant to chronic lung diseases. Apart from this, R. mucilaginosa has been associated with severe infections. However, its metabolic capabilities and genotype-phenotype relationships remain largely unknown. To gain insights into its cellular metabolism and genetic content, we developed the first manually curated genome-scale metabolic model, iRM23NL. Through growth kinetics and high-throughput phenotypic microarray testings, we defined its complete catabolic phenome. Subsequently, we assessed the model's effectiveness in accurately predicting growth behaviors and utilizing multiple substrates. We used constraint-based modeling techniques to formulate novel hypotheses that could expedite the development of antimicrobial strategies. More specifically, we detected putative essential genes and assessed their effect on metabolism under varying nutritional conditions. These predictions could offer novel potential antimicrobial targets without laborious large-scale screening of knockouts and mutant transposon libraries. Overall, iRM23NL demonstrates a solid capability to predict cellular phenotypes and holds immense potential as a valuable resource for accurate predictions in advancing antimicrobial therapies. Moreover, it can guide metabolic engineering to tailor R. mucilaginosa's metabolism for desired performance.IMPORTANCECystic fibrosis (CF) is a genetic disorder characterized by thick mucosal secretions, leading to chronic lung infections. Rothia mucilaginosa is a common bacterium found in various parts of the human body, acting as a normal part of the flora. In people with weakened immune systems, it can become an opportunistic pathogen, while it is prevalent and active in CF airways. Recent studies have highlighted its anti-inflammatory properties in the lower pulmonary system, indicating the intricate relationship between microbes and human health. Herein, we have developed the first manually curated metabolic model of R. mucilaginosa. Our study examined the previously unknown relationships between the bacterium's genotype and phenotype and identified essential genes that impact the metabolism under various conditions. With this, we opt for paving the way for developing new strategies in antimicrobial therapy and metabolic engineering, leading to enhanced therapeutic outcomes in cystic fibrosis and related conditions.
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Affiliation(s)
- Nantia Leonidou
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karl University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard Karl University of Tübingen, Tübingen, Germany
- Cluster of Excellence ‘Controlling Microbes to Fight Infections’, Eberhard Karl University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
- Quantitative Biology Center (QBiC), Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Lisa Ostyn
- Laboratory of Pharmaceutical Microbiology (LPM), Ghent University, Ghent, Belgium
| | - Tom Coenye
- Laboratory of Pharmaceutical Microbiology (LPM), Ghent University, Ghent, Belgium
| | - Aurélie Crabbé
- Laboratory of Pharmaceutical Microbiology (LPM), Ghent University, Ghent, Belgium
| | - Andreas Dräger
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karl University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
- Data Analytics and Bioinformatics, Institute of Computer Science, Martin Luther University Halle-Wittenberg, Halle (Saale), Germany
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13
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Lopes W, Amor DR, Gore J. Cooperative growth in microbial communities is a driver of multistability. Nat Commun 2024; 15:4709. [PMID: 38830891 PMCID: PMC11148146 DOI: 10.1038/s41467-024-48521-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 05/03/2024] [Indexed: 06/05/2024] Open
Abstract
Microbial communities often exhibit more than one possible stable composition for the same set of external conditions. In the human microbiome, these persistent changes in species composition and abundance are associated with health and disease states, but the drivers of these alternative stable states remain unclear. Here we experimentally demonstrate that a cross-kingdom community, composed of six species relevant to the respiratory tract, displays four alternative stable states each dominated by a different species. In pairwise coculture, we observe widespread bistability among species pairs, providing a natural origin for the multistability of the full community. In contrast with the common association between bistability and antagonism, experiments reveal many positive interactions within and between community members. We find that multiple species display cooperative growth, and modeling predicts that this could drive the observed multistability within the community as well as non-canonical pairwise outcomes. A biochemical screening reveals that glutamate either reduces or eliminates cooperativity in the growth of several species, and we confirm that such supplementation reduces the extent of bistability across pairs and reduces multistability in the full community. Our findings provide a mechanistic explanation of how cooperative growth rather than competitive interactions can underlie multistability in microbial communities.
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Affiliation(s)
- William Lopes
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Daniel R Amor
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA
- Institute of Biology, University of Graz, Graz, Austria
- LPENS, Département de physique, Ecole normale supérieure, Université PSL, Sorbonne Université, Université Paris Cité, CNRS, Paris, France
- IAME, Université de Paris Cité, Université Sorbonne Paris Nord, INSERM, Paris, France
| | - Jeff Gore
- Physics of Living Systems, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA.
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14
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Zelasko S, Swaney MH, Sandstrom S, Davenport TC, Seroogy CM, Gern JE, Kalan LR, Currie CR. Upper respiratory microbial communities of healthy populations are shaped by niche and age. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.14.589416. [PMID: 38645133 PMCID: PMC11030450 DOI: 10.1101/2024.04.14.589416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Background Alterations in upper respiratory microbiomes have been implicated in shaping host health trajectories, including by limiting mucosal pathogen colonization. However, limited comparative studies of respiratory microbiome development and functioning across age groups have been performed. Herein, we perform shotgun metagenomic sequencing paired with pathogen inhibition assays to elucidate differences in nasal and oral microbiome composition and functioning across healthy 24-month-old infant (n=229) and adult (n=100) populations. Results We find that beta diversity of nasal and oral microbiomes varies with age, with nasal microbiomes showing greater population-level variation compared to oral microbiomes. Infant microbiome alpha diversity was significantly lower across nasal samples and higher in oral samples, relative to adults. Accordingly, we demonstrate significant differences in genus- and species-level composition of microbiomes between sites and age groups. Antimicrobial resistome patterns likewise varied across body sites, with oral microbiomes showing higher resistance gene abundance compared to nasal microbiomes. Biosynthetic gene clusters encoding specialized metabolite production were found in higher abundance across infant oral microbiomes, relative to adults. Investigation of pathogen inhibition revealed greater inhibition of gram-negative and gram-positive bacteria by oral commensals, while nasal isolates had higher antifungal activity. Conclusions In summary, we identify significant differences in the microbial communities inhabiting nasal and oral cavities of healthy infants relative to adults. These findings inform our understanding of the interactions impacting respiratory microbiome composition and functioning, with important implications for host health across the lifespan.
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Affiliation(s)
- Susan Zelasko
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mary Hannah Swaney
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Shelby Sandstrom
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Timothy C. Davenport
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Christine M. Seroogy
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - James E. Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Lindsay R. Kalan
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Cameron R. Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- M.G. DeGroote Institute for Infectious Disease Research, David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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15
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Bertrand BP, Shinde D, Thomas VC, Whiteley M, Ibberson CB, Kielian T. Metabolic diversity of human macrophages: potential influence on Staphylococcus aureus intracellular survival. Infect Immun 2024; 92:e0047423. [PMID: 38179975 PMCID: PMC10863412 DOI: 10.1128/iai.00474-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 12/04/2023] [Indexed: 01/06/2024] Open
Abstract
Staphylococcus aureus is a leading cause of medical device-associated biofilm infections. This is influenced by the ability of S. aureus biofilm to evade the host immune response, which is partially driven by the anti-inflammatory cytokine interleukin-10 (IL-10). Here, we show that treatment of human monocyte-derived macrophages (HMDMs) with IL-10 enhanced biofilm formation, suggesting that macrophage anti-inflammatory programming likely plays an important role during the transition from planktonic to biofilm growth. To identify S. aureus genes that were important for intracellular survival in HMDMs and how this was affected by IL-10, transposon sequencing was performed. The size of the S. aureus essential genome was similar between unstimulated HMDMs and the outgrowth control (18.5% vs 18.4%, respectively, with 54.4% overlap) but increased to 22.5% in IL-10-treated macrophages, suggesting that macrophage polarization status exerts differential pressure on S. aureus. Essential genes for S. aureus survival within IL-10-polarized HMDMs were dominated by negative regulatory pathways, including nitrogen and RNA metabolism, whereas S. aureus essential genes within untreated HMDMs were enriched in biosynthetic pathways such as purine and pyrimidine biosynthesis. To explore how IL-10 altered the macrophage intracellular metabolome, targeted metabolomics was performed on HMDMs from six individual donors. IL-10 treatment led to conserved alterations in distinct metabolites that were increased (dihydroxyacetone phosphate, glyceraldehyde-3-phosphate, and acetyl-CoA) or reduced (fructose-6-phosphate, aspartic acid, and ornithine) across donors, whereas other metabolites were variable. Collectively, these findings highlight an important aspect of population-level heterogeneity in human macrophage responsiveness that should be considered when translating results to a patient population.IMPORTANCEOne mechanism that Staphylococcus aureus biofilm elicits in the host to facilitate infection persistence is the production of the anti-inflammatory cytokine interleukin-10 (IL-10). Here, we show that exposure of human monocyte-derived macrophages (HMDMs) to IL-10 promotes S. aureus biofilm formation and programs intracellular bacteria to favor catabolic pathways. Examination of intracellular metabolites in HMDMs revealed heterogeneity between donors that may explain the observed variability in essential genes for S. aureus survival based on nutrient availability for bacteria within the intracellular compartment. Collectively, these studies provide novel insights into how IL-10 polarization affects S. aureus intracellular survival in HMDMs and the importance of considering macrophage heterogeneity between human donors as a variable when examining effector mechanisms.
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Affiliation(s)
- Blake P. Bertrand
- Department of Pathology, Microbiology, and Immunology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Dhananjay Shinde
- Department of Pathology, Microbiology, and Immunology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Vinai C. Thomas
- Department of Pathology, Microbiology, and Immunology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Marvin Whiteley
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Carolyn B. Ibberson
- School of Biological Sciences, University of Oklahoma, Norman, Oklahoma, USA
| | - Tammy Kielian
- Department of Pathology, Microbiology, and Immunology, University of Nebraska Medical Center, Omaha, Nebraska, USA
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16
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Brown S, Evans SJ, Burgum MJ, Meldrum K, Herridge J, Akinbola B, Harris LG, Jenkins R, Doak SH, Clift MJD, Wilkinson TS. An In Vitro Model to Assess Early Immune Markers Following Co-Exposure of Epithelial Cells to Carbon Black (Nano)Particles in the Presence of S. aureus: A Role for Stressed Cells in Toxicological Testing. Biomedicines 2024; 12:128. [PMID: 38255233 PMCID: PMC10813740 DOI: 10.3390/biomedicines12010128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/21/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
The exposure of human lung and skin to carbon black (CB) is continuous due to its widespread applications. Current toxicological testing uses 'healthy' cellular systems; however, questions remain whether this mimics the everyday stresses that human cells are exposed to, including infection. Staphylococcus aureus lung and skin infections remain prevalent in society, and include pneumonia and atopic dermatitis, respectively, but current in vitro toxicological testing does not consider infection stress. Therefore, investigating the effects of CB co-exposure in 'stressed' infected epithelial cells in vitro may better approximate true toxicity. This work aims to study the impact of CB exposure during Staphylococcus aureus infection stress in A549 (lung) and HaCaT (skin) epithelial cells. Physicochemical characterisation of CB confirmed its dramatic polydispersity and potential to aggregate. CB significantly inhibited S. aureus growth in cell culture media. CB did not induce cytokines or antimicrobial peptides from lung and skin epithelial cells, when given alone, but did reduce HaCaT and A549 cell viability to 55% and 77%, respectively. In contrast, S. aureus induced a robust interleukin (IL)-8 response in both lung and skin epithelial cells. IL-6 and human beta defensin (hβD)-2 could only be detected when cells were stimulated with S. aureus with no decreases in cell viability. However, co-exposure to CB (100 µg/mL) and S. aureus resulted in significant inhibition of IL-8 (compared to S. aureus alone) without further reduction in cell viability. Furthermore, the same co-exposure induced significantly more hβD-2 (compared to S. aureus alone). This work confirms that toxicological testing in healthy versus stressed cells gives significantly different responses. This has significant implications for toxicological testing and suggests that cell stresses (including infection) should be included in current models to better represent the diversity of cell viabilities found in lung and skin within a general population. This model will have significant application when estimating CB exposure in at-risk groups, such as factory workers, the elderly, and the immunocompromised.
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Affiliation(s)
- Scott Brown
- Microbiology and Infectious Disease, Institute of Life Science, Swansea University Medical School (SUMS), Swansea SA2 8PP, UK
| | - Stephen J. Evans
- In Vitro Toxicology Group, Institute of Life Science, Swansea University Medical School (SUMS), Swansea SA2 8PP, UK (M.J.D.C.)
| | - Michael J. Burgum
- In Vitro Toxicology Group, Institute of Life Science, Swansea University Medical School (SUMS), Swansea SA2 8PP, UK (M.J.D.C.)
| | - Kirsty Meldrum
- In Vitro Toxicology Group, Institute of Life Science, Swansea University Medical School (SUMS), Swansea SA2 8PP, UK (M.J.D.C.)
| | - Jack Herridge
- Microbiology and Infectious Disease, Institute of Life Science, Swansea University Medical School (SUMS), Swansea SA2 8PP, UK
| | - Blessing Akinbola
- Microbiology and Infectious Disease, Institute of Life Science, Swansea University Medical School (SUMS), Swansea SA2 8PP, UK
| | - Llinos G. Harris
- Microbiology and Infectious Disease, Institute of Life Science, Swansea University Medical School (SUMS), Swansea SA2 8PP, UK
| | - Rowena Jenkins
- Microbiology and Infectious Disease, Institute of Life Science, Swansea University Medical School (SUMS), Swansea SA2 8PP, UK
| | - Shareen H. Doak
- In Vitro Toxicology Group, Institute of Life Science, Swansea University Medical School (SUMS), Swansea SA2 8PP, UK (M.J.D.C.)
| | - Martin J. D. Clift
- In Vitro Toxicology Group, Institute of Life Science, Swansea University Medical School (SUMS), Swansea SA2 8PP, UK (M.J.D.C.)
| | - Thomas S. Wilkinson
- Microbiology and Infectious Disease, Institute of Life Science, Swansea University Medical School (SUMS), Swansea SA2 8PP, UK
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17
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Torres Salazar BO, Dema T, Schilling NA, Janek D, Bornikoel J, Berscheid A, Elsherbini AMA, Krauss S, Jaag SJ, Lämmerhofer M, Li M, Alqahtani N, Horsburgh MJ, Weber T, Beltrán-Beleña JM, Brötz-Oesterhelt H, Grond S, Krismer B, Peschel A. Commensal production of a broad-spectrum and short-lived antimicrobial peptide polyene eliminates nasal Staphylococcus aureus. Nat Microbiol 2024; 9:200-213. [PMID: 38110697 PMCID: PMC11310079 DOI: 10.1038/s41564-023-01544-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 11/03/2023] [Indexed: 12/20/2023]
Abstract
Antagonistic bacterial interactions often rely on antimicrobial bacteriocins, which attack only a narrow range of target bacteria. However, antimicrobials with broader activity may be advantageous. Here we identify an antimicrobial called epifadin, which is produced by nasal Staphylococcus epidermidis IVK83. It has an unprecedented architecture consisting of a non-ribosomally synthesized peptide, a polyketide component and a terminal modified amino acid moiety. Epifadin combines a wide antimicrobial target spectrum with a short life span of only a few hours. It is highly unstable under in vivo-like conditions, potentially as a means to limit collateral damage of bacterial mutualists. However, Staphylococcus aureus is eliminated by epifadin-producing S. epidermidis during co-cultivation in vitro and in vivo, indicating that epifadin-producing commensals could help prevent nasal S. aureus carriage. These insights into a microbiome-derived, previously unknown antimicrobial compound class suggest that limiting the half-life of an antimicrobial may help to balance its beneficial and detrimental activities.
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Affiliation(s)
- Benjamin O Torres Salazar
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Taulant Dema
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Nadine A Schilling
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Daniela Janek
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Jan Bornikoel
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Anne Berscheid
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Ahmed M A Elsherbini
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Sophia Krauss
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
| | - Simon J Jaag
- Institute of Pharmaceutical Sciences, University of Tübingen, Tübingen, Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, University of Tübingen, Tübingen, Germany
| | - Min Li
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Norah Alqahtani
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Malcolm J Horsburgh
- Department of Infection Biology and Microbiomes, University of Liverpool, Liverpool, UK
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - José Manuel Beltrán-Beleña
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany
| | - Heike Brötz-Oesterhelt
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
- Department of Microbial Bioactive Compounds, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Stephanie Grond
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany.
- Institute of Organic Chemistry, University of Tübingen, Tübingen, Germany.
| | - Bernhard Krismer
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany.
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany.
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany.
| | - Andreas Peschel
- Department of Infection Biology, Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, Tübingen, Germany
- German Center for Infection Research (DZIF), partner site Tübingen, Tübingen, Germany
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18
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Pruitt EL, Zhang R, Ross DH, Ashford NK, Chen X, Alonzo F, Bush MF, Werth BJ, Xu L. Elucidating the impact of bacterial lipases, human serum albumin, and FASII inhibition on the utilization of exogenous fatty acids by Staphylococcus aureus. mSphere 2023; 8:e0036823. [PMID: 38014966 PMCID: PMC10732024 DOI: 10.1128/msphere.00368-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 10/26/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE Incorporation of host-derived exogenous fatty acids (eFAs), particularly unsaturated fatty acids (UFAs), by Staphylococcus aureus could affect the bacterial membrane fluidity and susceptibility to antimicrobials. In this work, we found that glycerol ester hydrolase (Geh) is the primary lipase hydrolyzing cholesteryl esters and, to a lesser extent, triglycerides and that human serum albumin (HSA) could serve as a buffer of eFAs, where low levels of HSA facilitate the utilization of eFAs but high levels of HSA inhibit it. The fact that the type II fatty acid synthesis (FASII) inhibitor, AFN-1252, leads to an increase in UFA content even in the absence of eFA suggests that membrane property modulation is part of its mechanism of action. Thus, Geh and/or the FASII system look to be promising targets to enhance S. aureus killing in a host environment by restricting eFA utilization or modulating membrane properties, respectively.
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Affiliation(s)
- Emily L. Pruitt
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Rutan Zhang
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Dylan H. Ross
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | | | - Xi Chen
- Department of Microbiology and Immunology, Loyola University Chicago-Stritch School of Medicine, Maywood, Illinois, USA
| | - Francis Alonzo
- Department of Microbiology and Immunology, Loyola University Chicago-Stritch School of Medicine, Maywood, Illinois, USA
| | - Matthew F. Bush
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Brian J. Werth
- Department of Pharmacy, University of Washington, Seattle, Washington, USA
| | - Libin Xu
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
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19
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Vanderpool EJ, Rumbaugh KP. Host-microbe interactions in chronic rhinosinusitis biofilms and models for investigation. Biofilm 2023; 6:100160. [PMID: 37928619 PMCID: PMC10622848 DOI: 10.1016/j.bioflm.2023.100160] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 11/07/2023] Open
Abstract
Chronic rhinosinusitis (CRS) is a debilitating condition characterized by long-lasting inflammation of the paranasal sinuses. It affects a significant portion of the population, causing a considerable burden on individuals and healthcare systems. The pathogenesis of CRS is multifactorial, with bacterial infections playing a crucial role in CRS development and persistence. In recent years, the presence of biofilms has emerged as a key contributor to the chronicity of sinusitis, further complicating treatment and exacerbating symptoms. This review aims to explore the role of biofilms in CRS, focusing on the involvement of the bacterial species Staphylococcus aureus and Pseudomonas aeruginosa, their interactions in chronic infections, and model systems for studying biofilms in CRS. These species serve as an example of how microbial interplay can influence disease progression and exemplify the need for continued investigation and innovation in CRS research.
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Affiliation(s)
- Emily J. Vanderpool
- Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Burn Center of Research Excellence, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Kendra P. Rumbaugh
- Department of Surgery, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Burn Center of Research Excellence, Texas Tech University Health Sciences Center, Lubbock, TX, USA
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX, USA
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20
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Wang Q, Nurxat N, Zhang L, Liu Y, Wang Y, Zhang L, Zhao N, Dai Y, Jian Y, He L, Wang H, Bae T, Li M, Liu Q. Diabetes mellitus promotes the nasal colonization of high virulent Staphylococcus aureus through the regulation of SaeRS two-component system. Emerg Microbes Infect 2023; 12:2276335. [PMID: 37882148 PMCID: PMC10796126 DOI: 10.1080/22221751.2023.2276335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 10/23/2023] [Indexed: 10/27/2023]
Abstract
Diabetic foot infections are a common complication of diabetes. Staphylococcus aureus is frequently isolated from diabetic foot infections and commonly colonizes human nares. According to the study, the nasal microbiome analysis revealed that diabetic patients had a significantly altered nasal microbial composition and diversity. Typically, the fasting blood glucose (FBG) level had an impact on the abundance and sequence type (ST) of S. aureus in diabetic patients. We observed that highly virulent S. aureus ST7 strains were more frequently colonized in diabetic patients, especially those with poorly controlled FBG, while ST59 was dominant in healthy individuals. S. aureus ST7 strains were more resistant to human antimicrobial peptides and formed stronger biofilms than ST59 strains. Critically, S. aureus ST7 strains displayed higher virulence compared to ST59 strains in vivo. The dominance of S. aureus ST7 strains in hyperglycemic environment is due to the higher activity of the SaeRS two-component system (TCS). S. aureus ST7 strains outcompeted ST59 both in vitro, and in nasal colonization model in diabetic mice, which was abolished by the deletion of the SaeRS TCS. Our data indicated that highly virulent S. aureus strains preferentially colonize diabetic patients with poorly controlled FBG through SaeRS TCS. Detection of S. aureus colonization and elimination of colonizing S. aureus are critical in the care of diabetic patients with high FBG.
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Affiliation(s)
- Qichen Wang
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Nadira Nurxat
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Lei Zhang
- Department of Vascular Surgery, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, People’s Republic of China
| | - Yao Liu
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yanan Wang
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Lei Zhang
- Department of Otorhinolaryngology, Head and Neck Surgery, The Second Hospital of Anhui Medical University, Hefei, People’s Republic of China
| | - Na Zhao
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yingxin Dai
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Ying Jian
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Lei He
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Hua Wang
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Taeok Bae
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, IN, USA
| | - Min Li
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
- Faculty of Medical Laboratory Science, Shanghai Jiao Tong University School of Medicine, Shanghai, People’s Republic of China
| | - Qian Liu
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
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21
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Yin F, Hu Y, Bu Z, Liu Y, Zhang H, Hu Y, Xue Y, Li S, Tan C, Chen X, Li L, Zhou R, Huang Q. Genome-wide identification of genes critical for in vivo fitness of multi-drug resistant porcine extraintestinal pathogenic Escherichia coli by transposon-directed insertion site sequencing using a mouse infection model. Virulence 2023; 14:2158708. [PMID: 36537189 PMCID: PMC9828833 DOI: 10.1080/21505594.2022.2158708] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Extraintestinal pathogenic Escherichia coli (ExPEC) is an important zoonotic pathogen. Recently, ExPEC has been reported to be an emerging problem in pig farming. However, the mechanism of pathogenicity of porcine ExPEC remains to be revealed. In this study, we constructed a transposon (Tn) mutagenesis library covering Tn insertion in over 72% of the chromosome-encoded genes of a virulent and multi-drug resistant porcine ExPEC strain PCN033. By using a mouse infection model, a transposon-directed insertion site sequencing (TraDIS) assay was performed to identify in vivo fitness factors. By comparing the Tn insertion frequencies between the input Tn library and the recovered library from different organs, 64 genes were identified to be involved in fitness during systemic infection. 15 genes were selected and individual gene deletion mutants were constructed. The in vivo fitness was evaluated by using a competitive infection assay. Among them, ΔfimG was significantly outcompeted by the WT strain in vivo and showed defective adhesion to host cells. rfa which was involved in lipopolysaccharide biosynthesis was shown to be critical for in vivo fitness which may have resulted from its role in the resistance to serum killing. In addition, several metabolic genes including fepB, sdhC, fepG, gltS, dcuA, ccmH, ddpD, narU, glpD, malM, and yabL and two regulatory genes metJ and baeS were shown as important determinants of in vivo fitness of porcine ExPEC. Collectively, this study performed a genome-wide screening for in vivo fitness factors which will be important for understanding the pathogenicity of porcine ExPEC.
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Affiliation(s)
- Fan Yin
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yan Hu
- College of Animal Sciences & Technology, Huazhong Agricultural University, Wuhan, China
| | - Zixuan Bu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yuying Liu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Hui Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Yawen Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Ying Xue
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Shaowen Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Chen Tan
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Ministry of Science and Technology, International Research Center for Animal Disease, Wuhan, China
| | - Xiabing Chen
- Institute of Animal Husbandry and Veterinary Science, Wuhan Academy of Agricultural Science and Technology, Wuhan, China
| | - Lu Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Ministry of Science and Technology, International Research Center for Animal Disease, Wuhan, China
| | - Rui Zhou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Ministry of Science and Technology, International Research Center for Animal Disease, Wuhan, China,The HZAU-HVSEN Institute, Wuhan, China,CONTACT Rui Zhou
| | - Qi Huang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Cooperative Innovation Center for Sustainable Pig Production, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China,Ministry of Science and Technology, International Research Center for Animal Disease, Wuhan, China,Qi Huang
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22
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Boardman ER, Palmer T, Alcock F. Interbacterial competition mediated by the type VIIb secretion system. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001420. [PMID: 38116759 PMCID: PMC10765036 DOI: 10.1099/mic.0.001420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 12/06/2023] [Indexed: 12/21/2023]
Abstract
Successful occupancy of a given niche requires the colonising bacteria to interact extensively with the biotic and abiotic environment, including other resident microbes. Bacteria have evolved a range of protein secretion machines for this purpose with eleven such systems identified to date. The type VIIb secretion system (T7SSb) is utilised by Bacillota to secrete a range of protein substrates, including antibacterial toxins targeting closely related strains, and the system as a whole has been implicated in a range of activities such as iron acquisition, intercellular signalling, host colonisation and virulence. This review covers the components and secretion mechanism of the T7SSb, the substrates of these systems and their roles in Gram-positive bacteria, with a focus on interbacterial competition.
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Affiliation(s)
- Eleanor R. Boardman
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Tracy Palmer
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Felicity Alcock
- Microbes in Health and Disease Theme, Newcastle University Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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23
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Houtak G, Bouras G, Nepal R, Shaghayegh G, Cooksley C, Psaltis AJ, Wormald PJ, Vreugde S. The intra-host evolutionary landscape and pathoadaptation of persistent Staphylococcus aureus in chronic rhinosinusitis. Microb Genom 2023; 9:001128. [PMID: 38010322 PMCID: PMC10711304 DOI: 10.1099/mgen.0.001128] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/23/2023] [Indexed: 11/29/2023] Open
Abstract
Chronic rhinosinusitis (CRS) is a common chronic sinonasal mucosal inflammation associated with Staphylococcus aureus biofilm and relapsing infections. This study aimed to determine rates of S. aureus persistence and pathoadaptation in CRS patients by investigating the genomic relatedness and antibiotic resistance/tolerance in longitudinally collected S. aureus clinical isolates. A total of 68 S. aureus paired isolates (34 pairs) were sourced from 34 CRS patients at least 6 months apart. Isolates were grown into 48 h biofilms and tested for tolerance to antibiotics. A hybrid sequencing strategy was used to obtain high-quality reference-grade assemblies of all isolates. Single nucleotide variants (SNV) divergence in the core genome and sequence type clustering were used to analyse the relatedness of the isolate pairs. Single nucleotide and structural genome variations, plasmid similarity, and plasmid copy numbers between pairs were examined. Our analysis revealed that 41 % (14/34 pairs) of S. aureus isolates were persistent, while 59 % (20/34 pairs) were non-persistent. Persistent isolates showed episode-specific mutational changes over time with a bias towards events in genes involved in adhesion to the host and mobile genetic elements such as plasmids, prophages, and insertion sequences. Furthermore, a significant increase in the copy number of conserved plasmids of persistent strains was observed. This was accompanied by a significant increase in biofilm tolerance against all tested antibiotics, which was linked to a significant increase in biofilm biomass over time, indicating a potential biofilm pathoadaptive process in persistent isolates. In conclusion, our study provides important insights into the mutational changes during S. aureus persistence in CRS patients highlighting potential pathoadaptive mechanisms in S. aureus persistent isolates culminating in increased biofilm biomass.
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Affiliation(s)
- Ghais Houtak
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - George Bouras
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Roshan Nepal
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Gohar Shaghayegh
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Clare Cooksley
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Alkis James Psaltis
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Peter-John Wormald
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
| | - Sarah Vreugde
- Adelaide Medical School, Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, Australia
- The Department of Surgery - Otolaryngology Head and Neck Surgery, University of Adelaide and the Basil Hetzel Institute for Translational Health Research, Central Adelaide Local Health Network, Adelaide, Australia
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24
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Bäuerle F, Döbel GO, Camus L, Heilbronner S, Dräger A. Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium striatum. FRONTIERS IN BIOINFORMATICS 2023; 3:1214074. [PMID: 37936955 PMCID: PMC10626998 DOI: 10.3389/fbinf.2023.1214074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 10/02/2023] [Indexed: 11/09/2023] Open
Abstract
Introduction: Genome-scale metabolic models (GEMs) are organism-specific knowledge bases which can be used to unravel pathogenicity or improve production of specific metabolites in biotechnology applications. However, the validity of predictions for bacterial proliferation in in vitro settings is hardly investigated. Methods: The present work combines in silico and in vitro approaches to create and curate strain-specific genome-scale metabolic models of Corynebacterium striatum. Results: We introduce five newly created strain-specific genome-scale metabolic models (GEMs) of high quality, satisfying all contemporary standards and requirements. All these models have been benchmarked using the community standard test suite Metabolic Model Testing (MEMOTE) and were validated by laboratory experiments. For the curation of those models, the software infrastructure refineGEMs was developed to work on these models in parallel and to comply with the quality standards for GEMs. The model predictions were confirmed by experimental data and a new comparison metric based on the doubling time was developed to quantify bacterial growth. Discussion: Future modeling projects can rely on the proposed software, which is independent of specific environmental conditions. The validation approach based on the growth rate calculation is now accessible and closely aligned with biological questions. The curated models are freely available via BioModels and a GitHub repository and can be used. The open-source software refineGEMs is available from https://github.com/draeger-lab/refinegems.
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Affiliation(s)
- Famke Bäuerle
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karl University of Tübingen, Tübingen, Germany
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Eberhard Karl University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Gwendolyn O. Döbel
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karl University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard Karl University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
| | - Laura Camus
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Eberhard Karl University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, Eberhard Karl University of Tübingen, Tübingen, Germany
| | - Simon Heilbronner
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen (IMIT), Eberhard Karl University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, Eberhard Karl University of Tübingen, Tübingen, Germany
- Faculty of Biology, Microbiology, Ludwig Maximilian University of Munich, Munich, Germany
| | - Andreas Dräger
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), Eberhard Karl University of Tübingen, Tübingen, Germany
- Department of Computer Science, Eberhard Karl University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Cluster of Excellence “Controlling Microbes to Fight Infections (CMFI)”, Eberhard Karl University of Tübingen, Tübingen, Germany
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25
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van Dalen R, Elsherbini AMA, Harms M, Alber S, Stemmler R, Peschel A. Secretory IgA impacts the microbiota density in the human nose. MICROBIOME 2023; 11:233. [PMID: 37865781 PMCID: PMC10589987 DOI: 10.1186/s40168-023-01675-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 09/24/2023] [Indexed: 10/23/2023]
Abstract
BACKGROUND Respiratory mucosal host defense relies on the production of secretory IgA (sIgA) antibodies, but we currently lack a fundamental understanding of how sIgA is induced by contact with microbes and how such immune responses may vary between humans. Defense of the nasal mucosal barrier through sIgA is critical to protect from infection and to maintain homeostasis of the microbiome, which influences respiratory disorders and hosts opportunistic pathogens. METHODS We applied IgA-seq analysis to nasal microbiota samples from male and female healthy volunteers, to identify which bacterial genera and species are targeted by sIgA on the level of the individual host. Furthermore, we used nasal sIgA from the same individuals in sIgA deposition experiments to validate the IgA-seq outcomes. CONCLUSIONS We observed that the amount of sIgA secreted into the nasal mucosa by the host varied substantially and was negatively correlated with the bacterial density, suggesting that nasal sIgA limits the overall bacterial capacity to colonize. The interaction between mucosal sIgA antibodies and the nasal microbiota was highly individual with no obvious differences between potentially invasive and non-invasive bacterial species. Importantly, we could show that for the clinically relevant opportunistic pathogen and frequent nasal resident Staphylococcus aureus, sIgA reactivity was in part the result of epitope-independent interaction of sIgA with the antibody-binding protein SpA through binding of sIgA Fab regions. This study thereby offers a first comprehensive insight into the targeting of the nasal microbiota by sIgA antibodies. It thereby helps to better understand the shaping and homeostasis of the nasal microbiome by the host and may guide the development of effective mucosal vaccines against bacterial pathogens. Video Abstract.
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Affiliation(s)
- Rob van Dalen
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany.
- Cluster of Excellence EXC2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.
- Present Address: Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands.
| | - Ahmed M A Elsherbini
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Mareike Harms
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Svenja Alber
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Regine Stemmler
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany
| | - Andreas Peschel
- Interfaculty Institute of Microbiology and Infection Medicine, Department of Infection Biology, University of Tübingen, Tübingen, Germany.
- Cluster of Excellence EXC2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany.
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany.
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26
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Deusenbery C, Carneiro O, Oberkfell C, Shukla A. Synergy of Antibiotics and Antibiofilm Agents against Methicillin-Resistant Staphylococcus aureus Biofilms. ACS Infect Dis 2023; 9:1949-1963. [PMID: 37646612 DOI: 10.1021/acsinfecdis.3c00239] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Methicillin-resistant Staphylococcus aureus (MRSA) infections are some of the most common antibiotic-resistant infections, often exacerbated by the formation of biofilms. Here, we evaluated six compounds, three common antibiotics used against MRSA and three antibiofilm compounds, in nine combinations to investigate the mechanisms of synergistic eradication of MRSA biofilms. Using metabolic assessment, colony enumeration, confocal fluorescence microscopy, and scanning electron microscopy, we identified two promising combinations of antibiotics with antibiofilm agents against preformed MRSA biofilms. The broad-spectrum protease, proteinase K, and membrane-targeting antibiotic, daptomycin, worked in synergy against MRSA biofilms by manipulating the protein content, increasing access to the cell membrane of biofilm bacteria. We also found that the combination of cationic peptide, IDR-1018, with the cell wall cross-linking inhibitor, vancomycin, exhibited synergy against MRSA biofilms by causing bacterial damage and preventing repair. Our findings identify synergistic combinations of antibiotics and antibiofilm agents, providing insight into mechanisms that may be explored further for the development of effective treatments against MRSA biofilm.
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Affiliation(s)
- Carly Deusenbery
- School of Engineering, Center for Biomedical Engineering, Brown University, Providence, Rhode Island 02912, United States
| | - Olivia Carneiro
- Therapeutic Sciences Graduate Program, Division of Biology and Medicine, Brown University, Providence, Rhode Island 02912, United States
| | - Carleigh Oberkfell
- School of Engineering, Center for Biomedical Engineering, Brown University, Providence, Rhode Island 02912, United States
| | - Anita Shukla
- School of Engineering, Center for Biomedical Engineering, Brown University, Providence, Rhode Island 02912, United States
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27
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Bastakoti S, Ajayi C, Julin K, Johannessen M, Hanssen AM. Exploring differentially expressed genes of Staphylococcus aureus exposed to human tonsillar cells using RNA sequencing. BMC Microbiol 2023; 23:185. [PMID: 37438716 PMCID: PMC10337072 DOI: 10.1186/s12866-023-02919-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/28/2023] [Indexed: 07/14/2023] Open
Abstract
BACKGROUND The nose and the throat are the most predominant colonizing sites of Staphylococcus aureus, and colonization is a risk factor for infection. Nasal colonization is well described; however, we have limited knowledge about S. aureus throat colonization. The main objective of this study was to explore differentially expressed genes (DEGs) in S. aureus throat isolate TR145 exposed to human tonsil epithelial cells (HTEpiC) by using RNA sequencing (RNA-seq) and pathway analysis. DEGs in S. aureus at 1 or 3 hours (h) interaction with its host were explored. RESULTS S. aureus was co-cultured in absence and presence of tonsillar cells at 1 or 3 h. Over the 3 h time frame, the bacteria multiplied, but still caused only minor cytotoxicity. Upon exposure to tonsillar cell line, S. aureus changed its transcriptomic profile. A total of 508 DEGs were identified including unique (1 h, 160 DEGs and 3 h, 78 DEGs) and commonly shared genes (1 and 3 h, 270 DEGs). Among the DEGs, were genes encoding proteins involved in adhesion and immune evasion, as well as iron acquisition and transport. Reverse transcription qPCR was done on selected genes, and the results correlated with the RNA-seq data. CONCLUSION We have shown the suitability of using HTEpiC as an in vitro model for investigating key determinants in S. aureus during co-incubation with host cells. Several DEGs were unique after 1 or 3 h exposure to host cells, while others were commonly expressed at both time points. As their expression is induced upon meeting with the host, they might be explored further for future targets for intervention to prevent either colonization or infection in the throat.
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Affiliation(s)
- Srijana Bastakoti
- Department of Medical Biology, Host-Microbe Interaction (HMI) research group, UiT - The Arctic University of Norway, Tromsø, Norway.
| | - Clement Ajayi
- Department of Medical Biology, Host-Microbe Interaction (HMI) research group, UiT - The Arctic University of Norway, Tromsø, Norway
- Center for Research and Education, University Hospital of North Norway (UNN), Tromsø, Norway
| | - Kjersti Julin
- Department of Medical Biology, Host-Microbe Interaction (HMI) research group, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Mona Johannessen
- Department of Medical Biology, Host-Microbe Interaction (HMI) research group, UiT - The Arctic University of Norway, Tromsø, Norway
- Center for Research and Education, University Hospital of North Norway (UNN), Tromsø, Norway
| | - Anne-Merethe Hanssen
- Department of Medical Biology, Host-Microbe Interaction (HMI) research group, UiT - The Arctic University of Norway, Tromsø, Norway.
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Lensmire JM, Wischer MR, Kraemer-Zimpel C, Kies PJ, Sosinski L, Ensink E, Dodson JP, Shook JC, Delekta PC, Cooper CC, Havlichek DH, Mulks MH, Lunt SY, Ravi J, Hammer ND. The glutathione import system satisfies the Staphylococcus aureus nutrient sulfur requirement and promotes interspecies competition. PLoS Genet 2023; 19:e1010834. [PMID: 37418503 PMCID: PMC10355420 DOI: 10.1371/journal.pgen.1010834] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 06/21/2023] [Indexed: 07/09/2023] Open
Abstract
Sulfur is an indispensable element for bacterial proliferation. Prior studies demonstrated that the human pathogen Staphylococcus aureus utilizes glutathione (GSH) as a source of nutrient sulfur; however, mechanisms of GSH acquisition are not defined. Here, we identify a five-gene locus comprising a putative ABC-transporter and predicted γ-glutamyl transpeptidase (ggt) that promotes S. aureus proliferation in medium supplemented with either reduced or oxidized GSH (GSSG) as the sole source of nutrient sulfur. Based on these phenotypes, we name this transporter operon the glutathione import system (gisABCD). Ggt is encoded within the gisBCD operon, and we show that the enzyme is capable of liberating glutamate using either GSH or GSSG as substrates, demonstrating it is a bona fide γ-glutamyl transpeptidase. We also determine that Ggt is expressed in the cytoplasm, representing only the second example of cytoplasmic Ggt localization, the other being Neisseria meningitidis. Bioinformatic analyses revealed that Staphylococcus species closely related to S. aureus encode GisABCD-Ggt homologs. However, homologous systems were not detected in Staphylococcus epidermidis. Consequently, we establish that GisABCD-Ggt provides a competitive advantage for S. aureus over S. epidermidis in a GSH- and GSSG-dependent manner. Overall, this study describes the discovery of a nutrient sulfur acquisition system in S. aureus that targets GSSG in addition to GSH and promotes competition against other staphylococci commonly associated with the human microbiota.
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Affiliation(s)
- Joshua M Lensmire
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Michael R Wischer
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Cristina Kraemer-Zimpel
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Paige J Kies
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Lo Sosinski
- Department of Pathobiology and Diagnostic Investigation, Michigan State University, East Lansing, Michigan, United States of America
| | - Elliot Ensink
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
| | - Jack P Dodson
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - John C Shook
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Phillip C Delekta
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Christopher C Cooper
- Department of Medicine, Division of Infectious Disease, Michigan State University, East Lansing, Michigan, United States of America
| | - Daniel H Havlichek
- Department of Medicine, Division of Infectious Disease, Michigan State University, East Lansing, Michigan, United States of America
| | - Martha H Mulks
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
| | - Sophia Y Lunt
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan, United States of America
- Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, Michigan, United States of America
| | - Janani Ravi
- Department of Biomedical Informatics, Center for Health Artificial Intelligence, University of Colorado Anschutz, Aurora, Colorado, United States of America
| | - Neal D Hammer
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America
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Pruitt EL, Zhang R, Ross DH, Ashford NK, Chen X, Alonzo F, Bush MF, Werth BJ, Xu L. Elucidating the Impact of Bacterial Lipases, Human Serum Albumin, and FASII Inhibition on the Utilization of Exogenous Fatty Acids by Staphylococcus aureus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.29.547085. [PMID: 37425828 PMCID: PMC10327171 DOI: 10.1101/2023.06.29.547085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Staphylococcus aureus only synthesizes straight-chain or branched-chain saturated fatty acids (SCFAs or BCFAs) via the type II fatty acid synthesis (FASII) pathway, but as a highly adaptive pathogen, S. aureus can also utilize host-derived exogenous fatty acids (eFAs), including SCFAs and unsaturated fatty acids (UFAs). S. aureus secretes three lipases, Geh, sal1, and SAUSA300_0641, which could perform the function of releasing fatty acids from host lipids. Once released, the FAs are phosphorylated by the fatty acid kinase, FakA, and incorporated into the bacterial lipids. In this study, we determined the substrate specificity of S. aureus secreted lipases, the effect of human serum albumin (HSA) on eFA incorporation, and the effect of FASII inhibitor, AFN-1252, on eFA incorporation using comprehensive lipidomics. When grown with major donors of fatty acids, cholesteryl esters (CEs) and triglycerides (TGs), Geh was found to be the primary lipase responsible for hydrolyzing CEs, but other lipases could compensate for the function of Geh in hydrolyzing TGs. Lipidomics showed that eFAs were incorporated into all major S. aureus lipid classes and that fatty acid-containing HSA can serve as a source of eFAs. Furthermore, S. aureus grown with UFAs displayed decreased membrane fluidity and increased production of reactive oxygen species (ROS). Exposure to AFN-1252 enhanced UFAs in the bacterial membrane, even without a source of eFAs, indicating a FASII pathway modification. Thus, the incorporation of eFAs alters the S. aureus lipidome, membrane fluidity, and ROS formation, which could affect host-pathogen interactions and susceptibility to membrane-targeting antimicrobials.
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Affiliation(s)
- Emily L. Pruitt
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Rutan Zhang
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | - Dylan H. Ross
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
| | | | - Xi Chen
- Department of Microbiology and Immunology, Loyola University Chicago-Stritch School of Medicine, Maywood, Illinois, USA
| | - Francis Alonzo
- Department of Microbiology and Immunology, Loyola University Chicago-Stritch School of Medicine, Maywood, Illinois, USA
| | - Matthew F. Bush
- Department of Chemistry, University of Washington, Seattle, Washington, USA
| | - Brian J. Werth
- Department of Pharmacy, University of Washington, Seattle, Washington, USA
| | - Libin Xu
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington, USA
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Patel H, Rawat S. A genetic regulatory see-saw of biofilm and virulence in MRSA pathogenesis. Front Microbiol 2023; 14:1204428. [PMID: 37434702 PMCID: PMC10332168 DOI: 10.3389/fmicb.2023.1204428] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/30/2023] [Indexed: 07/13/2023] Open
Abstract
Staphylococcus aureus is one of the most common opportunistic human pathogens causing several infectious diseases. Ever since the emergence of the first methicillin-resistant Staphylococcus aureus (MRSA) strain decades back, the organism has been a major cause of hospital-acquired infections (HA-MRSA). The spread of this pathogen across the community led to the emergence of a more virulent subtype of the strain, i.e., Community acquired Methicillin resistant Staphylococcus aureus (CA-MRSA). Hence, WHO has declared Staphylococcus aureus as a high-priority pathogen. MRSA pathogenesis is remarkable because of the ability of this "superbug" to form robust biofilm both in vivo and in vitro by the formation of polysaccharide intercellular adhesin (PIA), extracellular DNA (eDNA), wall teichoic acids (WTAs), and capsule (CP), which are major components that impart stability to a biofilm. On the other hand, secretion of a diverse array of virulence factors such as hemolysins, leukotoxins, enterotoxins, and Protein A regulated by agr and sae two-component systems (TCS) aids in combating host immune response. The up- and downregulation of adhesion genes involved in biofilm formation and genes responsible for synthesizing virulence factors during different stages of infection act as a genetic regulatory see-saw in the pathogenesis of MRSA. This review provides insight into the evolution and pathogenesis of MRSA infections with a focus on genetic regulation of biofilm formation and virulence factors secretion.
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Affiliation(s)
| | - Seema Rawat
- Microbiology Laboratory, School of Life Sciences, Central University of Gujarat, Gandhinagar, Gujarat, India
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31
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Stubbendieck RM, Dissanayake E, Burnham PM, Zelasko SE, Temkin MI, Wisdorf SS, Vrtis RF, Gern JE, Currie CR. Rothia from the Human Nose Inhibit Moraxella catarrhalis Colonization with a Secreted Peptidoglycan Endopeptidase. mBio 2023; 14:e0046423. [PMID: 37010413 PMCID: PMC10128031 DOI: 10.1128/mbio.00464-23] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 04/04/2023] Open
Abstract
Moraxella catarrhalis is found almost exclusively within the human respiratory tract. This pathobiont is associated with ear infections and the development of respiratory illnesses, including allergies and asthma. Given the limited ecological distribution of M. catarrhalis, we hypothesized that we could leverage the nasal microbiomes of healthy children without M. catarrhalis to identify bacteria that may represent potential sources of therapeutics. Rothia was more abundant in the noses of healthy children compared to children with cold symptoms and M. catarrhalis. We cultured Rothia from nasal samples and determined that most isolates of Rothia dentocariosa and "Rothia similmucilaginosa" were able to fully inhibit the growth of M. catarrhalis in vitro, whereas isolates of Rothia aeria varied in their ability to inhibit M. catarrhalis. Using comparative genomics and proteomics, we identified a putative peptidoglycan hydrolase called secreted antigen A (SagA). This protein was present at higher relative abundance in the secreted proteomes of R. dentocariosa and R. similmucilaginosa than in those from non-inhibitory R. aeria, suggesting that it may be involved in M. catarrhalis inhibition. We produced SagA from R. similmucilaginosa in Escherichia coli and confirmed its ability to degrade M. catarrhalis peptidoglycan and inhibit its growth. We then demonstrated that R. aeria and R. similmucilaginosa reduced M. catarrhalis levels in an air-liquid interface culture model of the respiratory epithelium. Together, our results suggest that Rothia restricts M. catarrhalis colonization of the human respiratory tract in vivo. IMPORTANCE Moraxella catarrhalis is a pathobiont of the respiratory tract, responsible for ear infections in children and wheezing illnesses in children and adults with chronic respiratory diseases. Detection of M. catarrhalis during wheezing episodes in early life is associated with the development of persistent asthma. There are currently no effective vaccines for M. catarrhalis, and most clinical isolates are resistant to the commonly prescribed antibiotics amoxicillin and penicillin. Given the limited niche of M. catarrhalis, we hypothesized that other nasal bacteria have evolved mechanisms to compete against M. catarrhalis. We found that Rothia are associated with the nasal microbiomes of healthy children without Moraxella. Next, we demonstrated that Rothia inhibit M. catarrhalis in vitro and on airway cells. We identified an enzyme produced by Rothia called SagA that degrades M. catarrhalis peptidoglycan and inhibits its growth. We suggest that Rothia or SagA could be developed as highly specific therapeutics against M. catarrhalis.
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Affiliation(s)
- Reed M. Stubbendieck
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Microbiology and Molecular Genetics, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Eishika Dissanayake
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Peter M. Burnham
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Susan E. Zelasko
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Mia I. Temkin
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Sydney S. Wisdorf
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Rose F. Vrtis
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - James E. Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Cameron R. Currie
- Department of Bacteriology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- David Braley Centre for Antibiotic Discovery, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
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32
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Kengmo Tchoupa A, Kretschmer D, Schittek B, Peschel A. The epidermal lipid barrier in microbiome-skin interaction. Trends Microbiol 2023:S0966-842X(23)00027-6. [PMID: 36822953 DOI: 10.1016/j.tim.2023.01.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 01/24/2023] [Accepted: 01/24/2023] [Indexed: 02/25/2023]
Abstract
The corneocyte layers forming the upper surface of mammalian skin are embedded in a lamellar-membrane matrix which repels harmful molecules while retaining solutes from subcutaneous tissues. Only certain bacterial and fungal taxa colonize skin surfaces. They have ways to use epidermal lipids as nutrients while resisting antimicrobial fatty acids. Skin microorganisms release lipophilic microbe-associated molecular pattern (MAMP) molecules which are largely retained by the epidermal lipid barrier. Skin barrier defects, as in atopic dermatitis, impair lamellar-membrane integrity, resulting in altered skin microbiomes, which then include the pathogen Staphylococcus aureus. The resulting increased penetration of MAMPs and toxins promotes skin inflammation. Elucidating how microorganisms manipulate the epidermal lipid barrier will be key for better ways of preventing inflammatory skin disorders.
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Affiliation(s)
- Arnaud Kengmo Tchoupa
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany; Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany; German Center for Infection Research (DZIF), partner site Tübingen, Germany
| | - Dorothee Kretschmer
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany; Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany; German Center for Infection Research (DZIF), partner site Tübingen, Germany
| | - Birgit Schittek
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany; Dermatology Department, University Hospital Tübingen, Tübingen, Germany
| | - Andreas Peschel
- Interfaculty Institute of Microbiology and Infection Medicine Tübingen, Infection Biology Section, University of Tübingen, Tübingen, Germany; Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, University of Tübingen, Tübingen, Germany; German Center for Infection Research (DZIF), partner site Tübingen, Germany.
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Carfrae LA, Brown ED. Nutrient stress is a target for new antibiotics. Trends Microbiol 2023; 31:571-585. [PMID: 36709096 DOI: 10.1016/j.tim.2023.01.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/05/2023] [Accepted: 01/09/2023] [Indexed: 01/28/2023]
Abstract
Novel approaches are required to address the looming threat of pan-resistant Gram-negative pathogens and forestall the rise of untreatable infections. Unconventional targets that are uniquely important during infection and tractable to high-throughput drug discovery methods hold high potential for innovation in antibiotic discovery programs. In this context, inhibitors of bacterial nutrient stress are particularly exciting candidates for future antibiotic development. Amino acid, nucleotide, and vitamin biosynthesis pathways are critical for bacterial growth in nutrient-limiting conditions in the laboratory and the host. Although historically dismissed as dispensable for pathogens, a wealth of transposon mutagenesis and single-mutant studies have emerged which demonstrate that several such pathways are critical for infection. Indeed, high-throughput screens of diverse synthetic compounds and natural products have uncovered inhibitors of nutrient biosynthesis. Herein, we review bacterial nutrient biosynthesis and its role during host infection. Further, we explore screening platforms developed to search for inhibitors of these targets and highlight successes among these. Finally, we feature important and sometimes surprising connections between bacterial nutrient biosynthesis, antibiotic activity, and antibiotic resistance.
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Affiliation(s)
- Lindsey A Carfrae
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4L8, Canada
| | - Eric D Brown
- Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4L8, Canada; Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, L8S 4L8, Canada; Present address: Institute of Infectious Disease Research, McMaster University, Hamilton, Ontario, L8S 4L8, Canada.
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Fernández-Fernández R, Abdullahi IN, González-Azcona C, Ulloa A, Martínez A, García-Vela S, Höfle U, Zarazaga M, Lozano C, Torres C. Detection of antimicrobial producing Staphylococcus from migratory birds: Potential role in nasotracheal microbiota modulation. Front Microbiol 2023; 14:1144975. [PMID: 37113241 PMCID: PMC10126283 DOI: 10.3389/fmicb.2023.1144975] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/06/2023] [Indexed: 04/29/2023] Open
Abstract
A collection of 259 staphylococci of 13 different species [212 coagulase-negative (CoNS) and 47 coagulase-positive (CoPS)] recovered from nasotracheal samples of 87 healthy nestling white storks was tested by the spot-on-lawn method for antimicrobial-activity (AA) against 14 indicator bacteria. Moreover, extracts of AP isolates were obtained [cell-free-supernatants (CFS) both crude and concentrated and butanol extracts] and tested against the 14 indicator bacteria. The microbiota modulation capacity of AP isolates was tested considering: (a) intra-sample AA, against all Gram-positive bacteria recovered in the same stork nasotracheal sample; (b) inter-sample AA against a selection of representative Gram-positive bacteria of the nasotracheal microbiota of all the storks (30 isolates of 29 different species and nine genera). In addition, enzymatic susceptibility test was carried out in selected AP isolates and bacteriocin encoding genes was studied by PCR/sequencing. In this respect, nine isolates (3.5%; seven CoNS and two CoPS) showed AA against at least one indicator bacteria and were considered antimicrobial-producing (AP) isolates. The AP isolates showed AA only for Gram-positive bacteria. Three of these AP isolates (S. hominis X3764, S. sciuri X4000, and S. chromogenes X4620) revealed AA on all extract conditions; other four AP isolates only showed activity in extracts after concentration; the remaining two AP isolates did not show AA in any of extract conditions. As for the microbiota modulation evaluation, three of the nine AP-isolates revealed intra-sample AA. It is to highlight the potent inter-sample AA of the X3764 isolate inhibiting 73% of the 29 representative Gram-positive species of the nasotracheal stork microbiota population. On the other hand, enzymatic analysis carried out in the two highest AP isolates (X3764 and X4000) verified the proteinaceous nature of the antimicrobial compound and PCR analysis revealed the presence of lantibiotic-like encoding genes in the nine AP isolates. In conclusion, these results show that nasotracheal staphylococci of healthy storks, and especially CoNS, produce antimicrobial substances that could be important in the modulations of their nasal microbiota.
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Affiliation(s)
- Rosa Fernández-Fernández
- Area of Biochemistry and Molecular Biology, One Health-UR Research Group, University of La Rioja, Logroño, Spain
| | - Idris Nasir Abdullahi
- Area of Biochemistry and Molecular Biology, One Health-UR Research Group, University of La Rioja, Logroño, Spain
| | - Carmen González-Azcona
- Area of Biochemistry and Molecular Biology, One Health-UR Research Group, University of La Rioja, Logroño, Spain
| | - Adriana Ulloa
- Area of Biochemistry and Molecular Biology, One Health-UR Research Group, University of La Rioja, Logroño, Spain
| | - Agustí Martínez
- Area of Biochemistry and Molecular Biology, One Health-UR Research Group, University of La Rioja, Logroño, Spain
| | - Sara García-Vela
- Area of Biochemistry and Molecular Biology, One Health-UR Research Group, University of La Rioja, Logroño, Spain
- Department of Food Science, University of Laval, Québec City, QC, Canada
| | - Ursula Höfle
- SaBio (Health and Biotechnology) Research Group, Game and Wildlife Research Institute, Spanish National Research Council/University of Castilla–La Mancha, Ciudad Real, Spain
| | - Myriam Zarazaga
- Area of Biochemistry and Molecular Biology, One Health-UR Research Group, University of La Rioja, Logroño, Spain
| | - Carmen Lozano
- Area of Biochemistry and Molecular Biology, One Health-UR Research Group, University of La Rioja, Logroño, Spain
| | - Carmen Torres
- Area of Biochemistry and Molecular Biology, One Health-UR Research Group, University of La Rioja, Logroño, Spain
- *Correspondence: Carmen Torres,
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Platt MP, Lin YH, Penix T, Wiscovitch-Russo R, Vashee I, Mares CA, Rosch JW, Yu Y, Gonzalez-Juarbe N. A multiomics analysis of direct interkingdom dynamics between influenza A virus and Streptococcus pneumoniae uncovers host-independent changes to bacterial virulence fitness. PLoS Pathog 2022; 18:e1011020. [PMID: 36542660 PMCID: PMC9815659 DOI: 10.1371/journal.ppat.1011020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 01/05/2023] [Accepted: 11/22/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND For almost a century, it has been recognized that influenza A virus (IAV) infection can promote the development of secondary bacterial infections (SBI) mainly caused by Streptococcus pneumoniae (Spn). Recent observations have shown that IAV is able to directly bind to the surface of Spn. To gain a foundational understanding of how direct IAV-Spn interaction alters bacterial biological fitness we employed combinatorial multiomic and molecular approaches. RESULTS Here we show IAV significantly remodels the global transcriptome, proteome and phosphoproteome profiles of Spn independently of host effectors. We identified Spn surface proteins that interact with IAV proteins (hemagglutinin, nucleoprotein, and neuraminidase). In addition, IAV was found to directly modulate expression of Spn virulence determinants such as pneumococcal surface protein A, pneumolysin, and factors associated with antimicrobial resistance among many others. Metabolic pathways were significantly altered leading to changes in Spn growth rate. IAV was also found to drive Spn capsule shedding and the release of pneumococcal surface proteins. Released proteins were found to be involved in evasion of innate immune responses and actively reduced human complement hemolytic and opsonizing activity. IAV also led to phosphorylation changes in Spn proteins associated with metabolism and bacterial virulence. Validation of proteomic data showed significant changes in Spn galactose and glucose metabolism. Furthermore, supplementation with galactose rescued bacterial growth and promoted bacterial invasion, while glucose supplementation led to enhanced pneumolysin production and lung cell apoptosis. CONCLUSIONS Here we demonstrate that IAV can directly modulate Spn biology without the requirement of host effectors and support the notion that inter-kingdom interactions between human viruses and commensal pathobionts can promote bacterial pathogenesis and microbiome dysbiosis.
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Affiliation(s)
- Maryann P. Platt
- Infectious Diseases and Genomic Medicine Group, J Craig Venter Institute, Rockville, Maryland, United States of America
| | - Yi-Han Lin
- Infectious Diseases and Genomic Medicine Group, J Craig Venter Institute, Rockville, Maryland, United States of America
| | - Trevor Penix
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Rosana Wiscovitch-Russo
- Infectious Diseases and Genomic Medicine Group, J Craig Venter Institute, Rockville, Maryland, United States of America
| | - Isha Vashee
- Infectious Diseases and Genomic Medicine Group, J Craig Venter Institute, Rockville, Maryland, United States of America
| | - Chris A. Mares
- Department of Life Sciences, Texas A&M University-San Antonio, Texas, United States of America
| | - Jason W. Rosch
- Department of Infectious Diseases, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Yanbao Yu
- Infectious Diseases and Genomic Medicine Group, J Craig Venter Institute, Rockville, Maryland, United States of America
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware, United States of America
| | - Norberto Gonzalez-Juarbe
- Infectious Diseases and Genomic Medicine Group, J Craig Venter Institute, Rockville, Maryland, United States of America
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Zhao N, Cheng D, Yang Z, Liu Y, Wang Y, Jian Y, Wang H, Li M, Bae T, Liu Q. Virulence adaption to environment promotes the age-dependent nasal colonization of Staphylococcus aureus. Emerg Microbes Infect 2022; 11:1402-1415. [PMID: 35508433 PMCID: PMC9132443 DOI: 10.1080/22221751.2022.2074316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/03/2022] [Indexed: 11/25/2022]
Abstract
Staphylococcus aureus is an important human commensal bacteria colonizing the human body, especially the nasal cavity. The nasal carriage can be a source of S. aureus bacteremia. However, the bacterial factors contributing to nasal colonization are not completely understood. By analysing S. aureus strains from the nasal cavity of the children, young adults, and seniors, we found that the low activity of the SaeRS two-component system (TCS) is an important determinant for S. aureus to colonize in seniors. The senior group isolates of S. aureus showed a rather distinct sequence type composition as compared with other age group isolates. The senior group isolates showed not only a lower gene carriage of enterotoxins a, c, and q but also lower hemolytic activity against human red blood cells. Of regulators affecting hemolysin production (i.e. agr, saeRS, rot, rsp, and sarS), only the SaeRS TCS showed an age-dependent decrease of activity. The decreased virulence and better colonization ability of the senior group isolates of S. aureus were confirmed in the mouse model. The senior group isolates showed the lowest survival and the best adhesion and colonizing ability. Also, the senior nasal secretions supported S. aureus survival better than the child and young adult nasal secretions. These results indicated that the senior nasal cavity favours colonization of S. aureus with higher adhesion and lower virulence, to which the reduced SaeRS TCS activity contributes. Taken together, our results illustrate an example of bacterial adaptation to the changing host environment.
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Affiliation(s)
- Na Zhao
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Danhong Cheng
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Ziyu Yang
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yao Liu
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yanan Wang
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Ying Jian
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Hua Wang
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Min Li
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Taeok Bae
- Department of Microbiology and Immunology, Indiana University School of Medicine-Northwest, Gary, IN, USA
| | - Qian Liu
- Department of Laboratory Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
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Burian M, Wolz C, Yazdi AS. Transcriptional adaptation of staphylococci during colonization of the authentic human environment: An overview of transcriptomic changes and their relationship to physiological conditions. Front Cell Infect Microbiol 2022; 12:1062329. [PMID: 36467739 PMCID: PMC9712997 DOI: 10.3389/fcimb.2022.1062329] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/02/2022] [Indexed: 12/06/2023] Open
Abstract
Staphylococci are commensals of human skin and mucous membranes, but some species can also cause serious infections. Host niches during both colonization and infection differ greatly and are characterized by specific environmental conditions (pH, temperature, oxygen, nutrient availability, and microbiota) that can affect gene expression and virulence of microbes. To successfully occupy extremely different habitats at different anatomical sites, Staphylococci are equipped with a variety of regulatory elements that allow specific adaptation to the changing environments. Not surprisingly, gene expression in vivo can be significantly different from the expression pattern observed in vitro. Niche specific stimuli that influence the bacterial ability to either cause infection or maintain colonization are only partially understood. Here, we describe habitat specific conditions and discuss the available literature analyzing staphylococcal gene expression, focusing on Staphylococcus aureus and S. epidermidis during colonization of the nose and skin.
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Affiliation(s)
- Marc Burian
- Department of Dermatology and Allergology, RWTH University Hospital Aachen, Aachen, Germany
| | - Christiane Wolz
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
- Cluster of Excellence EXC 2124 “Controlling Microbes to Fight Infections”, University of Tübingen, Tübingen, Germany
| | - Amir S. Yazdi
- Department of Dermatology and Allergology, RWTH University Hospital Aachen, Aachen, Germany
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Fuji N, Pichichero M, Kaur R. Pathogenesis of Streptococcus pneumoniae serotype 3 during natural colonization and infections among children and its IgG correlate of protection in a mouse model. Vaccine 2022; 40:6412-6421. [PMID: 36192274 DOI: 10.1016/j.vaccine.2022.09.062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 09/07/2022] [Accepted: 09/20/2022] [Indexed: 01/27/2023]
Abstract
Current licensed pneumococcal conjugate vaccines (PCVs) are effective against pneumococcal diseases caused by the serotypes contained in the PCvs However; several studies evaluating pneumococcal colonization and acute otitis-media (AOM) prevention in young children vaccinated with PCV13, observed less effectiveness against serotype-3. One possible reason for less effectiveness may be release of the capsular polysaccharide (CPS) of serotype-3 (CPS-3) as an immune evasion mechanism. Here we evaluated free CPS-3 levels released from 6 clinical isolates from young children compared to WU2 strain and to serotype-19A CPS (CPS-19A) released in vitro when interacting with nasopharyngeal, middle-ear and lung cell-lines. Clinical serotype-3 strains showed greater release of CPS than WU2 with the interaction to 2 cell-lines and all 6 clinical serotype-19A strains. We next evaluated CPS-3 vs CPS-19A levels in middle-ear fluid (MEF) and the nasopharynx (NP) of young children and found higher levels of CPS-3 compared to CPS-19A in MEF during AOM but not in NP secretions during colonization. With anti-CPS-3 IgG in MEF and NP secretions at time of health and onset of AOM, a significant negative correlation (r = -0.75, p < 0.05) between unbound anti-CPS-3 IgG levels and free- anti-CPS-3 in MEF were found, and a significant lower detection of unbound anti-CPS-3 IgG in NP at the time of health with serotype-3 SPN (p < 0.05) compared to irrelevant SPN serotypes were found. In a mouse model of AOM and pneumonia, we sought a correlate of protection against serotype-3 infection using human serum-derived anti-CPS-3 IgG. We conclude that serotype-3 clinical isolates from children release more capsule than WU2 strains or 19A strains during in vitro testing; release more capsule in the MEF of children during AOM than serotype 19A; unbound anti-CPS-3 IgG levels negatively correlate with free-anti-CPS-3; and a level of 2.8 µg/ml anti-CPS-3 antibody protects mice from AOM and pneumonia but not colonization.
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Affiliation(s)
- Naoko Fuji
- Center for Infectious Diseases and Immunology, Rochester General Hospital Research Institute, Rochester, NY, United States
| | - Michael Pichichero
- Center for Infectious Diseases and Immunology, Rochester General Hospital Research Institute, Rochester, NY, United States
| | - Ravinder Kaur
- Center for Infectious Diseases and Immunology, Rochester General Hospital Research Institute, Rochester, NY, United States.
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Glucose Mediates Niche-Specific Repression of Staphylococcus aureus Toxic Shock Syndrome Toxin-1 through the Activity of CcpA in the Vaginal Environment. J Bacteriol 2022; 204:e0026922. [PMID: 36106854 PMCID: PMC9578429 DOI: 10.1128/jb.00269-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus chronically colonizes up to 30% of the human population on the skin or mucous membranes, including the nasal tract or vaginal canal. While colonization is often benign, this bacterium also has the capability to cause serious infections. Menstrual toxic shock syndrome (mTSS) is a serious toxinosis associated with improper use of tampons, which can induce an environment that is favorable to the production of the superantigen known as toxic shock syndrome toxin-1 (TSST-1). To better understand environmental signaling that influences TSST-1 production, we analyzed expression in the prototype mTSS strain S. aureus MN8. Using transcriptional and protein-based analysis in two niche-related media, we observed that TSST-1 expression was significantly higher in synthetic nasal medium (SNM) than in vaginally defined medium (VDM). One major divergence in medium composition was high glucose concentration in VDM. The glucose-dependent virulence regulator gene ccpA was deleted in MN8, and, compared with wild-type MN8, we observed increased TSST-1 expression in the ΔccpA mutant when grown in VDM, suggesting that TSST-1 is repressed by catabolite control protein A (CcpA) in the vaginal environment. We were able to relieve CcpA-mediated repression by modifying the glucose level in vaginal conditions, confirming that changes in nutritional conditions contribute to the overexpression of TSST-1 that can lead to mTSS. We also compared CcpA-mediated repression to other key regulators of tst, finding that CcpA regulation is dominant compared to other characterized regulatory mechanisms. This study underlines the importance of environmental signaling for S. aureus pathogenesis in the context of mTSS. IMPORTANCE Menstrual toxic shock syndrome (mTSS) is caused by strains of Staphylococcus aureus that overproduce a toxin known as toxic shock syndrome toxin-1 (TSST-1). This work studied how glucose levels in a model vaginal environment could influence the amount of TSST-1 that is produced by S. aureus. We found that high levels of glucose repress TSST-1 production, and this is done by a regulatory protein called catabolite control protein A (CcpA). The research also demonstrated that, compared with other regulatory proteins, the CcpA regulator appears to be the most important for maintaining low levels of TSST-1 in the vaginal environment, and this information helps to understand how changes in the vaginal environmental can lead to mTSS.
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Mostolizadeh R, Glöckler M, Dräger A. Towards the human nasal microbiome: Simulating D. pigrum and S. aureus. Front Cell Infect Microbiol 2022; 12:925215. [PMID: 36605126 PMCID: PMC9810029 DOI: 10.3389/fcimb.2022.925215] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 08/15/2022] [Indexed: 01/12/2023] Open
Abstract
The human nose harbors various microbes that decisively influence the wellbeing and health of their host. Among the most threatening pathogens in this habitat is Staphylococcus aureus. Multiple epidemiological studies identify Dolosigranulum pigrum as a likely beneficial bacterium based on its positive association with health, including negative associations with S. aureus. Carefully curated GEMs are available for both bacterial species that reliably simulate their growth behavior in isolation. To unravel the mutual effects among bacteria, building community models for simulating co-culture growth is necessary. However, modeling microbial communities remains challenging. This article illustrates how applying the NCMW fosters our understanding of two microbes' joint growth conditions in the nasal habitat and their intricate interplay from a metabolic modeling perspective. The resulting community model combines the latest available curated GEMs of D. pigrum and S. aureus. This uses case illustrates how to incorporate genuine GEM of participating microorganisms and creates a basic community model mimicking the human nasal environment. Our analysis supports the role of negative microbe-microbe interactions involving D. pigrum examined experimentally in the lab. By this, we identify and characterize metabolic exchange factors involved in a specific interaction between D. pigrum and S. aureus as an in silico candidate factor for a deep insight into the associated species. This method may serve as a blueprint for developing more complex microbial interaction models. Its direct application suggests new ways to prevent disease-causing infections by inhibiting the growth of pathogens such as S. aureus through microbe-microbe interactions.
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Affiliation(s)
- Reihaneh Mostolizadeh
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany,Department of Computer Science, University of Tübingen, Tübingen, Germany,German Center for Infection Research (DZIF), Partner site, Tübingen, Germany,Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, Tübingen, Germany,*Correspondence: Reihaneh Mostolizadeh,
| | - Manuel Glöckler
- Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Andreas Dräger
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany,Department of Computer Science, University of Tübingen, Tübingen, Germany,German Center for Infection Research (DZIF), Partner site, Tübingen, Germany,Cluster of Excellence ‘Controlling Microbes to Fight Infections’, University of Tübingen, Tübingen, Germany
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Pederick JL, Horsfall AJ, Jovcevski B, Klose J, Abell AD, Pukala TL, Bruning JB. Discovery of an ʟ-amino acid ligase implicated in Staphylococcal sulfur amino acid metabolism. J Biol Chem 2022; 298:102392. [PMID: 35988643 PMCID: PMC9486568 DOI: 10.1016/j.jbc.2022.102392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/10/2022] [Accepted: 08/15/2022] [Indexed: 11/06/2022] Open
Abstract
Enzymes involved in Staphylococcus aureus amino acid metabolism have recently gained traction as promising targets for the development of new antibiotics, however, not all aspects of this process are understood. The ATP-grasp superfamily includes enzymes that predominantly catalyze the ATP-dependent ligation of various carboxylate and amine substrates. One subset, ʟ-amino acid ligases (LALs), primarily catalyze the formation of dipeptide products in Gram-positive bacteria, however, their involvement in S. aureus amino acid metabolism has not been investigated. Here, we present the characterization of the putative ATP-grasp enzyme (SAOUHSC_02373) from S. aureus NCTC 8325 and its identification as a novel LAL. First, we interrogated the activity of SAOUHSC_02373 against a panel of ʟ-amino acid substrates. As a result, we identified SAOUHSC_02373 as an LAL with high selectivity for ʟ-aspartate and ʟ-methionine substrates, specifically forming an ʟ-aspartyl–ʟ-methionine dipeptide. Thus, we propose that SAOUHSC_02373 be assigned as ʟ-aspartate–ʟ-methionine ligase (LdmS). To further understand this unique activity, we investigated the mechanism of LdmS by X-ray crystallography, molecular modeling, and site-directed mutagenesis. Our results suggest that LdmS shares a similar mechanism to other ATP-grasp enzymes but possesses a distinctive active site architecture that confers selectivity for the ʟ-Asp and ʟ-Met substrates. Phylogenetic analysis revealed LdmS homologs are highly conserved in Staphylococcus and closely related Gram-positive Firmicutes. Subsequent genetic analysis upstream of the ldmS operon revealed several trans-acting regulatory elements associated with control of Met and Cys metabolism. Together, these findings support a role for LdmS in Staphylococcal sulfur amino acid metabolism.
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Affiliation(s)
- Jordan L Pederick
- Institute for Photonics and Advanced Sensing, (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Aimee J Horsfall
- Institute for Photonics and Advanced Sensing, (IPAS), School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia; ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, South Australia 5005, Australia
| | - Blagojce Jovcevski
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia; School of Agriculture, Food and Wine, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jack Klose
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Andrew D Abell
- Institute for Photonics and Advanced Sensing, (IPAS), School of Physical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia; ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Adelaide, South Australia 5005, Australia
| | - Tara L Pukala
- Department of Chemistry, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - John B Bruning
- Institute for Photonics and Advanced Sensing, (IPAS), School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia.
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Stamm J, Weißelberg S, Both A, Failla AV, Nordholt G, Büttner H, Linder S, Aepfelbacher M, Rohde H. Development of an artificial synovial fluid useful for studying Staphylococcus epidermidis joint infections. Front Cell Infect Microbiol 2022; 12:948151. [PMID: 35967857 PMCID: PMC9374174 DOI: 10.3389/fcimb.2022.948151] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 07/04/2022] [Indexed: 11/24/2022] Open
Abstract
Staphylococcus epidermidis is a major causative agent of prosthetic joint infections (PJI). The ability to form biofilms supports this highly selective pathogenic potential. In vitro studies essentially relying on phenotypic assays and genetic approaches have provided a detailed picture of the molecular events contributing to biofilm assembly. A major limitation in these studies is the use of synthetic growth media, which significantly differs from the environmental conditions S. epidermidis encounters during host invasion. Building on evidence showing that growth in serum substantially affects S. epidermidis gene expression profiles and phenotypes, the major aim of this study was to develop and characterize a growth medium mimicking synovial fluid, thereby facilitating research addressing specific aspects related to PJI. Using fresh human plasma, a protocol was established allowing for the large-scale production of a medium that by biochemical analysis matches key characteristics of synovial fluid and therefore is referred to as artificial synovial fluid (ASF). By analysis of biofilm-positive, polysaccharide intercellular adhesion (PIA)-producing S. epidermidis 1457 and its isogenic, PIA- and biofilm-negative mutant 1457-M10, evidence is provided that the presence of ASF induces cluster formation in S. epidermidis 1457 and mutant 1457-M10. Consistent with the aggregative properties, both strains formed multilayered biofilms when analyzed by confocal laser scanning microscopy. In parallel to the phenotypic findings, expression analysis after growth in ASF found upregulation of genes encoding for intercellular adhesins (icaA, aap, and embp) as well as atlE, encoding for the major cell wall autolysin being responsible for eDNA release. In contrast, growth in ASF was associated with reduced expression of the master regulator agr. Collectively, these results indicate that ASF induces expression profiles that are able to support intercellular adhesion in both PIA-positive and PIA-negative S. epidermidis. Given the observation that ASF overall induced biofilm formation in a collection of S. epidermidis isolates from PJI, the results strongly support the idea of using growth media mimicking host environments. ASF may play an important role in future studies related to the pathogenesis of S. epidermidis PJI.
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Affiliation(s)
- Johanna Stamm
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Hamburg, Germany
| | - Samira Weißelberg
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Hamburg, Germany
| | - Anna Both
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Hamburg, Germany
| | | | - Gerhard Nordholt
- Institute for Clinical Chemistry, Universitätsklinikum Hamburg-Eppendorf, Hamburg, Germany
| | - Henning Büttner
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Hamburg, Germany
| | - Stefan Linder
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Hamburg, Germany
| | - Martin Aepfelbacher
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Hamburg, Germany
| | - Holger Rohde
- Institut für Medizinische Mikrobiologie, Virologie und Hygiene, Hamburg, Germany
- Deutsches Zentrum für Infektionsmedizin, Standort Hamburg-Lübeck-Borstel, Hamburg, Germany
- *Correspondence: Holger Rohde,
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Forecasting Staphylococcus aureus Infections Using Genome-Wide Association Studies, Machine Learning, and Transcriptomic Approaches. mSystems 2022; 7:e0037822. [PMID: 35862809 PMCID: PMC9426533 DOI: 10.1128/msystems.00378-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Staphylococcus aureus is a major human and animal pathogen, colonizing diverse ecological niches within its hosts. Predicting whether an isolate will infect a specific host and its subsequent clinical fate remains unknown. In this study, we investigated the S. aureus pangenome using a curated set of 356 strains, spanning a wide range of hosts, origins, and clinical display and antibiotic resistance profiles. We used genome-wide association study (GWAS) and random forest (RF) algorithms to discriminate strains based on their origins and clinical sources. Here, we show that the presence of sak and scn can discriminate strains based on their host specificity, while other genes such as mecA are often associated with virulent outcomes. Both GWAS and RF indicated the importance of intergenic regions (IGRs) and coding DNA sequence (CDS) but not sRNAs in forecasting an outcome. Additional transcriptomic analyses performed on the most prevalent clonal complex 8 (CC8) clonal types, in media mimicking nasal colonization or bacteremia, indicated three RNAs as potential RNA markers to forecast infection, followed by 30 others that could serve as infection severity predictors. Our report shows that genetic association and transcriptomics are complementary approaches that will be combined in a single analytical framework to improve our understanding of bacterial pathogenesis and ultimately identify potential predictive molecular markers. IMPORTANCE Predicting the outcome of bacterial colonization and infections, based on extensive genomic and transcriptomic data from a given pathogen, would be of substantial help for clinicians in treating and curing patients. In this report, genome-wide association studies and random forest algorithms have defined gene combinations that differentiate human from animal strains, colonization from diseases, and nonsevere from severe diseases, while it revealed the importance of IGRs and CDS, but not small RNAs (sRNAs), in anticipating an outcome. In addition, transcriptomic analyses performed on the most prevalent clonal types, in media mimicking either nasal colonization or bacteremia, revealed significant differences and therefore potent RNA markers. Overall, the use of both genomic and transcriptomic data in a single analytical framework can enhance our understanding of bacterial pathogenesis.
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Adolf LA, Heilbronner S. Nutritional Interactions between Bacterial Species Colonising the Human Nasal Cavity: Current Knowledge and Future Prospects. Metabolites 2022; 12:489. [PMID: 35736422 PMCID: PMC9229137 DOI: 10.3390/metabo12060489] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/16/2022] [Accepted: 05/25/2022] [Indexed: 12/10/2022] Open
Abstract
The human nasal microbiome can be a reservoir for several pathogens, including Staphylococcus aureus. However, certain harmless nasal commensals can interfere with pathogen colonisation, an ability that could be exploited to prevent infection. Although attractive as a prophylactic strategy, manipulation of nasal microbiomes to prevent pathogen colonisation requires a better understanding of the molecular mechanisms of interaction that occur between nasal commensals as well as between commensals and pathogens. Our knowledge concerning the mechanisms of pathogen exclusion and how stable community structures are established is patchy and incomplete. Nutrients are scarce in nasal cavities, which makes competitive or mutualistic traits in nutrient acquisition very likely. In this review, we focus on nutritional interactions that have been shown to or might occur between nasal microbiome members. We summarise concepts of nutrient release from complex host molecules and host cells as well as of intracommunity exchange of energy-rich fermentation products and siderophores. Finally, we discuss the potential of genome-based metabolic models to predict complex nutritional interactions between members of the nasal microbiome.
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Affiliation(s)
- Lea A. Adolf
- Interfaculty Institute for Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, UKT Tübingen, 72076 Tübingen, Germany;
| | - Simon Heilbronner
- Interfaculty Institute for Microbiology and Infection Medicine, Institute for Medical Microbiology and Hygiene, UKT Tübingen, 72076 Tübingen, Germany;
- German Centre for Infection Research (DZIF), Partner Site Tübingen, 72076 Tübingen, Germany
- Cluster of Excellence EXC 2124 Controlling Microbes to Fight Infections, 72076 Tübingen, Germany
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45
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Zheng Y, Hunt RL, Villaruz AE, Fisher EL, Liu R, Liu Q, Cheung GYC, Li M, Otto M. Commensal Staphylococcus epidermidis contributes to skin barrier homeostasis by generating protective ceramides. Cell Host Microbe 2022; 30:301-313.e9. [PMID: 35123653 PMCID: PMC8917079 DOI: 10.1016/j.chom.2022.01.004] [Citation(s) in RCA: 133] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 12/07/2021] [Accepted: 01/11/2022] [Indexed: 12/19/2022]
Abstract
Previously either regarded as insignificant or feared as potential sources of infection, the bacteria living on our skin are increasingly recognized for their role in benefitting human health. Skin commensals modulate mucosal immune defenses and directly interfere with pathogens; however, their contribution to the skin's physical integrity is less understood. Here, we show that the abundant skin commensal Staphylococcus epidermidis contributes to skin barrier integrity. S. epidermidis secretes a sphingomyelinase that acquires essential nutrients for the bacteria and assists the host in producing ceramides, the main constituent of the epithelial barrier that averts skin dehydration and aging. In mouse models, S. epidermidis significantly increases skin ceramide levels and prevents water loss of damaged skin in a fashion entirely dependent on its sphingomyelinase. Our findings reveal a symbiotic mechanism that demonstrates an important role of the skin microbiota in the maintenance of the skin's protective barrier.
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Affiliation(s)
- Yue Zheng
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, MD 20814, USA
| | - Rachelle L Hunt
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, MD 20814, USA
| | - Amer E Villaruz
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, MD 20814, USA
| | - Emilie L Fisher
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, MD 20814, USA
| | - Ryan Liu
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, MD 20814, USA
| | - Qian Liu
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Gordon Y C Cheung
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, MD 20814, USA
| | - Min Li
- Department of Laboratory Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Michael Otto
- Pathogen Molecular Genetics Section, Laboratory of Bacteriology, National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Bethesda, MD 20814, USA.
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46
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Ortega-Peña S, Rodríguez-Martínez S, Cancino-Diaz ME, Cancino-Diaz JC. Staphylococcus epidermidis Controls Opportunistic Pathogens in the Nose, Could It Help to Regulate SARS-CoV-2 (COVID-19) Infection? Life (Basel) 2022; 12:341. [PMID: 35330092 PMCID: PMC8954679 DOI: 10.3390/life12030341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/14/2022] [Accepted: 02/21/2022] [Indexed: 02/06/2023] Open
Abstract
Staphylococcus epidermidis is more abundant in the anterior nares than internal parts of the nose, but its relative abundance changes along with age; it is more abundant in adolescents than in children and adults. Various studies have shown that S. epidermidis is the guardian of the nasal cavity because it prevents the colonization and infection of respiratory pathogens (bacteria and viruses) through the secretion of antimicrobial molecules and inhibitors of biofilm formation, occupying the space of the membrane mucosa and through the stimulation of the host's innate and adaptive immunity. There is a strong relationship between the low number of S. epidermidis in the nasal cavity and the increased risk of serious respiratory infections. The direct application of S. epidermidis into the nasal cavity could be an effective therapeutic strategy to prevent respiratory infections and to restore nasal cavity homeostasis. This review shows the mechanisms that S. epidermidis uses to eliminate respiratory pathogens from the nasal cavity, also S. epidermidis is proposed to be used as a probiotic to prevent the development of COVID-19 because S. epidermidis induces the production of interferon type I and III and decreases the expression of the entry receptors of SARS-CoV-2 (ACE2 and TMPRSS2) in the nasal epithelial cells.
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Affiliation(s)
- Silvestre Ortega-Peña
- Laboratorio Tejido Conjuntivo, Centro Nacional de Investigación y Atención de Quemados, Instituto Nacional de Rehabilitación “Luís Guillermo Ibarra Ibarra”, Ciudad de México 14389, Mexico
| | - Sandra Rodríguez-Martínez
- Laboratorio de Inmunidad Innata, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (S.R.-M.); (M.E.C.-D.)
| | - Mario E. Cancino-Diaz
- Laboratorio de Inmunidad Innata, Departamento de Inmunología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico; (S.R.-M.); (M.E.C.-D.)
| | - Juan C. Cancino-Diaz
- Laboratorio de Inmunomicrobiología, Departamento Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México 11340, Mexico
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Glöckler M, Dräger A, Mostolizadeh R. NCMW: A Python Package to Analyze Metabolic Interactions in the Nasal Microbiome. FRONTIERS IN BIOINFORMATICS 2022; 2:827024. [PMID: 36304309 PMCID: PMC9580955 DOI: 10.3389/fbinf.2022.827024] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/19/2022] [Indexed: 11/13/2022] Open
Abstract
The human upper respiratory tract is the reservoir of a diverse community of commensals and potential pathogens (pathobionts), including Streptococcus pneumoniae (pneumococcus), Haemophilus influenzae, Moraxella catarrhalis, and Staphylococcus aureus, which occasionally turn into pathogens causing infectious diseases, while the contribution of many nasal microorganisms to human health remains undiscovered. To better understand the composition of the nasal microbiome community, we create a workflow of the community model, which mimics the human nasal environment. To address this challenge, constraint-based reconstruction of biochemically accurate genome-scale metabolic models (GEMs) networks of microorganisms is mandatory. Our workflow applies constraint-based modeling (CBM), simulates the metabolism between species in a given microbiome, and facilitates generating novel hypotheses on microbial interactions. Utilizing this workflow, we hope to gain a better understanding of interactions from the metabolic modeling perspective. This article presents nasal community modeling workflow (NCMW)—a python package based on GEMs of species as a starting point for understanding the composition of the nasal microbiome community. The package is constructed as a step-by-step mathematical framework for metabolic modeling and analysis of the nasal microbial community. Using constraint-based models reduces the need for culturing species in vitro, a process that is not convenient in the environment of human noses.Availability: NCMW is freely available on the Python Package Index (PIP) via pip install NCMW. The source code, documentation, and usage examples (Jupyter Notebook and example files) are available at https://github.com/manuelgloeckler/ncmw.
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Affiliation(s)
- Manuel Glöckler
- Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Andreas Dräger
- Department of Computer Science, University of Tübingen, Tübingen, Germany
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Cluster of Excellence “Controlling Microbes to Fight Infections”, University of Tübingen, Tübingen, Germany
| | - Reihaneh Mostolizadeh
- Department of Computer Science, University of Tübingen, Tübingen, Germany
- Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens, Institute for Bioinformatics and Medical Informatics (IBMI), University of Tübingen, Tübingen, Germany
- German Center for Infection Research (DZIF), Partner Site Tübingen, Tübingen, Germany
- Cluster of Excellence “Controlling Microbes to Fight Infections”, University of Tübingen, Tübingen, Germany
- *Correspondence: Reihaneh Mostolizadeh,
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Salgado BAB, Waters EM, Moran JC, Kadioglu A, Horsburgh MJ. Selection of Staphylococcus aureus in a murine nasopharyngeal colonization model. Front Cell Infect Microbiol 2022; 12:874138. [PMID: 35992161 PMCID: PMC9386156 DOI: 10.3389/fcimb.2022.874138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
Staphylococcus aureus nasal colonization is a risk factor for infection. A large proportion of the population are identified as potential S. aureus carriers yet we only partially understand the repertoire of genetic factors that promote long-term nasal colonization. Here we present a murine model of nasopharyngeal colonization that requires a low S. aureus inoculum and is amenable to experimental evolution approaches. We used this model to experimentally evolve S. aureus using successive passages in the nasopharynx to identify those genetic loci under selection. After 3 cycles of colonization, mutations were identified in mannitol, sorbitol, arginine, nitrite and lactate metabolism genes promoting key pathways in nasal colonization. Stress responses were identified as being under selective pressure, with mutations in DNA repair genes including dnaJ and recF and key stress response genes clpL, rpoB and ahpF. Peptidoglycan synthesis pathway genes also revealed mutations indicating potential selection for alteration of the cell surface. The murine model used here is versatile to question colonization, persistence and evolution studies. We studied the human pathogen Staphylococcus aureus in our search to determine factors that contribute to its ability to live in the human nose and throat. The anterior nares and nasopharynx are considered primary habitats but we do not understand how the pathogen adapts as it moves from one person to the next. We first determined sustained survival of the pathogen over multiple days in the nasopharynx that might act as a good model for human persistence due to the low numbers of bacteria needed for it to establish. By using successive rounds of colonization of the nasopharynx across different mice we revealed that multiple genetic changes in the S. aureus occurred. These changes were found in genes associated with the cell surface and metabolism and might indicate adaptation to the niche. One gene showed an accumulation of multiple mutations supporting a key contribution in adaptation but the role of the protein it encodes is not yet known. The contribution of these genes and genetic changes are unclear but indicate an area for future research to better understand how this common human pathogen is so successful at human colonization and survival.
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Maurin C, Courrier E, He Z, Rigaill J, Josse J, Laurent F, Gain P, Thuret G, Verhoeven PO. Key Role of Staphylococcal Fibronectin-Binding Proteins During the Initial Stage of Staphylococcus aureus Keratitis in Humans. Front Cell Infect Microbiol 2021; 11:745659. [PMID: 34858871 PMCID: PMC8630648 DOI: 10.3389/fcimb.2021.745659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/04/2021] [Indexed: 12/25/2022] Open
Abstract
Objectives Staphylococcus aureus is one of the main causes of bacterial keratitis in humans. This study was aimed at investigating the mechanisms of S. aureus adhesion to the human corneal epithelium involved during the initial stage of infectious keratitis. Methods Human corneas stored in a specific active storage machine that restores a normal pluristratified epithelium were used to assess S. aureus adhesion level to intact and injured tissues using immunostaining. S. aureus adhesion to immobilized fibronectin was measured in microtiter plate. Internalization of S. aureus clinical isolates recovered from keratitis was assessed on human corneal epithelial HCE-2 cells. Results Superficial corneal injury unmasked fibronectin molecules expressed within the human corneal epithelium. S. aureus adhesion level was increased by 117-fold in the area of injured epithelium (p < 0.0001). The deletion of staphylococcal fnbA/B genes decreased by 71% the adhesion level to immobilized fibronectin (p < 0.001). The deletion of fnbA/B genes and the incubation of the corneas with anti-fibronectin blocking antibodies prior to the infection significantly reduced the S. aureus adhesion level to injured corneal epithelium (p < 0.001). Finally, S. aureus clinical isolates triggered its internalization in human corneal epithelial cells as efficiently as the 8325-4 wt. Conclusion S. aureus was almost unable to bind the intact corneal epithelium, whereas a superficial epithelial injury of the corneal epithelium strongly increased S. aureus adhesion, which is mainly driven by the interaction between staphylococcal fibronectin-binding proteins and unmasked fibronectin molecules located underneath the most superficial layer of the corneal epithelium.
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Affiliation(s)
- Corantin Maurin
- Corneal Graft Biology, Engineering and Imaging Laboratory (BiiGC), University of St-Etienne, St-Etienne, France
| | - Emilie Courrier
- Corneal Graft Biology, Engineering and Imaging Laboratory (BiiGC), University of St-Etienne, St-Etienne, France
| | - Zhiguo He
- Corneal Graft Biology, Engineering and Imaging Laboratory (BiiGC), University of St-Etienne, St-Etienne, France
| | - Josselin Rigaill
- CIRI, Centre International de Recherche en Infectiologie, GIMAP Team, University of Lyon, University of St-Etienne, INSERM U1111, CNRS UMR5308, ENS de Lyon, UCBL1, St-Etienne, France.,Laboratory of Infectious Agents and Hygiene, University Hospital of St-Etienne, St-Etienne, France
| | - Jérôme Josse
- CIRI, Centre International de Recherche en Infectiologie, Staphylococcal Pathogenesis Team, University of Lyon, INSERM U1111, CNRS UMR5308, ENS de Lyon, UCBL1, Lyon, France
| | - Frédéric Laurent
- CIRI, Centre International de Recherche en Infectiologie, Staphylococcal Pathogenesis Team, University of Lyon, INSERM U1111, CNRS UMR5308, ENS de Lyon, UCBL1, Lyon, France.,Department of Bacteriology, Institute for Infectious Agents, Hospices Civiles de Lyon, Lyon, France.,Centre National de Référence des Staphylocoques, Hospices Civils de Lyon, Lyon, France
| | - Philippe Gain
- Corneal Graft Biology, Engineering and Imaging Laboratory (BiiGC), University of St-Etienne, St-Etienne, France.,Department of Ophthalmology, University Hospital, St-Etienne, France
| | - Gilles Thuret
- Corneal Graft Biology, Engineering and Imaging Laboratory (BiiGC), University of St-Etienne, St-Etienne, France.,Department of Ophthalmology, University Hospital, St-Etienne, France
| | - Paul O Verhoeven
- CIRI, Centre International de Recherche en Infectiologie, GIMAP Team, University of Lyon, University of St-Etienne, INSERM U1111, CNRS UMR5308, ENS de Lyon, UCBL1, St-Etienne, France.,Laboratory of Infectious Agents and Hygiene, University Hospital of St-Etienne, St-Etienne, France
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50
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Casillas-Ituarte NN, Staats AM, Lower BH, Stoodley P, Lower SK. Host blood proteins as bridging ligand in bacterial aggregation as well as anchor point for adhesion in the molecular pathogenesis of Staphylococcus aureus infections. Micron 2021; 150:103137. [PMID: 34392091 PMCID: PMC8484042 DOI: 10.1016/j.micron.2021.103137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/09/2021] [Accepted: 08/03/2021] [Indexed: 11/20/2022]
Abstract
Fibronectin (Fn) and fibrinogen (Fg) are major host proteins present in the extracellular matrix, blood, and coatings on indwelling medical devices. The ability of Staphylococcus aureus to cause infections in humans depends on favorable interactions with these host ligands. Closely related bacterial adhesins, fibronectin-binding proteins A and B (FnBPA, FnBPB) were evaluated for two key steps in pathogenesis: clumping and adhesion. Experiments utilized optical spectrophotometry, flow cytometry, and atomic force microscopy to probe FnBPA/B alone or in combination in seven different strains of S. aureus and Lactococcus lactis, a Gram-positive surrogate that naturally lacks adhesins to mammalian ligands. In the absence of soluble ligands, both FnBPA and FnBPB were capable of interacting with adjacent FnBPs from neighboring bacteria to mediate clumping. In the presence of soluble host ligands, clumping was enhanced particularly under shear stress and with Fn present in the media. FnBPB exhibited greater ability to clump compared to FnBPA. The strength of adhesion was similar for immobilized Fn to FnBPA and FnBPB. These findings suggest that these two distinct but closely related bacterial adhesins, have different functional capabilities to interact with host ligands in different settings (e.g., soluble vs. immobilized). Survival and persistence of S. aureus in a human host may depend on complementary roles of FnBPA and FnBPB as they interact with different conformations of Fn or Fg (compact in solution vs. extended on a surface) present in different physiological spaces.
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Affiliation(s)
- Nadia N Casillas-Ituarte
- School of Earth Sciences, The Ohio State University, Columbus, OH, 43210, USA; School of Environment and Natural Resources, The Ohio State University, Columbus, OH, 43210, USA.
| | - Amelia M Staats
- Departments of Microbiology and Microbial Infection and Immunity, The Ohio State University, 43210, Columbus, OH, USA
| | - Brian H Lower
- School of Environment and Natural Resources, The Ohio State University, Columbus, OH, 43210, USA
| | - Paul Stoodley
- Departments of Microbiology and Microbial Infection and Immunity, The Ohio State University, 43210, Columbus, OH, USA; Department of Orthopaedics, The Ohio State University, Columbus, OH, 43210, USA
| | - Steven K Lower
- School of Earth Sciences, The Ohio State University, Columbus, OH, 43210, USA; School of Environment and Natural Resources, The Ohio State University, Columbus, OH, 43210, USA; Departments of Microbiology and Microbial Infection and Immunity, The Ohio State University, 43210, Columbus, OH, USA
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