1
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Socarras KM, Marino MC, Earl JP, Ehrlich RL, Cramer NA, Mell JC, Sen B, Ahmed A, Marconi RT, Ehrlich GD. Characterization of the family-level Borreliaceae pan-genome and development of an episomal typing protocol. RESEARCH SQUARE 2024:rs.3.rs-4491589. [PMID: 38947078 PMCID: PMC11213207 DOI: 10.21203/rs.3.rs-4491589/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Background The Borreliaceae family includes many obligate parasitic bacterial species which are etiologically associated with a myriad of zoonotic borrelioses including Lyme disease and vector-borne relapsing fevers. Infections by the Borreliaceae are difficult to detect by both direct and indirect methods, often leading to delayed and missed diagnoses. Efforts to improve diagnoses center around the development of molecular diagnostics (MDx), but due to deep tissue sequestration of the causative spirochaetes and the lack of persistent bacteremias, even MDx assays suffer from a lack of sensitivity. Additionally, the highly extensive genomic heterogeneity among isolates, even within the same species, contributes to the lack of assay sensitivity as single target assays cannot provide universal coverage. This within-species heterogeneity is partly due to differences in replicon repertoires and genomic structures that have likely arisen to support the complex Borreliaceae lifecycle in which these parasites have to survive in multiple hosts each with unique immune responses. Results We constructed a Borreliaceae family-level pangenome and characterized the phylogenetic relationships among the constituent taxa which supports the recent taxonomy of splitting the family into at least two genera. Gene content pro les were created for the majority of the Borreliaceae replicons, providing for the first time their unambiguous molecular typing. Conclusion Our characterization of the Borreliaceae pan-genome supports the splitting of the former Borrelia genus into two genera and provides for the phylogenetic placement of several non-species designated isolates. Mining this family-level pangenome will enable precision diagnostics corresponding to gene content-driven clinical outcomes while also providing targets for interventions.
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Affiliation(s)
- Kayla M Socarras
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
| | - Mary C Marino
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
| | - Joshua P Earl
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
| | | | - Nicholas A Cramer
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center
| | - Joshua C Mell
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
| | - Bhaswati Sen
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
| | - Azad Ahmed
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
| | - Richard T Marconi
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center
| | - Garth D Ehrlich
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine
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2
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Tzani-Tzanopoulou P, Skliros D, Megremis S, Xepapadaki P, Andreakos E, Chanishvili N, Flemetakis E, Kaltsas G, Taka S, Lebessi E, Doudoulakakis A, Papadopoulos NG. Interactions of Bacteriophages and Bacteria at the Airway Mucosa: New Insights Into the Pathophysiology of Asthma. FRONTIERS IN ALLERGY 2021; 1:617240. [PMID: 35386933 PMCID: PMC8974763 DOI: 10.3389/falgy.2020.617240] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 12/29/2020] [Indexed: 12/16/2022] Open
Abstract
The airway epithelium is the primary site where inhaled and resident microbiota interacts between themselves and the host, potentially playing an important role on allergic asthma development and pathophysiology. With the advent of culture independent molecular techniques and high throughput technologies, the complex composition and diversity of bacterial communities of the airways has been well-documented and the notion of the lungs' sterility definitively rejected. Recent studies indicate that the microbial composition of the asthmatic airways across the spectrum of disease severity, differ significantly compared with healthy individuals. In parallel, a growing body of evidence suggests that bacterial viruses (bacteriophages or simply phages), regulating bacterial populations, are present in almost every niche of the human body and can also interact directly with the eukaryotic cells. The triptych of airway epithelial cells, bacterial symbionts and resident phages should be considered as a functional and interdependent unit with direct implications on the respiratory and overall homeostasis. While the role of epithelial cells in asthma pathophysiology is well-established, the tripartite interactions between epithelial cells, bacteria and phages should be scrutinized, both to better understand asthma as a system disorder and to explore potential interventions.
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Affiliation(s)
- Panagiota Tzani-Tzanopoulou
- Allergy and Clinical Immunology Unit, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
| | - Dimitrios Skliros
- Laboratory of Molecular Biology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece
| | - Spyridon Megremis
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
| | - Paraskevi Xepapadaki
- Allergy and Clinical Immunology Unit, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
| | - Evangelos Andreakos
- Center for Clinical, Experimental Surgery and Translational Research of the Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Nina Chanishvili
- Laboratory for Genetics of Microorganisms and Bacteriophages, Eliava Institute of Bacteriophage, Microbiology & Virology, Tbilisi, GA, United States
| | - Emmanouil Flemetakis
- Laboratory of Molecular Biology, Department of Biotechnology, School of Food, Biotechnology and Development, Agricultural University of Athens, Athens, Greece
| | - Grigoris Kaltsas
- Department of Electrical and Electronic Engineering, University of West Attica, Athens, Greece
| | - Styliani Taka
- Allergy and Clinical Immunology Unit, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece
| | - Evangelia Lebessi
- Department of Microbiology, P. & A. Kyriakou Children's Hospital, Athens, Greece
| | | | - Nikolaos G Papadopoulos
- Allergy and Clinical Immunology Unit, 2nd Pediatric Clinic, National and Kapodistrian University of Athens, Athens, Greece.,Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
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3
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Hammond JA, Gordon EA, Socarras KM, Chang Mell J, Ehrlich GD. Beyond the pan-genome: current perspectives on the functional and practical outcomes of the distributed genome hypothesis. Biochem Soc Trans 2020; 48:2437-2455. [PMID: 33245329 PMCID: PMC7752077 DOI: 10.1042/bst20190713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/28/2020] [Accepted: 10/29/2020] [Indexed: 01/08/2023]
Abstract
The principle of monoclonality with regard to bacterial infections was considered immutable prior to 30 years ago. This view, espoused by Koch for acute infections, has proven inadequate regarding chronic infections as persistence requires multiple forms of heterogeneity among the bacterial population. This understanding of bacterial plurality emerged from a synthesis of what-were-then novel technologies in molecular biology and imaging science. These technologies demonstrated that bacteria have complex life cycles, polymicrobial ecologies, and evolve in situ via the horizontal exchange of genic characters. Thus, there is an ongoing generation of diversity during infection that results in far more highly complex microbial communities than previously envisioned. This perspective is based on the fundamental tenet that the bacteria within an infecting population display genotypic diversity, including gene possession differences, which result from horizontal gene transfer mechanisms including transformation, conjugation, and transduction. This understanding is embodied in the concepts of the supragenome/pan-genome and the distributed genome hypothesis (DGH). These paradigms have fostered multiple researches in diverse areas of bacterial ecology including host-bacterial interactions covering the gamut of symbiotic relationships including mutualism, commensalism, and parasitism. With regard to the human host, within each of these symbiotic relationships all bacterial species possess attributes that contribute to colonization and persistence; those species/strains that are pathogenic also encode traits for invasion and metastases. Herein we provide an update on our understanding of bacterial plurality and discuss potential applications in diagnostics, therapeutics, and vaccinology based on perspectives provided by the DGH with regard to the evolution of pathogenicity.
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Affiliation(s)
- Jocelyn A. Hammond
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
| | - Emma A. Gordon
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
| | - Kayla M. Socarras
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Surgical Infections and Biofilms, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
| | - Joshua Chang Mell
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Meta-omics Shared Resource Facility, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, U.S.A
| | - Garth D. Ehrlich
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Advanced Microbial Processing, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Center for Surgical Infections and Biofilms, Institute for Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, U.S.A
- Meta-omics Shared Resource Facility, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, U.S.A
- Department of Otolaryngology – Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, PA, U.S.A
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4
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Santos-Cortez RLP, Bhutta MF, Earl JP, Hafrén L, Jennings M, Mell JC, Pichichero ME, Ryan AF, Tateossian H, Ehrlich GD. Panel 3: Genomics, precision medicine and targeted therapies. Int J Pediatr Otorhinolaryngol 2020; 130 Suppl 1:109835. [PMID: 32007292 PMCID: PMC7155947 DOI: 10.1016/j.ijporl.2019.109835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
OBJECTIVE To review the most recent advances in human and bacterial genomics as applied to pathogenesis and clinical management of otitis media. DATA SOURCES PubMed articles published since the last meeting in June 2015 up to June 2019. REVIEW METHODS A panel of experts in human and bacterial genomics of otitis media was formed. Each panel member reviewed the literature in their respective fields and wrote draft reviews. The reviews were shared with all panel members, and a merged draft was created. The panel met at the 20th International Symposium on Recent Advances in Otitis Media in June 2019, discussed the review and refined the content. A final draft was made, circulated, and approved by the panel members. CONCLUSION Trans-disciplinary approaches applying pan-omic technologies to identify human susceptibility to otitis media and to understand microbial population dynamics, patho-adaptation and virulence mechanisms are crucial to the development of novel, personalized therapeutics and prevention strategies for otitis media. IMPLICATIONS FOR PRACTICE In the future otitis media prevention strategies may be augmented by mucosal immunization, combination vaccines targeting multiple pathogens, and modulation of the middle ear microbiome. Both treatment and vaccination may be tailored to an individual's otitis media phenotype as defined by molecular profiles obtained by using rapidly developing techniques in microbial and host genomics.
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Affiliation(s)
- Regie Lyn P. Santos-Cortez
- Department of Otolaryngology, School of Medicine, University of Colorado Anschutz Medical Campus, 12700 E. 19 Ave., Aurora, CO 80045, USA
| | - Mahmood F. Bhutta
- Department of ENT, Royal Sussex County Hospital, Eastern Road, Brighton BN2 5BE, UK
| | - Joshua P. Earl
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease; Department of Microbiology and Immunology; Drexel University College of Medicine, 245 N. 15 St., Philadelphia, PA 19102, USA
| | - Lena Hafrén
- Department of Otorhinolaryngology, Head & Neck Surgery, University of Helsinki and Helsinki University Hospital, Helsinki, Tukholmankatu 8A, 00290 Helsinki, Finland
| | - Michael Jennings
- Institute for Glycomics, Gold Coast campus, Griffith University, QLD 4222, Australia
| | - Joshua C. Mell
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease; Department of Microbiology and Immunology; Drexel University College of Medicine, 245 N. 15 St., Philadelphia, PA 19102, USA
| | - Michael E. Pichichero
- Center for Infectious Diseases and Immunology, Rochester General Hospital Research Institute, 1425 Portland Ave., Rochester, NY 14621, USA
| | - Allen F. Ryan
- Department of Surgery/Otolaryngology, University of California San Diego, 9500 Gilman Dr., La Jolla, CA 92093, USA
| | - Hilda Tateossian
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell, Oxford, Didcot OX11 0RD, UK
| | - Garth D. Ehrlich
- Center for Genomic Sciences, Institute for Molecular Medicine and Infectious Disease; Department of Microbiology and Immunology; Drexel University College of Medicine, 245 N. 15 St., Philadelphia, PA 19102, USA
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5
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Murphy TF, Brauer AL, Pettigrew MM, LaFontaine ER, Tettelin H. Persistence of Moraxella catarrhalis in Chronic Obstructive Pulmonary Disease and Regulation of the Hag/MID Adhesin. J Infect Dis 2020; 219:1448-1455. [PMID: 30496439 DOI: 10.1093/infdis/jiy680] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/26/2018] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Persistence of bacterial pathogens in the airways has profound consequences on the course and pathogenesis of chronic obstructive pulmonary disease (COPD). Patients with COPD continuously acquire and clear strains of Moraxella catarrhalis, a major pathogen in COPD. Some strains are cleared quickly and some persist for months to years. The mechanism of the variability in duration of persistence is unknown. METHODS Guided by genome sequences of selected strains, we studied the expression of Hag/MID, hag/mid gene sequences, adherence to human cells, and autoaggregation in longitudinally collected strains of M. catarrhalis from adults with COPD. RESULTS Twenty-eight of 30 cleared strains of M. catarrhalis expressed Hag/MID whereas 17 of 30 persistent strains expressed Hag/MID upon acquisition by patients. All persistent strains ceased expression of Hag/MID during persistence. Expression of Hag/MID in human airways was regulated by slipped-strand mispairing. Virulence-associated phenotypes (adherence to human respiratory epithelial cells and autoaggregation) paralleled Hag/MID expression in airway isolates. CONCLUSIONS Most strains of M. catarrhalis express Hag/MID upon acquisition by adults with COPD and all persistent strains shut off expression during persistence. These observations suggest that Hag/MID is important for initial colonization by M. catarrhalis and that cessation of expression facilitates persistence in COPD airways.
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Affiliation(s)
- Timothy F Murphy
- Division of Infectious Diseases, Department of Medicine, The State University of New York, Buffalo.,Department of Microbiology and Immunology, The State University of New York, Buffalo.,Clinical and Translational Research Center, University at Buffalo, The State University of New York, Buffalo
| | - Aimee L Brauer
- Division of Infectious Diseases, Department of Medicine, The State University of New York, Buffalo.,Clinical and Translational Research Center, University at Buffalo, The State University of New York, Buffalo
| | - Melinda M Pettigrew
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, Yale University, New Haven, Connecticut
| | - Eric R LaFontaine
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens
| | - Hervé Tettelin
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore.,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore
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6
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Genotypic differences in CC224, CC363, CC449 and CC446 of Moraxella catarrhalis isolates based on whole genome SNP, MLST and PFGE typing. Int J Med Microbiol 2019; 310:151357. [PMID: 31570247 DOI: 10.1016/j.ijmm.2019.151357] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 08/15/2019] [Accepted: 09/15/2019] [Indexed: 10/26/2022] Open
Abstract
Understanding the evolutionary path of M. catarrhalis from macrolide-susceptible to macrolide-resistant organism, is important for hindering macrolide resistance from propagation. Multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE) and whole genome SNP typing (WGST), as useful and practical typing tools, have both advantages and disadvantages. We studied the utility of these 3 typing methods, including the level of agreement, consistency and drawbacks, in characterizing M. catarrhalis clones and clonal complexes. We focused on four clonal complexes [CC224, CC363, CC449 (CCN10) and CC446 (CCN08)] and found that PFGE and WGST had a high level of agreement and a proper consistency of the same clone or very closely related clones, while MLST is less discriminatory for different clones. Furthermore, we also established an evolutionary distance cut-off value for "The same clone". Moreover, we detected macrolide-resistant M. catarrhalis in CC224, which had previously been considered as a macrolide-susceptible clonal complex. A higher number of isolates belonged to ST215 compared to ST446, implying that ST215 is more likely to be the primary founder. Our study also demonstrated that all the four clonal complexes belong to the M. catarrhalis lineage 1, which is considered to be related to increased virulence potential and serum resistance. We also observed that copB II was highly related to CC449 and LOS type B was mainly confined in CC224. In conclusion, these findings provide further insight into the evolutionary characteristics of M. catarrhalis.
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7
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Warnke P, Köller T, Kreikemeyer B, Barrantes I, Mach H, Podbielski A. Molecular epidemiology study of a nosocomial Moraxella catarrhalis outbreak in a neurological rehabilitation unit. J Hosp Infect 2019; 103:27-34. [PMID: 31054937 DOI: 10.1016/j.jhin.2019.04.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 04/25/2019] [Indexed: 12/16/2022]
Abstract
BACKGROUND Moraxella catarrhalis is a common agent causing upper and lower respiratory tract infections, particularly of ventilated patients. The bacteria are transmitted between humans by direct and indirect contacts. However, reports of nosocomial outbreaks by this pathogen are scarce. AIM To analyse M. catarrhalis strains isolated during an outbreak in a medical rehabilitation centre to reveal their clonal relationship and to elucidate potential transmission routes. METHODS Extensive environmental and medical staff sampling was performed. Phenotypic and genotypic analyses of 15 isolates were executed, including repetitive element palindromic polymerase chain reaction (repPCR) and whole-genome sequencing. Furthermore, an intensified hygiene regimen was installed. FINDINGS The clonal nature of nine patient isolates and a simultaneous presence of separate entities including a strain isolated from a physician during staff screening was confirmed. Although neither asymptomatic carriers among the staff persons nor outbreak strain-contaminated fomites were identified for a specific intervention, the outbreak ceased due to maximum general and specific hygiene precautions. Retrospective analysis showed the increasing prevalence of M. catarrhalis strains over a period of two years before the incidence. Since then and after returning to the regular hygiene regimen, only one patient with a phenotypically diverse M. catarrhalis isolate has been documented. CONCLUSION The first M. catarrhalis outbreak involving nine patients of a neurological and trauma rehabilitation centre was reported. Potential transmission pathways were discussed. Comprehensive outbreak analyses insinuated the extension of routine laboratory storage time for defined species.
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Affiliation(s)
- P Warnke
- Institute of Medical Microbiology, Virology & Hygiene, University Medicine Rostock, Germany.
| | - T Köller
- Institute of Medical Microbiology, Virology & Hygiene, University Medicine Rostock, Germany
| | - B Kreikemeyer
- Institute of Medical Microbiology, Virology & Hygiene, University Medicine Rostock, Germany
| | - I Barrantes
- Institute for Biostatistics and Informatics in Medicine and Ageing Research, University Medicine Rostock, Germany
| | - H Mach
- Center for Medical Rehabilitation, Waldeck-Schwaan, Germany
| | - A Podbielski
- Institute of Medical Microbiology, Virology & Hygiene, University Medicine Rostock, Germany
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8
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Augustyniak D, Seredyński R, McClean S, Roszkowiak J, Roszniowski B, Smith DL, Drulis-Kawa Z, Mackiewicz P. Virulence factors of Moraxella catarrhalis outer membrane vesicles are major targets for cross-reactive antibodies and have adapted during evolution. Sci Rep 2018; 8:4955. [PMID: 29563531 PMCID: PMC5862889 DOI: 10.1038/s41598-018-23029-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/05/2018] [Indexed: 12/31/2022] Open
Abstract
Moraxella catarrhalis is a common human respiratory tract pathogen. Its virulence factors associated with whole bacteria or outer membrane vesicles (OMVs) aid infection, colonization and may induce specific antibodies. To investigate pathogen-host interactions, we applied integrated bioinformatic and immunoproteomic (2D-electrophoresis, immunoblotting, LC-MS/MS) approaches. We showed that OMV proteins engaged exclusively in complement evasion and colonization strategies, but not those involved in iron transport and metabolism, are major targets for cross-reacting antibodies produced against phylogenetically divergent M. catarrhalis strains. The analysis of 31 complete genomes of M. catarrhalis and other Moraxella revealed that OMV protein-coding genes belong to 64 orthologous groups, five of which are restricted to M. catarrhalis. This species showed a two-fold increase in the number of OMV protein-coding genes relative to its ancestors and animal-pathogenic Moraxella. The appearance of specific OMV factors and the increase in OMV-associated virulence proteins during M. catarrhalis evolution is an interesting example of pathogen adaptation to optimize colonization. This precisely targeted cross-reactive immunity against M. catarrhalis may be an important strategy of host defences to counteract this phenomenon. We demonstrate that cross-reactivity is closely associated with the anti-virulent antibody repertoire which we have linked with adaptation of this pathogen to the host.
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Affiliation(s)
- Daria Augustyniak
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland.
| | - Rafał Seredyński
- Department of Physiology, Wroclaw Medical University, T. Chalubinskiego 10, 50-368, Wroclaw, Poland.,Department of Physical Chemistry of Microorganisms, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland
| | - Siobhán McClean
- School of Biomolecular and Biomedical Sciences, UCD O'Brien Centre for Science West, B304, Dublin, Ireland
| | - Justyna Roszkowiak
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland
| | - Bartosz Roszniowski
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland
| | - Darren L Smith
- Applied Sciences, University of Northumbria, Ellison Building EBD222, Newcastle upon Tyne, NE1 8ST, UK
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland
| | - Paweł Mackiewicz
- Department of Genomics, Faculty of Biotechnology, University of Wrocław, Joliot-Curie 14a, 50-383, Wrocław, Poland.
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9
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Blakeway LV, Tan A, Peak IRA, Seib KL. Virulence determinants of Moraxella catarrhalis: distribution and considerations for vaccine development. MICROBIOLOGY-SGM 2017; 163:1371-1384. [PMID: 28893369 DOI: 10.1099/mic.0.000523] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Moraxella catarrhalis is a human-restricted opportunistic bacterial pathogen of the respiratory mucosa. It frequently colonizes the nasopharynx asymptomatically, but is also an important causative agent of otitis media (OM) in children, and plays a significant role in acute exacerbations of chronic obstructive pulmonary disease (COPD) in adults. As the current treatment options for M. catarrhalis infection in OM and exacerbations of COPD are often ineffective, the development of an efficacious vaccine is warranted. However, no vaccine candidates for M. catarrhalis have progressed to clinical trials, and information regarding the distribution of M. catarrhalis virulence factors and vaccine candidates is inconsistent in the literature. It is largely unknown if virulence is associated with particular strains or subpopulations of M. catarrhalis, or if differences in clinical manifestation can be attributed to the heterogeneous expression of specific M. catarrhalis virulence factors in the circulating population. Further investigation of the distribution of M. catarrhalis virulence factors in the context of carriage and disease is required so that vaccine development may be targeted at relevant antigens that are conserved among disease-causing strains. The challenge of determining which of the proposed M. catarrhalis virulence factors are relevant to human disease is amplified by the lack of a standardized M. catarrhalis typing system to facilitate direct comparisons of worldwide isolates. Here we summarize and evaluate proposed relationships between M. catarrhalis subpopulations and specific virulence factors in the context of colonization and disease, as well as the current methods used to infer these associations.
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Affiliation(s)
- Luke V Blakeway
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Aimee Tan
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
| | - Ian R A Peak
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia.,School of Medical Science, Griffith University, Gold Coast, Queensland, Australia
| | - Kate L Seib
- Institute for Glycomics, Griffith University, Gold Coast, Queensland, Australia
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10
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Tan A, Blakeway LV, Bakaletz LO, Boitano M, Clark TA, Korlach J, Jennings MP, Peak IR, Seib KL. Complete Genome Sequence of Moraxella catarrhalis Strain CCRI-195ME, Isolated from the Middle Ear. GENOME ANNOUNCEMENTS 2017; 5:e00384-17. [PMID: 28546484 PMCID: PMC5477397 DOI: 10.1128/genomea.00384-17] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 04/07/2017] [Indexed: 11/21/2022]
Abstract
Moraxella catarrhalis is an important bacterial pathogen that causes otitis media and exacerbations of chronic obstructive pulmonary disease. Here, we report the complete genome sequence of M. catarrhalis strain CCRI-195ME, which contains the phase-variable epigenetic regulator ModM3.
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Affiliation(s)
- Aimee Tan
- Institute for Glycomics, Griffith University, Gold Coast, Australia
| | - Luke V Blakeway
- Institute for Glycomics, Griffith University, Gold Coast, Australia
| | - Lauren O Bakaletz
- Center for Microbial Pathogenesis, Research Institute at Nationwide Children's Hospital, Ohio State University College of Medicine, Columbus, Ohio, USA
| | | | | | | | | | - Ian R Peak
- Institute for Glycomics, Griffith University, Gold Coast, Australia
| | - Kate L Seib
- Institute for Glycomics, Griffith University, Gold Coast, Australia
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11
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Barenkamp SJ, Chonmaitree T, Hakansson AP, Heikkinen T, King S, Nokso-Koivisto J, Novotny LA, Patel JA, Pettigrew M, Swords WE. Panel 4: Report of the Microbiology Panel. Otolaryngol Head Neck Surg 2017; 156:S51-S62. [PMID: 28372529 PMCID: PMC5490388 DOI: 10.1177/0194599816639028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 02/24/2016] [Indexed: 12/12/2022]
Abstract
Objective To perform a comprehensive review of the literature from July 2011 until June 2015 on the virology and bacteriology of otitis media in children. Data Sources PubMed database of the National Library of Medicine. Review Methods Two subpanels comprising experts in the virology and bacteriology of otitis media were created. Each panel reviewed the relevant literature in the fields of virology and bacteriology and generated draft reviews. These initial reviews were distributed to all panel members prior to meeting together at the Post-symposium Research Conference of the 18th International Symposium on Recent Advances in Otitis Media, National Harbor, Maryland, in June 2015. A final draft was created, circulated, and approved by all panel members. Conclusions Excellent progress has been made in the past 4 years in advancing our understanding of the microbiology of otitis media. Numerous advances were made in basic laboratory studies, in animal models of otitis media, in better understanding the epidemiology of disease, and in clinical practice. Implications for Practice (1) Many viruses cause acute otitis media without bacterial coinfection, and such cases do not require antibiotic treatment. (2) When respiratory syncytial virus, metapneumovirus, and influenza virus peak in the community, practitioners can expect to see an increase in clinical otitis media cases. (3) Biomarkers that predict which children with upper respiratory tract infections will develop otitis media may be available in the future. (4) Compounds that target newly identified bacterial virulence determinants may be available as future treatment options for children with otitis media.
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Affiliation(s)
- Stephen J. Barenkamp
- Department of Pediatrics, St Louis University School of Medicine, St Louis, Missouri, USA
| | - Tasnee Chonmaitree
- Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas, USA
| | | | - Terho Heikkinen
- Department of Pediatrics, University of Turku and Turku University Hospital, Turku, Finland
| | - Samantha King
- The Research Institute at Nationwide Children’s Hospital and Ohio State University, Columbus, Ohio, USA
| | - Johanna Nokso-Koivisto
- Department of Otorhinolaryngology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Laura A. Novotny
- The Research Institute at Nationwide Children’s Hospital and Ohio State University, Columbus, Ohio, USA
| | - Janak A. Patel
- Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas, USA
| | - Melinda Pettigrew
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - W. Edward Swords
- Department of Microbiology and Immunology, Wake Forest University, Winston-Salem, North Carolina, USA
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12
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Liu YL, Li DF, Xu HP, Xiao M, Cheng JW, Zhang L, Xu ZP, Chen XX, Zhang G, Kudinha T, Kong F, Gong YP, Wang XY, Zhang YX, Wu HL, Xu YC. Use of next generation sequence to investigate potential novel macrolide resistance mechanisms in a population of Moraxella catarrhalis isolates. Sci Rep 2016; 6:35711. [PMID: 27774989 PMCID: PMC5075928 DOI: 10.1038/srep35711] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 10/04/2016] [Indexed: 01/01/2023] Open
Abstract
Although previous studies have confirmed that 23S rRNA gene mutation could be responsible for most of macrolide resistance in M. catarrhalis, a recent study suggested otherwise. Next generation sequence based comparative genomics has revolutionized the mining of potential novel drug resistant mechanisms. In this study, two pairs of resistant and susceptible M. catarrhalis isolates with different multilocus sequence types, were investigated for potential differential genes or informative single nucleotide polymorphisms (SNPs). The identified genes and SNPs were evaluated in 188 clinical isolates. From initially 12 selected differential genes and 12 informative SNPs, 10 differential genes (mboIA, mcbC, mcbI, mboIB, MCR_1794, MCR_1795, lgt2B/C, dpnI, mcbB, and mcbA) and 6 SNPs (C619T of rumA, T140C of rplF, G643A of MCR_0020, T270G of MCR_1465, C1348A of copB, and G238A of rrmA) were identified as possibly linked to macrolide resistance in M. catarrhalis. Most of the identified differential genes and SNPs are related to methylation of ribosomal RNA (rRNA) or DNA, especially MCR_0020 and rrmA. Further studies are needed to determine the function and/or evolution process, of the identified genes or SNPs, to establish whether some novel or combined mechanisms are truly involved in M. catarrhalis macrolide resistance mechanism.
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Affiliation(s)
- Ya-Li Liu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100736, China
| | - Dong-Fang Li
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China.,Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - He-Ping Xu
- Department of Clinical Laboratory, the First Affiliated Hospital of Xiamen University, Xiamen, China
| | - Meng Xiao
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100736, China
| | - Jing-Wei Cheng
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100736, China
| | - Li Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100736, China
| | - Zhi-Peng Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100736, China
| | - Xin-Xin Chen
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100736, China
| | - Ge Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100736, China
| | - Timothy Kudinha
- Charles Sturt University, Leeds Parade, Orange, New South Wales 2687, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR - Pathology West, Westmead Hospital, University of Sydney, Darcy Road, Westmead, New South Wales 2145, Australia
| | - Fanrong Kong
- Centre for Infectious Diseases and Microbiology Laboratory Services, ICPMR - Pathology West, Westmead Hospital, University of Sydney, Darcy Road, Westmead, New South Wales 2145, Australia
| | - Yan-Ping Gong
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China.,Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Xin-Ying Wang
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China.,Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Yin-Xin Zhang
- Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China.,Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Hong-Long Wu
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.,Binhai Genomics Institute, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China.,Tianjin Translational Genomics Center, BGI-Tianjin, BGI-Shenzhen, Tianjin 300308, China
| | - Ying-Chun Xu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing 100736, China
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13
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Earl JP, de Vries SPW, Ahmed A, Powell E, Schultz MP, Hermans PWM, Hill DJ, Zhou Z, Constantinidou CI, Hu FZ, Bootsma HJ, Ehrlich GD. Comparative Genomic Analyses of the Moraxella catarrhalis Serosensitive and Seroresistant Lineages Demonstrate Their Independent Evolution. Genome Biol Evol 2016; 8:955-74. [PMID: 26912404 PMCID: PMC4860680 DOI: 10.1093/gbe/evw039] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/18/2016] [Indexed: 02/07/2023] Open
Abstract
The bacterial speciesMoraxella catarrhalishas been hypothesized as being composed of two distinct lineages (referred to as the seroresistant [SR] and serosensitive [SS]) with separate evolutionary histories based on several molecular typing methods, whereas 16S ribotyping has suggested an additional split within the SS lineage. Previously, we characterized whole-genome sequences of 12 SR-lineage isolates, which revealed a relatively small supragenome when compared with other opportunistic nasopharyngeal pathogens, suggestive of a relatively short evolutionary history. Here, we performed whole-genome sequencing on 18 strains from both ribotypes of the SS lineage, an additional SR strain, as well as four previously identified highly divergent strains based on multilocus sequence typing analyses. All 35 strains were subjected to a battery of comparative genomic analyses which clearly show that there are three lineages-the SR, SS, and the divergent. The SR and SS lineages are closely related, but distinct from each other based on three different methods of comparison: Allelic differences observed among core genes; possession of lineage-specific sets of core and distributed genes; and by an alignment of concatenated core sequences irrespective of gene annotation. All these methods show that the SS lineage has much longer interstrain branches than the SR lineage indicating that this lineage has likely been evolving either longer or faster than the SR lineage. There is evidence of extensive horizontal gene transfer (HGT) within both of these lineages, and to a lesser degree between them. In particular, we identified very high rates of HGT between these two lineages for ß-lactamase genes. The four divergent strains aresui generis, being much more distantly related to both the SR and SS groups than these other two groups are to each other. Based on average nucleotide identities, gene content, GC content, and genome size, this group could be considered as a separate taxonomic group. The SR and SS lineages, although distinct, clearly form a single species based on multiple criteria including a large common core genome, average nucleotide identity values, GC content, and genome size. Although neither of these lineages arose from within the other based on phylogenetic analyses, the question of how and when these lineages split and then subsequently reunited in the human nasopharynx is explored.
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Affiliation(s)
- Joshua P Earl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA Center for Genomic Sciences, Allegheny-Singer Research Institute, Allegheny General Hospital, Pittsburgh, PA
| | - Stefan P W de Vries
- Present address: Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Azad Ahmed
- Center for Genomic Sciences, Allegheny-Singer Research Institute, Allegheny General Hospital, Pittsburgh, PA
| | - Evan Powell
- Center for Genomic Sciences, Allegheny-Singer Research Institute, Allegheny General Hospital, Pittsburgh, PA
| | - Matthew P Schultz
- Center for Genomic Sciences, Allegheny-Singer Research Institute, Allegheny General Hospital, Pittsburgh, PA
| | - Peter W M Hermans
- Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Darryl J Hill
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Zhemin Zhou
- Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | | | - Fen Z Hu
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA Center for Genomic Sciences, Allegheny-Singer Research Institute, Allegheny General Hospital, Pittsburgh, PA Department of Otolaryngology Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, PA
| | - Hester J Bootsma
- Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Garth D Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA Center for Genomic Sciences and Center for Advanced Microbial Processing, Institute of Molecular Medicine and Infectious Disease, Drexel University College of Medicine, Philadelphia, PA Center for Genomic Sciences, Allegheny-Singer Research Institute, Allegheny General Hospital, Pittsburgh, PA Department of Otolaryngology Head and Neck Surgery, Drexel University College of Medicine, Philadelphia, PA
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14
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Fouts DE, Matthias MA, Adhikarla H, Adler B, Amorim-Santos L, Berg DE, Bulach D, Buschiazzo A, Chang YF, Galloway RL, Haake DA, Haft DH, Hartskeerl R, Ko AI, Levett PN, Matsunaga J, Mechaly AE, Monk JM, Nascimento ALT, Nelson KE, Palsson B, Peacock SJ, Picardeau M, Ricaldi JN, Thaipandungpanit J, Wunder EA, Yang XF, Zhang JJ, Vinetz JM. What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira. PLoS Negl Trop Dis 2016; 10:e0004403. [PMID: 26890609 PMCID: PMC4758666 DOI: 10.1371/journal.pntd.0004403] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 01/03/2016] [Indexed: 12/20/2022] Open
Abstract
Leptospirosis, caused by spirochetes of the genus Leptospira, is a globally widespread, neglected and emerging zoonotic disease. While whole genome analysis of individual pathogenic, intermediately pathogenic and saprophytic Leptospira species has been reported, comprehensive cross-species genomic comparison of all known species of infectious and non-infectious Leptospira, with the goal of identifying genes related to pathogenesis and mammalian host adaptation, remains a key gap in the field. Infectious Leptospira, comprised of pathogenic and intermediately pathogenic Leptospira, evolutionarily diverged from non-infectious, saprophytic Leptospira, as demonstrated by the following computational biology analyses: 1) the definitive taxonomy and evolutionary relatedness among all known Leptospira species; 2) genomically-predicted metabolic reconstructions that indicate novel adaptation of infectious Leptospira to mammals, including sialic acid biosynthesis, pathogen-specific porphyrin metabolism and the first-time demonstration of cobalamin (B12) autotrophy as a bacterial virulence factor; 3) CRISPR/Cas systems demonstrated only to be present in pathogenic Leptospira, suggesting a potential mechanism for this clade's refractoriness to gene targeting; 4) finding Leptospira pathogen-specific specialized protein secretion systems; 5) novel virulence-related genes/gene families such as the Virulence Modifying (VM) (PF07598 paralogs) proteins and pathogen-specific adhesins; 6) discovery of novel, pathogen-specific protein modification and secretion mechanisms including unique lipoprotein signal peptide motifs, Sec-independent twin arginine protein secretion motifs, and the absence of certain canonical signal recognition particle proteins from all Leptospira; and 7) and demonstration of infectious Leptospira-specific signal-responsive gene expression, motility and chemotaxis systems. By identifying large scale changes in infectious (pathogenic and intermediately pathogenic) vs. non-infectious Leptospira, this work provides new insights into the evolution of a genus of bacterial pathogens. This work will be a comprehensive roadmap for understanding leptospirosis pathogenesis. More generally, it provides new insights into mechanisms by which bacterial pathogens adapt to mammalian hosts.
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Affiliation(s)
- Derrick E. Fouts
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Michael A. Matthias
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Haritha Adhikarla
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Ben Adler
- Australian Research Council Centre of Excellence in Structural and Functional Microbial Genomics, Department of Microbiology, Monash University, Clayton, Australia
| | - Luciane Amorim-Santos
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia, Brazil
| | - Douglas E. Berg
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
| | - Dieter Bulach
- Victorian Bioinformatics Consortium, Monash University, Clayton, Victoria, Australia
| | - Alejandro Buschiazzo
- Institut Pasteur de Montevideo, Laboratory of Molecular and Structural Microbiology, Montevideo, Uruguay
- Institut Pasteur, Department of Structural Biology and Chemistry, Paris, France
| | - Yung-Fu Chang
- Department of Population Medicine & Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Renee L. Galloway
- Centers for Disease Control and Prevention (DHHS, CDC, OID, NCEZID, DHCPP, BSPB), Atlanta, Georgia, United States of America
| | - David A. Haake
- VA Greater Los Angeles Healthcare System, Los Angeles, California, United States of America
- David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Daniel H. Haft
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Rudy Hartskeerl
- WHO/FAO/OIE and National Collaborating Centre for Reference and Research on Leptospirosis, KIT Biomedical Research, Royal Tropical Institute (KIT), Amsterdam, The Netherlands
| | - Albert I. Ko
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia, Brazil
| | - Paul N. Levett
- Government of Saskatchewan, Disease Control Laboratory Regina, Canada
| | - James Matsunaga
- VA Greater Los Angeles Healthcare System, Los Angeles, California, United States of America
- David Geffen School of Medicine at UCLA, Los Angeles, California, United States of America
| | - Ariel E. Mechaly
- Institut Pasteur de Montevideo, Laboratory of Molecular and Structural Microbiology, Montevideo, Uruguay
| | - Jonathan M. Monk
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Ana L. T. Nascimento
- Centro de Biotecnologia, Instituto Butantan, São Paulo, SP, Brazil
- Programa Interunidades em Biotecnologia, Instituto de Ciências Biomédicas, USP, São Paulo, SP, Brazil
| | - Karen E. Nelson
- J. Craig Venter Institute, Rockville, Maryland, United States of America
| | - Bernhard Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Sharon J. Peacock
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Mathieu Picardeau
- Institut Pasteur, Biology of Spirochetes Unit, National Reference Centre and WHO Collaborating Center for Leptospirosis, Paris, France
| | - Jessica N. Ricaldi
- Instituto de Medicina Tropical Alexander von Humboldt; Facultad de Medicina Alberto Hurtado, Universidd Peruana Cayetano Heredia, Lima, Peru
| | | | - Elsio A. Wunder
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Centro de Pesquisas Gonçalo Moniz, Fundação Oswaldo Cruz/MS, Salvador, Bahia, Brazil
| | - X. Frank Yang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Jun-Jie Zhang
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana, United States of America
| | - Joseph M. Vinetz
- Division of Infectious Diseases, Department of Medicine, University of California San Diego School of Medicine, La Jolla, California, United States of America
- Instituto de Medicina Tropical Alexander von Humboldt; Facultad de Medicina Alberto Hurtado, Universidd Peruana Cayetano Heredia, Lima, Peru
- Instituto de Medicina “Alexander von Humboldt,” Universidad Peruana Cayetano Heredia, Lima, Peru
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15
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Ariff A, Wise MJ, Kahler CM, Tay CY, Peters F, Perkins TT, Chang BJ. Novel Moraxella catarrhalis prophages display hyperconserved non-structural genes despite their genomic diversity. BMC Genomics 2015; 16:860. [PMID: 26497500 PMCID: PMC4619438 DOI: 10.1186/s12864-015-2104-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/16/2015] [Indexed: 11/25/2022] Open
Abstract
Background Moraxella catarrhalis is an important pathogen that often causes otitis media in children, a disease that is not currently vaccine preventable. Asymptomatic colonisation of the human upper respiratory tract is common and lack of clearance by the immune system is likely due to the emergence of seroresistant genetic lineages. No active bacteriophages or prophages have been described in this species. This study was undertaken to identify and categorise prophages in M. catarrhalis, their genetic diversity and the relationship of such diversity with the host-species phylogeny. Results This study presents a comparative analysis of 32 putative prophages identified in 95 phylogenetically variable, newly sequenced M. catarrhalis genomes. The prophages were genotypically classified into four diverse clades. The genetic synteny of each clade is similar to the group 1 phage family Siphoviridae, however, they form genotypic clusters that are distinct from other members of this family. No core genetic sequences exist across the 32 prophages despite clades 2, 3, and 4 sharing the most sequence identity. The analysis of non-structural prophage genes (coding the integrase, and terminase), and portal gene showed that the respective genes were identical for clades 2, 3, and 4, but unique for clade 1. Empirical analysis calculated that these genes are unexpectedly hyperconserved, under purifying selection, suggesting a tightly regulated functional role. As such, it is improbable that the prophages are decaying remnants but stable components of a fluctuating, flexible and unpredictable system ultimately maintained by functional constraints on non-structural and packaging genes. Additionally, the plate encoding genes were well conserved across all four prophage clades, and the tail fibre genes, commonly responsible for receptor recognition, were clustered into three major groups distributed across the prophage clades. A pan-genome of 283,622 bp was identified, and the prophages were mapped onto the diverse M. catarrhalis multi-locus sequence type (MLST) backbone. Conclusion This study has provided the first evidence of putatively mobile prophages in M. catarrhalis, identifying a diverse and fluctuating system dependent on the hyperconservation of a few key, non-structural genes. Some prophages harbour virulence-related genes, and potentially influence the physiology and virulence of M. catarrhalis. Importantly our data will provide supporting information on the identification of novel prophages in other species by adding greater weight to the identification of non-structural genes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2104-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amir Ariff
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
| | - Michael J Wise
- School of Chemistry and Biochemistry, The University of Western Australia, Perth, WA, Australia.
| | - Charlene M Kahler
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
| | - Chin Yen Tay
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
| | - Fanny Peters
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
| | - Timothy T Perkins
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
| | - Barbara J Chang
- School of Pathology and Laboratory Medicine, The University of Western Australia, Perth, WA, Australia.
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16
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A novel method of consensus pan-chromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii. Genome Biol 2015. [PMID: 26195261 PMCID: PMC4507327 DOI: 10.1186/s13059-015-0701-6] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Background Infections by pan-drug resistant Acinetobacter baumannii plague military and civilian healthcare systems. Previous A. baumannii pan-genomic studies used modest sample sizes of low diversity and comparisons to a single reference genome, limiting our understanding of gene order and content. A consensus representation of multiple genomes will provide a better framework for comparison. A large-scale comparative study will identify genomic determinants associated with their diversity and adaptation as a successful pathogen. Results We determine draft-level genomic sequence of 50 diverse military isolates and conduct the largest bacterial pan-genome analysis of 249 genomes. The pan-genome of A. baumannii is open when the input genomes are normalized for diversity with 1867 core proteins and a paralog-collapsed pan-genome size of 11,694 proteins. We developed a novel graph-based algorithm and use it to assemble the first consensus pan-chromosome, identifying both the order and orientation of core genes and flexible genomic regions. Comparative genome analyses demonstrate the existence of novel resistance islands and isolates with increased numbers of resistance island insertions over time, from single insertions in the 1950s to triple insertions in 2011. Gene clusters responsible for carbon utilization, siderophore production, and pilus assembly demonstrate frequent gain or loss among isolates. Conclusions The highly variable and dynamic nature of the A. baumannii genome may be the result of its success in rapidly adapting to both abiotic and biotic environments through the gain and loss of gene clusters controlling fitness. Importantly, some archaic adaptation mechanisms appear to have reemerged among recent isolates. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0701-6) contains supplementary material, which is available to authorized users.
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17
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Kadam A, Janto B, Eutsey R, Earl JP, Powell E, Dahlgren ME, Hu FZ, Ehrlich GD, Hiller NL. Streptococcus pneumoniae Supragenome Hybridization Arrays for Profiling of Genetic Content and Gene Expression. ACTA ACUST UNITED AC 2015; 36:9D.4.1-9D.4.20. [PMID: 25641101 DOI: 10.1002/9780471729259.mc09d04s36] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
There is extensive genomic diversity among Streptococcus pneumoniae isolates. Approximately half of the comprehensive set of genes in the species (the supragenome or pangenome) is present in all the isolates (core set), and the remaining is unevenly distributed among strains (distributed set). The Streptococcus pneumoniae Supragenome Hybridization (SpSGH) array provides coverage for an extensive set of genes and polymorphisms encountered within this species, capturing this genomic diversity. Further, the capture is quantitative. In this manner, the SpSGH array allows for both genomic and transcriptomic analyses of diverse S. pneumoniae isolates on a single platform. In this unit, we present the SpSGH array, and describe in detail its design and implementation for both genomic and transcriptomic analyses. The methodology can be applied to construction and modification of SpSGH array platforms, as well to other bacterial species as long as multiple whole-genome sequences are available that collectively capture the vast majority of the species supragenome.
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Affiliation(s)
- Anagha Kadam
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Benjamin Janto
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Rory Eutsey
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania
| | - Joshua P Earl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Evan Powell
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania
| | - Margaret E Dahlgren
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania
| | - Fen Z Hu
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Garth D Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - N Luisa Hiller
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania.,Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania
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18
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Vernikos G, Medini D, Riley DR, Tettelin H. Ten years of pan-genome analyses. Curr Opin Microbiol 2014; 23:148-54. [PMID: 25483351 DOI: 10.1016/j.mib.2014.11.016] [Citation(s) in RCA: 298] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 11/19/2014] [Accepted: 11/20/2014] [Indexed: 10/24/2022]
Abstract
Next generation sequencing technologies have engendered a genome sequence data deluge in public databases. Genome analyses have transitioned from single or few genomes to hundreds to thousands of genomes. Pan-genome analyses provide a framework for estimating the genomic diversity of the dataset at hand and predicting the number of additional whole genomes sequences that would be necessary to fully characterize that diversity. We review recent implementations of the pan-genome approach, its impact and limits, and we propose possible extensions, including analyses at the whole genome multiple sequence alignment level.
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Affiliation(s)
- George Vernikos
- Novartis (Hellas) S.A.C.I., 12th Km Athens-Lamia North Road, 14451 Metamorfossi, Athens, Greece
| | - Duccio Medini
- Novartis Vaccines Research, Via Fiorentina 1, 53100 Siena, Italy
| | - David R Riley
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, 801 West Baltimore Street, Baltimore, MD 21201, USA
| | - Hervé Tettelin
- Institute for Genome Sciences, Department of Microbiology and Immunology, University of Maryland School of Medicine, 801 West Baltimore Street, Baltimore, MD 21201, USA.
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19
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Whitehouse CA, Ladner JT, Palacios GF. Molecular characterization of plasmid pMoma1of Moraxella macacae, a newly described bacterial pathogen of macaques. Folia Microbiol (Praha) 2014; 60:235-9. [PMID: 25398380 DOI: 10.1007/s12223-014-0364-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/06/2014] [Indexed: 10/24/2022]
Abstract
We report the complete nucleotide sequence and characterization of a small cryptic plasmid of Moraxella macacae 0408225, a newly described bacterial species within the family Moraxellaceae and a causative agent of epistaxis in macaques. The complete nucleotide sequence of the plasmid pMoma1 was determined and found to be 5,375 bp in size with a GC content of 37.4 %. Computer analysis of the sequence data revealed five open reading frames encoding putative proteins of 54.4 kDa (ORF1), 17.6 kDa (ORF2), 13.3 kDa (ORF3), 51.6 kDa (ORF4), and 25.0 kDa (ORF5). ORF1, ORF2, and ORF3 encode putative proteins with high identity (72, 42, and 55 %, respectively) to mobilization proteins of plasmids found in other Moraxella species. ORF3 encodes a putative protein with similarity (about 40 %) to several plasmid replicase (RepA) proteins. The fifth open reading frames (ORF) was most similar to hypothetical proteins with unknown functions, although domain analysis of this sequence suggests it belongs to the Abi-like protein family. Upstream of the repA gene, a 470-bp intergenic region, was identified that contained an AT-rich section and two sets of tandem direct and indirect repeats, consistent with a putative origin of replication site. In contrast to other plasmids of Moraxella, the occurrence of pMoma1 in M. macacae isolates appears to be common as PCR testing of 14 clinical isolates from two different research institutions all contained the plasmid.
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Affiliation(s)
- Chris A Whitehouse
- Center for Genome Sciences, U.S. Army Medical Research Institute of Infectious Diseases, Fort Detrick, MD, USA,
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A Moraxella catarrhalis two-component signal transduction system necessary for growth in liquid media affects production of two lysozyme inhibitors. Infect Immun 2014; 83:146-60. [PMID: 25312959 DOI: 10.1128/iai.02486-14] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
There are a paucity of data concerning gene products that could contribute to the ability of Moraxella catarrhalis to colonize the human nasopharynx. Inactivation of a gene (mesR) encoding a predicted response regulator of a two-component signal transduction system in M. catarrhalis yielded a mutant unable to grow in liquid media. This mesR mutant also exhibited increased sensitivity to certain stressors, including polymyxin B, SDS, and hydrogen peroxide. Inactivation of the gene (mesS) encoding the predicted cognate sensor (histidine) kinase yielded a mutant with the same inability to grow in liquid media as the mesR mutant. DNA microarray and real-time reverse transcriptase PCR analyses indicated that several genes previously shown to be involved in the ability of M. catarrhalis to persist in the chinchilla nasopharynx were upregulated in the mesR mutant. Two other open reading frames upregulated in the mesR mutant were shown to encode small proteins (LipA and LipB) that had amino acid sequence homology to bacterial adhesins and structural homology to bacterial lysozyme inhibitors. Inactivation of both lipA and lipB did not affect the ability of M. catarrhalis O35E to attach to a human bronchial epithelial cell line in vitro. Purified recombinant LipA and LipB fusion proteins were each shown to inhibit human lysozyme activity in vitro and in saliva. A lipA lipB deletion mutant was more sensitive than the wild-type parent strain to killing by human lysozyme in the presence of human apolactoferrin. This is the first report of the production of lysozyme inhibitors by M. catarrhalis.
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Development and validation of an Haemophilus influenzae supragenome hybridization (SGH) array for transcriptomic analyses. PLoS One 2014; 9:e105493. [PMID: 25290153 PMCID: PMC4188559 DOI: 10.1371/journal.pone.0105493] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 07/23/2014] [Indexed: 01/04/2023] Open
Abstract
We previously carried out the design and testing of a custom-built Haemophilus influenzae supragenome hybridization (SGH) array that contains probe sequences to 2,890 gene clusters identified by whole genome sequencing of 24 strains of H. influenzae. The array was originally designed as a tool to interrogate the gene content of large numbers of clinical isolates without the need for sequencing, however, the data obtained is quantitative and is thus suitable for transcriptomic analyses. In the current study RNA was extracted from H. influenzae strain CZ4126/02 (which was not included in the design of the array) converted to cDNA, and labelled and hybridized to the SGH arrays to assess the quality and reproducibility of data obtained from these custom-designed chips to serve as a tool for transcriptomics. Three types of experimental replicates were analyzed with all showing very high degrees of correlation, thus validating both the array and the methods used for RNA profiling. A custom filtering pipeline for two-condition unpaired data using five metrics was developed to minimize variability within replicates and to maximize the identification of the most significant true transcriptional differences between two samples. These methods can be extended to transcriptional analysis of other bacterial species utilizing supragenome-based arrays.
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22
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Blakeway LV, Power PM, Jen FEC, Worboys SR, Boitano M, Clark TA, Korlach J, Bakaletz LO, Jennings MP, Peak IR, Seib KL. ModM DNA methyltransferase methylome analysis reveals a potential role for Moraxella catarrhalis phasevarions in otitis media. FASEB J 2014; 28:5197-207. [PMID: 25183669 DOI: 10.1096/fj.14-256578] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Moraxella catarrhalis is a significant cause of otitis media and exacerbations of chronic obstructive pulmonary disease. Here, we characterize a phase-variable DNA methyltransferase (ModM), which contains 5'-CAAC-3' repeats in its open reading frame that mediate high-frequency mutation resulting in reversible on/off switching of ModM expression. Three modM alleles have been identified (modM1-3), with modM2 being the most commonly found allele. Using single-molecule, real-time (SMRT) genome sequencing and methylome analysis, we have determined that the ModM2 methylation target is 5'-GAR(m6)AC-3', and 100% of these sites are methylated in the genome of the M. catarrhalis 25239 ModM2 on strain. Proteomic analysis of ModM2 on and off variants revealed that ModM2 regulates expression of multiple genes that have potential roles in colonization, infection, and protection against host defenses. Investigation of the distribution of modM alleles in a panel of M. catarrhalis strains, isolated from the nasopharynx of healthy children or middle ear effusions from patients with otitis media, revealed a statistically significant association of modM3 with otitis media isolates. The modulation of gene expression via the ModM phase-variable regulon (phasevarion), and the significant association of the modM3 allele with otitis media, suggests a key role for ModM phasevarions in the pathogenesis of this organism.
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Affiliation(s)
| | | | | | | | | | - Tyson A Clark
- Pacific Biosciences, Menlo Park, California, USA; and
| | - Jonas Korlach
- Pacific Biosciences, Menlo Park, California, USA; and
| | - Lauren O Bakaletz
- Center for Microbial Pathogenesis, Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA
| | | | - Ian R Peak
- Institute for Glycomics and School of Medical Science, Griffith University, Southport, Queensland, Australia
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Luke-Marshall NR, Mang TS, Hansen LA, Campagnari AA. Moraxella catarrhalisis susceptible to antimicrobial photodynamic therapy with Photofrin. Lasers Surg Med 2014; 46:712-7. [DOI: 10.1002/lsm.22287] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Nicole R. Luke-Marshall
- Department of Microbiology and Immunology; State University of New York at Buffalo; Buffalo New York
| | - Thomas S. Mang
- Department of Oral and Maxillofacial Surgery; State University of New York at Buffalo; Buffalo New York
| | - Lisa A. Hansen
- Department of Microbiology and Immunology; State University of New York at Buffalo; Buffalo New York
| | - Anthony A. Campagnari
- Department of Microbiology and Immunology; State University of New York at Buffalo; Buffalo New York
- Department of Medicine; State University of New York at Buffalo; Buffalo New York
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24
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Substrate binding protein SBP2 of a putative ABC transporter as a novel vaccine antigen of Moraxella catarrhalis. Infect Immun 2014; 82:3503-12. [PMID: 24914218 DOI: 10.1128/iai.01832-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Moraxella catarrhalis is a common respiratory tract pathogen that causes otitis media in children and infections in adults with chronic obstructive pulmonary disease. Since the introduction of the pneumococcal conjugate vaccines with/without protein D of nontypeable Haemophilus influenzae, M. catarrhalis has become a high-priority pathogen in otitis media. For the development of antibacterial vaccines and therapies, substrate binding proteins of ATP-binding cassette transporters are important targets. In this study, we identified and characterized a substrate binding protein, SBP2, of M. catarrhalis. Among 30 clinical isolates tested, the sbp2 gene sequence was highly conserved. In 2 different analyses (whole-cell enzyme-linked immunosorbent assay and flow cytometry), polyclonal antibodies raised to recombinant SBP2 demonstrated that SBP2 expresses epitopes on the bacterial surface of the wild type but not the sbp2 mutant. Mice immunized with recombinant SBP2 showed significantly enhanced clearance of M. catarrhalis from the lung compared to that in the control group at both 25-μg and 50-μg doses (P < 0.001). We conclude that SBP2 is a novel, attractive candidate as a vaccine antigen against M. catarrhalis.
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25
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Identification of an outer membrane lipoprotein involved in nasopharyngeal colonization by Moraxella catarrhalis in an animal model. Infect Immun 2014; 82:2287-99. [PMID: 24643539 DOI: 10.1128/iai.01745-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Colonization of the human nasopharynx by Moraxella catarrhalis is presumed to involve attachment of this bacterium to the mucosa. DNA microarray analysis was used to determine whether attachment of M. catarrhalis to human bronchial epithelial (HBE) cells in vitro affected gene expression in this bacterium. Attachment affected expression of at least 454 different genes, with 163 being upregulated and 291 being downregulated. Among the upregulated genes was one (ORF113) previously annotated as encoding a protein with some similarity to outer membrane protein A (OmpA). The protein encoded by ORF113 was predicted to have a signal peptidase II cleavage site, and globomycin inhibition experiments confirmed that this protein was indeed a lipoprotein. The ORF113 protein also contained a predicted peptidoglycan-binding domain in its C-terminal half. The use of mutant and recombinant M. catarrhalis strains confirmed that the ORF113 protein was present in outer membrane preparations, and this protein was also shown to be at least partially exposed on the bacterial cell surface. A mutant unable to produce the ORF113 protein showed little or no change in its growth rate in vitro, in its ability to attach to HBE cells in vitro, or in its autoagglutination characteristics, but it did exhibit a reduced ability to survive in the chinchilla nasopharynx. This is the first report of a lipoprotein essential to the ability of M. catarrhalis to persist in an animal model.
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26
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de Vries SPW, Rademakers RJA, van der Gaast-de Jongh CE, Eleveld MJ, Hermans PWM, Bootsma HJ. Deciphering the genetic basis ofMoraxella catarrhaliscomplement resistance: a critical role for the disulphide bond formation system. Mol Microbiol 2013; 91:522-37. [DOI: 10.1111/mmi.12475] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2013] [Indexed: 12/14/2022]
Affiliation(s)
- Stefan P. W. de Vries
- Laboratory of Pediatric Infectious Diseases; Radboud University Medical Centre; Nijmegen The Netherlands
| | - Rob J. A. Rademakers
- Laboratory of Pediatric Infectious Diseases; Radboud University Medical Centre; Nijmegen The Netherlands
| | | | - Marc J. Eleveld
- Laboratory of Pediatric Infectious Diseases; Radboud University Medical Centre; Nijmegen The Netherlands
| | - Peter W. M. Hermans
- Laboratory of Pediatric Infectious Diseases; Radboud University Medical Centre; Nijmegen The Netherlands
| | - Hester J. Bootsma
- Laboratory of Pediatric Infectious Diseases; Radboud University Medical Centre; Nijmegen The Netherlands
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27
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Moraxella catarrhalis expresses a cardiolipin synthase that impacts adherence to human epithelial cells. J Bacteriol 2013; 196:107-20. [PMID: 24142255 DOI: 10.1128/jb.00298-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The major phospholipid constituents of Moraxella catarrhalis membranes are phosphatidylglycerol, phosphatidylethanolamine, and cardiolipin (CL). However, very little is known regarding the synthesis and function of these phospholipids in M. catarrhalis. In this study, we discovered that M. catarrhalis expresses a cardiolipin synthase (CLS), termed MclS, that is responsible for the synthesis of CL within the bacterium. The nucleotide sequence of mclS is highly conserved among M. catarrhalis isolates and is predicted to encode a protein with significant amino acid similarity to the recently characterized YmdC/ClsC protein of Escherichia coli. Isogenic mclS mutant strains were generated in M. catarrhalis isolates O35E, O12E, and McGHS1 and contained no observable levels of CL. Site-directed mutagenesis of a highly conserved HKD motif of MclS also resulted in a CL-deficient strain. Moraxella catarrhalis, which depends on adherence to epithelial cells for colonization of the human host, displays significantly reduced levels of adherence to HEp-2 and A549 cell lines in the mclS mutant strains compared to wild-type bacteria. The reduction in adherence appears to be attributed to the absence of CL. These findings mark the first instance in which a CLS has been related to a virulence-associated trait.
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28
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Eutsey RA, Hiller NL, Earl JP, Janto BA, Dahlgren ME, Ahmed A, Powell E, Schultz MP, Gilsdorf JR, Zhang L, Smith A, Murphy TF, Sethi S, Shen K, Post JC, Hu FZ, Ehrlich GD. Design and validation of a supragenome array for determination of the genomic content of Haemophilus influenzae isolates. BMC Genomics 2013; 14:484. [PMID: 23865594 PMCID: PMC3723446 DOI: 10.1186/1471-2164-14-484] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Accepted: 07/10/2013] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Haemophilus influenzae colonizes the human nasopharynx as a commensal, and is etiologically associated with numerous opportunistic infections of the airway; it is also less commonly associated with invasive disease. Clinical isolates of H. influenzae display extensive genomic diversity and plasticity. The development of strategies to successfully prevent, diagnose and treat H. influenzae infections depends on tools to ascertain the gene content of individual isolates. RESULTS We describe and validate a Haemophilus influenzae supragenome hybridization (SGH) array that can be used to characterize the full genic complement of any strain within the species, as well as strains from several highly related species. The array contains 31,307 probes that collectively cover essentially all alleles of the 2890 gene clusters identified from the whole genome sequencing of 24 clinical H. influenzae strains. The finite supragenome model predicts that these data include greater than 85% of all non-rare genes (where rare genes are defined as those present in less than 10% of sequenced strains). The veracity of the array was tested by comparing the whole genome sequences of eight strains with their hybridization data obtained using the supragenome array. The array predictions were correct and reproducible for ~ 98% of the gene content of all of the sequenced strains. This technology was then applied to an investigation of the gene content of 193 geographically and clinically diverse H. influenzae clinical strains. These strains came from multiple locations from five different continents and Papua New Guinea and include isolates from: the middle ears of persons with otitis media and otorrhea; lung aspirates and sputum samples from pneumonia and COPD patients, blood specimens from patients with sepsis; cerebrospinal fluid from patients with meningitis, as well as from pharyngeal specimens from healthy persons. CONCLUSIONS These analyses provided the most comprehensive and detailed genomic/phylogenetic look at this species to date, and identified a subset of highly divergent strains that form a separate lineage within the species. This array provides a cost-effective and high-throughput tool to determine the gene content of any H. influenzae isolate or lineage. Furthermore, the method for probe selection can be applied to any species, given a group of available whole genome sequences.
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Affiliation(s)
- Rory A Eutsey
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
| | - N Luisa Hiller
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Joshua P Earl
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
| | - Benjamin A Janto
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
| | - Margaret E Dahlgren
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
| | - Azad Ahmed
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
| | - Evan Powell
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
| | - Matthew P Schultz
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
| | - Janet R Gilsdorf
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MC, USA
- Department of Pediatrics and Communicable Diseases, University of Michigan School of Public Health, Ann Arbor, MC, USA
| | - Lixin Zhang
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor, MC, USA
| | - Arnold Smith
- Center for Childhood Infections, Seattle Children’s Hospital Research Institute, Seattle, WA, USA
| | - Timothy F Murphy
- Department of Medicine, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Sanjay Sethi
- Department of Medicine, University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Kai Shen
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
- Department of Otolaryngology Head and Neck Surgery, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
| | - J Christopher Post
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
- Department of Otolaryngology Head and Neck Surgery, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
| | - Fen Z Hu
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
- Department of Otolaryngology Head and Neck Surgery, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
| | - Garth D Ehrlich
- Center for Genomic Sciences, Allegheny Singer Research Institute, Allegheny General Hospital, 320 East North Avenue, 11th Floor, South Tower, Pittsburgh, PA 15212, USA
- Department of Microbiology and Immunology, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
- Department of Otolaryngology Head and Neck Surgery, Drexel University College of Medicine, Allegheny Campus, Pittsburgh, PA, USA
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Role of the zinc uptake ABC transporter of Moraxella catarrhalis in persistence in the respiratory tract. Infect Immun 2013; 81:3406-13. [PMID: 23817618 DOI: 10.1128/iai.00589-13] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Moraxella catarrhalis is a human respiratory tract pathogen that causes otitis media in children and lower respiratory tract infections in adults with chronic obstructive pulmonary disease. We have identified and characterized a zinc uptake ABC transporter that is present in all strains of M. catarrhalis tested. A mutant in which the znu gene cluster is knocked out shows markedly impaired growth compared to the wild type in medium that contains trace zinc; growth is restored to wild-type levels by supplementing medium with zinc but not with other divalent cations. Thermal-shift assays showed that the purified recombinant substrate binding protein ZnuA binds zinc but does not bind other divalent cations. Invasion assays with human respiratory epithelial cells demonstrated that the zinc ABC transporter of M. catarrhalis is critical for invasion of respiratory epithelial cells, an observation that is especially relevant because an intracellular reservoir of M. catarrhalis is present in the human respiratory tract and this reservoir is important for persistence. The znu knockout mutant showed marked impairment in its capacity to persist in the respiratory tract compared to the wild type in a mouse pulmonary clearance model. We conclude that the zinc uptake ABC transporter mediates uptake of zinc in environments with very low zinc concentrations and is critical for full virulence of M. catarrhalis in the respiratory tract in facilitating intracellular invasion of epithelial cells and persistence in the respiratory tract.
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Murphy TF, Chonmaitree T, Barenkamp S, Kyd J, Nokso-Koivisto J, Patel JA, Heikkinen T, Yamanaka N, Ogra P, Swords WE, Sih T, Pettigrew MM. Panel 5: Microbiology and immunology panel. Otolaryngol Head Neck Surg 2013; 148:E64-89. [PMID: 23536533 DOI: 10.1177/0194599812459636] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
OBJECTIVE The objective is to perform a comprehensive review of the literature from January 2007 through June 2011 on the virology, bacteriology, and immunology related to otitis media. DATA SOURCES PubMed database of the National Library of Medicine. REVIEW METHODS Three subpanels with co-chairs comprising experts in the virology, bacteriology, and immunology of otitis media were formed. Each of the panels reviewed the literature in their respective fields and wrote draft reviews. The reviews were shared with all panel members, and a second draft was created. The entire panel met at the 10th International Symposium on Recent Advances in Otitis Media in June 2011 and discussed the review and refined the content further. A final draft was created, circulated, and approved by the panel. CONCLUSION Excellent progress has been made in the past 4 years in advancing an understanding of the microbiology and immunology of otitis media. Advances include laboratory-based basic studies, cell-based assays, work in animal models, and clinical studies. IMPLICATIONS FOR PRACTICE The advances of the past 4 years formed the basis of a series of short-term and long-term research goals in an effort to guide the field. Accomplishing these goals will provide opportunities for the development of novel interventions, including new ways to better treat and prevent otitis media.
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Affiliation(s)
- Timothy F Murphy
- Clinical and Translational Research Center, University at Buffalo, State University of New York, Buffalo, New York 14203, USA.
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31
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Su YC, Hallström BM, Bernhard S, Singh B, Riesbeck K. Impact of sequence diversity in the Moraxella catarrhalis UspA2/UspA2H head domain on vitronectin binding and antigenic variation. Microbes Infect 2013; 15:375-87. [DOI: 10.1016/j.micinf.2013.02.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 01/15/2013] [Accepted: 02/11/2013] [Indexed: 12/31/2022]
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Genome sequence of Moraxella catarrhalis RH4, an isolate of seroresistant lineage. J Bacteriol 2013; 194:6969. [PMID: 23209224 DOI: 10.1128/jb.01833-12] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here we report the annotated genome sequence of Moraxella catarrhalis strain RH4, a seroresistant-lineage strain isolated from the blood of an infected patient. This genome sequence will allow us to gain further insight into the genetic diversity of clinical M. catarrhalis isolates and will facilitate study of M. catarrhalis pathogenesis.
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33
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Kunthalert D, Henghiranyawong K, Sistayanarain A, Khoothiam K. A single-step polymerase chain reaction for simultaneous detection and differentiation of nontypeable and serotypeable Haemophilus influenzae, Moraxella catarrhalis and Streptococcus pneumoniae. Int J Pediatr Otorhinolaryngol 2013; 77:275-80. [PMID: 23245490 DOI: 10.1016/j.ijporl.2012.11.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 11/19/2012] [Accepted: 11/20/2012] [Indexed: 10/27/2022]
Abstract
OBJECTIVE The critically high prevalence of bacterial otitis media worldwide has prompted a proper disease management. While vaccine development for otitis media is promising, the reliable and effective methods for diagnosis of such etiologic agents are of importance. METHODS We developed a multiplex polymerase chain reaction assay for simultaneous detection and differentiation of nontypeable and serotypeable Haemophilus influenzae, Moraxella catarrhalis and Streptococcus pneumoniae. Five primer pairs targeting genes fumarate reductase (H. influenzae), outer membrane protein B (M. catarrhalis), major autolysin (S. pneumoniae), capsulation-associated BexA protein (all encapsulated H. influenzae) and 16S rRNA were incorporated in this single-step PCR. Validation of the multiplex PCR was also performed on clinical isolates. RESULTS The developed multiplex PCR was highly specific, enabling the detection of the target pathogens in a specific manner, either individually or as a mixture of all target organisms. The assay was also found to be sensitive with the lowest detection limit of 1 ng of bacterial DNA. When applied to clinical isolates from diverse specimen sources, the multiplex PCR developed in this study correctly identified each microorganism individually or in a combination of two or more target organisms. All results matched with conventional culture identification. In addition, the ability of such assay to differentiate H. influenzae encapsulation from the study clinical isolates was 100%. CONCLUSION Our multiplex PCR provides a rapid and accurate diagnostic tool for detection of the 4 target organisms. Such assay would serve as a useful tool for clinicians and epidemiologists in their efforts to the proper treatment and disease management caused by these organisms.
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Affiliation(s)
- Duangkamol Kunthalert
- Department of Microbiology and Parasitology, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand.
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Su YC, Singh B, Riesbeck K. Moraxella catarrhalis: from interactions with the host immune system to vaccine development. Future Microbiol 2013; 7:1073-100. [PMID: 22953708 DOI: 10.2217/fmb.12.80] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Moraxella catarrhalis is a human-restricted commensal that over the last two decades has developed into an emerging respiratory tract pathogen. The bacterial species is equipped with various adhesins to facilitate its colonization. Successful evasion of the human immune system is a prerequisite for Moraxella infection. This strategy involves induction of an excessive proinflammatory response, intervention of granulocyte recruitment to the infection site, activation of selected pattern recognition receptors and cellular adhesion molecules to counteract the host bacteriolytic attack, as well as, finally, reprogramming of antigen presenting cells. Host immunomodulator molecules are also exploited by Moraxella to aid in resistance against complement killing and host bactericidal molecules. Thus, breaking the basis of Moraxella immune evasion mechanisms is fundamental for future invention of effective therapy in controlling Moraxella infection.
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Affiliation(s)
- Yu-Ching Su
- Medical Microbiology, Department of Laboratory Medicine Malmö, Lund University, Skåne University Hospital, Malmö, Sweden
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Evans AS, Pybus C, Hansen EJ. Development of a LacZ-based transcriptional reporter system for use with Moraxella catarrhalis. Plasmid 2012; 69:180-5. [PMID: 23219721 DOI: 10.1016/j.plasmid.2012.11.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 11/20/2012] [Indexed: 01/13/2023]
Abstract
The lack of a transcriptional reporter system for use in Moraxella catarrhalis has hindered studies of gene regulation in this pathogen. PCR and recombinant DNA methods were used to insert a multicloning site (MCS) and promoterless full-length Escherichia coli lacZ gene, flanked by transcriptional terminators both immediately upstream and downstream, into the M. catarrhalis recombinant plasmid pWW115. Insertion into the MCS in the newly constructed plasmid pASE222 of M. catarrhalis promoter regions controlled by either a repressor (i.e., NsrR) or activator (i.e., PhoB) yielded transcriptional fusion constructs that were appropriately responsive to signal inputs dependent on the host strain genotype, as measured quantitatively by means of a Miller β-galactosidase assay. The transcriptional reporter plasmid pASE222 should prove to be a useful tool for rapid screening of factors affecting gene expression in M. catarrhalis.
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Affiliation(s)
- Amanda S Evans
- Department of Pediatrics, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA.
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36
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de Vries SPW, Burghout P, Langereis JD, Zomer A, Hermans PWM, Bootsma HJ. Genetic requirements for Moraxella catarrhalis growth under iron-limiting conditions. Mol Microbiol 2012; 87:14-29. [PMID: 23163337 DOI: 10.1111/mmi.12081] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/20/2012] [Indexed: 11/26/2022]
Abstract
Iron sequestration by the human host is a first line defence against respiratory pathogens like Moraxella catarrhalis, which consequently experiences a period of iron starvation during colonization. We determined the genetic requirements for M. catarrhalis BBH18 growth during iron starvation using the high-throughput genome-wide screening technology genomic array footprinting (GAF). By subjecting a large random transposon mutant library to growth under iron-limiting conditions, mutants of the MCR_0996-rhlB-yggW operon, rnd, and MCR_0457 were negatively selected. Growth experiments using directed mutants confirmed the GAF phenotypes with ΔyggW (putative haem-shuttling protein) and ΔMCR_0457 (hypothetical protein) most severely attenuated during iron starvation, phenotypes which were restored upon genetic complementation of the deleted genes. Deletion of yggW resulted in similar attenuated phenotypes in three additional strains. Transcriptional profiles of ΔyggW and ΔMCR_0457 were highly altered with 393 and 192 differentially expressed genes respectively. In all five mutants, expression of nitrate reductase genes was increased and of nitrite reductase decreased, suggesting an impaired aerobic respiration. Alteration of iron metabolism may affect nasopharyngeal colonization as adherence of all mutants to respiratory tract epithelial cells was attenuated. In conclusion, we elucidated the genetic requirements for M. catarrhalis growth during iron starvation and characterized the roles of the identified genes in bacterial growth and host interaction.
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Affiliation(s)
- Stefan P W de Vries
- Laboratory of Pediatric Infectious Diseases, Radboud University Medical Centre, Nijmegen, the Netherlands
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37
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Broadbent JR, Neeno-Eckwall EC, Stahl B, Tandee K, Cai H, Morovic W, Horvath P, Heidenreich J, Perna NT, Barrangou R, Steele JL. Analysis of the Lactobacillus casei supragenome and its influence in species evolution and lifestyle adaptation. BMC Genomics 2012; 13:533. [PMID: 23035691 PMCID: PMC3496567 DOI: 10.1186/1471-2164-13-533] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Accepted: 09/27/2012] [Indexed: 12/26/2022] Open
Abstract
Background The broad ecological distribution of L. casei makes it an insightful subject for research on genome evolution and lifestyle adaptation. To explore evolutionary mechanisms that determine genomic diversity of L. casei, we performed comparative analysis of 17 L. casei genomes representing strains collected from dairy, plant, and human sources. Results Differences in L. casei genome inventory revealed an open pan-genome comprised of 1,715 core and 4,220 accessory genes. Extrapolation of pan-genome data indicates L. casei has a supragenome approximately 3.2 times larger than the average genome of individual strains. Evidence suggests horizontal gene transfer from other bacterial species, particularly lactobacilli, has been important in adaptation of L. casei to new habitats and lifestyles, but evolution of dairy niche specialists also appears to involve gene decay. Conclusions Genome diversity in L. casei has evolved through gene acquisition and decay. Acquisition of foreign genomic islands likely confers a fitness benefit in specific habitats, notably plant-associated niches. Loss of unnecessary ancestral traits in strains collected from bacterial-ripened cheeses supports the hypothesis that gene decay contributes to enhanced fitness in that niche. This study gives the first evidence for a L. casei supragenome and provides valuable insights into mechanisms for genome evolution and lifestyle adaptation of this ecologically flexible and industrially important lactic acid bacterium. Additionally, our data confirm the Distributed Genome Hypothesis extends to non-pathogenic, ecologically flexible species like L. casei.
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Affiliation(s)
- Jeff R Broadbent
- Department of Nutrition, Dietetics, and Food Sciences, Utah State University, 8700 Old Main Hill, Logan, UT 84322-8700, USA.
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Akochy PM, Lapointe J, Roy PH. Natural insertion of the bro-1 β-lactamase gene into the gatCAB operon affects Moraxella catarrhalis aspartyl-tRNAAsn amidotransferase activity. Microbiology (Reading) 2012; 158:2363-2371. [DOI: 10.1099/mic.0.060095-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Pierre-Marie Akochy
- Centre de Recherche en Infectiologie, CHUQ Pavillon CHUL, 2705 boul. Laurier, RC-709, QC G1V 4G2, Canada
- Institut Pasteur de Côte d’Ivoire, 01 BP 490 Abidjan, Côte d’Ivoire
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, QC G1V 0A6, Canada
| | - Jacques Lapointe
- Institut de biologie intégrative et des systèmes (IBIS), Pavillon Charles-Eugène-Marchand, G1V 0A6, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, QC G1V 0A6, Canada
| | - Paul H. Roy
- Centre de Recherche en Infectiologie, CHUQ Pavillon CHUL, 2705 boul. Laurier, RC-709, QC G1V 4G2, Canada
- Département de Biochimie, de Microbiologie et de Bio-informatique, Université Laval, QC G1V 0A6, Canada
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Swords WE. Quorum signaling and sensing by nontypeable Haemophilus influenzae. Front Cell Infect Microbiol 2012; 2:100. [PMID: 22919689 PMCID: PMC3417591 DOI: 10.3389/fcimb.2012.00100] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2012] [Accepted: 07/02/2012] [Indexed: 01/06/2023] Open
Abstract
Quorum signals are diffusible factors produced by bacteria that coordinate communal responses. For nontypeable Haemophilus influenzae (NTHi), a series of recent papers indicate that production and sensing of quorum signals are determinants of biofilm formation/maturation and persistence in vivo. In this mini-review I will summarize the current knowledge about quorum signaling/sensing by this organism, and identify specific topics for additional study.
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Affiliation(s)
- W Edward Swords
- Department of Microbiology and Immunology, Wake Forest University Health Sciences Winston-Salem, NC, USA.
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Comparative genomic analyses of 17 clinical isolates of Gardnerella vaginalis provide evidence of multiple genetically isolated clades consistent with subspeciation into genovars. J Bacteriol 2012; 194:3922-37. [PMID: 22609915 DOI: 10.1128/jb.00056-12] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Gardnerella vaginalis is associated with a spectrum of clinical conditions, suggesting high degrees of genetic heterogeneity among stains. Seventeen G. vaginalis isolates were subjected to a battery of comparative genomic analyses to determine their level of relatedness. For each measure, the degree of difference among the G. vaginalis strains was the highest observed among 23 pathogenic bacterial species for which at least eight genomes are available. Genome sizes ranged from 1.491 to 1.716 Mb; GC contents ranged from 41.18% to 43.40%; and the core genome, consisting of only 746 genes, makes up only 51.6% of each strain's genome on average and accounts for only 27% of the species supragenome. Neighbor-grouping analyses, using both distributed gene possession data and core gene allelic data, each identified two major sets of strains, each of which is composed of two groups. Each of the four groups has its own characteristic genome size, GC ratio, and greatly expanded core gene content, making the genomic diversity of each group within the range for other bacterial species. To test whether these 4 groups corresponded to genetically isolated clades, we inferred the phylogeny of each distributed gene that was present in at least two strains and absent in at least two strains; this analysis identified frequent homologous recombination within groups but not between groups or sets. G. vaginalis appears to include four nonrecombining groups/clades of organisms with distinct gene pools and genomic properties, which may confer distinct ecological properties. Consequently, it may be appropriate to treat these four groups as separate species.
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Liu Y, Zhao C, Zhang F, Chen H, Chen M, Wang H. High prevalence and molecular analysis of macrolide-nonsusceptible Moraxella catarrhalis isolated from nasopharynx of healthy children in China. Microb Drug Resist 2012; 18:417-26. [PMID: 22394083 DOI: 10.1089/mdr.2011.0175] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Three hundred eighty-three isolates of Moraxella catarrhalis were collected from healthy children aged less than 2 years in China and assessed for antimicrobial resistance. We found that 92.2% (n=353) produced a β-lactamase. Nonsusceptibility rates to erythromycin and azithromycin, determined using Clinical Laboratory Standards Institute (CLSI) breakpoints, were 40.3% and 22.5%, respectively; nonsusceptibility rates determined using pharmacokinetics/pharmacodynamics breakpoints, however, were 59% and 60.1%. The minimal inhibitory concentration (MIC)(90) values were >256 μg/ml. Nonsusceptibility rates varied by region from 9.7% in Dongguan to 75.9% in Jinan. Further, concomitant resistance to β-lactam antibiotics was also observed. Pulsed-field gel electrophoresis analysis of 27/37 high-level macrolide-resistant M. catarrhalis isolates showed that closely related pulsotypes dominated, with a total of 11 different pulsotypes being observed. The closely related pulsotypes were observed in isolates originating from all six Chinese cities investigated, possibly as a consequence of the mobility of the Chinese population. Sixteen patterns of 23S rRNA mutations were found among 97 selected isolates using polymerase chain reaction and sequencing, but no known ermA, ermB, mefA, or mefE genes could be detected. Mutations A2982T and A2796T in 23S rRNA were related to high-level macrolide resistance (MICs ranging from 24 to >256 μg/ml), while an A2983T mutation was associated with low-level macrolide resistance (MICs ranging from 0.19 to 16 μg/ml).
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Affiliation(s)
- Yali Liu
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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Use of the chinchilla model for nasopharyngeal colonization to study gene expression by Moraxella catarrhalis. Infect Immun 2011; 80:982-95. [PMID: 22184412 DOI: 10.1128/iai.05918-11] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Young adult chinchillas were atraumatically inoculated with Moraxella catarrhalis via the nasal route. Detailed histopathologic examination of nasopharyngeal tissues isolated from these M. catarrhalis-infected animals revealed the presence of significant inflammation within the epithelium. Absence of similar histopathologic findings in sham-inoculated animals confirmed that M. catarrhalis was exposed to significant host-derived factors in this environment. Twenty-four hours after inoculation, viable M. catarrhalis organisms were recovered from the nasal cavity and nasopharynx of the animals in numbers sufficient for DNA microarray analysis. More than 100 M. catarrhalis genes were upregulated in vivo, including open reading frames (ORFs) encoding proteins that are involved in a truncated denitrification pathway or in the oxidative stress response, as well as several putative transcriptional regulators. Additionally, 200 M. catarrhalis genes were found to be downregulated when this bacterium was introduced into the nasopharynx. These downregulated genes included ORFs encoding several well-characterized M. catarrhalis surface proteins including Hag, McaP, and MchA1. Real-time reverse transcriptase PCR (RT-PCR) was utilized as a stringent control to validate the results of in vivo gene expression patterns as measured by DNA microarray analysis. Inactivation of one of the genes (MC ORF 1550) that was upregulated in vivo resulted in a decrease in the ability of M. catarrhalis to survive in the chinchilla nasopharynx over a 3-day period. This is the first evaluation of global transcriptome expression by M. catarrhalis cells in vivo.
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Hays J. Mobile genetic elements in Moraxella catarrhalis. Mob Genet Elements 2011; 1:155-158. [PMID: 22016866 DOI: 10.4161/mge.1.2.17632] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 08/04/2011] [Accepted: 08/04/2011] [Indexed: 12/26/2022] Open
Abstract
Moraxella catarrhalis is a Gram-negative diplococcus that is a strict human pathogen, which for a long period of time was regarded as a simple commensal. Research now shows that this organism is a pathogen its own right and is associated with both upper and lower respiratory tract infections. Further, there appears to be a dichotomy in the pathogenic potential of M. catarrhalis with upper respiratory tract infections mainly occurring in children, and lower respiratory tract infections mainly occurring in adults with predisposing pulmonary complications e.g., chronic obstructive pulmonary disease (COPD).
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Affiliation(s)
- John Hays
- Deptartment of Medical Microbiology and Infectious Disease; Erasmus MC; Rotterdam, The Netherlands
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Toward an efficient method of identifying core genes for evolutionary and functional microbial phylogenies. PLoS One 2011; 6:e24704. [PMID: 21931822 PMCID: PMC3171473 DOI: 10.1371/journal.pone.0024704] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Accepted: 08/16/2011] [Indexed: 02/04/2023] Open
Abstract
Microbial community metagenomes and individual microbial genomes are becoming increasingly accessible by means of high-throughput sequencing. Assessing organismal membership within a community is typically performed using one or a few taxonomic marker genes such as the 16S rDNA, and these same genes are also employed to reconstruct molecular phylogenies. There is thus a growing need to bioinformatically catalog strongly conserved core genes that can serve as effective taxonomic markers, to assess the agreement among phylogenies generated from different core gene, and to characterize the biological functions enriched within core genes and thus conserved throughout large microbial clades. We present a method to recursively identify core genes (i.e. genes ubiquitous within a microbial clade) in high-throughput from a large number of complete input genomes. We analyzed over 1,100 genomes to produce core gene sets spanning 2,861 bacterial and archaeal clades, ranging in size from one to >2,000 genes in inverse correlation with the α-diversity (total phylogenetic branch length) spanned by each clade. These cores are enriched as expected for housekeeping functions including translation, transcription, and replication, in addition to significant representations of regulatory, chaperone, and conserved uncharacterized proteins. In agreement with previous manually curated core gene sets, phylogenies constructed from one or more of these core genes agree with those built using 16S rDNA sequence similarity, suggesting that systematic core gene selection can be used to optimize both comparative genomics and determination of microbial community structure. Finally, we examine functional phylogenies constructed by clustering genomes by the presence or absence of orthologous gene families and show that they provide an informative complement to standard sequence-based molecular phylogenies.
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Abstract
During most of recorded history, the application of knowledge to the care of individual patients was founded on the experience of individual medical practitioners; when published, it basically took the form of case reports. Not until the middle of the 20th Century did randomized controlled trials (RCTs) come to be the gold standard. By the beginning of the 21st Century, however, the limitations of RCTs and their syntheses, the meta-analyses, have come to be recognized, and their applicability to the individual patient questioned and, indeed, challenged. The intense increase in our knowledge base and in accompanying technology has made possible the personalization of medicine beyond the possibilities of earlier periods. The approach of personalized medicine requires evaluation of four parameters: the individual patient’s intrinsic susceptibility, intrinsic morbidity, extrinsic susceptibility, and extrinsic morbidity. The characteristics of the disease agent—how much (duration) and how virulent—also must be factored in. These individualized data define the appropriate intervention: high susceptibility and/or morbidity or low susceptibility and/or morbidity and the aggregate of the intrinsic and extrinsic risk factors are cofactored in medical decision making.
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Affiliation(s)
- Robert J. Ruben
- Departments of Otorhinolaryngology–Head and Neck Surgery and Pediatrics, Albert Einstein College of Medicine, Montefiore Medical Center, Bronx, New York, USA
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