1
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Chou RT, Ouattara A, Adams M, Berry AA, Takala-Harrison S, Cummings MP. Positive-unlabeled learning identifies vaccine candidate antigens in the malaria parasite Plasmodium falciparum. NPJ Syst Biol Appl 2024; 10:44. [PMID: 38678051 PMCID: PMC11055854 DOI: 10.1038/s41540-024-00365-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 03/29/2024] [Indexed: 04/29/2024] Open
Abstract
Malaria vaccine development is hampered by extensive antigenic variation and complex life stages of Plasmodium species. Vaccine development has focused on a small number of antigens, many of which were identified without utilizing systematic genome-level approaches. In this study, we implement a machine learning-based reverse vaccinology approach to predict potential new malaria vaccine candidate antigens. We assemble and analyze P. falciparum proteomic, structural, functional, immunological, genomic, and transcriptomic data, and use positive-unlabeled learning to predict potential antigens based on the properties of known antigens and remaining proteins. We prioritize candidate antigens based on model performance on reference antigens with different genetic diversity and quantify the protein properties that contribute most to identifying top candidates. Candidate antigens are characterized by gene essentiality, gene ontology, and gene expression in different life stages to inform future vaccine development. This approach provides a framework for identifying and prioritizing candidate vaccine antigens for a broad range of pathogens.
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Affiliation(s)
- Renee Ti Chou
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA
| | - Amed Ouattara
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Matthew Adams
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Andrea A Berry
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Shannon Takala-Harrison
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA.
| | - Michael P Cummings
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, College Park, MD, USA.
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2
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Podda M, Bonechi S, Palladino A, Scaramuzzino M, Brozzi A, Roma G, Muzzi A, Priami C, Sîrbu A, Bodini M. Classification of Neisseria meningitidis genomes with a bag-of-words approach and machine learning. iScience 2024; 27:109257. [PMID: 38439962 PMCID: PMC10910294 DOI: 10.1016/j.isci.2024.109257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/13/2023] [Accepted: 02/13/2024] [Indexed: 03/06/2024] Open
Abstract
Whole genome sequencing of bacteria is important to enable strain classification. Using entire genomes as an input to machine learning (ML) models would allow rapid classification of strains while using information from multiple genetic elements. We developed a "bag-of-words" approach to encode, using SentencePiece or k-mer tokenization, entire bacterial genomes and analyze these with ML. Initial model selection identified SentencePiece with 8,000 and 32,000 words as the best approach for genome tokenization. We then classified in Neisseria meningitidis genomes the capsule B group genotype with 99.6% accuracy and the multifactor invasive phenotype with 90.2% accuracy, in an independent test set. Subsequently, in silico knockouts of 2,808 genes confirmed that the ML model predictions aligned with our current understanding of the underlying biology. To our knowledge, this is the first ML method using entire bacterial genomes to classify strains and identify genes considered relevant by the classifier.
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Affiliation(s)
- Marco Podda
- Vaccines Discovery Data Sciences, GSK Vaccines, GSK, 53100 Siena, Italy
| | - Simone Bonechi
- Vaccines Discovery Data Sciences, GSK Vaccines, GSK, 53100 Siena, Italy
- Department of Computer Science, University of Pisa, 56127 Pisa, Italy
| | - Andrea Palladino
- Vaccines Discovery Data Sciences, GSK Vaccines, GSK, 53100 Siena, Italy
| | | | - Alessandro Brozzi
- Vaccines Discovery Data Sciences, GSK Vaccines, GSK, 53100 Siena, Italy
| | - Guglielmo Roma
- Vaccines Discovery Data Sciences, GSK Vaccines, GSK, 53100 Siena, Italy
| | - Alessandro Muzzi
- Vaccines Discovery Data Sciences, GSK Vaccines, GSK, 53100 Siena, Italy
| | - Corrado Priami
- Department of Computer Science, University of Pisa, 56127 Pisa, Italy
| | - Alina Sîrbu
- Department of Computer Science, University of Pisa, 56127 Pisa, Italy
| | - Margherita Bodini
- Vaccines Discovery Data Sciences, GSK Vaccines, GSK, 53100 Siena, Italy
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3
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Nguyen PNT, Thai PQ, Dien TM, Hai DT, Dai VTT, Luan NH, Mathur G, Badur S, Truyen DM, Le Minh NH. 4CMenB Vaccination to Prevent Meningococcal B Disease in Vietnam: Expert Review and Opinion. Infect Dis Ther 2024; 13:423-437. [PMID: 38430327 DOI: 10.1007/s40121-023-00905-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 12/13/2023] [Indexed: 03/03/2024] Open
Abstract
An advisory board meeting was held with experts in Vietnam (Hanoi, August 2022), to review the evidence on invasive meningococcal disease (IMD) epidemiology, clinical management, and meningococcal vaccines to reach a consensus on recommendations for meningococcal vaccination in Vietnam. IMD is a severe disease, with the highest burden in infants and children. IMD presents as meningitis and/or meningococcemia and can progress extremely rapidly. Almost 90% of deaths in children occur within the first 24 h, and disabling sequelae (e.g., limb amputations and neurological damage) occur in up to 20% of survivors. IMD patients are often hospitalized late, due to mild and nonspecific early symptoms and misdiagnosis. Difficulties related to diagnosis and antibiotic misuse mean that the number of reported IMD cases in Vietnam is likely to be underestimated. Serogroup B IMD is predominant in many regions of the world, including Vietnam, where 82% of IMD cases were due to serogroup B (surveillance data from 2012 to 2021). Four component meningococcal B vaccine (4CMenB) is used in many countries (and is part of the pediatric National Immunization Program in 13 countries), with infant vaccination starting from two months of age, and a 2 + 1 dosing schedule. Experts recommend 4CMenB vaccination as soon as possible in Vietnam, starting from two months of age, with a 2 + 1 dosing schedule, and at least completing one dose before 6 months of age.
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Affiliation(s)
- Phung Nguyen The Nguyen
- Pediatrics Department, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Pham Quang Thai
- Communicable Diseases Control and Prevention Department, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | - Do Thien Hai
- Center for Tropical Diseases, National Pediatric Hospital, Hanoi, Vietnam
| | - Vo Thi Trang Dai
- Respiratory Microbiology Bacteria Laboratory, Department of Immunology and Microbiology, the Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Nguyen Huy Luan
- Immunization Unit of University of Medicine and Pharmacy Hospital, Pediatrics Department, University of Medicine and Pharmacy at Ho Chi Minh City, Ho Chi Minh City, Vietnam
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4
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Montero DA, Vidal RM, Velasco J, Carreño LJ, Torres JP, Benachi O. MA, Tovar-Rosero YY, Oñate AA, O'Ryan M. Two centuries of vaccination: historical and conceptual approach and future perspectives. Front Public Health 2024; 11:1326154. [PMID: 38264254 PMCID: PMC10803505 DOI: 10.3389/fpubh.2023.1326154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 12/13/2023] [Indexed: 01/25/2024] Open
Abstract
Over the past two centuries, vaccines have been critical for the prevention of infectious diseases and are considered milestones in the medical and public health history. The World Health Organization estimates that vaccination currently prevents approximately 3.5-5 million deaths annually, attributed to diseases such as diphtheria, tetanus, pertussis, influenza, and measles. Vaccination has been instrumental in eradicating important pathogens, including the smallpox virus and wild poliovirus types 2 and 3. This narrative review offers a detailed journey through the history and advancements in vaccinology, tailored for healthcare workers. It traces pivotal milestones, beginning with the variolation practices in the early 17th century, the development of the first smallpox vaccine, and the continuous evolution and innovation in vaccine development up to the present day. We also briefly review immunological principles underlying vaccination, as well as the main vaccine types, with a special mention of the recently introduced mRNA vaccine technology. Additionally, we discuss the broad benefits of vaccines, including their role in reducing morbidity and mortality, and in fostering socioeconomic development in communities. Finally, we address the issue of vaccine hesitancy and discuss effective strategies to promote vaccine acceptance. Research, collaboration, and the widespread acceptance and use of vaccines are imperative for the continued success of vaccination programs in controlling and ultimately eradicating infectious diseases.
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Affiliation(s)
- David A. Montero
- Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
- Centro Integrativo de Biología y Química Aplicada, Universidad Bernardo O'Higgins, Santiago, Chile
| | - Roberto M. Vidal
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Instituto Milenio de Inmunología e Inmunoterapia, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Juliana Velasco
- Unidad de Paciente Crítico, Clínica Hospital del Profesor, Santiago, Chile
- Programa de Formación de Especialista en Medicina de Urgencia, Universidad Andrés Bello, Santiago, Chile
| | - Leandro J. Carreño
- Instituto Milenio de Inmunología e Inmunoterapia, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Programa de Inmunología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Juan P. Torres
- Departamento de Pediatría y Cirugía Pediátrica, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Manuel A. Benachi O.
- Área de Biotecnología, Tecnoacademia Neiva, Servicio Nacional de Aprendizaje, Regional Huila, Neiva, Colombia
| | - Yenifer-Yadira Tovar-Rosero
- Departamento de Biología, Facultad de Ciencias Naturales, Exactas y de la Educación, Universidad del Cauca, Popayán, Colombia
| | - Angel A. Oñate
- Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Miguel O'Ryan
- Programa de Microbiología y Micología, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
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5
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Takahashi H, Morita M, Yasuda M, Ohama Y, Kobori Y, Kojima M, Shimuta K, Akeda Y, Ohnishi M. Detection of Novel US Neisseria meningitidis Urethritis Clade Subtypes in Japan. Emerg Infect Dis 2023; 29:2210-2217. [PMID: 37877502 PMCID: PMC10617353 DOI: 10.3201/eid2911.231082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023] Open
Abstract
Neisseria meningitidis causes invasive meningococcal diseases and has also been identified as a causative agent of sexually transmitted infections, including urethritis. Unencapsulated sequence type 11 meningococci containing the gonococcal aniA-norB locus and belonging to the United States N. meningitidis urethritis clade (US_NmUC) are causative agents of urethral infections in the United States, predominantly among men who have sex with men. We identified 2 subtypes of unencapsulated sequence type 11 meningococci in Japan that were phylogenetically close to US_NmUC, designated as the Japan N. meningitidis urethritis clade (J_NmUC). The subtypes were characterized by PCR, serologic testing, and whole-genome sequencing. Our study suggests that an ancestor of US_NmUC and J_NmUS urethritis-associated meningococci is disseminated worldwide. Global monitoring of urethritis-associated N. meningitidis isolates should be performed to further characterize microbiologic and epidemiologic characteristics of urethritis clade meningococci.
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6
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Fohmann I, Weinmann A, Schumacher F, Peters S, Prell A, Weigel C, Spiegel S, Kleuser B, Schubert-Unkmeir A. Sphingosine kinase 1/S1P receptor signaling axis is essential for cellular uptake of Neisseria meningitidis in brain endothelial cells. PLoS Pathog 2023; 19:e1011842. [PMID: 38033162 PMCID: PMC10715668 DOI: 10.1371/journal.ppat.1011842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Revised: 12/12/2023] [Accepted: 11/18/2023] [Indexed: 12/02/2023] Open
Abstract
Invasion of brain endothelial cells (BECs) is central to the pathogenicity of Neisseria meningitidis infection. Here, we established a key role for the bioactive sphingolipid sphingosine-1-phosphate (S1P) and S1P receptor (S1PR) 2 in the uptake process. Quantitative sphingolipidome analyses of BECs infected with N. meningitidis revealed elevated S1P levels, which could be attributed to enhanced expression of the enzyme sphingosine kinase 1 and its activity. Increased activity was dependent on the interaction of meningococcal type IV pilus with the endothelial receptor CD147. Concurrently, infection led to increased expression of the S1PR2. Blocking S1PR2 signaling impaired epidermal growth factor receptor (EGFR) phosphorylation, which has been shown to be involved in cytoskeletal remodeling and bacterial endocytosis. Strikingly, targeting S1PR1 or S1PR3 also interfered with bacterial uptake. Collectively, our data support a critical role of the SphK/S1P/S1PR axis in the invasion of N. meningitidis into BECs, defining a potential target for adjuvant therapy.
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Affiliation(s)
- Ingo Fohmann
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Alina Weinmann
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Fabian Schumacher
- Institute of Pharmacy, Pharmacology and Toxicology, Freie Universität Berlin, Berlin, Germany
| | - Simon Peters
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Agata Prell
- Institute of Pharmacy, Pharmacology and Toxicology, Freie Universität Berlin, Berlin, Germany
| | - Cynthia Weigel
- Department of Biochemistry and Molecular Biology and the Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, United States of America
| | - Sarah Spiegel
- Department of Biochemistry and Molecular Biology and the Massey Cancer Center, Virginia Commonwealth University School of Medicine, Richmond, Virginia, United States of America
| | - Burkhard Kleuser
- Institute of Pharmacy, Pharmacology and Toxicology, Freie Universität Berlin, Berlin, Germany
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7
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Koff WC, Rappuoli R, Plotkin SA. Historical advances in structural and molecular biology and how they impacted vaccine development. J Mol Biol 2023; 435:168113. [PMID: 37080423 DOI: 10.1016/j.jmb.2023.168113] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/11/2023] [Accepted: 04/11/2023] [Indexed: 04/22/2023]
Abstract
Vaccines are among the greatest tools for prevention and control of disease. They have eliminated smallpox from the planet, decreased morbidity and mortality for major infectious diseases like polio, measles, mumps, and rubella, significantly blunted the impact of the COVID-19 pandemic, and prevented viral induced cancers such as cervical cancer caused by human papillomavirus. Recent technological advances, in genomics, structural biology, and human immunology have transformed vaccine development, enabling new technologies such as mRNA vaccines to greatly accelerate development of new and improved vaccines. In this review, we briefly highlight the history of vaccine development, and provide examples of where advances in genomics and structural biology, paved the way for development of vaccines for bacterial and viral diseases.
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Affiliation(s)
- Wayne C Koff
- President and CEO, Human Immunome Project, New York, NY, USA
| | - Rino Rappuoli
- Chief Scientific Officer, Fondazione Biotechnopolo, Siena, Italy
| | - Stanley A Plotkin
- Emeritus Professor of Pediatrics, University of Pennsylvania and Children's Hospital of Philadelphia, Philadelphia, PA, USA
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8
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Naidu A, Nayak SS, Lulu S S, Sundararajan V. Advances in computational frameworks in the fight against TB: The way forward. Front Pharmacol 2023; 14:1152915. [PMID: 37077815 PMCID: PMC10106641 DOI: 10.3389/fphar.2023.1152915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 03/20/2023] [Indexed: 04/05/2023] Open
Abstract
Around 1.6 million people lost their life to Tuberculosis in 2021 according to WHO estimates. Although an intensive treatment plan exists against the causal agent, Mycobacterium Tuberculosis, evolution of multi-drug resistant strains of the pathogen puts a large number of global populations at risk. Vaccine which can induce long-term protection is still in the making with many candidates currently in different phases of clinical trials. The COVID-19 pandemic has further aggravated the adversities by affecting early TB diagnosis and treatment. Yet, WHO remains adamant on its "End TB" strategy and aims to substantially reduce TB incidence and deaths by the year 2035. Such an ambitious goal would require a multi-sectoral approach which would greatly benefit from the latest computational advancements. To highlight the progress of these tools against TB, through this review, we summarize recent studies which have used advanced computational tools and algorithms for-early TB diagnosis, anti-mycobacterium drug discovery and in the designing of the next-generation of TB vaccines. At the end, we give an insight on other computational tools and Machine Learning approaches which have successfully been applied in biomedical research and discuss their prospects and applications against TB.
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Affiliation(s)
| | | | | | - Vino Sundararajan
- Department of Biotechnology, School of Bio Sciences and Technology, VIT University, Vellore, India
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9
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Man-Bovenkerk S, Schipper K, van Sorge NM, Speijer D, van der Ende A, Pannekoek Y. Neisseria meningitidis Sibling Small Regulatory RNAs Connect Metabolism with Colonization by Controlling Propionate Use. J Bacteriol 2023; 205:e0046222. [PMID: 36856428 PMCID: PMC10029713 DOI: 10.1128/jb.00462-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/09/2023] [Indexed: 03/02/2023] Open
Abstract
Neisseria meningitidis (meningococcus) colonizes the human nasopharynx, primarily as a commensal, but sporadically causing septicemia and meningitis. During colonization and invasion, it encounters different niches with specific nutrient compositions. Small noncoding RNAs (sRNAs) are used to fine-tune expression of genes, allowing adaptation to their physiological differences. We have previously characterized sRNAs (Neisseria metabolic switch regulators [NmsRs]) controlling switches between cataplerotic and anaplerotic metabolism. Here, we extend the NmsR regulon by studying methylcitrate lyase (PrpF) and propionate kinase (AckA-1) involved in the methylcitrate cycle and serine hydroxymethyltransferase (GlyA) and 3-hydroxyacid dehydrogenase (MmsB) involved in protein degradation. These proteins were previously shown to be dysregulated in a ΔnmsRs strain. Levels of transcription of target genes and NmsRs were assessed by reverse transcriptase quantitative PCR (RT-qPCR). We also used a novel gene reporter system in which the 5' untranslated region (5' UTR) of the target gene is fused to mcherry to study NmsRs-target gene interaction in the meningococcus. Under nutrient-rich conditions, NmsRs downregulate expression of PrpF and AckA-1 by direct interaction with the 5' UTR of their mRNA. Overexpression of NmsRs impaired growth under nutrient-limiting growth conditions with pyruvate and propionic acid as the only carbon sources. Our data strongly suggest that NmsRs downregulate propionate metabolism by lowering methylcitrate enzyme activity under nutrient-rich conditions. Under nutrient-poor conditions, NmsRs are downregulated, increasing propionate metabolism, resulting in higher tricarboxylic acid (TCA) activities. IMPORTANCE Neisseria meningitidis colonizes the human nasopharynx, forming a reservoir for the sporadic occurrence of epidemic invasive meningococcal disease like septicemia and meningitis. Propionic acid generated by other bacteria that coinhabit the human nasopharynx can be utilized by meningococci for replication in this environment. Here, we showed that sibling small RNAs, designated NmsRs, riboregulate propionic acid utilization by meningococci and, thus, colonization. Under conditions mimicking the nasopharyngeal environment, NmsRs are downregulated. This leads to the conversion of propionic acid to pyruvate and succinate, resulting in higher tricarboxylic acid cycle activity, allowing colonization of the nasopharynx. NmsRs link metabolic state with colonization, which is a crucial step on the trajectory to invasive meningococcal disease.
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Affiliation(s)
- Sandra Man-Bovenkerk
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Kim Schipper
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Nina M. van Sorge
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
- Amsterdam UMC, Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam, The Netherlands
| | - Dave Speijer
- Department of Medical Biochemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Arie van der Ende
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
| | - Yvonne Pannekoek
- Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Institute for Infection and Immunity, Infectious Diseases, Amsterdam, The Netherlands
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10
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Khan MA, Amin A, Farid A, Ullah A, Waris A, Shinwari K, Hussain Y, Alsharif KF, Alzahrani KJ, Khan H. Recent Advances in Genomics-Based Approaches for the Development of Intracellular Bacterial Pathogen Vaccines. Pharmaceutics 2022; 15:pharmaceutics15010152. [PMID: 36678781 PMCID: PMC9863128 DOI: 10.3390/pharmaceutics15010152] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 12/12/2022] [Accepted: 12/19/2022] [Indexed: 01/04/2023] Open
Abstract
Infectious diseases continue to be a leading cause of morbidity and mortality worldwide. The majority of infectious diseases are caused by intracellular pathogenic bacteria (IPB). Historically, conventional vaccination drives have helped control the pathogenesis of intracellular bacteria and the emergence of antimicrobial resistance, saving millions of lives. However, in light of various limitations, many diseases that involve IPB still do not have adequate vaccines. In response to increasing demand for novel vaccine development strategies, a new area of vaccine research emerged following the advent of genomics technology, which changed the paradigm of vaccine development by utilizing the complete genomic data of microorganisms against them. It became possible to identify genes related to disease virulence, genetic patterns linked to disease virulence, as well as the genetic components that supported immunity and favorable vaccine responses. Complete genomic databases, and advancements in transcriptomics, metabolomics, structural genomics, proteomics, immunomics, pan-genomics, synthetic genomics, and population biology have allowed researchers to identify potential vaccine candidates and predict their effects in patients. New vaccines have been created against diseases for which previously there were no vaccines available, and existing vaccines have been improved. This review highlights the key issues and explores the evolution of vaccines. The increasing volume of IPB genomic data, and their application in novel genome-based techniques for vaccine development, were also examined, along with their characteristics, and the opportunities and obstacles involved. Critically, the application of genomics technology has helped researchers rapidly select and evaluate candidate antigens. Novel vaccines capable of addressing the limitations associated with conventional vaccines have been developed and pressing healthcare issues are being addressed.
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Affiliation(s)
- Muhammad Ajmal Khan
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
- Correspondence: (M.A.K.); or (H.K.)
| | - Aftab Amin
- Division of Life Science, Center for Cancer Research, and State Key Lab of Molecular Neuroscience, Hong Kong University of Science and Technology, Hong Kong, China
| | - Awais Farid
- Division of Environment and Sustainability, Hong Kong University of Science and Technology, Hong Kong, China
| | - Amin Ullah
- Molecular Virology Laboratory, Department of Microbiology and Biotechnology, Abasyn University, Peshawar 25000, Pakistan
| | - Abdul Waris
- Department of Biomedical Sciences, City University of Hong Kong, Hong Kong, China
| | - Khyber Shinwari
- Institute of Chemical Engineering, Department Immuno-Chemistry, Ural Federal University, Yekaterinbiurg 620002, Russia
| | - Yaseen Hussain
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan 23200, Pakistan
| | - Khalaf F. Alsharif
- Department of Clinical Laboratory, College of Applied Medical Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Khalid J. Alzahrani
- Department of Clinical Laboratory, College of Applied Medical Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
| | - Haroon Khan
- Department of Clinical Laboratory, College of Applied Medical Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
- Correspondence: (M.A.K.); or (H.K.)
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11
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Pathogenic Neisseria Bind the Complement Protein CFHR5 via Outer Membrane Porins. Infect Immun 2022; 90:e0037722. [PMID: 36194022 PMCID: PMC9584296 DOI: 10.1128/iai.00377-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Neisseria meningitidis and Neisseria gonorrhoeae are important human pathogens that have evolved to bind the major negative regulator of the complement system, complement factor H (CFH). However, little is known about the interaction of pathogens with CFH-related proteins (CFHRs) which are structurally similar to CFH but lack the main complement regulatory domains found in CFH. Insights into the role of CFHRs have been hampered by a lack of specific reagents. We generated a panel of CFHR-specific monoclonal antibodies and demonstrated that CFHR5 was bound by both pathogenic Neisseria spp. We showed that CFHR5 bound to PorB expressed by both pathogens in the presence of sialylated lipopolysaccharide and enhanced complement activation on the surface of N. gonorrhoeae. Our study furthered our understanding of the interactions of CFHRs with bacterial pathogens and revealed that CFHR5 bound the meningococcus and gonococcus via similar mechanisms.
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12
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Talà A, Guerra F, Calcagnile M, Romano R, Resta SC, Paiano A, Chiariello M, Pizzolante G, Bucci C, Alifano P. HrpA anchors meningococci to the dynein motor and affects the balance between apoptosis and pyroptosis. J Biomed Sci 2022; 29:45. [PMID: 35765029 PMCID: PMC9241232 DOI: 10.1186/s12929-022-00829-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 06/22/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In Neisseria meningitidis the HrpA/HrpB two-partner secretion system (TPS) was implicated in diverse functions including meningococcal competition, biofilm formation, adherence to epithelial cells, intracellular survival and vacuolar escape. These diverse functions could be attributed to distinct domains of secreted HrpA. METHODS A yeast two-hybrid screening, in vitro pull-down assay and immunofluorescence microscopy experiments were used to investigate the interaction between HrpA and the dynein light-chain, Tctex-type 1 (DYNLT1). In silico modeling was used to analyze HrpA structure. Western blot analysis was used to investigate apoptotic and pyroptotic markers. RESULTS The HrpA carboxy-terminal region acts as a manganese-dependent cell lysin, while the results of a yeast two-hybrid screening demonstrated that the HrpA middle region has the ability to bind the dynein light-chain, Tctex-type 1 (DYNLT1). This interaction was confirmed by in vitro pull-down assay and immunofluorescence microscopy experiments showing co-localization of N. meningitidis with DYNLT1 in infected epithelial cells. In silico modeling revealed that the HrpA-M interface interacting with the DYNLT1 has similarity with capsid proteins of neurotropic viruses that interact with the DYNLT1. Indeed, we found that HrpA plays a key role in infection of and meningococcal trafficking within neuronal cells, and is implicated in the modulation of the balance between apoptosis and pyroptosis. CONCLUSIONS Our findings revealed that N. meningitidis is able to effectively infect and survive in neuronal cells, and that this ability is dependent on HrpA, which establishes a direct protein-protein interaction with DYNLTI in these cells, suggesting that the HrpA interaction with dynein could be fundamental for N. meningitidis spreading inside the neurons. Moreover, we found that the balance between apoptotic and pyroptotic pathways is heavily affected by HrpA.
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Affiliation(s)
- Adelfia Talà
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy
| | - Flora Guerra
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy
| | - Matteo Calcagnile
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy
| | - Roberta Romano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy
| | - Silvia Caterina Resta
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy
| | - Aurora Paiano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy
| | - Mario Chiariello
- Core Research Laboratory-Siena, Institute for Cancer Research and Prevention (ISPRO), 53100, Siena, Italy.,Institute of Clinical Physiology (IFC), National Research Council (CNR), 53100, Siena, Italy
| | - Graziano Pizzolante
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy
| | - Cecilia Bucci
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy.
| | - Pietro Alifano
- Department of Biological and Environmental Sciences and Technologies (DiSTeBA), University of Salento, Via Provinciale Monteroni n. 165, 73100, Lecce, Italy.
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13
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Shao Y, Chen M, Luo J, Li D, Yuan L, Yang X, Wang M, Chen M, Guo Q. Serogroup Y Clonal Complex 23 Meningococcus in China Acquiring Penicillin Resistance from Commensal Neisseria lactamica Species. Antimicrob Agents Chemother 2022; 66:e0238321. [PMID: 35652645 PMCID: PMC9211434 DOI: 10.1128/aac.02383-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 05/16/2022] [Indexed: 11/20/2022] Open
Abstract
Invasive meningococcal disease (IMD) due to serogroup Y Neisseria meningitidis (NmY) is rare in China; recently, an invasive NmY isolate, Nm512, was discovered in Shanghai with decreased susceptibility to penicillin (PenNS). Here, we investigated the epidemiology of NmY isolates in Shanghai and explored the potential commensal Neisseria lactamica donor of the PenNS NmY isolate. A total of 491 N. meningitidis and 724 commensal Neisseria spp. isolates were collected. Eleven NmY isolates were discovered from IMD (n = 1) and carriers (n = 10), including two PenNS isolates with five-key-mutation-harboring (F504L-A510V-I515V-H541N-I566V) penA genes. Five of the eight ST-175 complex (CC175) isolates had a genotype [Y:P1.5-1,2-2:F5-8:ST-175(CC175)] identical to that of the predominant invasive clone found in South Africa. Only one invasive NmY CC23 isolate (Nm512) was discovered; this isolate carried a novel PenNSpenA832 allele, which was identified in commensal N. lactamica isolates locally. Recombination analysis and transformation of the penA allele highlighted that N. meningitidis Nm512 may acquire resistance from its commensal donor; this was supported by the similar distribution of transformation-required DNA uptake sequence variants and the highly cognate receptor ComP between N. meningitidis and N. lactamica. In 2,309 NmY CC23 genomes from the PubMLST database, isolates with key-mutation-harboring penA genes comprised 12% and have been increasing since the 1990s, accompanied by recruitment of the blaROB-1 and/or quinolone resistance allele. Moreover, penA22 was predominant among genomes without key mutations in penA. These results strongly suggest that Nm512 is a descendant of the penA22-harboring CC23 isolate from Europe and acquired its penicillin resistance locally from commensal N. lactamica species by natural transformation.
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Affiliation(s)
- Youxing Shao
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People’s Republic of China, Shanghai, People’s Republic of China
| | - Mingliang Chen
- Department of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People’s Republic of China
- Department of Microbiology, Shanghai Institutes of Preventive Medicine, Shanghai, People’s Republic of China
| | - Jiayuan Luo
- Department of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People’s Republic of China
| | - Dan Li
- Department of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People’s Republic of China
| | - Lingyue Yuan
- Department of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People’s Republic of China
| | - Xiaoying Yang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People’s Republic of China, Shanghai, People’s Republic of China
| | - Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People’s Republic of China, Shanghai, People’s Republic of China
| | - Min Chen
- Department of Microbiology, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, People’s Republic of China
| | - Qinglan Guo
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People’s Republic of China
- Key Laboratory of Clinical Pharmacology of Antibiotics, National Heath Commission of the People’s Republic of China, Shanghai, People’s Republic of China
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14
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Yan L, Tang C, Cai Y, Nong J, Zhang K, Zhu L, Wang P, Wu L, Zhao F, Hu S. Ultra-efficient multiple cross displacement amplification-lateral flow biosensor (MCDA-LFB) for serogroup identification of prevalent Neisseria meningitidis. Anal Biochem 2022; 654:114740. [PMID: 35623396 DOI: 10.1016/j.ab.2022.114740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/16/2022] [Accepted: 05/17/2022] [Indexed: 11/18/2022]
Abstract
Meningococcal disease caused by Neisseria meningitidis remains a major global public health concern. Serogroup A, B, C and W135 were the major disease-causing serogroups. It is vital to timely and efficiently detect and differentiate these four serogroups. Herein, we developed multiple cross displacement amplification-lateral flow biosensor (MCDA-LFB) assays targeting ctrA, sacB, siaD, siaD and synG gene respectively for detection and subtyping of four N. meningitidis serogroups. This assay utilizes LFB to detect FITC and biotin-labeled target amplicons produced by MCDA through double antibody sandwich principle, to allow sensitive and specific detection under a constant temperature. The detection limit was as low as 10 fg or 100 fg genomic DNA in pure cultures and 5.5 CFUs or 36 CFUs in spiked cerebrospinal fluid (CSF) specimens, which were overall 100 to 1000-fold more sensitive than conventional PCR. High specificity of these assays was also validated through type strains and clinical isolates, with no cross-reactions. MCDA-LFB testing procedure can be finished within 1 h. In conclusion, the N. meningitidis- and serogroup-MCDA-LFB assays established in this study are simple, rapid and efficient, providing valuable molecular methods for diagnosis and surveillance of meningococcal disease, especially in resource-limited regions and when specimen culture fails.
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Affiliation(s)
- Linlin Yan
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, 100144, China
| | - Chong Tang
- Department of Orthopaedic Surgery, Peking University Shougang Hospital, Beijing, 100144, China
| | - Yu Cai
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, 100144, China
| | - Jinqing Nong
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, 100144, China
| | - Ke Zhang
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, 100144, China
| | - Linlin Zhu
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, 100144, China
| | - Pengfei Wang
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, 100144, China
| | - Lei Wu
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, 100144, China
| | - Fan Zhao
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, 100144, China.
| | - Shoukui Hu
- Department of Clinical Laboratory, Peking University Shougang Hospital, Beijing, 100144, China.
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15
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Abstract
The genus Neisseria includes two pathogenic species, N. gonorrhoeae and N. meningitidis, and numerous commensal species. Neisseria species frequently exchange DNA with one another, primarily via transformation and homologous recombination and via multiple types of mobile genetic elements (MGEs). Few Neisseria bacteriophages (phages) have been identified, and their impact on bacterial physiology is poorly understood. Furthermore, little is known about the range of species that Neisseria phages can infect. In this study, we used three virus prediction tools to scan 248 genomes of 21 different Neisseria species and identified 1,302 unique predicted prophages. Using comparative genomics, we found that many predictions are dissimilar from prophages and other MGEs previously described to infect Neisseria species. We also identified similar predicted prophages in genomes of different Neisseria species. Additionally, we examined CRISPR-Cas targeting of each Neisseria genome and predicted prophage. While CRISPR targeting of chromosomal DNA appears to be common among several Neisseria species, we found that 20% of the prophages we predicted are targeted significantly more than the rest of the bacterial genome in which they were identified (i.e., backbone). Furthermore, many predicted prophages are targeted by CRISPR spacers encoded by other species. We then used these results to infer additional host species of known Neisseria prophages and predictions that are highly targeted relative to the backbone. Together, our results suggest that we have identified novel Neisseria prophages, several of which may infect multiple Neisseria species. These findings have important implications for understanding horizontal gene transfer between members of this genus. IMPORTANCE Drug-resistant Neisseria gonorrhoeae is a major threat to human health. Commensal Neisseria species are thought to serve as reservoirs of antibiotic resistance and virulence genes for the pathogenic species N. gonorrhoeae and N. meningitidis. Therefore, it is important to understand both the diversity of mobile genetic elements (MGEs) that can mediate horizontal gene transfer within this genus and the breadth of species these MGEs can infect. In particular, few bacteriophages (phages) are known to infect Neisseria species. In this study, we identified a large number of candidate phages integrated in the genomes of commensal and pathogenic Neisseria species, many of which appear to be novel phages. Importantly, we discovered extensive interspecies targeting of predicted phages by Neisseria CRISPR-Cas systems, which may reflect their movement between different species. Uncovering the diversity and host range of phages is essential for understanding how they influence the evolution of their microbial hosts.
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16
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The Retrospective on Atypical Brucella Species Leads to Novel Definitions. Microorganisms 2022; 10:microorganisms10040813. [PMID: 35456863 PMCID: PMC9025488 DOI: 10.3390/microorganisms10040813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 02/01/2023] Open
Abstract
The genus Brucella currently comprises twelve species of facultative intracellular bacteria with variable zoonotic potential. Six of them have been considered as classical, causing brucellosis in terrestrial mammalian hosts, with two species originated from marine mammals. In the past fifteen years, field research as well as improved pathogen detection and typing have allowed the identification of four new species, namely Brucella microti, Brucella inopinata, Brucella papionis, Brucella vulpis, and of numerous strains, isolated from a wide range of hosts, including for the first time cold-blooded animals. While their genome sequences are still highly similar to those of classical strains, some of them are characterized by atypical phenotypes such as higher growth rate, increased resistance to acid stress, motility, and lethality in the murine infection model. In our review, we provide an overview of state-of-the-art knowledge about these novel Brucella sp., with emphasis on their phylogenetic positions in the genus, their metabolic characteristics, acid stress resistance mechanisms, and their behavior in well-established in cellulo and in vivo infection models. Comparison of phylogenetic classification and phenotypical properties between classical and novel Brucella species and strains finally lead us to propose a more adapted terminology, distinguishing between core and non-core, and typical versus atypical brucellae, respectively.
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17
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Product review on the IMD serogroup B vaccine Bexsero®. Hum Vaccin Immunother 2022; 18:2020043. [PMID: 35192786 PMCID: PMC8986181 DOI: 10.1080/21645515.2021.2020043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Bexsero® is a multicomponent vaccine composed of four major proteins of Neisseria meningitidis: the fHbp, NHBA, NadA and PorA. This vaccine was licensed against invasive meningococcal disease (IMD) due to serogroup B isolates. When administered alone, Bexsero® showed a safety profile similar to other childhood vaccines. It provides an excellent immunogenicity but that requires booster doses in infants and young children. Although the vaccine does not seem to impact on acquisition of carriage of serogroup B isolates, it confers protection against isolates of serogroup B harboring distinct but cross-reactive variants of fHbp, NadA and NHBA. Primary vaccination schemes in infancy underwent a rapid increase after a toddler booster suggesting an anamnestic response and the establishment of a memory response. As Bexsero® targets sub-capsular proteins that can be conserved regardless the capsule, the vaccine can be effective against non-B isolates such as isolates of serogroups W and X.
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18
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Spoerry C, Karlsson J, Aschtgen MS, Loh E. Neisseria meningitidis IgA1-specific serine protease exhibits novel cleavage activity against IgG3. Virulence 2021; 12:389-403. [PMID: 33459578 PMCID: PMC7834093 DOI: 10.1080/21505594.2021.1871822] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 11/16/2022] Open
Abstract
Neisseria meningitidis (meningococcus) is a common bacterial colonizer of the human nasopharynx but can occasionally cause very severe systemic infections with rapid onset. Meningococci are able to degrade IgA encountered during colonization of mucosal membranes using their IgA1-specific serine protease. During systemic infection, specific IgG can induce complement-mediated lysis of the bacterium. However, meningococcal immune evasion mechanisms in thwarting IgG remain undescribed. In this study, we report for the first time that the meningococcal IgA1-specific serine protease is able to degrade IgG3 in addition to IgA. The IgG3 heavy chain is specifically cleaved in the lower hinge region thereby separating the antigen binding part from its effector binding part. Through molecular characterization, we demonstrate that meningococcal IgA1-specific serine protease of cleavage type 1 degrades both IgG3 and IgA, whereas cleavage type 2 only degrades IgA. Epidemiological analysis of 7581 clinical meningococcal isolates shows a significant higher proportion of cleavage type 1 among isolates from invasive cases compared to carrier cases, regardless of serogroup. Notably, serogroup W cc11 which is an increasing cause of invasive meningococcal disease globally harbors almost exclusively cleavage type 1 protease. Our study also shows an increasing prevalence of meningococcal isolates encoding IgA1P cleavage type 1 compared to cleavage type 2 during the observed decade (2010-2019). Altogether, our work describes a novel mechanism of IgG3 degradation by meningococci and its association to invasive meningococcal disease.
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Affiliation(s)
- Christian Spoerry
- Department of Microbiology, Tumor, and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Jens Karlsson
- Department of Microbiology, Tumor, and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Marie-Stephanie Aschtgen
- Department of Microbiology, Tumor, and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Edmund Loh
- Department of Microbiology, Tumor, and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
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19
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Ruiz García Y, Sohn WY, Seib KL, Taha MK, Vázquez JA, de Lemos APS, Vadivelu K, Pizza M, Rappuoli R, Bekkat-Berkani R. Looking beyond meningococcal B with the 4CMenB vaccine: the Neisseria effect. NPJ Vaccines 2021; 6:130. [PMID: 34716336 PMCID: PMC8556335 DOI: 10.1038/s41541-021-00388-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/01/2021] [Indexed: 11/30/2022] Open
Abstract
Infections with Neisseria meningitidis and Neisseria gonorrhoeae have different clinical manifestations, but the bacteria share up to 80-90% genome sequence identity. The recombinant meningococcal serogroup B (MenB) vaccine 4CMenB consists of four antigenic components that can be present in non-B meningococcal and gonococcal strains. This comprehensive review summarizes scientific evidence on the genotypic and phenotypic similarities between vaccine antigens and their homologs expressed by non-B meningococcal and gonococcal strains. It also includes immune responses of 4CMenB-vaccinated individuals and effectiveness and impact of 4CMenB against these strains. Varying degrees of strain coverage were estimated depending on the non-B meningococcal serogroup and antigenic repertoire. 4CMenB elicits immune responses against non-B meningococcal serogroups and N. gonorrhoeae. Real-world evidence showed risk reductions of 69% for meningococcal serogroup W clonal complex 11 disease and 40% for gonorrhea after 4CMenB immunization. In conclusion, functional antibody activity and real-world evidence indicate that 4CMenB has the potential to provide some protection beyond MenB disease.
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Affiliation(s)
| | - Woo-Yun Sohn
- grid.418019.50000 0004 0393 4335GSK, Rockville, MD USA
| | - Kate L. Seib
- grid.1022.10000 0004 0437 5432Institute for Glycomics, Griffith University, Gold Coast, QLD Australia
| | | | - Julio A. Vázquez
- grid.413448.e0000 0000 9314 1427National Centre of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
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20
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Mullally CA, Mikucki A, Wise MJ, Kahler CM. Modelling evolutionary pathways for commensalism and hypervirulence in Neisseria meningitidis. Microb Genom 2021; 7. [PMID: 34704920 PMCID: PMC8627216 DOI: 10.1099/mgen.0.000662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Neisseria meningitidis, the meningococcus, resides exclusively in humans and causes invasive meningococcal disease (IMD). The population of N. meningitidis is structured into stable clonal complexes by limited horizontal recombination in this naturally transformable species. N. meningitidis is an opportunistic pathogen, with some clonal complexes, such as cc53, effectively acting as commensal colonizers, while other genetic lineages, such as cc11, are rarely colonizers but are over-represented in IMD and are termed hypervirulent. This study examined theoretical evolutionary pathways for pathogenic and commensal lineages by examining the prevalence of horizontally acquired genomic islands (GIs) and loss-of-function (LOF) mutations. Using a collection of 4850 genomes from the BIGSdb database, we identified 82 GIs in the pan-genome of 11 lineages (10 hypervirulent and one commensal lineage). A new computational tool, Phaser, was used to identify frameshift mutations, which were examined for statistically significant association with genetic lineage. Phaser identified a total of 144 frameshift loci of which 105 were shown to have a statistically significant non-random distribution in phase status. The 82 GIs, but not the LOF loci, were associated with genetic lineage and invasiveness using the disease carriage ratio metric. These observations have been integrated into a new model that infers the early events of the evolution of the human adapted meningococcus. These pathways are enriched for GIs that are involved in modulating attachment to the host, growth rate, iron uptake and toxin expression which are proposed to increase competition within the meningococcal population for the limited environmental niche of the human nasopharynx. We surmise that competition for the host mucosal surface with the nasopharyngeal microbiome has led to the selection of isolates with traits that enable access to cell types (non-phagocytic and phagocytic) in the submucosal tissues leading to an increased risk for IMD.
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Affiliation(s)
- Christopher A. Mullally
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Science, University of Western Australia, Perth, Australia
| | - August Mikucki
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Science, University of Western Australia, Perth, Australia
| | - Michael J. Wise
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Science, University of Western Australia, Perth, Australia
- School of Physics, Mathematics and Computing, University of Western Australia, Perth, Australia
| | - Charlene M. Kahler
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Science, University of Western Australia, Perth, Australia
- Telethon Kids Institute, Perth Children’s Hospital, Perth, Australia
- *Correspondence: Charlene M. Kahler,
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21
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Karlsson J, Eichner H, Loh E. Invasive meningococcal disease and genome databases. THE LANCET MICROBE 2021; 2:e421-e422. [DOI: 10.1016/s2666-5247(21)00172-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 11/28/2022] Open
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22
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Amemiya HM, Schroeder J, Freddolino PL. Nucleoid-associated proteins shape chromatin structure and transcriptional regulation across the bacterial kingdom. Transcription 2021; 12:182-218. [PMID: 34499567 PMCID: PMC8632127 DOI: 10.1080/21541264.2021.1973865] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/15/2021] [Accepted: 08/18/2021] [Indexed: 01/21/2023] Open
Abstract
Genome architecture has proven to be critical in determining gene regulation across almost all domains of life. While many of the key components and mechanisms of eukaryotic genome organization have been described, the interplay between bacterial DNA organization and gene regulation is only now being fully appreciated. An increasing pool of evidence has demonstrated that the bacterial chromosome can reasonably be thought of as chromatin, and that bacterial chromosomes contain transcriptionally silent and transcriptionally active regions analogous to heterochromatin and euchromatin, respectively. The roles played by histones in eukaryotic systems appear to be shared across a range of nucleoid-associated proteins (NAPs) in bacteria, which function to compact, structure, and regulate large portions of bacterial chromosomes. The broad range of extant NAPs, and the extent to which they differ from species to species, has raised additional challenges in identifying and characterizing their roles in all but a handful of model bacteria. Here we review the regulatory roles played by NAPs in several well-studied bacteria and use the resulting state of knowledge to provide a working definition for NAPs, based on their function, binding pattern, and expression levels. We present a screening procedure which can be applied to any species for which transcriptomic data are available. Finally, we note that NAPs tend to play two major regulatory roles - xenogeneic silencers and developmental regulators - and that many unrecognized potential NAPs exist in each bacterial species examined.
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Affiliation(s)
- Haley M. Amemiya
- University of Michigan Medical School, Ann Arbor, MI, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Jeremy Schroeder
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Peter L. Freddolino
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA
- Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA
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23
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Laver JR, Gbesemete D, Dale AP, Pounce ZC, Webb CN, Roche EF, Guy JM, Berreen G, Belogiannis K, Hill AR, Ibrahim MM, Ahmed M, Cleary DW, Pandey AK, Humphries HE, Allen L, de Graaf H, Maiden MC, Faust SN, Gorringe AR, Read RC. A recombinant commensal bacteria elicits heterologous antigen-specific immune responses during pharyngeal carriage. Sci Transl Med 2021; 13:eabe8573. [PMID: 34233953 PMCID: PMC7615050 DOI: 10.1126/scitranslmed.abe8573] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 03/22/2021] [Accepted: 05/25/2021] [Indexed: 12/25/2022]
Abstract
The human nasopharynx contains a stable microbial ecosystem of commensal and potentially pathogenic bacteria, which can elicit protective primary and secondary immune responses. Experimental intranasal infection of human adults with the commensal Neisseria lactamica produced safe, sustained pharyngeal colonization. This has potential utility as a vehicle for sustained release of antigen to the human mucosa, but commensals in general are thought to be immunologically tolerated. Here, we show that engineered N. lactamica, chromosomally transformed to express a heterologous vaccine antigen, safely induces systemic, antigen-specific immune responses during carriage in humans. When the N. lactamica expressing the meningococcal antigen Neisseria Adhesin A (NadA) was inoculated intranasally into human volunteers, all colonized participants carried the bacteria asymptomatically for at least 28 days, with most (86%) still carrying the bacteria at 90 days. Compared to an otherwise isogenic but phenotypically wild-type strain, colonization with NadA-expressing N. lactamica generated NadA-specific immunoglobulin G (IgG)- and IgA-secreting plasma cells within 14 days of colonization and NadA-specific IgG memory B cells within 28 days of colonization. NadA-specific IgG memory B cells were detected in peripheral blood of colonized participants for at least 90 days. Over the same period, there was seroconversion against NadA and generation of serum bactericidal antibody activity against a NadA-expressing meningococcus. The controlled infection was safe, and there was no transmission to adult bedroom sharers during the 90-day period. Genetically modified N. lactamica could therefore be used to generate beneficial immune responses to heterologous antigens during sustained pharyngeal carriage.
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Affiliation(s)
- Jay R Laver
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK.
- NIHR Southampton Biomedical Research Centre and NIHR Southampton Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Diane Gbesemete
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
- NIHR Southampton Biomedical Research Centre and NIHR Southampton Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Adam P Dale
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
- NIHR Southampton Biomedical Research Centre and NIHR Southampton Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Zoe C Pounce
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Carl N Webb
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
- NIHR Southampton Biomedical Research Centre and NIHR Southampton Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Eleanor F Roche
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Jonathan M Guy
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Graham Berreen
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Konstantinos Belogiannis
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Alison R Hill
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
- NIHR Southampton Biomedical Research Centre and NIHR Southampton Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Muktar M Ibrahim
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Muhammad Ahmed
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - David W Cleary
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
- NIHR Southampton Biomedical Research Centre and NIHR Southampton Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Anish K Pandey
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
- NIHR Southampton Biomedical Research Centre and NIHR Southampton Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | | | - Lauren Allen
- Public Health England, Porton Down, Salisbury SP4 0JG, UK
| | - Hans de Graaf
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
- NIHR Southampton Biomedical Research Centre and NIHR Southampton Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | - Martin C Maiden
- Department of Zoology, University of Oxford, Oxford OX1 3SZ, UK
| | - Saul N Faust
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
- NIHR Southampton Biomedical Research Centre and NIHR Southampton Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
| | | | - Robert C Read
- Faculty of Medicine and Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK
- NIHR Southampton Biomedical Research Centre and NIHR Southampton Clinical Research Facility, University Hospital Southampton NHS Foundation Trust, Southampton SO16 6YD, UK
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24
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Custodio R, Ford RM, Ellison CJ, Liu G, Mickute G, Tang CM, Exley RM. Type VI secretion system killing by commensal Neisseria is influenced by expression of type four pili. eLife 2021; 10:63755. [PMID: 34232858 PMCID: PMC8263058 DOI: 10.7554/elife.63755] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 06/27/2021] [Indexed: 12/14/2022] Open
Abstract
Type VI Secretion Systems (T6SSs) are widespread in bacteria and can dictate the development and organisation of polymicrobial ecosystems by mediating contact dependent killing. In Neisseria species, including Neisseria cinerea a commensal of the human respiratory tract, interbacterial contacts are mediated by Type four pili (Tfp) which promote formation of aggregates and govern the spatial dynamics of growing Neisseria microcolonies. Here, we show that N. cinerea expresses a plasmid-encoded T6SS that is active and can limit growth of related pathogens. We explored the impact of Tfp on N. cinerea T6SS-dependent killing within a colony and show that pilus expression by a prey strain enhances susceptibility to T6SS compared to a non-piliated prey, by preventing segregation from a T6SS-wielding attacker. Our findings have important implications for understanding how spatial constraints during contact-dependent antagonism can shape the evolution of microbial communities.
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Affiliation(s)
- Rafael Custodio
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Rhian M Ford
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Cara J Ellison
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Guangyu Liu
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Gerda Mickute
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Rachel M Exley
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
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25
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Xie J, Zi W, Li Z, He Y. Ontology-based Precision Vaccinology for Deep Mechanism Understanding and Precision Vaccine Development. Curr Pharm Des 2021; 27:900-910. [PMID: 33238868 DOI: 10.2174/1381612826666201125112131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 10/08/2020] [Indexed: 11/22/2022]
Abstract
Vaccination is one of the most important innovations in human history. It has also become a hot research area in a new application - the development of new vaccines against non-infectious diseases such as cancers. However, effective and safe vaccines still do not exist for many diseases, and where vaccines exist, their protective immune mechanisms are often unclear. Although licensed vaccines are generally safe, various adverse events, and sometimes severe adverse events, still exist for a small population. Precision medicine tailors medical intervention to the personal characteristics of individual patients or sub-populations of individuals with similar immunity-related characteristics. Precision vaccinology is a new strategy that applies precision medicine to the development, administration, and post-administration analysis of vaccines. Several conditions contribute to make this the right time to embark on the development of precision vaccinology. First, the increased level of research in vaccinology has generated voluminous "big data" repositories of vaccinology data. Secondly, new technologies such as multi-omics and immunoinformatics bring new methods for investigating vaccines and immunology. Finally, the advent of AI and machine learning software now makes possible the marriage of Big Data to the development of new vaccines in ways not possible before. However, something is missing in this marriage, and that is a common language that facilitates the correlation, analysis, and reporting nomenclature for the field of vaccinology. Solving this bioinformatics problem is the domain of applied biomedical ontology. Ontology in the informatics field is human- and machine-interpretable representation of entities and the relations among entities in a specific domain. The Vaccine Ontology (VO) and Ontology of Vaccine Adverse Events (OVAE) have been developed to support the standard representation of vaccines, vaccine components, vaccinations, host responses, and vaccine adverse events. Many other biomedical ontologies have also been developed and can be applied in vaccine research. Here, we review the current status of precision vaccinology and how ontological development will enhance this field, and propose an ontology-based precision vaccinology strategy to support precision vaccine research and development.
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Affiliation(s)
- Jiangan Xie
- Chongqing Engineering Research Center of Medical Electronics and Information Technology, School of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Wenrui Zi
- Chongqing engineering research center of medical electronics and information technology, School of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Zhangyong Li
- Chongqing engineering research center of medical electronics and information technology, School of Bioinformatics, Chongqing University of Posts and Telecommunications, Chongqing, China
| | - Yongqun He
- Unit of Laboratory Animal Medicine, Development of Microbiology and Immunology, Center of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, Michigan, United States
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26
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The serogroup B meningococcal outer membrane vesicle-based vaccine 4CMenB induces cross-species protection against Neisseria gonorrhoeae. PLoS Pathog 2020; 16:e1008602. [PMID: 33290434 PMCID: PMC7748408 DOI: 10.1371/journal.ppat.1008602] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 12/18/2020] [Accepted: 10/08/2020] [Indexed: 12/15/2022] Open
Abstract
There is a pressing need for a gonorrhea vaccine due to the high disease burden associated with gonococcal infections globally and the rapid evolution of antibiotic resistance in Neisseria gonorrhoeae (Ng). Current gonorrhea vaccine research is in the stages of antigen discovery and the identification of protective immune responses, and no vaccine has been tested in clinical trials in over 30 years. Recently, however, it was reported in a retrospective case-control study that vaccination of humans with a serogroup B Neisseria meningitidis (Nm) outer membrane vesicle (OMV) vaccine (MeNZB) was associated with reduced rates of gonorrhea. Here we directly tested the hypothesis that Nm OMVs induce cross-protection against gonorrhea in a well-characterized female mouse model of Ng genital tract infection. We found that immunization with the licensed Nm OMV-based vaccine 4CMenB (Bexsero) significantly accelerated clearance and reduced the Ng bacterial burden compared to administration of alum or PBS. Serum IgG and vaginal IgA and IgG that cross-reacted with Ng OMVs were induced by 4CMenB vaccination by either the subcutaneous or intraperitoneal routes. Antibodies from vaccinated mice recognized several Ng surface proteins, including PilQ, BamA, MtrE, NHBA (known to be recognized by humans), PorB, and Opa. Immune sera from both mice and humans recognized Ng PilQ and several proteins of similar apparent molecular weight, but MtrE was only recognized by mouse serum. Pooled sera from 4CMenB-immunized mice showed a 4-fold increase in serum bactericidal50 titers against the challenge strain; in contrast, no significant difference in bactericidal activity was detected when sera from 4CMenB-immunized and unimmunized subjects were compared. Our findings directly support epidemiological evidence that Nm OMVs confer cross-species protection against gonorrhea, and implicate several Ng surface antigens as potentially protective targets. Additionally, this study further defines the usefulness of murine infection model as a relevant experimental system for gonorrhea vaccine development.
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27
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Interactions and Signal Transduction Pathways Involved during Central Nervous System Entry by Neisseria meningitidis across the Blood-Brain Barriers. Int J Mol Sci 2020; 21:ijms21228788. [PMID: 33233688 PMCID: PMC7699760 DOI: 10.3390/ijms21228788] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 11/18/2020] [Indexed: 11/20/2022] Open
Abstract
The Gram-negative diplococcus Neisseria meningitidis, also called meningococcus, exclusively infects humans and can cause meningitis, a severe disease that can lead to the death of the afflicted individuals. To cause meningitis, the bacteria have to enter the central nervous system (CNS) by crossing one of the barriers protecting the CNS from entry by pathogens. These barriers are represented by the blood–brain barrier separating the blood from the brain parenchyma and the blood–cerebrospinal fluid (CSF) barriers at the choroid plexus and the meninges. During the course of meningococcal disease resulting in meningitis, the bacteria undergo several interactions with host cells, including the pharyngeal epithelium and the cells constituting the barriers between the blood and the CSF. These interactions are required to initiate signal transduction pathways that are involved during the crossing of the meningococci into the blood stream and CNS entry, as well as in the host cell response to infection. In this review we summarize the interactions and pathways involved in these processes, whose understanding could help to better understand the pathogenesis of meningococcal meningitis.
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28
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Juscamayta-López E, Valdivia F, Morales S, Donaires LF, Fiestas-Solórzano V, Oré M, Pachas P, León-Janampa N, Gavilán R. Emergence of ciprofloxacin-resistant Neisseria meningitidis B from asymptomatic carriers during an outbreak in Peru, 2017. J Med Microbiol 2020; 70. [PMID: 33196407 DOI: 10.1099/jmm.0.001245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Asymptomatic carriers are a likely source of transmission of Neisseria meningitidis to close contacts who are placed at a higher risk for invasive meningococcal disease (IMD). Although N. meningitidis ciprofloxacin-resistance is rare, there have been an increase in the reports of resistant isolates mainly in patients diagnosed with IMD, and little is known about the N. meningitidis ciprofloxacin-resistance in the carrier populations. We performed a pharyngeal carriage study during a 2017 military setting outbreak in Peru, caused by a ciprofloxacin-resistant N. meningitidis B. The isolates analysed came from two hospitalized cases and six asymptomatic carriers. Whole-genome sequence-based analysis was performed and showed that strains carrying the Thr91Ile mutation, in the gene encoding for subunit A of DNA gyrase (gyrA), were responsible for the fluoroquinolone resistance (MICs ≥0.256 µg ml-1) and were closely related to highly virulent strains from France, Norway and the UK. Phylogenetic analysis of the gyrA gene revealed that likely these Peruvian isolates acquired resistance through horizontal gene transfer from Neisseria lactamica. Our study provides evidence for the emergence and propagation of ciprofloxacin-resistant N. meningitidis B from asymptomatic carriers, and recommends the introduction of serogroup B vaccines for high-risk populations.
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Affiliation(s)
| | - Faviola Valdivia
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Sara Morales
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | | | | | - Marianela Oré
- Epidemiología, Comando de Salud del Ejército, Lima, Peru
| | - Paul Pachas
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Nancy León-Janampa
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
| | - Ronnie Gavilán
- Centro Nacional de Salud Pública, Instituto Nacional de Salud, Lima, Peru
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29
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Kremer PHC, Lees JA, Ferwerda B, van de Ende A, Brouwer MC, Bentley SD, van de Beek D. Genetic Variation in Neisseria meningitidis Does Not Influence Disease Severity in Meningococcal Meningitis. Front Med (Lausanne) 2020; 7:594769. [PMID: 33262994 PMCID: PMC7686797 DOI: 10.3389/fmed.2020.594769] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
Neisseria meningitidis causes sepsis and meningitis in humans. It has been suggested that pathogen genetic variation determines variance in disease severity. Here we report results of a genome-wide association study of 486 N. meningitidis genomes from meningococcal meningitis patients and their association with disease severity. Of 369 meningococcal meningitis patients for whom clinical data was available, 44 (12%) had unfavorable outcome and 24 (7%) died. To increase power, thrombocyte count was used as proxy marker for disease severity. Bacterial genetic variants were called as k-mers, SNPs, insertions and deletions and clusters of orthologous genes (COGs). Population-level meningococcal genetic variation did not explain variance in disease severity (unfavorable outcome or thrombocyte count) in this cohort (h2 = 0.0%; 95% confidence interval: 0.0–0.9). Genetic variants in the bacterial uppS gene represented the top signal associated with thrombocyte count (p-value = 9.96e-07) but this did not reach statistical significance. We did not find an association between previously published variants in lpxL1, fHbp, and tps genes and unfavorable outcome or thrombocyte count. A power analysis based on simulated phenotypes based on real genetic data from 880 N. meningitidis genomes showed that we would be able to detect a continuous phenotype with h2 > = 0.5 with the population size available in this study. This rules out a major contribution of pathogen genetic variation to disease severity in meningococcal meningitis, and shows that much larger sample sizes are required to find specific low-effect genetic variants modulating disease outcome in meningococcal meningitis.
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Affiliation(s)
- Philip H C Kremer
- Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - John A Lees
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, United Kingdom.,Department of Infectious Disease Epidemiology, Medical Research Council Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom
| | - Bart Ferwerda
- Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Arie van de Ende
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands.,The Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam, Netherlands
| | - Matthijs C Brouwer
- Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Stephen D Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, United Kingdom
| | - Diederik van de Beek
- Department of Neurology, Amsterdam Neuroscience, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
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30
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Azimi S, Wheldon LM, Oldfield NJ, Ala'Aldeen DAA, Wooldridge KG. A role for fibroblast growth factor receptor 1 in the pathogenesis of Neisseria meningitidis. Microb Pathog 2020; 149:104534. [PMID: 33045339 DOI: 10.1016/j.micpath.2020.104534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 08/13/2020] [Accepted: 09/21/2020] [Indexed: 12/19/2022]
Abstract
Neisseria meningitidis (the meningococcus) remains an important cause of human disease, including meningitis and sepsis. Adaptation to the host environment includes many interactions with specific cell surface receptors, resulting in intracellular signalling and cytoskeletal rearrangements that contribute to pathogenesis. Here, we assessed the interactions between meningococci and Fibroblast Growth Factor Receptor 1-IIIc (FGFR1-IIIc): a receptor specific to endothelial cells of the microvasculature, including that of the blood-brain barrier. We show that the meningococcus recruits FGFR1-IIIc onto the surface of human blood microvascular endothelial cells (HBMECs). Furthermore, we demonstrate that expression of FGFR1-IIIc is required for optimal invasion of HBMECs by meningococci. We show that the ability of N. meningitidis to interact with the ligand-binding domain of FGFR1-IIIc is shared with the other pathogenic Neisseria species, N. gonorrhoeae, but not with commensal bacteria including non-pathogenic Neisseria species.
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Affiliation(s)
- Sheyda Azimi
- Molecular Bacteriology and Immunology Group, School of Life Sciences, University of Nottingham, UK
| | - Lee M Wheldon
- Molecular Bacteriology and Immunology Group, School of Life Sciences, University of Nottingham, UK
| | - Neil J Oldfield
- Molecular Bacteriology and Immunology Group, School of Life Sciences, University of Nottingham, UK
| | - Dlawer A A Ala'Aldeen
- Molecular Bacteriology and Immunology Group, School of Life Sciences, University of Nottingham, UK
| | - Karl G Wooldridge
- Molecular Bacteriology and Immunology Group, School of Life Sciences, University of Nottingham, UK.
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31
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Takahashi H, Dohmae N, Kim KS, Shimuta K, Ohnishi M, Yokoyama S, Yanagisawa T. Genetic incorporation of non-canonical amino acid photocrosslinkers in Neisseria meningitidis: New method provides insights into the physiological function of the function-unknown NMB1345 protein. PLoS One 2020; 15:e0237883. [PMID: 32866169 PMCID: PMC7458321 DOI: 10.1371/journal.pone.0237883] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/04/2020] [Indexed: 02/01/2023] Open
Abstract
Although whole-genome sequencing has provided novel insights into Neisseria meningitidis, many open reading frames have only been annotated as hypothetical proteins with unknown biological functions. Our previous genetic analyses revealed that the hypothetical protein, NMB1345, plays a crucial role in meningococcal infection in human brain microvascular endothelial cells; however, NMB1345 has no homology to any identified protein in databases and its physiological function could not be elucidated using pre-existing methods. Among the many biological technologies to examine transient protein-protein interaction in vivo, one of the developed methods is genetic code expansion with non-canonical amino acids (ncAAs) utilizing a pyrrolysyl-tRNA synthetase/tRNAPyl pair from Methanosarcina species: However, this method has never been applied to assign function-unknown proteins in pathogenic bacteria. In the present study, we developed a new method to genetically incorporate ncAAs-encoded photocrosslinking probes into N. meningitidis by utilizing a pyrrolysyl-tRNA synthetase/tRNAPyl pair and elucidated the biological function(s) of the NMB1345 protein. The results revealed that the NMB1345 protein directly interacts with PilE, a major component of meningococcal pili, and further physicochemical and genetic analyses showed that the interaction between the NMB1345 protein and PilE was important for both functional pilus formation and meningococcal infectious ability in N. meningitidis. The present study using this new methodology for N. meningitidis provides novel insights into meningococcal pathogenesis by assigning the function of a hypothetical protein.
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Affiliation(s)
- Hideyuki Takahashi
- National Institute of Infectious Diseases, Department of Bacteriology I, Shinjuku-ku, Japan
- * E-mail:
| | - Naoshi Dohmae
- Biomolecular Characterization Unit, RIKEN Center for Sustainable Resource Science, Wako, Japan
| | - Kwang Sik Kim
- Division of Pediatric Infectious Diseases, Department of Pediatrics, School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Ken Shimuta
- National Institute of Infectious Diseases, Department of Bacteriology I, Shinjuku-ku, Japan
| | - Makoto Ohnishi
- National Institute of Infectious Diseases, Department of Bacteriology I, Shinjuku-ku, Japan
| | - Shigeyuki Yokoyama
- RIKEN Structural Biology Laboratory, Yokohama, Japan
- RIKEN Cluster for Science, Technology and Innovation Hub, Yokohama, Japan
| | - Tatsuo Yanagisawa
- RIKEN Structural Biology Laboratory, Yokohama, Japan
- RIKEN Cluster for Science, Technology and Innovation Hub, Yokohama, Japan
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32
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Le TT, Tran TX, Trieu LP, Austin CM, Nguyen HM, Quyen DV. Genotypic characterization and genome comparison reveal insights into potential vaccine coverage and genealogy of Neisseria meningitidis in military camps in Vietnam. PeerJ 2020; 8:e9502. [PMID: 32742791 PMCID: PMC7380270 DOI: 10.7717/peerj.9502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 06/17/2020] [Indexed: 12/20/2022] Open
Abstract
Background Neisseria meningitidis remains the main cause of sporadic meningitis and sepsis in military camps in Vietnam. Yet, very limited molecular data of their genotypic and epidemiological characteristics are available from Vietnam, and particularly the military environment. Whole genome sequencing (WGS) has proven useful for meningococcal disease surveillance and guiding preventative vaccination programs. Previously, we characterized key genetic and epidemiological features of an invasive N. meningitidis B isolate from a military unit in Vietnam. Here, we extend these findings by sequencing two additional invasive N. meningitidis B isolated from cerebrospinal fluid (CSF) of two meningitis cases at another military unit and compared their genomic sequences and features. We also report the sequence types and antigenic profiles of 25 historical and more recently emerged N. meningitidis isolates from these units and other units in proximity. Methods Strains were sequenced using the Illumina HiSeq platform, de novo assembled and annotated. Genomes were compared within and between military units, as well as against the global N. meningitidis collection and other isolates from the Southeast Asia region using PubMLST. Variations at the nucleotide level were determined, and phylogenetic relationships were estimated. Antigenic genotypes and vaccine coverage were analyzed using gMATS and PubMLST. Susceptibility of isolates against commonly used antibiotic agents was examined using E-test. Results Genome comparison revealed a high level of similarity among isolates both within and between units. All isolates showed resistance to chloramphenicol and carried identical catP gene with other Southeast Asian isolates, suggesting a common lineage. Their antigenic genotypes predicted no coverage by either Bexsero®or Trumenba®, and nucleotide variation analysis revealed diverse new, unassigned alleles at multiple virulence loci of all strains. Groups of singleton and unique novel sequence types extending beyond individual camps were found from epidemiological data of 25 other isolates. Our results add to the sparse published molecular data of N. meningitidis in the military units in Vietnam, highlight their diversity, distinct genetic features and antibiotic resistance pattern, and emphasize the need for further studies on the molecular characteristics of N. meningitidis in Vietnam.
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Affiliation(s)
- Trang Thu Le
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Thach Xuan Tran
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Long Phi Trieu
- Laboratory of Microbiology, Military Institute of Preventive Medicine, Hanoi, Vietnam
| | - Christopher M Austin
- Deakin Genomics Centre, Deakin University, Geelong, Victoria, Australia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | - Huong Minh Nguyen
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | - Dong Van Quyen
- Laboratory of Molecular Microbiology, Institute of Biotechnology, Vietnam Academy of Science and Technology, Hanoi, Vietnam
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33
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Principato S, Pizza M, Rappuoli R. Meningococcal factor H binding protein as immune evasion factor and vaccine antigen. FEBS Lett 2020; 594:2657-2669. [PMID: 32298465 DOI: 10.1002/1873-3468.13793] [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: 02/11/2020] [Revised: 03/25/2020] [Accepted: 03/30/2020] [Indexed: 01/15/2023]
Abstract
Factor H binding protein (fHbp) is a key virulence factor of Neisseria meningitidis and a main component of the two licensed vaccines against serogroup B meningococcus (Bexsero and Trumenba). fHbp is a surface-exposed lipoprotein that enables the bacterium to survive in human blood by binding the human complement regulator factor H (fH). When used as vaccine, the protein induces antibodies with potent bactericidal activity. While the fHbp gene is present in the majority of N. meningitidis serogroup B isolates, the expression level varies up to 15 times between different strains and more than 700 different sequence variants have been described. Antigenically, the protein has been divided into three variants or two subfamilies. The 3D structure of fHbp alone, in combination with fH or in complex with bactericidal antibodies, has been key to understanding the molecular details of the protein. In this article, we will review the biochemical and immunological properties of fHbp, and its key role in meningococcal pathogenesis, complement regulation, and immune evasion.
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34
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Hughes-Games A, Roberts AP, Davis SA, Hill DJ. Identification of integrative and conjugative elements in pathogenic and commensal Neisseriaceae species via genomic distributions of DNA uptake sequence dialects. Microb Genom 2020; 6:e000372. [PMID: 32375974 PMCID: PMC7371117 DOI: 10.1099/mgen.0.000372] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 04/13/2020] [Indexed: 02/02/2023] Open
Abstract
Mobile genetic elements (MGEs) are key factors responsible for dissemination of virulence determinants and antimicrobial-resistance genes amongst pathogenic bacteria. Conjugative MGEs are notable for their high gene loads donated per transfer event, broad host ranges and phylogenetic ubiquity amongst prokaryotes, with the subclass of chromosomally inserted integrative and conjugative elements (ICEs) being particularly abundant. The focus on a small number of model systems has biased the study of ICEs towards those conferring readily selectable phenotypes to host cells, whereas the identification and characterization of integrated cryptic elements remains challenging. Even though antimicrobial resistance and horizontally acquired virulence genes are major factors aggravating neisserial infection, conjugative MGEs of Neisseria gonorrhoeae and Neisseria meningitidis remain poorly characterized. Using a phenotype-independent approach based on atypical distributions of DNA uptake sequences (DUSs) in MGEs relative to the chromosomal background, we have identified two groups of chromosomally integrated conjugative elements in Neisseria: one found almost exclusively in pathogenic species possibly deriving from the genus Kingella, the other belonging to a group of Neisseria mucosa-like commensals. The former element appears to enable transfer of traditionally gonococcal-specific loci such as the virulence-associated toxin-antitoxin system fitAB to N. meningitidis chromosomes, whilst the circular form of the latter possesses a unique attachment site (attP) sequence seemingly adapted to exploit DUS motifs as chromosomal integration sites. In addition to validating the use of DUS distributions in Neisseriaceae MGE identification, the >170 identified ICE sequences provide a valuable resource for future studies of ICE evolution and host adaptation.
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Affiliation(s)
- Alex Hughes-Games
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
- Bristol Centre for Functional Nanomaterials, HH Wills Physics Laboratory, University of Bristol, Bristol, UK
| | - Adam P. Roberts
- Centre for Drugs and Diagnostics, Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Sean A. Davis
- School of Chemistry, University of Bristol, Bristol, UK
| | - Darryl J. Hill
- School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
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35
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Beernink PT. Effect of complement Factor H on antibody repertoire and protection elicited by meningococcal capsular group B vaccines containing Factor H binding protein. Hum Vaccin Immunother 2020; 16:703-712. [PMID: 31526219 DOI: 10.1080/21645515.2019.1664241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
Abstract
Bacteria produce surface ligands for host complement regulators including Factor H (FH), which allows the bacteria to evade immunity. Meningococcal Factor H binding protein (FHbp) is both a virulence factor and a vaccine antigen. Antibodies to FHbp can neutralize its function by inhibiting binding of FH to the bacteria and confer robust complement-mediated protection. However, in the presence of human or primate FH, antibodies to FHbp do not inhibit FH binding and the protective antibody responses are decreased. This immune suppression can be overcome by modification of the FHbp antigen to decrease FH binding, which modulates the antibody repertoire to inhibit FH binding and increase protection. When FHbp is present at sufficient density on the bacterial surface, two or more antibodies can synergize to activate the complement system. Thus, modification of FHbp antigens to decrease FH binding expands the anti-FHbp antibody repertoire and increases the potential for synergistic activity.
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Affiliation(s)
- Peter T Beernink
- Center for Immunobiology and Vaccine Development, UCSF Benioff Children's Hospital Oakland, Oakland, CA, USA.,Department of Pediatrics, School of Medicine, University of California, San Francisco, San Francisco, CA, USA
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36
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Righetti F, Materne SL, Boss J, Eichner H, Charpentier E, Loh E. Characterization of a transcriptional TPP riboswitch in the human pathogen Neisseria meningitidis. RNA Biol 2020; 17:718-730. [PMID: 32079473 PMCID: PMC7237195 DOI: 10.1080/15476286.2020.1727188] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Increasing evidence has demonstrated that regulatory RNA elements such as riboswitches (RS) play a pivotal role in the fine-tuning of bacterial gene expression. In this study, we investigated and characterized a novel transcriptional thiamine pyrophosphate (TPP) RS in the obligate human pathogen N. meningitidis MC58 (serogroup B). This RS is located in the 5´ untranslated region upstream of thiC gene, encoding a protein involved in TPP biosynthesis, an essential cofactor for all living beings. Primer extension revealed the transcriptional start site of thiC. Northern blot analysis of thiC mRNA and reporter gene studies confirmed the presence of an active TPP-sensing RS. Expression patterns of the wild-type RS and site-specific mutants showed that it is an OFF switch that controls transcription elongation of thiC mRNA. Interestingly, the regulatory mechanism of the meningococcal thiC RS resembles the Gram-positive Bacillus subtilis thiC RS rather than the Gram-negative Escherichia coli thiC RS. Therefore, the meningococcal thiC RS represents a rare example of transcriptional RS in a Gram-negative bacterium. We further observed that the RS is actively involved in modulating gene expression in response to different growth media and to supplemented bacterial and eukaryotic cell lysates as possible sources of nutrients in the nasopharynx. Our results suggest that RS-mediated gene regulation could influence meningococcal fitness, through the fine-tuning of biosynthesis and scavenging of nutrients and cofactors, such as thiamine.
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Affiliation(s)
- Francesco Righetti
- Department of Microbiology, Tumor- and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Solange Lise Materne
- Department of Microbiology, Tumor- and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
| | - John Boss
- Department of Microbiology, Tumor- and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Hannes Eichner
- Department of Microbiology, Tumor- and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden
| | - Emmanuelle Charpentier
- Max Planck Unit for the Science of Pathogens, Berlin, Germany.,Department of Regulation in Infection Biology, Max Planck Institute for Infection Biology, Berlin, Germany.,Institute for Biology, Humboldt University, Berlin, Germany.,Department of Regulation in Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany.,The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå Centre for Microbial Research (UCMR), Department of Molecular Biology, Umeå University, Umeå, Sweden
| | - Edmund Loh
- Department of Microbiology, Tumor- and Cell Biology, BioClinicum, Karolinska University Hospital, Stockholm, Sweden.,SCELSE, Nanyang Technological University, Singapore, Singapore
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37
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PA0335, a Gene Encoding Histidinol Phosphate Phosphatase, Mediates Histidine Auxotrophy in Pseudomonas aeruginosa. Appl Environ Microbiol 2020; 86:AEM.02593-19. [PMID: 31862725 DOI: 10.1128/aem.02593-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 11/24/2019] [Indexed: 11/20/2022] Open
Abstract
The biosynthesis of histidine, a proteinogenic amino acid, has been extensively studied due to its importance in bacterial growth and survival. Histidinol-phosphate phosphatase (Hol-Pase), which is responsible for the penultimate step of histidine biosynthesis, is generally the last enzyme to be characterized in many bacteria because its origin and evolution are more complex compared to other enzymes in histidine biosynthesis. However, none of the enzymes in histidine biosynthesis, including Hol-Pase, have been characterized in Pseudomonas aeruginosa, which is an important opportunistic Gram-negative pathogen that can cause serious human infections. In our previous work, a transposon mutant of P. aeruginosa was found to display a growth defect on glucose-containing minimal solid medium. In this study, we found that the growth defect was due to incomplete histidine auxotrophy caused by PA0335 inactivation. Subsequently, PA0335 was shown to encode Hol-Pase, and its function and enzymatic activity were investigated using genetic and biochemical methods. In addition to PA0335, the roles of 12 other predicted genes involved in histidine biosynthesis in P. aeruginosa were examined. Among them, hisC2 (PA3165), hisH2 (PA3152), and hisF2 (PA3151) were found to be dispensable for histidine synthesis, whereas hisG (PA4449), hisE (PA5067), hisF1 (PA5140), hisB (PA5143), hisI (PA5066), hisC1 (PA4447), and hisA (PA5141) were essential because deletion of each resulted in complete histidine auxotrophy; similar to the case for PA0335, hisH1 (PA5142) or hisD (PA4448) deletion caused incomplete histidine auxotrophy. Taken together, our results outline the histidine synthesis pathway of P. aeruginosa IMPORTANCE Histidine is a common amino acid in proteins. Because it plays critical roles in bacterial metabolism, its biosynthetic pathway in many bacteria has been elucidated. However, the pathway remains unclear in Pseudomonas aeruginosa, an important opportunistic pathogen in clinical settings; in particular, there is scant knowledge about histidinol-phosphate phosphatase (Hol-Pase), which has a complex origin and evolution. In this study, P. aeruginosa Hol-Pase was identified and characterized. Furthermore, the roles of all other predicted genes involved in histidine biosynthesis were examined. Our results illustrate the histidine synthesis pathway of P. aeruginosa The knowledge obtained from this study may help in developing strategies to control P. aeruginosa-related infections. In addition, some enzymes of the histidine synthesis pathway from P. aeruginosa might be used as elements of histidine synthetic biology in other industrial microorganisms.
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Williams AH, Wheeler R, Deghmane AE, Santecchia I, Schaub RE, Hicham S, Moya Nilges M, Malosse C, Chamot-Rooke J, Haouz A, Dillard JP, Robins WP, Taha MK, Gomperts Boneca I. Defective lytic transglycosylase disrupts cell morphogenesis by hindering cell wall de- O-acetylation in Neisseria meningitidis. eLife 2020; 9:51247. [PMID: 32022687 PMCID: PMC7083599 DOI: 10.7554/elife.51247] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 02/04/2020] [Indexed: 12/17/2022] Open
Abstract
Lytic transglycosylases (LT) are enzymes involved in peptidoglycan (PG) remodeling. However, their contribution to cell-wall-modifying complexes and their potential as antimicrobial drug targets remains unclear. Here, we determined a high-resolution structure of the LT, an outer membrane lipoprotein from Neisseria species with a disordered active site helix (alpha helix 30). We show that deletion of the conserved alpha-helix 30 interferes with the integrity of the cell wall, disrupts cell division, cell separation, and impairs the fitness of the human pathogen Neisseria meningitidis during infection. Additionally, deletion of alpha-helix 30 results in hyperacetylated PG, suggesting this LtgA variant affects the function of the PG de-O-acetylase (Ape 1). Our study revealed that Ape 1 requires LtgA for optimal function, demonstrating that LTs can modulate the activity of their protein-binding partner. We show that targeting specific domains in LTs can be lethal, which opens the possibility that LTs are useful drug-targets.
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Affiliation(s)
- Allison Hillary Williams
- Unité Biologie et Génétique de la Paroi Bactérienne, Institut Pasteur; Groupe Avenir, INSERM 75015, Paris, France
| | - Richard Wheeler
- Unité Biologie et Génétique de la Paroi Bactérienne, Institut Pasteur; Groupe Avenir, INSERM 75015, Paris, France.,Tumour Immunology and Immunotherapy, Institut Gustave Roussy, Villejuif, France
| | | | - Ignacio Santecchia
- Unité Biologie et Génétique de la Paroi Bactérienne, Institut Pasteur; Groupe Avenir, INSERM 75015, Paris, France.,Universté Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Ryan E Schaub
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, United States
| | - Samia Hicham
- Unité Biologie et Génétique de la Paroi Bactérienne, Institut Pasteur; Groupe Avenir, INSERM 75015, Paris, France
| | - Maryse Moya Nilges
- Unité Technologie et Service BioImagerie Ultrastructural, Institut Pasteur, Paris, France
| | - Christian Malosse
- Unité Technologie et Service Spectrométrie de Masse pour la Biologie, Institut Pasteur; UMR 3528, CNRS 75015, Paris, France
| | - Julia Chamot-Rooke
- Unité Technologie et Service Spectrométrie de Masse pour la Biologie, Institut Pasteur; UMR 3528, CNRS 75015, Paris, France
| | - Ahmed Haouz
- Plate-forme de Cristallographie-C2RT, Institut Pasteur; UMR3528, CNRS 75015, Paris, France
| | - Joseph P Dillard
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, United States
| | - William P Robins
- Department of Microbiology, Harvard Medical School, Boston, United States
| | - Muhamed-Kheir Taha
- Unité des Infection Bactériennes Invasives, Institut Pasteur, Paris, France
| | - Ivo Gomperts Boneca
- Unité Biologie et Génétique de la Paroi Bactérienne, Institut Pasteur; Groupe Avenir, INSERM 75015, Paris, France
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Meningococcal Quinolone Resistance Originated from Several Commensal Neisseria Species. Antimicrob Agents Chemother 2020; 64:AAC.01494-19. [PMID: 31740556 DOI: 10.1128/aac.01494-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 11/11/2019] [Indexed: 02/07/2023] Open
Abstract
Quinolone resistance is increasing in Neisseria meningitidis, with its prevalence in China being high (>70%), but its origin remains unknown. The aim of this study was to investigate the donors of mutation-harboring gyrA alleles in N. meningitidis A total of 198 N. meningitidis isolates and 293 commensal Neisseria isolates were collected between 2005 and 2018 in Shanghai, China. The MICs of ciprofloxacin were determined using the agar dilution method. The resistance-associated genes gyrA and parC were sequenced for all isolates, while a few isolates were sequenced on the Illumina platform. The prevalences of quinolone resistance in the N. meningitidis and commensal Neisseria isolates were 67.7% (134/198) and 99.3% (291/293), respectively. All 134 quinolone-resistant N. meningitidis isolates possessed mutations in T91 (n = 123) and/or D95 (n = 12) of GyrA, with 7 isolates also harboring ParC mutations and exhibiting higher MICs. Phylogenetic analysis of the gyrA sequence identified six clusters. Among the 71 mutation-harboring gyrA alleles found in 221 N. meningitidis isolates and genomes (n = 221), 12 alleles (n = 103, 46.6%) were included in the N. meningitidis cluster, while 20 alleles (n = 56) were included in the N. lactamica cluster, 27 alleles (n = 49) were included in the N. cinerea cluster, and 9 alleles (n = 10) were included in the N. subflava cluster. Genomic analyses identified the exact N. lactamica donors of seven mutation-harboring gyrA alleles (gyrA92, gyrA97, gyrA98, gyrA114, gyrA116, gyrA151, and gyrA230) and the N. subflava donor isolate of gyrA171, with the sizes of the recombinant fragments ranging from 634 to 7,499 bp. Transformation of gyrA fragments from these donor strains into a meningococcal isolate increased its ciprofloxacin MIC from 0.004 μg/ml to 0.125 or 0.19 μg/ml and to 0.5 μg/ml with further transformation of an additional ParC mutation. Over half of the quinolone-resistant N. meningitidis isolates acquired resistance by horizontal gene transfer from three commensal Neisseria species. Quinolone resistance in N. meningitidis increases in a stepwise manner.
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40
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Tsang RSW, Ahmad T, Jamieson FB, Tyrrell GJ. WGS analysis of a penicillin-resistant Neisseria meningitidis strain containing a chromosomal ROB-1 β-lactamase gene. J Antimicrob Chemother 2020; 74:22-28. [PMID: 30295754 PMCID: PMC6293085 DOI: 10.1093/jac/dky391] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/28/2018] [Indexed: 11/14/2022] Open
Abstract
Objectives Neisseria meningitidis is rarely penicillin resistant. We describe WGS analysis of a penicillin-resistant N. meningitidis collected from a case of invasive meningococcal disease. Methods Serogrouping, serotyping and serosubtyping were performed with specific antibodies. β-Lactamase was detected by nitrocefin. MICs were determined by Etest and agar dilution. Sequencing of N. meningitidis genomes was done on the Illumina MiSeq platform and genome data were analysed using the Bacterial Isolate Genome Sequence Database (BIGSdb) on the PubMLST Neisseria website (https://pubmlst.org/neisseria/). Transformation was used to confirm the genetic basis of the penicillin resistance. Results An N. meningitidis blood isolate from a female patient in her mid-50s with a painful and septic left shoulder was found to have penicillin MIC values of 3–12 mg/L. The isolate was typed as Y: 14, 19: P1.– and ST3587, and was weakly β-lactamase positive. WGS analysis identified a full-length copy of the β-lactamase gene blaROB-1, which was contained on a 1719 bp insert with a G + C content of 41.7% (versus a G + C content of N. meningitidis of 51.7%), suggesting that the blaROB-1 gene came from a different bacterial species. A GenBank analysis of the blaROB-1 gene insert found 99.77% identity with a DNA segment found in plasmid pB1000′ from Haemophilus influenzae. Transformation of a penicillin-susceptible strain with the blaROB-1 gene conferred β-lactamase activity and penicillin resistance. Conclusions N. meningitidis serogroup Y, ST3587 can carry and express the blaROB-1 gene, leading to penicillin resistance. It is highly likely that the N. meningitidis isolate acquired the blaROB-1 gene from H. influenzae.
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Affiliation(s)
- Raymond S W Tsang
- Vaccine Preventable Bacterial Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Tauqeer Ahmad
- Vaccine Preventable Bacterial Diseases, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Frances B Jamieson
- Public Health Ontario, and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Gregory J Tyrrell
- Provincial Laboratory for Public Health and Division of Diagnostic and Applied Microbiology, Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
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41
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Monticolo F, Palomba E, Termolino P, Chiaiese P, de Alteriis E, Mazzoleni S, Chiusano ML. The Role of DNA in the Extracellular Environment: A Focus on NETs, RETs and Biofilms. FRONTIERS IN PLANT SCIENCE 2020; 11:589837. [PMID: 33424885 PMCID: PMC7793654 DOI: 10.3389/fpls.2020.589837] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/25/2020] [Indexed: 05/06/2023]
Abstract
The capacity to actively release genetic material into the extracellular environment has been reported for bacteria, archaea, fungi, and in general, for microbial communities, but it is also described in the context of multicellular organisms, animals and plants. This material is often present in matrices that locate outside the cells. Extracellular matrices have important roles in defense response and disease in microbes, animal and plants cells, appearing as barrier against pathogen invasion or for their recognition. Specifically, neutrophils extracellular traps (NETs) in animals and root extracellular traps (RETs) in plants, are recognized to be important players in immunity. A growing amount of evidence revealed that the extracellular DNA, in these contexts, plays an active role in the defense action. Moreover, the protective role of extracellular DNA against antimicrobials and mechanical stress also appears to be confirmed in bacterial biofilms. In parallel, recent efforts highlighted different roles of self (homologous) and non-self (heterologous) extracellular DNA, paving the way to discussions on its role as a "Damage-associated molecular pattern" (DAMP). We here provide an evolutionary overview on extracellular DNA in extracellular matrices like RETs, NETs, and microbial biofilms, discussing on its roles and inferring on possible novel functionalities.
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Affiliation(s)
- Francesco Monticolo
- Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, Portici, Italy
| | - Emanuela Palomba
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica “Anton Dohrn”, Naples, Italy
| | - Pasquale Termolino
- Institute of Biosciences and Bioresources, National Research Council, Portici, Italy
| | - Pasquale Chiaiese
- Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, Portici, Italy
| | | | - Stefano Mazzoleni
- Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, Portici, Italy
| | - Maria Luisa Chiusano
- Department of Agricultural Sciences, Università degli Studi di Napoli Federico II, Portici, Italy
- Department of Research Infrastructures for Marine Biological Resources, Stazione Zoologica “Anton Dohrn”, Naples, Italy
- *Correspondence: Maria Luisa Chiusano,
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42
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da Silva RAG, Karlyshev AV, Oldfield NJ, Wooldridge KG, Bayliss CD, Ryan A, Griffin R. Variant Signal Peptides of Vaccine Antigen, FHbp, Impair Processing Affecting Surface Localization and Antibody-Mediated Killing in Most Meningococcal Isolates. Front Microbiol 2019; 10:2847. [PMID: 31921030 PMCID: PMC6930937 DOI: 10.3389/fmicb.2019.02847] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/25/2019] [Indexed: 11/24/2022] Open
Abstract
Meningococcal lipoprotein, Factor H binding protein (FHbp), is the sole antigen of the Trumenba vaccine (Pfizer) and one of four antigens of the Bexsero vaccine (GSK) targeting Neisseria meningitidis serogroup B isolates. Lipidation of FHbp is assumed to occur for all isolates. We show in the majority of a collection of United Kingdom isolates (1742/1895) non-synonymous single nucleotide polymorphisms (SNPs) in the signal peptide (SP) of FHbp. A single SNP, common to all, alters a polar amino acid that abolishes processing: lipidation and SP cleavage. Whilst some of the FHbp precursor is retained in the cytoplasm due to reduced binding to SecA, remarkably some is translocated and further surface-localized by Slam. Thus we show Slam is not lipoprotein-specific. In a panel of isolates tested, the overall reduced surface localization of the precursor FHbp, compared to isolates with an intact SP, corresponded with decreased susceptibility to antibody-mediated killing. Our findings shed new light on the canonical pathway for lipoprotein processing and translocation of important relevance for lipoprotein-based vaccines in development and in particular for Trumenba.
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Affiliation(s)
- Ronni A G da Silva
- Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Andrey V Karlyshev
- School of Life Sciences, Pharmacy and Chemistry, Kingston University, Kingston upon Thames, United Kingdom
| | - Neil J Oldfield
- Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Karl G Wooldridge
- Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Christopher D Bayliss
- Department of Genetics and Genome Biology, University of Leicester, Leicester, United Kingdom
| | - Ali Ryan
- School of Life Sciences, Pharmacy and Chemistry, Kingston University, Kingston upon Thames, United Kingdom
| | - Ruth Griffin
- Centre for Biomolecular Sciences, University of Nottingham, Nottingham, United Kingdom
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43
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Pensar J, Puranen S, Arnold B, MacAlasdair N, Kuronen J, Tonkin-Hill G, Pesonen M, Xu Y, Sipola A, Sánchez-Busó L, Lees JA, Chewapreecha C, Bentley SD, Harris SR, Parkhill J, Croucher NJ, Corander J. Genome-wide epistasis and co-selection study using mutual information. Nucleic Acids Res 2019; 47:e112. [PMID: 31361894 PMCID: PMC6765119 DOI: 10.1093/nar/gkz656] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 07/09/2019] [Accepted: 07/19/2019] [Indexed: 01/19/2023] Open
Abstract
Covariance-based discovery of polymorphisms under co-selective pressure or epistasis has received considerable recent attention in population genomics. Both statistical modeling of the population level covariation of alleles across the chromosome and model-free testing of dependencies between pairs of polymorphisms have been shown to successfully uncover patterns of selection in bacterial populations. Here we introduce a model-free method, SpydrPick, whose computational efficiency enables analysis at the scale of pan-genomes of many bacteria. SpydrPick incorporates an efficient correction for population structure, which adjusts for the phylogenetic signal in the data without requiring an explicit phylogenetic tree. We also introduce a new type of visualization of the results similar to the Manhattan plots used in genome-wide association studies, which enables rapid exploration of the identified signals of co-evolution. Simulations demonstrate the usefulness of our method and give some insight to when this type of analysis is most likely to be successful. Application of the method to large population genomic datasets of two major human pathogens, Streptococcus pneumoniae and Neisseria meningitidis, revealed both previously identified and novel putative targets of co-selection related to virulence and antibiotic resistance, highlighting the potential of this approach to drive molecular discoveries, even in the absence of phenotypic data.
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Affiliation(s)
- Johan Pensar
- Department of Mathematics and Statistics, Helsinki Institute for Information Technology (HIIT), Faculty of Science, University of Helsinki, FI-00014 Helsinki, Finland
| | - Santeri Puranen
- Department of Mathematics and Statistics, Helsinki Institute for Information Technology (HIIT), Faculty of Science, University of Helsinki, FI-00014 Helsinki, Finland.,Department of Computer Science, Aalto University, Espoo, FI-00014, Finland
| | - Brian Arnold
- Division of Informatics, Faculty of Arts and Sciences, Harvard University, Cambridge, MA 02138, USA
| | - Neil MacAlasdair
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Juri Kuronen
- Department of Biostatistics, University of Oslo, Oslo, 0317, Norway
| | - Gerry Tonkin-Hill
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Maiju Pesonen
- Department of Mathematics and Statistics, Helsinki Institute for Information Technology (HIIT), Faculty of Science, University of Helsinki, FI-00014 Helsinki, Finland.,Department of Computer Science, Aalto University, Espoo, FI-00014, Finland
| | - Yingying Xu
- Department of Mathematics and Statistics, Helsinki Institute for Information Technology (HIIT), Faculty of Science, University of Helsinki, FI-00014 Helsinki, Finland.,Department of Computer Science, Aalto University, Espoo, FI-00014, Finland
| | - Aleksi Sipola
- Department of Mathematics and Statistics, Helsinki Institute for Information Technology (HIIT), Faculty of Science, University of Helsinki, FI-00014 Helsinki, Finland
| | | | - John A Lees
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA
| | - Claire Chewapreecha
- Department of Medicine, University of Cambridge, Cambridge CB2 0QQ, UK.,Bioinformatics & Systems Biology program, King Mongkut's University of Technology Thonburi, Bangkok 10150, Thailand
| | - Stephen D Bentley
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Simon R Harris
- Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, CB3 0ES, UK
| | - Nicholas J Croucher
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, St. Mary's Campus, Imperial College London, London, W2 1PG, UK
| | - Jukka Corander
- Department of Mathematics and Statistics, Helsinki Institute for Information Technology (HIIT), Faculty of Science, University of Helsinki, FI-00014 Helsinki, Finland.,Parasites and Microbes, Wellcome Sanger Institute, Cambridge, CB10 1SA, UK.,Department of Biostatistics, University of Oslo, Oslo, 0317, Norway
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44
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Caugant DA, Brynildsrud OB. Neisseria meningitidis: using genomics to understand diversity, evolution and pathogenesis. Nat Rev Microbiol 2019; 18:84-96. [PMID: 31705134 DOI: 10.1038/s41579-019-0282-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/25/2019] [Indexed: 01/30/2023]
Abstract
Meningococcal disease remains an important cause of morbidity and death worldwide despite the development and increasing implementation of effective vaccines. Elimination of the disease is hampered by the enormous diversity and antigenic variability of the causative agent, Neisseria meningitidis, one of the most variable bacteria in nature. These features are attained mainly through high rates of horizontal gene transfer and alteration of protein expression through phase variation. The recent availability of whole-genome sequencing (WGS) of large-scale collections of N. meningitidis isolates from various origins, databases to facilitate storage and sharing of WGS data and the concomitant development of effective bioinformatics tools have led to a much more thorough understanding of the diversity of the species, its evolution and population structure and how virulent traits may emerge. Implementation of WGS is already contributing to enhanced epidemiological surveillance and is essential to ascertain the impact of vaccination strategies. This Review summarizes the recent advances provided by WGS studies in our understanding of the biology of N. meningitidis and the epidemiology of meningococcal disease.
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Affiliation(s)
- Dominique A Caugant
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway. .,Department of Community Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway.
| | - Ola B Brynildsrud
- Division for Infection Control and Environmental Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Food Safety and Infection Biology, Faculty of Veterinary Science, Norwegian University of Life Science, Oslo, Norway
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45
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Rivero-Calle I, Raguindin PF, Gómez-Rial J, Rodriguez-Tenreiro C, Martinón-Torres F. Meningococcal Group B Vaccine For The Prevention Of Invasive Meningococcal Disease Caused By Neisseria meningitidis Serogroup B. Infect Drug Resist 2019; 12:3169-3188. [PMID: 31632103 PMCID: PMC6793463 DOI: 10.2147/idr.s159952] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Accepted: 09/12/2019] [Indexed: 12/13/2022] Open
Abstract
Invasive meningococcal disease (IMD) is a major public health concern because of its high case fatality, long-term morbidity, and potential to course with outbreaks. IMD caused by Nesseira meningitidis serogroup B has been predominant in different regions of the world like Europe and only recently broadly protective vaccines against B serogroup have become available. Two protein-based vaccines, namely 4CMenB (Bexsero®) and rLP2086 (Trumenba®) are currently licensed for use in different countries against MenB disease. These vaccines came from a novel technology on vaccine design (or antigen selection) using highly specific antigen targets identified through whole-genome sequence analysis. Moreover, it has the potential to confer protection against non-B meningococcus and against other Neisserial species such as gonococcus. Real-world data on the vaccine-use are rapidly accumulating from the UK and other countries which used the vaccine for control of outbreak or as part of routine immunization program, reiterating its safety and efficacy. Additional data on real-life effectiveness, long-term immunity, and eventual herd effects, including estimates on vaccine impact for cost-effectiveness assessment are further needed. Given the predominance of MenB in Europe and other parts of the world, these new vaccines are crucial for the prevention and public health control of the disease, and should be considered.
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Affiliation(s)
- Irene Rivero-Calle
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Galicia, Spain.,Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Hospital Clínico Universitario and Universidad de Santiago de Compostela (USC), Galicia, Spain
| | - Peter Francis Raguindin
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Hospital Clínico Universitario and Universidad de Santiago de Compostela (USC), Galicia, Spain
| | - Jose Gómez-Rial
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Hospital Clínico Universitario and Universidad de Santiago de Compostela (USC), Galicia, Spain
| | - Carmen Rodriguez-Tenreiro
- Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Hospital Clínico Universitario and Universidad de Santiago de Compostela (USC), Galicia, Spain
| | - Federico Martinón-Torres
- Translational Pediatrics and Infectious Diseases, Department of Pediatrics, Hospital Clínico Universitario de Santiago de Compostela, Galicia, Spain.,Genetics, Vaccines and Pediatric Infectious Diseases Research Group (GENVIP), Hospital Clínico Universitario and Universidad de Santiago de Compostela (USC), Galicia, Spain
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46
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Seib KL, Haag AF, Oriente F, Fantappiè L, Borghi S, Semchenko EA, Schulz BL, Ferlicca F, Taddei AR, Giuliani MM, Pizza M, Delany I. The meningococcal vaccine antigen GNA2091 is an analogue of YraP and plays key roles in outer membrane stability and virulence. FASEB J 2019; 33:12324-12335. [DOI: 10.1096/fj.201900669r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kate L. Seib
- Institute for GlycomicsGriffith UniversityGold CoastQueenslandAustralia
| | | | | | | | | | | | - Benjamin L. Schulz
- School of Chemistry and Molecular BiosciencesThe University of QueenslandBrisbaneQueenslandAustralia
| | | | - Anna Rita Taddei
- Interdepartmental Centre of Electron Microscopy (CIME)Tuscia UniversityTusciaItaly
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47
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Lin D, O'Callaghan CA. MetClo: methylase-assisted hierarchical DNA assembly using a single type IIS restriction enzyme. Nucleic Acids Res 2019; 46:e113. [PMID: 29986052 PMCID: PMC6212791 DOI: 10.1093/nar/gky596] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 06/27/2018] [Indexed: 01/05/2023] Open
Abstract
Efficient DNA assembly is of great value in biological research and biotechnology. Type IIS restriction enzyme-based assembly systems allow assembly of multiple DNA fragments in a one-pot reaction. However, large DNA fragments can only be assembled by alternating use of two or more type IIS restriction enzymes in a multi-step approach. Here, we present MetClo, a DNA assembly method that uses only a single type IIS restriction enzyme for hierarchical DNA assembly. The method is based on in vivo methylation-mediated on/off switching of type IIS restriction enzyme recognition sites that overlap with site-specific methylase recognition sequences. We have developed practical MetClo systems for the type IIS enzymes BsaI, BpiI and LguI, and demonstrated hierarchical assembly of large DNA fragments up to 218 kb. The MetClo approach substantially reduces the need to remove internal restriction sites from components to be assembled. The use of a single type IIS enzyme throughout the different stages of DNA assembly allows novel and powerful design schemes for rapid large-scale hierarchical DNA assembly. The BsaI-based MetClo system is backward-compatible with component libraries of most of the existing type IIS restriction enzyme-based assembly systems, and has potential to become a standard for modular DNA assembly.
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Affiliation(s)
- Da Lin
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Christopher A O'Callaghan
- Wellcome Trust Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
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48
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Pantano E, Marchi S, Biagini M, Di Fede M, Nardi Dei V, Rossi Paccani S, Pizza M, Cartocci E. NHBA is processed by kallikrein from human saliva. PLoS One 2019; 14:e0203234. [PMID: 31369555 PMCID: PMC6675046 DOI: 10.1371/journal.pone.0203234] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 06/28/2019] [Indexed: 11/18/2022] Open
Abstract
Neisserial Heparin Binding Antigen (NHBA) is a surface-exposed lipoprotein of Neisseria meningitidis and a component of the Bexsero vaccine. NHBA is characterized by the presence of a highly conserved Arg-rich region involved in binding to heparin and heparan sulphate proteoglycans present on the surface of host epithelial cells, suggesting a possible role of NHBA during N. meningitidis colonization. NHBA has been shown to be cleaved by the meningococcal protease NalP and by human lactoferrin (hLF), a host protease presents in different body fluids (saliva, breast milk and serum). Cleavage occurs upstream or downstream the Arg-rich region. Since the human nasopharynx is the only known reservoir of infection, we further investigated the susceptibility of NHBA to human proteases present in the saliva to assess whether proteolytic cleavage could happen during the initial steps of colonization. Here we show that human saliva proteolytically cleaves NHBA, and identified human kallikrein 1 (hK1), a serine protease, as responsible for this cleavage. Kallikrein-related peptidases (KLKs) have a distinct domain structure and exist as a family of 15 genes which are differentially expressed in many tissues and in the central nervous system. They are present in plasma, lymph, urine, saliva, pancreatic juices, and other body fluids where they catalyze the proteolysis of several human proteins. Here we report the characterization of NHBA cleavage by the tissue kallikrein, expressed in saliva and the identification of the cleavage site on NHBA both, as recombinant protein or as native protein, when expressed on live bacteria. Overall, these findings provide new insights on NHBA as target of host proteases, highlights thepotential role of NHBA in the Neisseria meningitidis nasopharyngeal colonization, and of kallikrein as a defensive agent against meningococcal infection.
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Silhan J, Zhao Q, Boura E, Thomson H, Förster A, Tang CM, Freemont PS, Baldwin GS. Structural basis for recognition and repair of the 3'-phosphate by NExo, a base excision DNA repair nuclease from Neisseria meningitidis. Nucleic Acids Res 2019; 46:11980-11989. [PMID: 30329088 PMCID: PMC6294502 DOI: 10.1093/nar/gky934] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 10/12/2018] [Indexed: 01/29/2023] Open
Abstract
NExo is an enzyme from Neisseria meningitidis that is specialized in the removal of the 3'-phosphate and other 3'-lesions, which are potential blocks for DNA repair. NExo is a highly active DNA 3'-phosphatase, and although it is from the class II AP family it lacks AP endonuclease activity. In contrast, the NExo homologue NApe, lacks 3'-phosphatase activity but is an efficient AP endonuclease. These enzymes act together to protect the meningococcus from DNA damage arising mainly from oxidative stress and spontaneous base loss. In this work, we present crystal structures of the specialized 3'-phosphatase NExo bound to DNA in the presence and absence of a 3'-phosphate lesion. We have outlined the reaction mechanism of NExo, and using point mutations we bring mechanistic insights into the specificity of the 3'-phosphatase activity of NExo. Our data provide further insight into the molecular origins of plasticity in substrate recognition for this class of enzymes. From this we hypothesize that these specialized enzymes lead to enhanced efficiency and accuracy of DNA repair and that this is important for the biological niche occupied by this bacterium.
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Affiliation(s)
- Jan Silhan
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Czech Republic
| | - Qiyuan Zhao
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Czech Republic
| | - Hellen Thomson
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
| | | | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Paul S Freemont
- Department of Medicine, Imperial College London, South Kensington, London SW7 2AZ, UK
| | - Geoff S Baldwin
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, UK
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50
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Vigué L, Eyre-Walker A. The comparative population genetics of Neisseria meningitidis and Neisseria gonorrhoeae. PeerJ 2019; 7:e7216. [PMID: 31293838 PMCID: PMC6599670 DOI: 10.7717/peerj.7216] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 05/30/2019] [Indexed: 12/31/2022] Open
Abstract
Neisseria meningitidis and N. gonorrhoeae are closely related pathogenic bacteria. To compare their population genetics, we compiled a dataset of 1,145 genes found across 20 N. meningitidis and 15 N. gonorrhoeae genomes. We find that N. meningitidis is seven-times more diverse than N. gonorrhoeae in their combined core genome. Both species have acquired the majority of their diversity by recombination with divergent strains, however, we find that N. meningitidis has acquired more of its diversity by recombination than N. gonorrhoeae. We find that linkage disequilibrium (LD) declines rapidly across the genomes of both species. Several observations suggest that N. meningitidis has a higher effective population size than N. gonorrhoeae; it is more diverse, the ratio of non-synonymous to synonymous polymorphism is lower, and LD declines more rapidly to a lower asymptote in N. meningitidis. The two species share a modest amount of variation, half of which seems to have been acquired by lateral gene transfer and half from their common ancestor. We investigate whether diversity varies across the genome of each species and find that it does. Much of this variation is due to different levels of lateral gene transfer. However, we also find some evidence that the effective population size varies across the genome. We test for adaptive evolution in the core genome using a McDonald–Kreitman test and by considering the diversity around non-synonymous sites that are fixed for different alleles in the two species. We find some evidence for adaptive evolution using both approaches.
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