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Long DR, Holmes EA, Lo HY, Penewit K, Almazan J, Hodgson T, Berger NF, Bishop ZH, Lewis JD, Waalkes A, Wolter DJ, Salipante SJ. Clinical and in vitro models identify distinct adaptations enhancing Staphylococcus aureus pathogenesis in human macrophages. PLoS Pathog 2024; 20:e1012394. [PMID: 38991026 PMCID: PMC11265673 DOI: 10.1371/journal.ppat.1012394] [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: 02/16/2024] [Revised: 07/23/2024] [Accepted: 07/04/2024] [Indexed: 07/13/2024] Open
Abstract
Staphylococcus aureus is a facultative intracellular pathogen of human macrophages, which facilitates chronic infection. The genotypes, pathways, and mutations influencing that phenotype remain incompletely explored. Here, we used two distinct strategies to ascertain S. aureus gene mutations affecting pathogenesis in macrophages. First, we analyzed isolates collected serially from chronic cystic fibrosis (CF) respiratory infections. We found that S. aureus strains evolved greater macrophage invasion capacity during chronic human infection. Bacterial genome-wide association studies (GWAS) identified 127 candidate genes for which mutation was significantly associated with macrophage pathogenesis in vivo. In parallel, we passaged laboratory S. aureus strains in vitro to select for increased infection of human THP-1 derived macrophages, which identified 15 candidate genes by whole-genome sequencing. Functional validation of candidate genes using isogenic transposon mutant knockouts and CRISPR interference (CRISPRi) knockdowns confirmed virulence contributions from 37 of 39 tested genes (95%) implicated by in vivo studies and 7 of 10 genes (70%) ascertained from in vitro selection, with one gene in common to the two strategies. Validated genes included 17 known virulence factors (39%) and 27 newly identified by our study (61%), some encoding functions not previously associated with macrophage pathogenesis. Most genes (80%) positively impacted macrophage invasion when disrupted, consistent with the phenotype readily arising from loss-of-function mutations in vivo. This work reveals genes and mechanisms that contribute to S. aureus infection of macrophages, highlights differences in mutations underlying convergent phenotypes arising from in vivo and in vitro systems, and supports the relevance of S. aureus macrophage pathogenesis during chronic respiratory infection in CF. Additional studies will be needed to illuminate the exact mechanisms by which implicated mutations affect their phenotypes.
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Affiliation(s)
- Dustin R. Long
- Division of Critical Care Medicine, Department of Anesthesiology and Pain Medicine, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Elizabeth A. Holmes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Hsin-Yu Lo
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Kelsi Penewit
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Jared Almazan
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Taylor Hodgson
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Nova F. Berger
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Zoe H. Bishop
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Janessa D. Lewis
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Adam Waalkes
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Daniel J. Wolter
- Department of Pediatrics, University of Washington School of Medicine, Seattle, Washington, United States of America
| | - Stephen J. Salipante
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, Washington, United States of America
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Nielsen TK, Petersen IB, Xu L, Barbuti MD, Mebus V, Justh A, Alqarzaee AA, Jacques N, Oury C, Thomas V, Kjos M, Henriksen C, Frees D. The Spx stress regulator confers high-level β-lactam resistance and decreases susceptibility to last-line antibiotics in methicillin-resistant Staphylococcus aureus. Antimicrob Agents Chemother 2024:e0033524. [PMID: 38690894 DOI: 10.1128/aac.00335-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/05/2024] [Indexed: 05/03/2024] Open
Abstract
Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are a leading cause of mortality worldwide. MRSA has acquired resistance to next-generation β-lactam antibiotics through the horizontal acquisition of the mecA resistance gene. Development of high resistance is, however, often associated with additional mutations in a set of chromosomal core genes, known as potentiators, which, through poorly described mechanisms, enhance resistance. The yjbH gene was recently identified as a hot spot for adaptive mutations during severe infections. Here, we show that inactivation of yjbH increased β-lactam MICs up to 16-fold and transformed MRSA cells with low levels of resistance to being homogenously highly resistant to β-lactams. The yjbH gene encodes an adaptor protein that targets the transcriptional stress regulator Spx for degradation by the ClpXP protease. Using CRISPR interference (CRISPRi) to knock down spx transcription, we unambiguously linked hyper-resistance to the accumulation of Spx. Spx was previously proposed to be essential; however, our data suggest that Spx is dispensable for growth at 37°C but becomes essential in the presence of antibiotics with various targets. On the other hand, high Spx levels bypassed the role of PBP4 in β-lactam resistance and broadly decreased MRSA susceptibility to compounds targeting the cell wall or the cell membrane, including vancomycin, daptomycin, and nisin. Strikingly, Spx potentiated resistance independently of its redox-sensing switch. Collectively, our study identifies a general stress pathway that, in addition to promoting the development of high-level, broad-spectrum β-lactam resistance, also decreases MRSA susceptibility to critical antibiotics of last resort.
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Affiliation(s)
- Tobias Krogh Nielsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ida Birkjær Petersen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lijuan Xu
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maria Disen Barbuti
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Viktor Mebus
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anni Justh
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Abdulelah Ahmed Alqarzaee
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Nicolas Jacques
- Laboratory of Cardiology, GIGA Institute, University of Liège Hospital, Liège, Belgium
| | - Cécile Oury
- Laboratory of Cardiology, GIGA Institute, University of Liège Hospital, Liège, Belgium
| | - Vinai Thomas
- Center for Staphylococcal Research, Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Morten Kjos
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Camilla Henriksen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dorte Frees
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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3
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Yamauchi S, Shimoda S, Kawahara A, Sugahara T, Yamamoto S, Kitabayashi M, Sogabe A, Jansen CA, Tobe R, Hirakawa R, Islam J, Furukawa M, Yoneyama H, Nochi T. Identification of four genes responsible for antimicrobial resistance of MEL-B against S. aureus. Biochem Biophys Res Commun 2024; 699:149566. [PMID: 38290176 DOI: 10.1016/j.bbrc.2024.149566] [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: 01/13/2024] [Accepted: 01/22/2024] [Indexed: 02/01/2024]
Abstract
There is increasing interest in the antimicrobial activity of mannosylerythritol lipids-B (MEL-B) against Gram-positive bacteria such as Staphylococcus aureus (S. aureus). However, the specific molecules involved in MEL-B's antimicrobial action against S. aureus have not been identified. This study utilized the Nebraska transposon mutant library (NTML), which contains 1920 mutants, each lacking three-quarters of the genes found in S. aureus. The NTML was screened to identify mutants resistant to MEL-B. Four mutants (Accession Number: SAUSA300_0904, SAUSA300_0752, SAUSA300_0387, and SAUSA300_2311) largely unaffected by incubation with MEL-B, indicating MEL-B resistance. Despite the strong binding of MEL-B to these mutants, the four molecules encoded by the deleted genes (yjbI, clpP, pbuX, or brpS) in each mutant were not directly recognized by MEL-B. Given that these molecules are not localized on the outer surface of S. aureus and that the antibacterial activity of MEL-B against S. aureus is facilitated by the effective transfer of two antibacterial fatty acids (caprylic acid and myristoleic acid) to S. aureus via ME, the deletion of each of the four molecules may alter the peptidoglycan structure, potentially inhibiting the effective transfer of these antimicrobial fatty acids into S. aureus.
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Affiliation(s)
- Shinya Yamauchi
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Miyagi, 980-8572, Japan; Laboratory of Animal Functional Morphology, Graduate School of Agricultural Science, Tohoku University, Miyagi, 980-8572, Japan
| | - So Shimoda
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Miyagi, 980-8572, Japan; Laboratory of Animal Microbiology, Graduate School of Agricultural Science, Tohoku University, Miyagi, 980-8572, Japan
| | - Akio Kawahara
- Toyobo Co., Ltd. Biotechnology Research Laboratory, Fukui, 914-8550, Japan
| | - Tomohiro Sugahara
- Toyobo Co., Ltd. Biotechnology Research Laboratory, Fukui, 914-8550, Japan
| | - Shuhei Yamamoto
- Toyobo Co., Ltd. Biotechnology Research Laboratory, Fukui, 914-8550, Japan; Toyobo Co., Ltd. Biotechnology Operating Department, Osaka, 530-0001, Japan
| | - Masao Kitabayashi
- Toyobo Co., Ltd. Biotechnology Research Laboratory, Fukui, 914-8550, Japan; Toyobo Co., Ltd. Biotechnology Operating Department, Osaka, 530-0001, Japan
| | - Atsushi Sogabe
- Toyobo Co., Ltd. Biotechnology Research Laboratory, Fukui, 914-8550, Japan; Toyobo Co., Ltd. Biotechnology Operating Department, Osaka, 530-0001, Japan
| | - Christine A Jansen
- Cell Biology and Immunology Group, Department of Animal Sciences, Wageningen University, Wageningen, 6708 WD, the Netherlands
| | - Ryuta Tobe
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Miyagi, 980-8572, Japan; Laboratory of Animal Microbiology, Graduate School of Agricultural Science, Tohoku University, Miyagi, 980-8572, Japan
| | - Ryota Hirakawa
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Miyagi, 980-8572, Japan; Laboratory of Animal Functional Morphology, Graduate School of Agricultural Science, Tohoku University, Miyagi, 980-8572, Japan; Laboratory of Animal Mucosal Immunology, Graduate School of Agricultural Science, Tohoku University, Miyagi, 980-8572, Japan
| | - Jahidul Islam
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Miyagi, 980-8572, Japan; Laboratory of Animal Functional Morphology, Graduate School of Agricultural Science, Tohoku University, Miyagi, 980-8572, Japan
| | - Mutsumi Furukawa
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Miyagi, 980-8572, Japan; Laboratory of Animal Functional Morphology, Graduate School of Agricultural Science, Tohoku University, Miyagi, 980-8572, Japan; Laboratory of Animal Mucosal Immunology, Graduate School of Agricultural Science, Tohoku University, Miyagi, 980-8572, Japan
| | - Hiroshi Yoneyama
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Miyagi, 980-8572, Japan; Laboratory of Animal Microbiology, Graduate School of Agricultural Science, Tohoku University, Miyagi, 980-8572, Japan
| | - Tomonori Nochi
- International Education and Research Center for Food and Agricultural Immunology, Graduate School of Agricultural Science, Tohoku University, Miyagi, 980-8572, Japan; Laboratory of Animal Functional Morphology, Graduate School of Agricultural Science, Tohoku University, Miyagi, 980-8572, Japan; Laboratory of Animal Mucosal Immunology, Graduate School of Agricultural Science, Tohoku University, Miyagi, 980-8572, Japan; Division of Mucosal Vaccines, International Vaccine Design Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan; Department of Animal Bioscience, University of Guelph, Ontario, N1G 2W1, Canada; Center for Professional Development, Institute for Excellence in Higher Education, Tohoku University, Miyagi, 980-8576, Japan.
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4
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Campbell AE, McCready-Vangi AR, Uberoi A, Murga-Garrido SM, Lovins VM, White EK, Pan JTC, Knight SAB, Morgenstern AR, Bianco C, Planet PJ, Gardner SE, Grice EA. Variable staphyloxanthin production by Staphylococcus aureus drives strain-dependent effects on diabetic wound-healing outcomes. Cell Rep 2023; 42:113281. [PMID: 37858460 PMCID: PMC10680119 DOI: 10.1016/j.celrep.2023.113281] [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: 10/21/2022] [Revised: 08/24/2023] [Accepted: 09/28/2023] [Indexed: 10/21/2023] Open
Abstract
Strain-level variation in Staphylococcus aureus is a factor that contributes to disease burden and clinical outcomes in skin disorders and chronic wounds. However, the microbial mechanisms that drive these variable host responses are poorly understood. To identify mechanisms underlying strain-specific outcomes, we perform high-throughput phenotyping screens on S. aureus isolates cultured from diabetic foot ulcers. Isolates from non-healing wounds produce more staphyloxanthin, a cell membrane pigment. In murine diabetic wounds, staphyloxanthin-producing isolates delay wound closure significantly compared with staphyloxanthin-deficient isolates. Staphyloxanthin promotes resistance to oxidative stress and enhances bacterial survival in neutrophils. Comparative genomic and transcriptomic analysis of genetically similar clinical isolates with disparate staphyloxanthin phenotypes reveals a mutation in the sigma B operon, resulting in marked differences in stress response gene expression. Our work illustrates a framework to identify traits that underlie strain-level variation in disease burden and suggests more precise targets for therapeutic intervention in S. aureus-positive wounds.
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Affiliation(s)
- Amy E Campbell
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Amelia R McCready-Vangi
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Aayushi Uberoi
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sofía M Murga-Garrido
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Victoria M Lovins
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ellen K White
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jamie Ting-Chun Pan
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Simon A B Knight
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alexis R Morgenstern
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Colleen Bianco
- Division of Infectious Disease, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Paul J Planet
- Division of Infectious Disease, Department of Pediatrics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Departments of Pediatrics and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sue E Gardner
- College of Nursing, University of Iowa, Iowa City, IA 52242, USA
| | - Elizabeth A Grice
- Departments of Dermatology and Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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5
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Walzl A, Marbach H, Belikova D, Vogl C, Ehling-Schulz M, Heilbronner S, Grunert T. Prevalence of the SigB-Deficient Phenotype among Clinical Staphylococcus aureus Isolates Linked to Bovine Mastitis. Antibiotics (Basel) 2023; 12:699. [PMID: 37107061 PMCID: PMC10135042 DOI: 10.3390/antibiotics12040699] [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: 03/01/2023] [Revised: 03/27/2023] [Accepted: 03/30/2023] [Indexed: 04/07/2023] Open
Abstract
Phenotypic adaptation has been associated with persistent, therapy-resistant Staphylococcus aureus infections. Recently, we described within-host evolution towards a Sigma factor B (SigB)-deficient phenotype in a non-human host, a naturally infected dairy cow with chronic, persistent mastitis. However, to our knowledge, the prevalence of SigB deficiency among clinical S. aureus isolates remains unknown. In this study, we screened a collection of bovine mastitis isolates for phenotypic traits typical for SigB deficiency: decreased carotenoid pigmentation, increased proteolysis, secretion of α-hemolysin and exoproteins. Overall, 8 out of 77 (10.4%) isolates of our bovine mastitis collection exhibited the SigB-deficient phenotype. These isolates were assigned to various clonal complexes (CC8, CC9, CC97, CC151, CC3666). We further demonstrated a strong positive correlation between asp23-expression (a marker of SigB activity) and carotenoid pigmentation (r = 0.6359, p = 0.0008), underlining the role of pigmentation as a valuable predictor of the functional status of SigB. Sequencing of the sigB operon (mazEF-rsbUVW-sigB) indicated the phosphatase domain of the RsbU protein as a primary target of mutations leading to SigB deficiency. Indeed, by exchanging single nucleotides in rsbU, we could either induce SigB deficiency or restore the SigB phenotype, demonstrating the pivotal role of RsbU for SigB functionality. The data presented highlight the clinical relevance of SigB deficiency, and future studies are needed to exploit its role in staphylococcal infections.
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Affiliation(s)
- Anna Walzl
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, A-1210 Vienna, Austria
| | - Helene Marbach
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, A-1210 Vienna, Austria
| | - Darya Belikova
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, D-72076 Tübingen, Germany
| | - Claus Vogl
- Molecular Genetics, Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine, A-1210 Vienna, Austria
| | - Monika Ehling-Schulz
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, A-1210 Vienna, Austria
| | - Simon Heilbronner
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, D-72076 Tübingen, Germany
| | - Tom Grunert
- Institute of Microbiology, Department of Pathobiology, University of Veterinary Medicine, A-1210 Vienna, Austria
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6
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Howden BP, Giulieri SG, Wong Fok Lung T, Baines SL, Sharkey LK, Lee JYH, Hachani A, Monk IR, Stinear TP. Staphylococcus aureus host interactions and adaptation. Nat Rev Microbiol 2023; 21:380-395. [PMID: 36707725 PMCID: PMC9882747 DOI: 10.1038/s41579-023-00852-y] [Citation(s) in RCA: 96] [Impact Index Per Article: 96.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/04/2023] [Indexed: 01/28/2023]
Abstract
Invasive Staphylococcus aureus infections are common, causing high mortality, compounded by the propensity of the bacterium to develop drug resistance. S. aureus is an excellent case study of the potential for a bacterium to be commensal, colonizing, latent or disease-causing; these states defined by the interplay between S. aureus and host. This interplay is multidimensional and evolving, exemplified by the spread of S. aureus between humans and other animal reservoirs and the lack of success in vaccine development. In this Review, we examine recent advances in understanding the S. aureus-host interactions that lead to infections. We revisit the primary role of neutrophils in controlling infection, summarizing the discovery of new immune evasion molecules and the discovery of new functions ascribed to well-known virulence factors. We explore the intriguing intersection of bacterial and host metabolism, where crosstalk in both directions can influence immune responses and infection outcomes. This Review also assesses the surprising genomic plasticity of S. aureus, its dualism as a multi-mammalian species commensal and opportunistic pathogen and our developing understanding of the roles of other bacteria in shaping S. aureus colonization.
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Affiliation(s)
- Benjamin P. Howden
- grid.1008.90000 0001 2179 088XCentre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria Australia ,grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia ,grid.410678.c0000 0000 9374 3516Department of Infectious Diseases, Austin Health, Heidelberg, Victoria Australia ,grid.416153.40000 0004 0624 1200Microbiology Department, Royal Melbourne Hospital, Melbourne, Victoria Australia
| | - Stefano G. Giulieri
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia ,grid.416153.40000 0004 0624 1200Victorian Infectious Diseases Service, Royal Melbourne Hospital, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Tania Wong Fok Lung
- grid.21729.3f0000000419368729Department of Paediatrics, Columbia University, New York, NY USA
| | - Sarah L. Baines
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Liam K. Sharkey
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Jean Y. H. Lee
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia ,grid.419789.a0000 0000 9295 3933Department of Infectious Diseases, Monash Health, Clayton, Victoria Australia
| | - Abderrahman Hachani
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Ian R. Monk
- grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
| | - Timothy P. Stinear
- grid.1008.90000 0001 2179 088XCentre for Pathogen Genomics, The University of Melbourne, Melbourne, Victoria Australia ,grid.1008.90000 0001 2179 088XDepartment of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria Australia
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7
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Herrera-Heredia SA, Hsu HP, Kao CY, Tsai YH, Yamaguchi Y, Roers A, Hsu CL, Dzhagalov IL. Heparin is required for the formation of granules in connective tissue mast cells. Front Immunol 2022; 13:1000405. [DOI: 10.3389/fimmu.2022.1000405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/17/2022] [Indexed: 11/10/2022] Open
Abstract
Mast cells are innate immune cells strategically positioned around blood vessels near body surfaces. Their primary weapons are bioactive amines, mast cell-specific proteases, and cytokines stored in preformed granules. Mast cells granules constituents are packaged efficiently with the help of the highly negatively charged Heparan sulfate-derivative, Heparin. Heparin is one of the most widely used drugs to treat coagulation disorders, yet, it is not found in the circulation at a steady state, casting doubt that the prevention of blood clotting is its physiological function. Early studies using Ndst2-/- mice have shown that Heparin is essential for mast cells granules formation. However, these mice could still produce less sulfated Heparan sulfate that could potentially replace Heparin. Here, we have created and validated a novel genetic model for Heparin deficiency, specifically in connective tissue mast cells, to address the physiological role of this molecule. Using this model, we have demonstrated that Heparin is required for mast cell granules formation; without it, mast cells are reduced in the peritoneal cavity and the skin. The absence of Heparin impaired the response to passive cutaneous anaphylaxis but, surprisingly, enhanced ear swelling in an irritant dermatitis model and reduced the lesion size and bacterial burden in a Staphylococcus aureus necrotizing dermatitis model. The altered function of Heparin-deficient mast cells in the latter two models was not mediated through enhanced Histamine or TNFα release. However, the Mrgprb2 receptor was up-regulated in knock-out mast cells, potentially explaining the enhanced response of mutant mice to irritant and necrotizing dermatitis. Altogether our results expand our current understanding of the physiological role of Heparin and provide unique tools to further dissect its importance.
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8
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Panthee S, Hamamoto H, Paudel A, Kaito C, Suzuki Y, Sekimizu K. Hybrid assembly using long reads resolves repeats and completes the genome sequence of a laboratory strain of Staphylococcus aureus subsp. Aureus RN4220. Heliyon 2022; 8:e11376. [PMID: 36387480 PMCID: PMC9660545 DOI: 10.1016/j.heliyon.2022.e11376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 06/30/2022] [Accepted: 10/27/2022] [Indexed: 11/07/2022] Open
Abstract
Staphylococcus aureus RN4220 has been extensively used by staphylococcal researchers as an intermediate strain for genetic manipulation due to its ability to accept foreign DNA. Despite its wide use in laboratories, its complete genome is not available. In this study, we used a hybrid genome assembly approach using minION long reads and Illumina short reads to sequence the complete genome of S. aureus RN4220. The comparative analysis of the annotated complete genome showed the presence of 39 genes fragmented in the previous assembly, many of which were located near the repeat regions. Using RNA-Seq reads, we showed that a higher number of reads could be mapped to the complete genome than the draft genome and the gene expression profile obtained using the complete genome also differs from that obtained from the draft genome. Furthermore, by comparative transcriptomic analysis, we showed the correlation between expression levels of staphyloxanthin biosynthetic genes and the production of yellow pigment. This study highlighted the importance of long reads in completing microbial genomes, especially those possessing repetitive elements. S. aureus RN4220 is used as an intermediate strain for genetic manipulation. We completed its genome and found 39 fragmented genes in previous genome assembly. RNA-Seq analysis improved mapping of the reads with the use of complete genome. Expression of staphyloxanthin biosynthetic genes was correlated with its production.
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Abstract
Duck infectious serositis, also known as Riemerella anatipestifer disease, infects domestic ducks, geese, and turkeys and wild birds. However, the regulatory mechanism of its pathogenicity remains unclear. The PhoPR two-component system (TCS) was first reported in Gram-negative bacteria in our previous research and was demonstrated to be involved in virulence and gene expression. Here, DNA affinity purification sequencing (DAP-seq) was applied to further explore the regulation of PhoPR in relation to pathogenicity in R. anatipestifer. A conserved motif was identified upstream of 583 candidate target genes which were directly regulated by PhoP. To further confirm the genes which are regulated by PhoR and PhoP, single-gene-deletion strains were constructed. The results of transcriptome analysis using next-generation RNA sequencing showed 136 differentially expressed genes (DEGs) between the ΔphoP strain and the wild type (WT) and 183 DEGs between the ΔphoR strain and the WT. The candidate target genes of PhoP were further identified by combining transcriptome analysis and DAP-seq, which revealed that the main direct regulons of PhoP are located on the membrane and PhoP is involved in regulating aerotolerance. Using the in vivo duck model, the pathogenicity of ΔphoP and ΔphoR mutants was found to be significantly lower than that of the WT. Together, our findings provide insight into the direct regulation of PhoP and suggest that phoPR is essential for the pathogenicity of R. anatipestifer. The gene deletion strains are expected to be candidate live vaccine strains of R. anatipestifer which can be used as ideal genetic engineering vector strains for the expression of foreign antigens. IMPORTANCE Riemerella anatipestifer is a significant pathogen with high mortality in the poultry industry that causes acute septicemia and infectious polyserositis in ducks, chickens, geese, and other avian species. Previously, we characterized the two-component system encoded by phoPR and found that R. anatipestifer almost completely lost its pathogenicity for ducklings when phoPR was deleted. However, the mechanism of PhoPR regulation of virulence in R. anatipestifer had not been deeply explored. In this study, we utilized DAP-seq to explore the DNA-binding sites of PhoP as a response regulator in the global genome. Furthermore, phoP and phoR were deleted separately, and transcriptomics analysis of the corresponding gene deletion strains was performed. We identified a series of directly regulated genes of the PhoPR two-component system. The duckling model showed that both PhoP and PhoR are essential virulence-related factors in R. anatipestifer.
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10
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Hamamoto H, Panthee S, Paudel A, Ohgi S, Suzuki Y, Makimura K, Sekimizu K. Transcriptome change of Staphylococcus aureus in infected mouse liver. Commun Biol 2022; 5:721. [PMID: 35859002 PMCID: PMC9300722 DOI: 10.1038/s42003-022-03674-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/05/2022] [Indexed: 12/13/2022] Open
Abstract
We performed in vivo RNA-sequencing analysis of Staphylococcus aureus in infected mouse liver using the 2-step cell-crush method. We compared the transcriptome of S. aureus at 6, 24, and 48 h post-infection (h.p.i) in mice and in culture medium. Genes related to anaerobic respiration were highly upregulated at 24 and 48 h.p.i. The gene expression patterns of virulence factors differed depending on the type of toxin. For example, hemolysins, but not leukotoxins and serine proteases, were highly upregulated at 6 h.p.i. Gene expression of metal transporters, such as iron transporters, gradually increased at 24 and 48 h.p.i. We also analyzed the transcriptome of mouse liver infected with S. aureus. Hypoxia response genes were upregulated at 24 and 48 h.p.i., and immune response genes were upregulated from 6 h.p.i. These findings suggest that gene expression of S. aureus in the host changes in response to changes in the host environment, such as the oxygenation status or immune system attacks during infection. An in vivo transcriptomic analysis of Staphylococcus aureus infection in mice provides further insight into how this pathogen responds to changes in the host environment over time.
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Affiliation(s)
- Hiroshi Hamamoto
- Teikyo University Institute of Medical Mycology, 359 Otsuka, Hachio-ji shi, Tokyo, 192-0395, Japan
| | - Suresh Panthee
- Drug Discoveries by Silkworm Models, Faculty of Pharma-Science, Teikyo University, 359 Otsuka, Hachio-ji shi, Tokyo, 192-0395, Japan.,GenEndeavor LLC, 26219 Eden Landing Rd, Hayward, CA, 94545, USA
| | - Atmika Paudel
- International Institute for Zoonosis Control, Hokkaido University, North 20, West 10, Kita-ku, Sapporo Hokkaido, 001-0020, Japan
| | - Suguru Ohgi
- Laboratory of Microbiology, Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 111-0033, Japan.,Kyowa Kirin Co., Ltd., 1-9-2 Otemachi, Chiyoda-ku, Tokyo, 100-0004, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa shi, Chiba, 277-8562, Japan
| | - Koichi Makimura
- Teikyo University Institute of Medical Mycology, 359 Otsuka, Hachio-ji shi, Tokyo, 192-0395, Japan
| | - Kazuhisa Sekimizu
- Drug Discoveries by Silkworm Models, Faculty of Pharma-Science, Teikyo University, 359 Otsuka, Hachio-ji shi, Tokyo, 192-0395, Japan.
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11
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Giulieri SG, Guérillot R, Duchene S, Hachani A, Daniel D, Seemann T, Davis JS, Tong SYC, Young BC, Wilson DJ, Stinear TP, Howden BP. Niche-specific genome degradation and convergent evolution shaping Staphylococcus aureus adaptation during severe infections. eLife 2022; 11:77195. [PMID: 35699423 PMCID: PMC9270034 DOI: 10.7554/elife.77195] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
During severe infections, Staphylococcus aureus moves from its colonising sites to blood and tissues and is exposed to new selective pressures, thus, potentially driving adaptive evolution. Previous studies have shown the key role of the agr locus in S. aureus pathoadaptation; however, a more comprehensive characterisation of genetic signatures of bacterial adaptation may enable prediction of clinical outcomes and reveal new targets for treatment and prevention of these infections. Here, we measured adaptation using within-host evolution analysis of 2590 S. aureus genomes from 396 independent episodes of infection. By capturing a comprehensive repertoire of single nucleotide and structural genome variations, we found evidence of a distinctive evolutionary pattern within the infecting populations compared to colonising bacteria. These invasive strains had up to 20-fold enrichments for genome degradation signatures and displayed significantly convergent mutations in a distinctive set of genes, linked to antibiotic response and pathogenesis. In addition to agr-mediated adaptation, we identified non-canonical, genome-wide significant loci including sucA-sucB and stp1. The prevalence of adaptive changes increased with infection extent, emphasising the clinical significance of these signatures. These findings provide a high-resolution picture of the molecular changes when S. aureus transitions from colonisation to severe infection and may inform correlation of infection outcomes with adaptation signatures. The bacterium Staphylococcus aureus lives harmlessly on our skin and noses. However, occasionally, it gets into our blood and internal organs, such as our bones and joints, where it causes severe, long-lasting infections that are difficult to treat. Over time, S. aureus acquire characteristics that help them to adapt to different locations, such as transitioning from the nose to the blood, and avoid being killed by antibiotics. Previous studies have identified changes, or ‘mutations’, in genes that are likely to play an important role in this evolutionary process. One of these genes, called accessory gene regulator (or agr for short), has been shown to control the mechanisms S. aureus use to infect cells and disseminate in the body. However, it is unclear if there are changes in other genes that also help S. aureus adapt to life inside the human body. To help resolve this mystery, Giulieri et al. collected 2,500 samples of S. aureus from almost 400 people. This included bacteria harmlessly living on the skin or in the nose, as well as strains that caused an infection. Gene sequencing revealed a small number of genes, referred to as ‘adaptive genes’, that often acquire mutations during infection. Of these, agr was the most commonly altered. However, mutations in less well-known genes were also identified: some of these genes are related to resistance to antibiotics, while others are involved in chemical processes that help the bacteria to process nutrients. Most mutations were caused by random errors being introduced in to the bacteria’s genetic code which stopped genes from working. However, in some cases, genes were turned off by small fragments of DNA moving around and inserting themselves into different parts of the genome. This study highlights a group of genes that help S. aureus to thrive inside the body and cause severe and prolonged infections. If these results can be confirmed, it may help to guide which antibiotics are used to treat different infections. Furthermore, understanding which genes are important for infection could lead to new strategies for eliminating this dangerous bacterium.
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Affiliation(s)
- Stefano G Giulieri
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Australia
| | - Romain Guérillot
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Abderrahman Hachani
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Diane Daniel
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Torsten Seemann
- Microbiological Diagnostic Unit, University of Melbourne, Melbourne, Australia
| | - Joshua S Davis
- Department of Infectious Diseases, John Hunter Hospital, Newcastle, Australia
| | - Steven Y C Tong
- Victorian Infectious Diseases Service, University of Melbourne, Melbourne, Australia
| | | | | | - Timothy P Stinear
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Benjamin P Howden
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
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12
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Liu S, Chen L, Wang L, Zhou B, Ye D, Zheng X, Lin Y, Zeng W, Zhou T, Ye J. Cluster Differences in Antibiotic Resistance, Biofilm Formation, Mobility, and Virulence of Clinical Enterobacter cloacae Complex. Front Microbiol 2022; 13:814831. [PMID: 35464993 PMCID: PMC9019753 DOI: 10.3389/fmicb.2022.814831] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 02/24/2022] [Indexed: 12/03/2022] Open
Abstract
Due to the lack of research on the characteristics of different clusters of Enterobacter cloacae complex (ECC), this study aimed to characterize and explore the differences among species of the ECC. An analysis based on hsp60 showed that Enterobacter hormaechei was predominant in ECC. Interestingly, the antibiotic resistance rates of clusters were different, among which E. hormaechei subsp. steigerwaltii (cluster VIII) and Enterobacter cloacae IX (cluster IX) possessed high resistant rates to ciprofloxacin and levofloxacin, but cluster II (Enterobacter kobei) had low resistant rates. Cluster II exhibited a strong biofilm formation ability. Different motility and protease production ability were shown for distinct clusters. A PCR analysis showed that clusters I, III, VI, VIII, and IX carried more virulence genes, while cluster II had fewer. Clusters I, VIII, and IX with high pathogenicity were evaluated using the Galleria mellonella infection model. Thus, the characteristics of resistance, biofilm-forming ability, mobility, and virulence differed among the clusters. The strains were divided into 12 subgroups based on hsp60. The main clusters of ECC clinical strains were I, II, III, VI, VIII, and IX, among which IX, VIII, and I were predominant with high resistance and pathogenicity, and cluster II (E. kobei) was a special taxon with a strong biofilm formation ability under nutrient deficiency, but was associated with low resistance, virulence, and pathogenicity. Hence, clinical classification methods to identify ECC subgroups are an urgent requirement to guide the treatment of clinical infections.
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Affiliation(s)
- Shixing Liu
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Liqiong Chen
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Lingbo Wang
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Beibei Zhou
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Dandan Ye
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiangkuo Zheng
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yishuai Lin
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Weiliang Zeng
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Tieli Zhou
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jianzhong Ye
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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13
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Subramanian D, Natarajan J. Leveraging big data bioinformatics approaches to extract knowledge from Staphylococcus aureus public omics data. Crit Rev Microbiol 2022; 49:391-413. [PMID: 35468027 DOI: 10.1080/1040841x.2022.2065905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Staphylococcus aureus is a notorious pathogen posing challenges in the medical industry due to drug resistance and biofilm formation. The horizon of knowledge on S. aureus pathogenesis has expanded with the advancement of data-driven bioinformatics techniques. Mining information from sequenced genomes and their expression data is an economic approach that alleviates wastage of resources and redundancy in experiments. The current review covers how big data bioinformatics has been used in the analysis of S. aureus from publicly available -omics data to uncover mechanisms of infection and inhibition. Particularly, advances in the past two decades in biomarker discovery, host responses, phenotype identification, consolidation of information, and drug development are discussed highlighting the challenges and shortcomings. Overall, the review summarizes the diverse aspects of scrupulous re-analysis of S. aureus proteomic and transcriptomic expression datasets retrieved from public repositories in terms of the efforts taken, benefits offered, and follow-up actions. The detailed review thus serves as a reference and aid for (i) Computational biologists by briefing the approaches utilized for bacterial omics re-analysis concerning S. aureus and (ii) Experimental biologists by elucidating the potential of bioinformatics in biological research to generate reliable postulates in a prompt and economical manner.
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Affiliation(s)
- Devika Subramanian
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, India
| | - Jeyakumar Natarajan
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, India
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14
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Celastrol mitigates staphyloxanthin biosynthesis and biofilm formation in Staphylococcus aureus via targeting key regulators of virulence; in vitro and in vivo approach. BMC Microbiol 2022; 22:106. [PMID: 35421933 PMCID: PMC9011992 DOI: 10.1186/s12866-022-02515-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/01/2022] [Indexed: 12/18/2022] Open
Abstract
Abstract
Background
Staphylococcus aureus is a leading cause of human infections. The spread of antibiotic-resistant staphylococci has driven the search for novel strategies to supersede antibiotics use. Thus, targeting bacterial virulence rather than viability could be a possible alternative.
Results
The influence of celastrol on staphyloxanthin (STX) biosynthesis, biofilm formation, antibiotic susceptibility and host pathogenesis in S. aureus has been investigated. Celastrol efficiently reduced STX biosynthesis in S. aureus. Liquid chromatography-mass spectrometry (LC–MS) and molecular docking revealed that celastrol inhibits STX biosynthesis through its effect on CrtM. Quantitative measurement of STX intermediates showed a significant pigment inhibition via interference of celastrol with CrtM and accumulation of its substrate, farnesyl diphosphate. Importantly, celastrol-treated S. aureus was more sensitive to environmental stresses and human blood killing than untreated bacteria. Similarly, inhibition of STX upon celastrol treatment rendered S. aureus more susceptible to membrane targeting antibiotics. In addition to its anti-pigment capability, celastrol exhibits significant anti-biofilm activity against S. aureus as indicated by crystal violet assay and microscopy. Celastrol-treated cells showed deficient exopolysaccharide production and cell hydrophobicity. Moreover, celastrol markedly synergized the action of conventional antibiotics against S. aureus and reduced bacterial pathogenesis in vivo using mice infection model. These findings were further validated using qRT-PCR, demonstrating that celastrol could alter the expression of STX biosynthesis genes as well as biofilm formation related genes and bacterial virulence.
Conclusions
Celastrol is a novel anti-virulent agent against S. aureus suggesting, a prospective therapeutic role for celastrol as a multi-targeted anti-pathogenic agent.
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15
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Paudel A, Furuta Y, Higashi H. Silkworm model for Bacillus anthracis infection and virulence determination. Virulence 2021; 12:2285-2295. [PMID: 34490836 PMCID: PMC8425766 DOI: 10.1080/21505594.2021.1965830] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/30/2021] [Accepted: 08/04/2021] [Indexed: 11/07/2022] Open
Abstract
Bacillus anthracis is an obligate pathogen and a causative agent of anthrax. Its major virulence factors are plasmid-coded; however, recent studies have revealed chromosome-encoded virulence factors, indicating that the current understanding of its virulence mechanism is elusive and needs further investigation. In this study, we established a silkworm (Bombyx mori) infection model of B. anthracis. We showed that silkworms were killed by B. anthracis Sterne and cured of the infection when administered with antibiotics. We quantitatively determined the lethal dose of the bacteria that kills 50% larvae and effective doses of antibiotics that cure 50% infected larvae. Furthermore, we demonstrated that B. anthracis mutants with disruption in virulence genes such as pagA, lef, and atxA had attenuated silkworm-killing ability and reduced colonization in silkworm hemolymph. The silkworm infection model established in this study can be utilized in large-scale infection experiments to identify novel virulence determinants and develop novel therapeutic options against B. anthracis infections.
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Affiliation(s)
- Atmika Paudel
- Division of Infection and Immunity, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Yoshikazu Furuta
- Division of Infection and Immunity, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
| | - Hideaki Higashi
- Division of Infection and Immunity, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Hokkaido, Japan
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16
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Novel Pathogenic Mucorales Identified Using the Silkworm Infection Model. J Fungi (Basel) 2021; 7:jof7110995. [PMID: 34829282 PMCID: PMC8621750 DOI: 10.3390/jof7110995] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 11/20/2021] [Indexed: 02/06/2023] Open
Abstract
Mucormycosis, a rare but highly fatal infection, is caused by fungi of the order Mucorales. Due to their ubiquitous nature, reduced susceptibility to antifungals, acid tolerance, and ability to infect immunocompromised patients through rapid dissemination, these fungi have been frequently reported to infect the COVID-19 patients. In order to develop strategies to overcome mucormycosis, it is essential to understand and identify novel Mucorales present in the environment. In this study, we report the identification of four novel pathogenic Mucorales using the silkworm (Bombyx mori) model. The strains’ phylogeny was analyzed using the genome sequence of the large subunit ribosomal ribonucleic acid (LSU rRNA) and the internal transcribed spacer (ITS) region, where strains 1-3, 5-3, and S286-1101 claded with Mucor orantomantidis, and strain 827-14 claded with Backusella lamprospora. All the strains had a cold-sensitive phenotype with their inability to grow prominently at 4 °C. Mucor sp. 1-3 and 5-3 were characterized by their filamentous and yeast-like growth under aerobic and anaerobic conditions, respectively. The yeast colonies of Mucor sp. 5-3 had multipolar budding cells often observed with cleaved cell surfaces under a scanning electron microscope. We further found that these strains were able to kill immunocompromised mice suggesting their pathogenicity to mammals. Our study established an invertebrate model-based screening system to identify novel pathogenic Mucorales from the natural environment and provided a clue towards the rapid increase in COVID-19 related mucormycosis.
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17
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Li W, Jiang L, Liu X, Guo R, Ma S, Wang J, Ma S, Li S, Li H. YhjC is a novel transcriptional regulator required for Shigella flexneri virulence. Virulence 2021; 12:1661-1671. [PMID: 34152261 PMCID: PMC8218686 DOI: 10.1080/21505594.2021.1936767] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Shigella is an intracellular pathogen that primarily infects the human colon and causes shigellosis. Shigella virulence relies largely on the type III secretion system (T3SS) and secreted effectors. VirF, the master Shigella virulence regulator, is essential for the expression of T3SS-related genes. In this study, we found that YhjC, a LysR-type transcriptional regulator, is required for Shigella virulence through activating the transcription of virF. Pathogenicity of the yhjC mutant, including colonization in the colons of guinea pigs as well as its ability for host cell adhesion and invasion, was significantly lowered. Expression levels of virF and nearly all VirF-dependent genes were downregulated by yhjC deletion, indicating that YhjC can activate virF transcription. Electrophoretic mobility shift assay analysis demonstrated that YhjC could bind directly to the virF promoter region. Therefore, YhjC is a novel virulence regulator that positively regulates the virF expression and promotes Shigella virulence. Additionally, genome-wide expression analysis identified the presence of other genes in the large virulence plasmid and a genome exhibiting differential expression in response to yhjC deletion, with 169 downregulated and 99 upregulated genes, indicating that YhjC also functioned as a global regulatory factor.
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Affiliation(s)
- Wanwu Li
- TEDA Institute of Biological Sciences and Biotechnology, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China.,Shandong Center for Food and Drug Evaluation & Certification, Jinan, China
| | - Lingyan Jiang
- TEDA Institute of Biological Sciences and Biotechnology, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Xiaoqian Liu
- TEDA Institute of Biological Sciences and Biotechnology, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Rui Guo
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan 250014, China
| | - Shuai Ma
- TEDA Institute of Biological Sciences and Biotechnology, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Jingting Wang
- TEDA Institute of Biological Sciences and Biotechnology, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Shuangshuang Ma
- TEDA Institute of Biological Sciences and Biotechnology, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Shujie Li
- TEDA Institute of Biological Sciences and Biotechnology, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Nankai University, Tianjin 300457, China
| | - Huiying Li
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Medicine and Health Key Laboratory of Laboratory Medicine, Jinan 250014, China.,School of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
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18
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Mikami K, Sonobe K, Ishino K, Noda T, Kato M, Hanao M, Hamamoto H, Sekimizu K, Okazaki M. Evaluation of pathogenicity and therapeutic effectiveness of antibiotics using silkworm Nocardia infection model. Drug Discov Ther 2021; 15:73-77. [PMID: 33952779 DOI: 10.5582/ddt.2021.01035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Nocardia is a ubiquitous environmental microbe that causes nocardiosis against immunosuppressed and immunocompromised hosts. The assay system for the quantitative evaluation of virulence of Nocardia sp. or therapeutic effectiveness of antimicrobials for treatment of nocardiosis is not established so far. In this study, we established an infection model of Nocardia sp. using silkworm as an alternative animal model. We found that all tested Nocardia sp. such as Nocardia asiatica, Nocardia elegans, Nocardia exalbida, Nocardia farcinica, and Nocardia nova killed silkworm and their killing ability were different by species. N. farcinica showed higher pathogenicity among tested strain, similar to the mouse model as previously reported. In addition, we found that antimicrobials such as amikacin and minocycline showed therapeutic effectiveness in silkworms infected with N. farcinica, and we could determine effective doses 50 (ED₅₀) values. These results suggest that silkworm is a useful alternative animal to evaluate the pathogenicity of Nocardia pathogen and the therapeutic effects of antimicrobials against Nocardia sp. in a quantitative manner.
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Affiliation(s)
- Kazuhiro Mikami
- Department of Medical Technology, School of Health Sciences, Tokyo University of Technology, Tokyo, Japan.,Drug Discoveries by Silkworm Models, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Kazunari Sonobe
- Department of Clinical Laboratory, Tokyo Medical and Dental University Medical Hospital, Tokyo, Japan
| | - Keiko Ishino
- Division of Infection Control Sciences, Department of Clinical Pharmacy, School of Pharmacy, Showa University, Tokyo, Japan
| | - Takumi Noda
- Department of Medical Technology, School of Health Sciences, Tokyo University of Technology, Tokyo, Japan
| | - Mami Kato
- Department of Medical Technology, School of Health Sciences, Tokyo University of Technology, Tokyo, Japan
| | - Mami Hanao
- Department of Medical Technology, School of Health Sciences, Tokyo University of Technology, Tokyo, Japan
| | | | - Kazuhisa Sekimizu
- Drug Discoveries by Silkworm Models, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan.,Genome Pharmaceuticals Institute, Tokyo, Japan
| | - Mitsuhiro Okazaki
- Department of Medical Technology, School of Health Sciences, Tokyo University of Technology, Tokyo, Japan
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19
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Panthee S, Paudel A, Hamamoto H, Ogasawara AA, Iwasa T, Blom J, Sekimizu K. Complete genome sequence and comparative genomic analysis of Enterococcus faecalis EF-2001, a probiotic bacterium. Genomics 2021; 113:1534-1542. [PMID: 33771633 DOI: 10.1016/j.ygeno.2021.03.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 03/10/2021] [Accepted: 03/21/2021] [Indexed: 12/22/2022]
Abstract
Enterococcus faecalis is a common human gut commensal bacterium. While some E. faecalis strains are probiotic, others are known to cause opportunistic infections, and clear distinction between these strains is difficult using traditional taxonomic approaches. In this study, we completed the genome sequencing of EF-2001, a probiotic strain, using our in-house hybrid assembly approach. Comparative analysis showed that EF-2001 was devoid of cytolysins, major factors associated with pathogenesis, and was phylogenetically distant from pathogenic E. faecalis V583. Genomic analysis of strains with a publicly available complete genome sequence predicted that drug-resistance genes- dfrE, efrA, efrB, emeA, and lsaA were present in all strains, and EF-2001 lacked additional drug-resistance genes. Core- and pan-genome analyses revealed a higher degree of genomic fluidity. We found 49 genes specific to EF-2001, further characterization of which may provide insights into its diverse biological activities. Our comparative genomic analysis approach could help predict the pathogenic or probiotic potential of E. faecalis leading to an early distinction based on genome sequences.
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Affiliation(s)
- Suresh Panthee
- Teikyo University Institute of Medical Mycology, Hachioji, Otsuka 359, Tokyo 192-0395, Japan.
| | - Atmika Paudel
- Teikyo University Institute of Medical Mycology, Hachioji, Otsuka 359, Tokyo 192-0395, Japan; Division of Infection and Immunity, Research Center for Zoonosis Control, Hokkaido University, North 20, West 10, Kita-ku, Sapporo Hokkaido 001-0020, Japan.
| | - Hiroshi Hamamoto
- Teikyo University Institute of Medical Mycology, Hachioji, Otsuka 359, Tokyo 192-0395, Japan.
| | | | - Toshihiro Iwasa
- NIHON BERUMU CO., LTD., 2-14-3 Nagatacho, Chiyoda-ku, Tokyo 100-0014, Japan.
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus-Liebig-University Giessen, Giessen, Germany.
| | - Kazuhisa Sekimizu
- Teikyo University Institute of Medical Mycology, Hachioji, Otsuka 359, Tokyo 192-0395, Japan.
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