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Mikucki A, Kahler CM. Microevolution and Its Impact on Hypervirulence, Antimicrobial Resistance, and Vaccine Escape in Neisseria meningitidis. Microorganisms 2023; 11:3005. [PMID: 38138149 PMCID: PMC10745880 DOI: 10.3390/microorganisms11123005] [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: 11/06/2023] [Revised: 12/07/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Neisseria meningitidis is commensal of the human pharynx and occasionally invades the host, causing the life-threatening illness invasive meningococcal disease. The meningococcus is a highly diverse and adaptable organism thanks to natural competence, a propensity for recombination, and a highly repetitive genome. These mechanisms together result in a high level of antigenic variation to invade diverse human hosts and evade their innate and adaptive immune responses. This review explores the ways in which this diversity contributes to the evolutionary history and population structure of the meningococcus, with a particular focus on microevolution. It examines studies on meningococcal microevolution in the context of within-host evolution and persistent carriage; microevolution in the context of meningococcal outbreaks and epidemics; and the potential of microevolution to contribute to antimicrobial resistance and vaccine escape. A persistent theme is the idea that the process of microevolution contributes to the development of new hyperinvasive meningococcal variants. As such, microevolution in this species has significant potential to drive future public health threats in the form of hypervirulent, antibiotic-resistant, vaccine-escape variants. The implications of this on current vaccination strategies are explored.
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Affiliation(s)
- August Mikucki
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA 6009, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia
| | - Charlene M. Kahler
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA 6009, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, University of Western Australia, Perth, WA 6009, Australia
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Eriksson L, Johannesen TB, Stenmark B, Jacobsson S, Säll O, Hedberg ST, Fredlund H, Stegger M, Mölling P. Genetic variants linked to the phenotypic outcome of invasive disease and carriage of Neisseria meningitidis. Microb Genom 2023; 9:001124. [PMID: 37874326 PMCID: PMC10634450 DOI: 10.1099/mgen.0.001124] [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: 05/16/2023] [Accepted: 10/10/2023] [Indexed: 10/25/2023] Open
Abstract
Neisseria meningitidis can be a human commensal in the upper respiratory tract but is also capable of causing invasive diseases such as meningococcal meningitis and septicaemia. No specific genetic markers have been detected to distinguish carriage from disease isolates. The aim here was to find genetic traits that could be linked to phenotypic outcomes associated with carriage versus invasive N. meningitidis disease through a bacterial genome-wide association study (GWAS). In this study, invasive N. meningitidis isolates collected in Sweden (n=103) and carriage isolates collected at Örebro University, Sweden (n=213) 2018-2019 were analysed. The GWAS analysis, treeWAS, was applied to single-nucleotide polymorphisms (SNPs), genes and k-mers. One gene and one non-synonymous SNP were associated with invasive disease and seven genes and one non-synonymous SNP were associated with carriage isolates. The gene associated with invasive disease encodes a phage transposase (NEIS1048), and the associated invasive SNP glmU S373C encodes the enzyme N-acetylglucosamine 1-phosphate (GlcNAC 1-P) uridyltransferase. Of the genes associated with carriage isolates, a gene variant of porB encoding PorB class 3, the genes pilE/pilS and tspB have known functions. The SNP associated with carriage was fkbp D33N, encoding a FK506-binding protein (FKBP). K-mers from PilS, tbpB and tspB were found to be associated with carriage, while k-mers from mtrD and tbpA were associated with invasiveness. In the genes fkbp, glmU, PilC and pilE, k-mers were found that were associated with both carriage and invasive isolates, indicating that specific variations within these genes could play a role in invasiveness. The data presented here highlight genetic traits that are significantly associated with invasive or carriage N. meningitidis across the species population. These traits could prove essential to our understanding of the pathogenicity of N. meningitidis and could help to identify future vaccine targets.
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Affiliation(s)
- Lorraine Eriksson
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Thor Bech Johannesen
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Bianca Stenmark
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Susanne Jacobsson
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Olof Säll
- Department of Infectious Diseases, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Sara Thulin Hedberg
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Hans Fredlund
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Marc Stegger
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Paula Mölling
- Department of Laboratory Medicine, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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Klonowska A, Ardley J, Moulin L, Zandberg J, Patrel D, Gollagher M, Marinova D, Reddy TBK, Varghese N, Huntemann M, Woyke T, Seshadri R, Ivanova N, Kyrpides N, Reeve W. Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018. Front Microbiol 2023; 14:1082107. [PMID: 36925474 PMCID: PMC10011098 DOI: 10.3389/fmicb.2023.1082107] [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: 10/27/2022] [Accepted: 01/24/2023] [Indexed: 03/08/2023] Open
Abstract
Integrated virus genomes (prophages) are commonly found in sequenced bacterial genomes but have rarely been described in detail for rhizobial genomes. Cupriavidus taiwanensis STM 6018 is a rhizobial Betaproteobacteria strain that was isolated in 2006 from a root nodule of a Mimosa pudica host in French Guiana, South America. Here we describe features of the genome of STM 6018, focusing on the characterization of two different types of prophages that have been identified in its genome. The draft genome of STM 6018 is 6,553,639 bp, and consists of 80 scaffolds, containing 5,864 protein-coding genes and 61 RNA genes. STM 6018 contains all the nodulation and nitrogen fixation gene clusters common to symbiotic Cupriavidus species; sharing >99.97% bp identity homology to the nod/nif/noeM gene clusters from C. taiwanensis LMG19424T and "Cupriavidus neocalidonicus" STM 6070. The STM 6018 genome contains the genomes of two prophages: one complete Mu-like capsular phage and one filamentous phage, which integrates into a putative dif site. This is the first characterization of a filamentous phage found within the genome of a rhizobial strain. Further examination of sequenced rhizobial genomes identified filamentous prophage sequences in several Beta-rhizobial strains but not in any Alphaproteobacterial rhizobia.
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Affiliation(s)
- Agnieszka Klonowska
- Université de Montpellier, IRD, CIRAD, INRAE, Institut AgroPHIM Plant Health Institute, Montpellier, France
| | - Julie Ardley
- Centre for Crop and Food Innovation, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Lionel Moulin
- Université de Montpellier, IRD, CIRAD, INRAE, Institut AgroPHIM Plant Health Institute, Montpellier, France
| | - Jaco Zandberg
- Centre for Crop and Food Innovation, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
| | - Delphine Patrel
- Université de Montpellier, IRD, CIRAD, INRAE, Institut AgroPHIM Plant Health Institute, Montpellier, France
| | - Margaret Gollagher
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA, Australia
| | - Dora Marinova
- Curtin University Sustainability Policy Institute, Curtin University, Bentley, WA, Australia
| | - T B K Reddy
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Neha Varghese
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Marcel Huntemann
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Rekha Seshadri
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Natalia Ivanova
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nikos Kyrpides
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Wayne Reeve
- Centre for Crop and Food Innovation, Food Futures Institute, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA, Australia
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Madariaga-Troncoso D, Leyton-Carcaman B, Garcia M, Kawai M, Abanto Marin M. Comprehensive Genome Analysis of Neisseria meningitidis from South America Reveals a Distinctive Pathogenicity-Related Prophage Repertoire. Int J Mol Sci 2022; 23:ijms232415731. [PMID: 36555373 PMCID: PMC9779448 DOI: 10.3390/ijms232415731] [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: 10/14/2022] [Revised: 11/15/2022] [Accepted: 11/25/2022] [Indexed: 12/14/2022] Open
Abstract
Neisseria meningitidis, a bacterium that colonizes in the human nasopharynx, occasionally causes invasive meningococcal disease leading to meningitis or septicemia. Different serogroups and lineages (clonal complexes) are related to the occurrence and epidemiology of N. meningitidis. Despite vaccines for most serogroups, N. meningitidis lineages causing unusual clinical manifestations and a higher fatality rate compared to other lineages have been reported in South America. The present study focused on exploring the diversity of N. meningitidis prophages from South America and their relationship with the epidemiological variables of these strains. We found a high diversity of prophages among the different clonal complexes. By comparing them with previously described N. meningitidis phages and prophages, we revealed groups of prophages sharing similar compositions, which could be useful for prophage comparison in N. meningitidis. Furthermore, we observed a high correlation between the prophage content and epidemiological features, e.g., pathogenicity or clonal complex. Additionally, a distinctive filamentous prophage named here as IMSAR-11 (Invasive Meningococci from South America Related to cc11) was identified. Interestingly, two versions of IMSAR-11, circular and chromosomally integrated, were found. Overall, this study reinforces the importance of the genomic characterization of circulating N. meningitidis lineages to generate new targets for lineage monitoring, diagnosis, or appropriateness of vaccine development. Further studies are necessary to understand the role of these prophages in the persistence, dispersal, and virulence of N. meningitidis in the world.
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Affiliation(s)
- David Madariaga-Troncoso
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
| | - Benjamin Leyton-Carcaman
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
| | - Matias Garcia
- Laboratory of Molecular Applied Biology, Center of Excellence in Translational Medicine, Universidad de La Frontera, Temuco 4811230, Chile
| | - Mikihiko Kawai
- Department of Interdisciplinary Environment, Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Michel Abanto Marin
- Scientific and Technological Bioresource Nucleus, Universidad de La Frontera, Temuco 4811230, Chile
- Correspondence:
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de Almeida JCF, da Silva Xavier A, Cascardo RDS, de Rezende RR, de Souza FO, Lopes CA, Alfenas-Zerbini P. Genomic and Biological Characterization of Ralstonia solanacearum Inovirus Brazil 1, an Inovirus that Alters the Pathogenicity of the Phytopathogen Ralstonia pseudosolanacearum. MICROBIAL ECOLOGY 2022; 84:527-538. [PMID: 34557947 DOI: 10.1007/s00248-021-01874-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Filamentous bacteriophages contain a single-stranded DNA genome and have a peculiar lifestyle, since they do not cause host cell lysis, but establish a persistent association with the host, often causing behavioral changes, with effects on bacterial ecology. Over the years, a gradual reduction in the incidence of bacterial wilt has been observed in some fields from Brazil. This event, which has been associated with the loss of pathogenicity of Rasltonia spp. isolates due to infection by filamentous viruses of the inovirus group, is widely reported for Ralstonia spp. Asian isolates infected by inoviruses. In an attempt to elucidate which factors are associated with the phenomenon reported in Brazil, we investigated one isolate of R. solanacearum (UB-2014), with unusual characteristics for R. solanacearum, obtained from eggplant with mild wilt symptoms. To verify if the presence of filamentous bacteriophage was related to this phenotype, we performed viral purification and nucleic acid extraction. The phage genome was sequenced, and phylogenetic analyses demonstrated that the virus belongs to the family Inoviridae and was named as Ralstonia solanacerarum inovirus Brazil 1 (RSIBR1). RSIBR1 was transmitted to R. pseudosolanacearum GMI1000, and the virus-infected GMI1000 (GMI1000 VI) isolate showed alterations in phenotypic characteristics, as well as loss of pathogenicity, similarly to that observed in R. solanacearum isolate UB-2014. The presence of virus-infected UB-2014 and GMI1000 VI plants without symptoms, after 3 months, confirms that the infected isolates can colonize the plant without causing disease, which demonstrates that the phage infection changed the behavior of these pathogens.
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Affiliation(s)
- Juliana Cristina Fraleon de Almeida
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | - André da Silva Xavier
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | - Renan de Souza Cascardo
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | - Rafael Reis de Rezende
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | - Flavia Oliveira de Souza
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil
| | - Carlos Alberto Lopes
- EMBRAPA - National Center for Research on Vegetables (CNPH), Gama, DF, 70359-970, Brazil
| | - Poliane Alfenas-Zerbini
- Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária (BIOAGRO), Universidade Federal de Viçosa, Viçosa, MG, 36570-000, Brazil.
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Rhodes KA, Ma MC, Rendón MA, So M. Neisseria genes required for persistence identified via in vivo screening of a transposon mutant library. PLoS Pathog 2022; 18:e1010497. [PMID: 35580146 PMCID: PMC9140248 DOI: 10.1371/journal.ppat.1010497] [Citation(s) in RCA: 2] [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: 11/17/2021] [Revised: 05/27/2022] [Accepted: 04/04/2022] [Indexed: 11/30/2022] Open
Abstract
The mechanisms used by human adapted commensal Neisseria to shape and maintain a niche in their host are poorly defined. These organisms are common members of the mucosal microbiota and share many putative host interaction factors with Neisseria meningitidis and Neisseria gonorrhoeae. Evaluating the role of these shared factors during host carriage may provide insight into bacterial mechanisms driving both commensalism and asymptomatic infection across the genus. We identified host interaction factors required for niche development and maintenance through in vivo screening of a transposon mutant library of Neisseria musculi, a commensal of wild-caught mice which persistently and asymptomatically colonizes the oral cavity and gut of CAST/EiJ and A/J mice. Approximately 500 candidate genes involved in long-term host interaction were identified. These included homologs of putative N. meningitidis and N. gonorrhoeae virulence factors which have been shown to modulate host interactions in vitro. Importantly, many candidate genes have no assigned function, illustrating how much remains to be learned about Neisseria persistence. Many genes of unknown function are conserved in human adapted Neisseria species; they are likely to provide a gateway for understanding the mechanisms allowing pathogenic and commensal Neisseria to establish and maintain a niche in their natural hosts. Validation of a subset of candidate genes confirmed a role for a polysaccharide capsule in N. musculi persistence but not colonization. Our findings highlight the potential utility of the Neisseria musculi-mouse model as a tool for studying the pathogenic Neisseria; our work represents a first step towards the identification of novel host interaction factors conserved across the genus. The Neisseria genus contains many genetically related commensals of animals and humans, and two human pathogens, Neisseria gonorrhoeae and Neisseria meningitidis. The mechanisms allowing commensal Neisseria to maintain a niche in their host is little understood. To identify genes required for persistence, we screened a library of transposon mutants of Neisseria musculi, a commensal of wild-caught mice, in CAST/EiJ mice, which persistently and asymptomatically colonizes. Approximately 500 candidate host interaction genes were identified. A subset of these are homologs of N. meningitidis and N. gonorrhoeae genes known to modulate pathogen-host interactions in vitro. Many candidate genes have no known function, demonstrating how much remains to be learned about N. musculi niche maintenance. As many genes of unknown function are conserved in human adapted Neisseria, they provide a gateway for understanding Neisseria persistence mechanisms in general.
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Affiliation(s)
- Katherine A. Rhodes
- Immunobiology Department, University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
- * E-mail:
| | - Man Cheong Ma
- Immunobiology Department, University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
| | - María A. Rendón
- Immunobiology Department, University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
| | - Magdalene So
- Immunobiology Department, University of Arizona, Tucson, Arizona, United States of America
- BIO5 Institute, University of Arizona, Tucson, Arizona, United States of America
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Mikucki A, McCluskey NR, Kahler CM. The Host-Pathogen Interactions and Epicellular Lifestyle of Neisseria meningitidis. Front Cell Infect Microbiol 2022; 12:862935. [PMID: 35531336 PMCID: PMC9072670 DOI: 10.3389/fcimb.2022.862935] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 02/28/2022] [Indexed: 01/17/2023] Open
Abstract
Neisseria meningitidis is a gram-negative diplococcus and a transient commensal of the human nasopharynx. It shares and competes for this niche with a number of other Neisseria species including N. lactamica, N. cinerea and N. mucosa. Unlike these other members of the genus, N. meningitidis may become invasive, crossing the epithelium of the nasopharynx and entering the bloodstream, where it rapidly proliferates causing a syndrome known as Invasive Meningococcal Disease (IMD). IMD progresses rapidly to cause septic shock and meningitis and is often fatal despite aggressive antibiotic therapy. While many of the ways in which meningococci survive in the host environment have been well studied, recent insights into the interactions between N. meningitidis and the epithelial, serum, and endothelial environments have expanded our understanding of how IMD develops. This review seeks to incorporate recent work into the established model of pathogenesis. In particular, we focus on the competition that N. meningitidis faces in the nasopharynx from other Neisseria species, and how the genetic diversity of the meningococcus contributes to the wide range of inflammatory and pathogenic potentials observed among different lineages.
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Affiliation(s)
- August Mikucki
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
| | - Nicolie R. McCluskey
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
- College of Science, Health, Engineering and Education, Telethon Kids Institute, Murdoch University, Perth, WA, Australia
| | - Charlene M. Kahler
- Marshall Centre for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Perth, WA, Australia
- *Correspondence: Charlene M. Kahler,
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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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Bettencourt C, Nunes A, Gomes JP, Simões MJ. Genomic surveillance of Neisseria meningitidis serogroup W in Portugal from 2003 to 2019. Eur J Clin Microbiol Infect Dis 2021; 41:289-298. [PMID: 34787749 DOI: 10.1007/s10096-021-04371-7] [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: 08/25/2021] [Accepted: 10/21/2021] [Indexed: 10/19/2022]
Abstract
In recent years, a change in the epidemiology of meningococcal disease caused by Neisseria meningitidis serogroup W (MenW) has been observed worldwide, with the emergence of new sublineages associated with a higher rate of fatal cases. The present study intends to describe the epidemiology of invasive meningococcal disease (IMD) due to MenW in Portugal between 2003 and 2019, and to genetically characterize population structure. Despite MenW has a low incidence in Portugal, having almost disappeared from 2008 to 2015, since 2016, the number of MenW cases has been steadily increasing at a rate of ~ twofold per year, with more than 80% of the characterized isolates belonging to clonal complex 11 (cc11). Core-genome phylogeny of 25 Portuguese (PT) MenW isolates showed a strain clustering mainly either with the Original UK or the UK 2013 sublineages. Our study also reported for the first time the presence of distinct prophages with a notable overrepresentation of an ~ 32-35-kb PS_1-like prophage found in MenW cc11 genomes. The presence of the PS_1-like prophage in almost all 4723 cc11 genomes selected from Neisseria PubMLST database regardless of the capsular group they belong to suggests an ancestral acquisition of this mobile element prior to capsular switching events. Overall, by mimicking the scenario observed worldwide, this study reinforces the importance of a close monitoring of MenW disease, especially from cc11, in order to promptly adapt the vaccination plan for IMD control in Portugal. Moreover, future studies are needed to understand the putative contribution of prophages to fitness and virulence of PT MenW strains.
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Affiliation(s)
- Célia Bettencourt
- National Reference Laboratory for Neisseria meningitidis, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal.
| | - Alexandra Nunes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal. .,CBIOS - Universidade Lusófona Research Center for Biosciences & Health Technologies, Lisbon, Portugal.
| | - João Paulo Gomes
- Bioinformatics Unit, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
| | - Maria João Simões
- National Reference Laboratory for Neisseria meningitidis, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge, Lisbon, Portugal
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Conners R, McLaren M, Łapińska U, Sanders K, Stone MRL, Blaskovich MAT, Pagliara S, Daum B, Rakonjac J, Gold VAM. CryoEM structure of the outer membrane secretin channel pIV from the f1 filamentous bacteriophage. Nat Commun 2021; 12:6316. [PMID: 34728631 PMCID: PMC8563730 DOI: 10.1038/s41467-021-26610-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/13/2021] [Indexed: 11/09/2022] Open
Abstract
The Ff family of filamentous bacteriophages infect gram-negative bacteria, but do not cause lysis of their host cell. Instead, new virions are extruded via the phage-encoded pIV protein, which has homology with bacterial secretins. Here, we determine the structure of pIV from the f1 filamentous bacteriophage at 2.7 Å resolution by cryo-electron microscopy, the first near-atomic structure of a phage secretin. Fifteen f1 pIV subunits assemble to form a gated channel in the bacterial outer membrane, with associated soluble domains projecting into the periplasm. We model channel opening and propose a mechanism for phage egress. By single-cell microfluidics experiments, we demonstrate the potential for secretins such as pIV to be used as adjuvants to increase the uptake and efficacy of antibiotics in bacteria. Finally, we compare the f1 pIV structure to its homologues to reveal similarities and differences between phage and bacterial secretins.
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Affiliation(s)
- Rebecca Conners
- Living Systems Institute, University of Exeter, Exeter, UK
- College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Exeter, UK
| | - Mathew McLaren
- Living Systems Institute, University of Exeter, Exeter, UK
- College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Exeter, UK
| | - Urszula Łapińska
- Living Systems Institute, University of Exeter, Exeter, UK
- College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Exeter, UK
| | - Kelly Sanders
- Living Systems Institute, University of Exeter, Exeter, UK
- College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Exeter, UK
| | - M Rhia L Stone
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Mark A T Blaskovich
- Centre for Superbug Solutions, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, Australia
| | - Stefano Pagliara
- Living Systems Institute, University of Exeter, Exeter, UK
- College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Exeter, UK
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Exeter, UK
- College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Exeter, UK
| | - Jasna Rakonjac
- School of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Exeter, UK.
- College of Life and Environmental Sciences, Geoffrey Pope, University of Exeter, Exeter, UK.
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11
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Earle SG, Lobanovska M, Lavender H, Tang C, Exley RM, Ramos-Sevillano E, Browning DF, Kostiou V, Harrison OB, Bratcher HB, Varani G, Tang CM, Wilson DJ, Maiden MCJ. Genome-wide association studies reveal the role of polymorphisms affecting factor H binding protein expression in host invasion by Neisseria meningitidis. PLoS Pathog 2021; 17:e1009992. [PMID: 34662348 PMCID: PMC8553145 DOI: 10.1371/journal.ppat.1009992] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 10/28/2021] [Accepted: 09/29/2021] [Indexed: 11/18/2022] Open
Abstract
Many invasive bacterial diseases are caused by organisms that are ordinarily harmless components of the human microbiome. Effective interventions against these microbes require an understanding of the processes whereby symbiotic or commensal relationships transition into pathology. Here, we describe bacterial genome-wide association studies (GWAS) of Neisseria meningitidis, a common commensal of the human respiratory tract that is nevertheless a leading cause of meningitis and sepsis. An initial GWAS discovered bacterial genetic variants, including single nucleotide polymorphisms (SNPs), associated with invasive meningococcal disease (IMD) versus carriage in several loci across the meningococcal genome, encoding antigens and other extracellular components, confirming the polygenic nature of the invasive phenotype. In particular, there was a significant peak of association around the fHbp locus, encoding factor H binding protein (fHbp), which promotes bacterial immune evasion of human complement by recruiting complement factor H (CFH) to the meningococcal surface. The association around fHbp with IMD was confirmed by a validation GWAS, and we found that the SNPs identified in the validation affected the 5' region of fHbp mRNA, altering secondary RNA structures, thereby increasing fHbp expression and enhancing bacterial escape from complement-mediated killing. This finding is consistent with the known link between complement deficiencies and CFH variation with human susceptibility to IMD. These observations demonstrate the importance of human and bacterial genetic variation across the fHbp:CFH interface in determining IMD susceptibility, the transition from carriage to disease.
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Affiliation(s)
- Sarah G. Earle
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Oxford, United Kingdom
| | - Mariya Lobanovska
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Hayley Lavender
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Changyan Tang
- Department of Chemistry, University of Washington, Seattle, Washington United States of America
| | - Rachel M. Exley
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | | | - Douglas F. Browning
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Vasiliki Kostiou
- Nuffield Department of Clinical Medicine, Experimental Medicine Division, John Radcliffe Hospital, Oxford, United Kingdom
| | | | | | - Gabriele Varani
- Department of Chemistry, University of Washington, Seattle, Washington United States of America
- * E-mail: (GV); (CMT); (DJW); (MCJM)
| | - Christoph M. Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
- * E-mail: (GV); (CMT); (DJW); (MCJM)
| | - Daniel J. Wilson
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Oxford, United Kingdom
- Department for Continuing Education, University of Oxford, Oxford, United Kingdom
- * E-mail: (GV); (CMT); (DJW); (MCJM)
| | - Martin C. J. Maiden
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail: (GV); (CMT); (DJW); (MCJM)
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12
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Spinsanti M, Brignoli T, Bodini M, Fontana LE, De Chiara M, Biolchi A, Muzzi A, Scarlato V, Delany I. Deconvolution of intergenic polymorphisms determining high expression of Factor H binding protein in meningococcus and their association with invasive disease. PLoS Pathog 2021; 17:e1009461. [PMID: 33770146 PMCID: PMC8026042 DOI: 10.1371/journal.ppat.1009461] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 04/07/2021] [Accepted: 03/09/2021] [Indexed: 12/11/2022] Open
Abstract
Neisseria meningitidis is a strictly human pathogen and is the major cause of septicemia and meningitis worldwide. Factor H binding protein (fHbp) is a meningococcal surface-exposed lipoprotein that binds the human Complement factor H allowing the bacterium to evade the host innate immune response. FHbp is also a key antigen in two vaccines against N. meningitidis serogroup B. Although the fHbp gene is present in most circulating meningococcal strains, level of fHbp expression varies among isolates and has been correlated to differences in promoter sequences upstream of the gene. Here we elucidated the sequence determinants that control fHbp expression in globally circulating strains. We analyzed the upstream fHbpintergenic region (fIR) of more than 5800 strains representative of the UK circulating isolates and we identified eleven fIR sequence alleles which represent 88% of meningococcal strains. By engineering isogenic recombinant strains where fHbp expression was under the control of each of the eleven fIR alleles, we confirmed that the fIR sequence determines a specific and distinct level of expression. Moreover, we identified the molecular basis for variation in expression through polymorphisms within key regulatory regions that are known to affect fHbp expression. We experimentally established three expression groups, high–medium–low, that correlated directly with the susceptibility to killing mediated by anti-fHbp antibodies and the ability of the meningococcal strain to survive within human serum. By using this sequence classification and information about the variant, we predicted fHbp expression in the panel of UK strains and we observed that strains with higher expressing fIR alleles are more likely associated with invasive disease. Overall, our findings can contribute to understand and predict vaccine coverage mediated by fHbp as well as to shed light on the role of this virulence factor in determining an invasive phenotype. Complement plays a key role in the immunity against Neisseria meningitidis. The meningococcus uses the Factor H binding protein (fHbp), to bind a negative regulator of the alternative complement pathway, factor H, to its surface thus preventing complement deposition and lysis. The use of fHbp as an antigen in two licensed vaccines highlights its public health relevance. Therefore the levels of this antigen produced by the bacterium are pivotal on the one hand for the survival of N. meningitidis in blood and on the other hand for the susceptibility to vaccine-induced killing antibodies. Here, we identify the predominant nucleotide sequences that drive distinct levels of the fHbp antigen in circulating meningococcal strains. We cluster them into distinct groups with increasing levels and observe that strains expressing higher fHbp amounts are associated with invasive disease. Our findings show that the nucleotide sequence of the fHbp promoter can be used for the prediction of antigen levels of any given strain and consequently for both the assessment of its sensitivity to killing by fHbp antibodies and its likelihood to cause invasive disease.
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Affiliation(s)
| | - Tarcisio Brignoli
- GSK, Siena, Italy
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
| | | | | | | | | | | | - Vincenzo Scarlato
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, Bologna, Italy
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13
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Al Suwayyid BA, Rankine-Wilson L, Speers DJ, Wise MJ, Coombs GW, Kahler CM. Meningococcal Disease-Associated Prophage-Like Elements Are Present in Neisseria gonorrhoeae and Some Commensal Neisseria Species. Genome Biol Evol 2020; 12:3938-3950. [PMID: 32031617 PMCID: PMC7058167 DOI: 10.1093/gbe/evaa023] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2020] [Indexed: 12/14/2022] Open
Abstract
Neisseria spp. possess four genogroups of filamentous prophages, termed Nf1 to 4. A filamentous bacteriophage from the Nf1 genogroup termed meningococcal disease-associated phage (MDA φ) is associated with clonal complexes of Neisseria meningitidis that cause invasive meningococcal disease. Recently, we recovered an isolate of Neisseria gonorrhoeae (ExNg63) from a rare case of gonococcal meningitis, and found that it possessed a region with 90% similarity to Nf1 prophages, specifically, the meningococcal MDA φ. This led to the hypothesis that the Nf1 prophage may be more widely distributed amongst the genus Neisseria. An analysis of 92 reference genomes revealed the presence of intact Nf1 prophages in the commensal species, Neisseria lactamica and Neisseria cinerea in addition to the pathogen N. gonorrhoeae. In N. gonorrhoeae, Nf1 prophages had a restricted distribution but were present in all representatives of MLST ST1918. Of the 160 phage integration sites identified, only one common insertion site was found between one isolate of N. gonorrhoeae and N. meningitidis. There was an absence of any obvious conservation of the receptor for prophage entry, PilE, suggesting that the phage may have been obtained by natural transformation. An examination of the restriction modification systems and mutated mismatch repair systems with prophage presence suggested that there was no obvious preference for these hosts. A timed phylogeny inferred that N. meningitidis was the donor of the Nf1 prophages in N. lactamica and N. gonorrhoeae. Further work is required to determine whether Nf1 prophages are active and can act as accessory colonization factors in these species.
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Affiliation(s)
- Barakat A Al Suwayyid
- The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Crawley, Australia.,School of Biomedical Sciences, The University of Western Australia, Crawley, Australia.,Ministry of Education, Riyadh, Saudi Arabia
| | - Leah Rankine-Wilson
- The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Crawley, Australia.,School of Biomedical Sciences, The University of Western Australia, Crawley, Australia
| | - David J Speers
- Department of Microbiology, PathWest Laboratory Medicine WA, Queen Elizabeth II Medical Centre, Nedlands, Australia.,School of Medicine and Pharmacology, University of Western Australia, Crawley, Australia
| | - Michael J Wise
- The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Crawley, Australia.,Computer Science and Software Engineering, The University of Western Australia, Crawley, Australia
| | - Geoffrey W Coombs
- Department of Microbiology, PathWest Laboratory Medicine WA, Fiona Stanley Hospital, Murdoch, Australia.,Antimicrobial Resistance and Infectious Diseases Research Laboratory, School of Veterinary Life Sciences, Murdoch University, Australia
| | - Charlene M Kahler
- The Marshall Centre for Infectious Diseases Research and Training, The University of Western Australia, Crawley, Australia.,School of Biomedical Sciences, The University of Western Australia, Crawley, Australia
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14
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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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15
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Piekarowicz A, Kłyż A, Adamczyk-Popławska M, Stein DC. Association of host proteins with the broad host range filamentous phage NgoΦ6 of Neisseria gonorrhoeae. PLoS One 2020; 15:e0240579. [PMID: 33057372 PMCID: PMC7561177 DOI: 10.1371/journal.pone.0240579] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 09/30/2020] [Indexed: 02/07/2023] Open
Abstract
All Neisseria gonorrhoeae strains contain multiple copies of integrated filamentous phage genomes with undefined structures. In this study, we sought to characterize the capsid proteins of filamentous N. gonorrhoeae bacteriophage NgoΦ6 and phagemids propagated in different bacteria. The data demonstrate that purified phage contain phage-encoded structural proteins and bacterial host proteins; host proteins consistently copurified with the phage particles. The bacterial host proteins associated with the phage filament (as identified by mass spectrometry) tended to be one of the predominant outer membrane components of the host strain, plus minor additional host proteins. We were able to copurify a functional ß-lactamase, a phagemid-encoded protein, with phage filaments. We used protein modeling and immunological analysis to identify the major phage encoded structural proteins. The antigenic properties of these proteins depended on the bacterium where the phages were propagated. Polyclonal antibodies against N. gonorrhoeae phage NgoΦ6 recognized phage-encoded proteins if the phage was propagated in N. gonorrhoeae or H. influenzae cells but not if it was propagated in Salmonella or E. coli. We show that the phage filaments isolated from gonococci and Haemophilus are glycosylated, and this may explain the antigenic diversity seen. Taken en toto, the data demonstrate that while the neisserial filamentous phage are similar to other Inovirus with respect to overall genomic organization, their ability to closely associate with host proteins suggests that they have unique surface properties and are secreted by a here-to-fore unknown secretory pathway.
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Affiliation(s)
- A. Piekarowicz
- Department of Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - A. Kłyż
- Department of Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - M. Adamczyk-Popławska
- Department of Virology, Institute of Microbiology, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - D. C. Stein
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, United States of America
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16
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Mauritzen JJ, Castillo D, Tan D, Svenningsen SL, Middelboe M. Beyond Cholera: Characterization of zot-Encoding Filamentous Phages in the Marine Fish Pathogen Vibrio anguillarum. Viruses 2020; 12:v12070730. [PMID: 32640584 PMCID: PMC7412436 DOI: 10.3390/v12070730] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 06/29/2020] [Accepted: 07/02/2020] [Indexed: 12/22/2022] Open
Abstract
Zonula occludens toxin (Zot) is a conserved protein in filamentous vibriophages and has been reported as a putative toxin in Vibrio cholerae. Recently, widespread distribution of zot-encoding prophages was found among marine Vibrio species, including environmental isolates. However, little is known about the dynamics of these prophages beyond V. cholerae. In this study, we characterized and quantified the zot-encoding filamentous phage VAIϕ, spontaneously induced from the fish pathogen V. anguillarum. VAIϕ contained 6117 bp encoding 11 ORFs, including ORF8pVAI, exhibiting 27%–73% amino acid identity to Inovirus Zot-like proteins. A qPCR method revealed an average of four VAIϕ genomes per host genome during host exponential growth phase, and PCR demonstrated dissemination of induced VAIϕ to other V. anguillarum strains through re-integration in non-lysogens. VAIϕ integrated into both chromosomes of V. anguillarum by recombination, causing changes in a putative ORF in the phage genome. Phylogenetic analysis of the V. anguillarumInoviridae elements revealed mosaic genome structures related to mainly V. cholerae. Altogether, this study contributes to the understanding of Inovirus infection dynamics and mobilization of zot-like genes beyond human pathogenic vibrios, and discusses their potential role in the evolution of the fish pathogen V. anguillarum.
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Affiliation(s)
- Jesper Juel Mauritzen
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark; (J.J.M.); (D.C.)
| | - Daniel Castillo
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark; (J.J.M.); (D.C.)
| | - Demeng Tan
- Section for Biomolecular Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200 København N, Denmark; (D.T.); (S.L.S.)
| | - Sine Lo Svenningsen
- Section for Biomolecular Sciences, University of Copenhagen, Ole Maaløes Vej 5, 2200 København N, Denmark; (D.T.); (S.L.S.)
| | - Mathias Middelboe
- Marine Biological Section, University of Copenhagen, Strandpromenaden 5, 3000 Helsingør, Denmark; (J.J.M.); (D.C.)
- Correspondence: ; Tel.: +45-35-32-19-91
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17
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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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18
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Delbaz A, Chen M, Jen FEC, Schulz BL, Gorse AD, Jennings MP, St John JA, Ekberg JAK. Neisseria meningitidis Induces Pathology-Associated Cellular and Molecular Changes in Trigeminal Schwann Cells. Infect Immun 2020; 88:e00955-19. [PMID: 31964742 PMCID: PMC7093114 DOI: 10.1128/iai.00955-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 02/06/2023] Open
Abstract
Neisseria meningitidis, a common cause of sepsis and bacterial meningitis, infects the meninges and central nervous system (CNS), primarily via paracellular traversal across the blood-brain barrier (BBB) or blood-cerebrospinal fluid barrier. N. meningitidis is often present asymptomatically in the nasopharynx, and the nerves extending between the nasal cavity and the brain constitute an alternative route by which the meningococci may reach the CNS. To date, the cellular mechanisms involved in nerve infection are not fully understood. Peripheral nerve glial cells are phagocytic and are capable of eliminating microorganisms, but some pathogens may be able to overcome this protection mechanism and instead infect the glia, causing cell death or pathology. Here, we show that N. meningitidis readily infects trigeminal Schwann cells (the glial cells of the trigeminal nerve) in vitro in both two-dimensional and three-dimensional cell cultures. Infection of trigeminal Schwann cells may be one mechanism by which N. meningitidis is able to invade the CNS. Infection of the cells led to multinucleation and the appearance of atypical nuclei, with the presence of horseshoe nuclei and the budding of nuclei increasing over time. Using sequential window acquisition of all theoretical mass spectra (SWATH-MS) proteomics followed by bioinformatics pathway analysis, we showed that N. meningitidis induced protein alterations in the glia that were associated with altered intercellular signaling, cell-cell interactions, and cellular movement. The analysis also suggested that the alterations in protein levels were consistent with changes occurring in cancer. Thus, infection of the trigeminal nerve by N. meningitidis may have ongoing adverse effects on the biology of Schwann cells, which may lead to pathology.
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Affiliation(s)
- Ali Delbaz
- Clem Jones Centre for Neurobiology and Stem Cell Research, Griffith University, Brisbane, QLD, Australia
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD, Australia
- Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia
| | - Mo Chen
- Clem Jones Centre for Neurobiology and Stem Cell Research, Griffith University, Brisbane, QLD, Australia
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD, Australia
- Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia
| | - Freda E-C Jen
- Institute for Glycomics, Griffith University, Southport, QLD, Australia
| | - Benjamin L Schulz
- Australian Infectious Diseases Research Centre, School of Chemistry and Molecular Biosciences, the University of Queensland, St. Lucia, Brisbane, Australia
| | - Alain-Dominique Gorse
- QFAB Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Brisbane, Australia
| | | | - James A St John
- Clem Jones Centre for Neurobiology and Stem Cell Research, Griffith University, Brisbane, QLD, Australia
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD, Australia
- Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia
| | - Jenny A K Ekberg
- Clem Jones Centre for Neurobiology and Stem Cell Research, Griffith University, Brisbane, QLD, Australia
- Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD, Australia
- Menzies Health Institute Queensland, Griffith University, Southport, QLD, Australia
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19
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Saber MM, Shapiro BJ. Benchmarking bacterial genome-wide association study methods using simulated genomes and phenotypes. Microb Genom 2020; 6:e000337. [PMID: 32100713 PMCID: PMC7200059 DOI: 10.1099/mgen.0.000337] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 01/23/2020] [Indexed: 11/18/2022] Open
Abstract
Genome-wide association studies (GWASs) have the potential to reveal the genetics of microbial phenotypes such as antibiotic resistance and virulence. Capitalizing on the growing wealth of bacterial sequence data, microbial GWAS methods aim to identify causal genetic variants while ignoring spurious associations. Bacteria reproduce clonally, leading to strong population structure and genome-wide linkage, making it challenging to separate true 'hits' (i.e. mutations that cause a phenotype) from non-causal linked mutations. GWAS methods attempt to correct for population structure in different ways, but their performance has not yet been systematically and comprehensively evaluated under a range of evolutionary scenarios. Here, we developed a bacterial GWAS simulator (BacGWASim) to generate bacterial genomes with varying rates of mutation, recombination and other evolutionary parameters, along with a subset of causal mutations underlying a phenotype of interest. We assessed the performance (recall and precision) of three widely used single-locus GWAS approaches (cluster-based, dimensionality-reduction and linear mixed models, implemented in plink, pyseer and gemma) and one relatively new multi-locus model implemented in pyseer, across a range of simulated sample sizes, recombination rates and causal mutation effect sizes. As expected, all methods performed better with larger sample sizes and effect sizes. The performance of clustering and dimensionality reduction approaches to correct for population structure were considerably variable according to the choice of parameters. Notably, the multi-locus elastic net (lasso) approach was consistently amongst the highest-performing methods, and had the highest power in detecting causal variants with both low and high effect sizes. Most methods reached the level of good performance (recall >0.75) for identifying causal mutations of strong effect size [log odds ratio (OR) ≥2] with a sample size of 2000 genomes. However, only elastic nets reached the level of reasonable performance (recall=0.35) for detecting markers with weaker effects (log OR ~1) in smaller samples. Elastic nets also showed superior precision and recall in controlling for genome-wide linkage, relative to single-locus models. However, all methods performed relatively poorly on highly clonal (low-recombining) genomes, suggesting room for improvement in method development. These findings show the potential for multi-locus models to improve bacterial GWAS performance. BacGWASim code and simulated data are publicly available to enable further comparisons and benchmarking of new methods.
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Affiliation(s)
- Morteza M. Saber
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada
| | - B. Jesse Shapiro
- Département de Sciences Biologiques, Université de Montréal, Montréal, QC, Canada
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20
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Complete genome and methylome analysis of Neisseria meningitidis associated with increased serogroup Y disease. Sci Rep 2020; 10:3644. [PMID: 32108139 PMCID: PMC7046676 DOI: 10.1038/s41598-020-59509-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 01/22/2020] [Indexed: 12/22/2022] Open
Abstract
Invasive meningococcal disease (IMD) due to serogroup Y Neisseria meningitidis emerged in Europe during the 2000s. Draft genomes of serogroup Y isolates in Sweden revealed that although the population structure of these isolates was similar to other serogroup Y isolates internationally, a distinct strain (YI) and more specifically a sublineage (1) of this strain was responsible for the increase of serogroup Y IMD in Sweden. We performed single molecule real-time (SMRT) sequencing on eight serogroup Y isolates from different sublineages to unravel the genetic and epigenetic factors delineating them, in order to understand the serogroup Y emergence. Extensive comparisons between the serogroup Y sublineages of all coding sequences, complex genomic regions, intergenic regions, and methylation motifs revealed small point mutations in genes mainly encoding hypothetical and metabolic proteins, and non-synonymous variants in genes involved in adhesion, iron acquisition, and endotoxin production. The methylation motif CACNNNNNTAC was only found in isolates of sublineage 2. Only seven genes were putatively differentially expressed, and another two genes encoding hypothetical proteins were only present in sublineage 2. These data suggest that the serogroup Y IMD increase in Sweden was most probably due to small changes in genes important for colonization and transmission.
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21
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San JE, Baichoo S, Kanzi A, Moosa Y, Lessells R, Fonseca V, Mogaka J, Power R, de Oliveira T. Current Affairs of Microbial Genome-Wide Association Studies: Approaches, Bottlenecks and Analytical Pitfalls. Front Microbiol 2020; 10:3119. [PMID: 32082269 PMCID: PMC7002396 DOI: 10.3389/fmicb.2019.03119] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/24/2019] [Indexed: 12/12/2022] Open
Abstract
Microbial genome-wide association studies (mGWAS) are a new and exciting research field that is adapting human GWAS methods to understand how variations in microbial genomes affect host or pathogen phenotypes, such as drug resistance, virulence, host specificity and prognosis. Several computational tools and methods have been developed or adapted from human GWAS to facilitate the discovery of novel mutations and structural variations that are associated with the phenotypes of interest. However, no comprehensive, end-to-end, user-friendly tool is currently available. The development of a broadly applicable pipeline presents a real opportunity among computational biologists. Here, (i) we review the prominent and promising tools, (ii) discuss analytical pitfalls and bottlenecks in mGWAS, (iii) provide insights into the selection of appropriate tools, (iv) highlight the gaps that still need to be filled and how users and developers can work together to overcome these bottlenecks. Use of mGWAS research can inform drug repositioning decisions as well as accelerate the discovery and development of more effective vaccines and antimicrobials for pressing infectious diseases of global health significance, such as HIV, TB, influenza, and malaria.
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Affiliation(s)
- James Emmanuel San
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Shakuntala Baichoo
- Department of Digital Technologies, FoICDT, University of Mauritius, Réduit, Mauritius
| | - Aquillah Kanzi
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Yumna Moosa
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Richard Lessells
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Vagner Fonseca
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Laboratório de Genética Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - John Mogaka
- Discipline of Public Health, University of Kwazulu-Natal, Durban, South Africa
| | - Robert Power
- St Edmund Hall, Oxford University, Oxford, United Kingdom
| | - Tulio de Oliveira
- Kwazulu-Natal Research and Innovation Sequencing Platform (KRISP), College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, United States
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22
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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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23
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Coureuil M, Jamet A, Bille E, Lécuyer H, Bourdoulous S, Nassif X. Molecular interactions between Neisseria meningitidis and its human host. Cell Microbiol 2019; 21:e13063. [PMID: 31167044 PMCID: PMC6899865 DOI: 10.1111/cmi.13063] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 05/21/2019] [Accepted: 05/30/2019] [Indexed: 02/06/2023]
Abstract
Neisseria meningitidis is a Gram‐negative bacterium that asymptomatically colonises the nasopharynx of humans. For an unknown reason, N. meningitidis can cross the nasopharyngeal barrier and invade the bloodstream where it becomes one of the most harmful extracellular bacterial pathogen. This infectious cycle involves the colonisation of two different environments. (a) In the nasopharynx, N. meningitidis grow on the top of mucus‐producing epithelial cells surrounded by a complex microbiota. To survive and grow in this challenging environment, the meningococcus expresses specific virulence factors such as polymorphic toxins and MDAΦ. (b) Meningococci have the ability to survive in the extra cellular fluids including blood and cerebrospinal fluid. The interaction of N. meningitidis with human endothelial cells leads to the formation of typical microcolonies that extend overtime and promote vascular injury, disseminated intravascular coagulation, and acute inflammation. In this review, we will focus on the interplay between N. meningitidis and these two different niches at the cellular and molecular level and discuss the use of inhibitors of piliation as a potent therapeutic approach.
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Affiliation(s)
- Mathieu Coureuil
- Inserm, Institut Necker Enfants Malades, U1151, Paris, France.,Université de Paris, UMR_S 1151, Paris, France.,CNRS, UMR 8253, Paris, France
| | - Anne Jamet
- Inserm, Institut Necker Enfants Malades, U1151, Paris, France.,Université de Paris, UMR_S 1151, Paris, France.,CNRS, UMR 8253, Paris, France.,Assistance Publique - Hôpitaux de Paris, Hôpital Necker Enfants Malades, Paris, France
| | - Emmanuelle Bille
- Inserm, Institut Necker Enfants Malades, U1151, Paris, France.,Université de Paris, UMR_S 1151, Paris, France.,CNRS, UMR 8253, Paris, France.,Assistance Publique - Hôpitaux de Paris, Hôpital Necker Enfants Malades, Paris, France
| | - Hervé Lécuyer
- Inserm, Institut Necker Enfants Malades, U1151, Paris, France.,Université de Paris, UMR_S 1151, Paris, France.,CNRS, UMR 8253, Paris, France.,Assistance Publique - Hôpitaux de Paris, Hôpital Necker Enfants Malades, Paris, France
| | - Sandrine Bourdoulous
- Université de Paris, UMR_S 1151, Paris, France.,Inserm, U1016, Institut Cochin, Paris, France.,CNRS, UMR8104, Paris, France
| | - Xavier Nassif
- Inserm, Institut Necker Enfants Malades, U1151, Paris, France.,Université de Paris, UMR_S 1151, Paris, France.,CNRS, UMR 8253, Paris, France.,Assistance Publique - Hôpitaux de Paris, Hôpital Necker Enfants Malades, Paris, France
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24
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Hay ID, Lithgow T. Filamentous phages: masters of a microbial sharing economy. EMBO Rep 2019; 20:embr.201847427. [PMID: 30952693 DOI: 10.15252/embr.201847427] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 01/30/2019] [Accepted: 03/19/2019] [Indexed: 12/11/2022] Open
Abstract
Bacteriophage ("bacteria eaters") or phage is the collective term for viruses that infect bacteria. While most phages are pathogens that kill their bacterial hosts, the filamentous phages of the sub-class Inoviridae live in cooperative relationships with their bacterial hosts, akin to the principal behaviours found in the modern-day sharing economy: peer-to-peer support, to offset any burden. Filamentous phages impose very little burden on bacteria and offset this by providing service to help build better biofilms, or provision of toxins and other factors that increase virulence, or modified behaviours that provide novel motile activity to their bacterial hosts. Past, present and future biotechnology applications have been built on this phage-host cooperativity, including DNA sequencing technology, tools for genetic engineering and molecular analysis of gene expression and protein production, and phage-display technologies for screening protein-ligand and protein-protein interactions. With the explosion of genome and metagenome sequencing surveys around the world, we are coming to realize that our knowledge of filamentous phage diversity remains at a tip-of-the-iceberg stage, promising that new biology and biotechnology are soon to come.
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Affiliation(s)
- Iain D Hay
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Melbourne, Vic., Australia
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25
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Sharma RS, Karmakar S, Kumar P, Mishra V. Application of filamentous phages in environment: A tectonic shift in the science and practice of ecorestoration. Ecol Evol 2019; 9:2263-2304. [PMID: 30847110 PMCID: PMC6392359 DOI: 10.1002/ece3.4743] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 08/25/2018] [Accepted: 10/30/2018] [Indexed: 02/06/2023] Open
Abstract
Theories in soil biology, such as plant-microbe interactions and microbial cooperation and antagonism, have guided the practice of ecological restoration (ecorestoration). Below-ground biodiversity (bacteria, fungi, invertebrates, etc.) influences the development of above-ground biodiversity (vegetation structure). The role of rhizosphere bacteria in plant growth has been largely investigated but the role of phages (bacterial viruses) has received a little attention. Below the ground, phages govern the ecology and evolution of microbial communities by affecting genetic diversity, host fitness, population dynamics, community composition, and nutrient cycling. However, few restoration efforts take into account the interactions between bacteria and phages. Unlike other phages, filamentous phages are highly specific, nonlethal, and influence host fitness in several ways, which make them useful as target bacterial inocula. Also, the ease with which filamentous phages can be genetically manipulated to express a desired peptide to track and control pathogens and contaminants makes them useful in biosensing. Based on ecology and biology of filamentous phages, we developed a hypothesis on the application of phages in environment to derive benefits at different levels of biological organization ranging from individual bacteria to ecosystem for ecorestoration. We examined the potential applications of filamentous phages in improving bacterial inocula to restore vegetation and to monitor changes in habitat during ecorestoration and, based on our results, recommend a reorientation of the existing framework of using microbial inocula for such restoration and monitoring. Because bacterial inocula and biomonitoring tools based on filamentous phages are likely to prove useful in developing cost-effective methods of restoring vegetation, we propose that filamentous phages be incorporated into nature-based restoration efforts and that the tripartite relationship between phages, bacteria, and plants be explored further. Possible impacts of filamentous phages on native microflora are discussed and future areas of research are suggested to preclude any potential risks associated with such an approach.
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Affiliation(s)
- Radhey Shyam Sharma
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental StudiesUniversity of DelhiDelhiIndia
| | - Swagata Karmakar
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental StudiesUniversity of DelhiDelhiIndia
| | - Pankaj Kumar
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental StudiesUniversity of DelhiDelhiIndia
| | - Vandana Mishra
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental StudiesUniversity of DelhiDelhiIndia
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26
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Abstract
Neisseria gonorrhoeae, the causative agent of the sexually transmitted disease gonorrhoeae, possesses several mobile genetic elements (MGEs). The MGEs such as transposable elements mediate intrachromosomal rearrangements, while plasmids and the gonococcal genetic island are involved in interchromosomal gene transfer. Additionally, gonococcal MGEs serve as hotspots for recombination and integration of other genetic elements such as bacteriophages, contribute to gene regulation or spread genes through gonococcal populations by horizontal gene transfer. In this review, we summarise the literature on the structure and biology of MGEs and discuss how these genetic elements may play a role in the pathogenesis and spread of antimicrobial resistance in N. gonorrhoeae. Although an abundance of information about gonococcal MGEs exists (mainly from whole genome sequencing and bioinformatic analysis), there are still many open questions on how MGEs influence the biology of N. gonorrhoeae.
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Affiliation(s)
- Ana Cehovin
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Steven B Lewis
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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27
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Acquisition of virulence genes by a carrier strain gave rise to the ongoing epidemics of meningococcal disease in West Africa. Proc Natl Acad Sci U S A 2018; 115:5510-5515. [PMID: 29735685 PMCID: PMC6003489 DOI: 10.1073/pnas.1802298115] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Historically, Neisseria meningitidis serogroup A strains have caused large epidemics of meningitis across sub-Saharan Africa. Following mass vaccination from 2010, serogroup A outbreaks have been mostly eliminated. Starting in 2013 however, yearly epidemics of a previously unknown serogroup C strain have led to tens of thousands of cases in Nigeria and Niger. We show how this new strain evolved from a benign ancestor through the acquisition of virulence genes encoding the serogroup C capsule and a phage linked to invasiveness, illustrating that minor genetic changes in a microbe can have major public health consequences. Our reconstruction of the spatiotemporal outbreak dynamics in the Niger–Nigeria border region suggests direct epidemiological consequences of contrasting outbreak responses in the two countries. In the African meningitis belt, a region of sub-Saharan Africa comprising 22 countries from Senegal in the west to Ethiopia in the east, large epidemics of serogroup A meningococcal meningitis have occurred periodically. After gradual introduction from 2010 of mass vaccination with a monovalent meningococcal A conjugate vaccine, serogroup A epidemics have been eliminated. Starting in 2013, the northwestern part of Nigeria has been affected by yearly outbreaks of meningitis caused by a novel strain of serogroup C Neisseria meningitidis (NmC). In 2015, the strain spread to the neighboring country Niger, where it caused a severe epidemic. Following a relative calm in 2016, the largest ever recorded epidemic of NmC broke out in Nigeria in 2017. Here, we describe the recent evolution of this new outbreak strain and show how the acquisition of capsule genes and virulence factors by a strain previously circulating asymptomatically in the African population led to the emergence of a virulent pathogen. This study illustrates the power of long-read whole-genome sequencing, combined with Illumina sequencing, for high-resolution epidemiological investigations.
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28
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Heidrich N, Bauriedl S, Barquist L, Li L, Schoen C, Vogel J. The primary transcriptome of Neisseria meningitidis and its interaction with the RNA chaperone Hfq. Nucleic Acids Res 2017; 45:6147-6167. [PMID: 28334889 PMCID: PMC5449619 DOI: 10.1093/nar/gkx168] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/02/2017] [Indexed: 12/15/2022] Open
Abstract
Neisseria meningitidis is a human commensal that can also cause life-threatening meningitis and septicemia. Despite growing evidence for RNA-based regulation in meningococci, their transcriptome structure and output of regulatory small RNAs (sRNAs) are incompletely understood. Using dRNA-seq, we have mapped at single-nucleotide resolution the primary transcriptome of N. meningitidis strain 8013. Annotation of 1625 transcriptional start sites defines transcription units for most protein-coding genes but also reveals a paucity of classical σ70-type promoters, suggesting the existence of activators that compensate for the lack of −35 consensus sequences in N. meningitidis. The transcriptome maps also reveal 65 candidate sRNAs, a third of which were validated by northern blot analysis. Immunoprecipitation with the RNA chaperone Hfq drafts an unexpectedly large post-transcriptional regulatory network in this organism, comprising 23 sRNAs and hundreds of potential mRNA targets. Based on this data, using a newly developed gfp reporter system we validate an Hfq-dependent mRNA repression of the putative colonization factor PrpB by the two trans-acting sRNAs RcoF1/2. Our genome-wide RNA compendium will allow for a better understanding of meningococcal transcriptome organization and riboregulation with implications for colonization of the human nasopharynx.
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Affiliation(s)
- Nadja Heidrich
- RNA Biology Group, Institute for Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Saskia Bauriedl
- Institute for Hygiene and Microbiology (IHM), University of Würzburg, D-97080 Würzburg, Germany
| | - Lars Barquist
- RNA Biology Group, Institute for Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany
| | - Lei Li
- Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Christoph Schoen
- Institute for Hygiene and Microbiology (IHM), University of Würzburg, D-97080 Würzburg, Germany
| | - Jörg Vogel
- RNA Biology Group, Institute for Molecular Infection Biology (IMIB), University of Würzburg, D-97080 Würzburg, Germany.,Helmholtz Institute for RNA-based Infection Research (HIRI), D-97080 Würzburg, Germany
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29
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Lees JA, Croucher NJ, Goldblatt D, Nosten F, Parkhill J, Turner C, Turner P, Bentley SD. Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration. eLife 2017; 6:e26255. [PMID: 28742023 PMCID: PMC5576492 DOI: 10.7554/elife.26255] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 07/21/2017] [Indexed: 01/04/2023] Open
Abstract
Streptococcus pneumoniae is a leading cause of invasive disease in infants, especially in low-income settings. Asymptomatic carriage in the nasopharynx is a prerequisite for disease, but variability in its duration is currently only understood at the serotype level. Here we developed a model to calculate the duration of carriage episodes from longitudinal swab data, and combined these results with whole genome sequence data. We estimated that pneumococcal genomic variation accounted for 63% of the phenotype variation, whereas the host traits considered here (age and previous carriage) accounted for less than 5%. We further partitioned this heritability into both lineage and locus effects, and quantified the amount attributable to the largest sources of variation in carriage duration: serotype (17%), drug-resistance (9%) and other significant locus effects (7%). A pan-genome-wide association study identified prophage sequences as being associated with decreased carriage duration independent of serotype, potentially by disruption of the competence mechanism. These findings support theoretical models of pneumococcal competition and antibiotic resistance.
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Affiliation(s)
- John A Lees
- Infection GenomicsWellcome Trust Sanger InstituteHinxtonUnited Kingdom
| | - Nicholas J Croucher
- Department of Infectious Disease EpidemiologySt. Mary’s Campus, Imperial College LondonLondonUnited Kingdom
| | - David Goldblatt
- Institute of Child HealthUniversity College LondonLondonUnited Kingdom
| | - François Nosten
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical MedicineMahidol UniversityMae SotThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Julian Parkhill
- Infection GenomicsWellcome Trust Sanger InstituteHinxtonUnited Kingdom
| | - Claudia Turner
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical MedicineMahidol UniversityMae SotThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Paul Turner
- Shoklo Malaria Research Unit, Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical MedicineMahidol UniversityMae SotThailand
- Centre for Tropical Medicine and Global Health, Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Stephen D Bentley
- Infection GenomicsWellcome Trust Sanger InstituteHinxtonUnited Kingdom
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30
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Bille E, Meyer J, Jamet A, Euphrasie D, Barnier JP, Brissac T, Larsen A, Pelissier P, Nassif X. A virulence-associated filamentous bacteriophage of Neisseria meningitidis increases host-cell colonisation. PLoS Pathog 2017; 13:e1006495. [PMID: 28704569 PMCID: PMC5526601 DOI: 10.1371/journal.ppat.1006495] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 07/25/2017] [Accepted: 06/27/2017] [Indexed: 01/31/2023] Open
Abstract
Neisseria meningitidis is a commensal of human nasopharynx. In some circumstances, this bacteria can invade the bloodstream and, after crossing the blood brain barrier, the meninges. A filamentous phage, designated MDAΦ for Meningococcal Disease Associated, has been associated with invasive disease. In this work we show that the prophage is not associated with a higher virulence during the bloodstream phase of the disease. However, looking at the interaction of N. meningitidis with epithelial cells, a step essential for colonization of the nasopharynx, we demonstrate that the presence of the prophage, via the production of viruses, increases colonization of encapsulated meningococci onto monolayers of epithelial cells. The analysis of the biomass covering the epithelial cells revealed that meningococci are bound to the apical surface of host cells by few layers of heavily piliated bacteria, whereas, in the upper layers, bacteria are non-piliated but surrounded by phage particles which (i) form bundles of filaments, and/or (ii) are in some places associated with bacteria. The latter are likely to correspond to growing bacteriophages during their extrusion through the outer membrane. These data suggest that, as the biomass increases, the loss of piliation in the upper layers of the biomass does not allow type IV pilus bacterial aggregation, but is compensated by a large production of phage particles that promote bacterial aggregation via the formation of bundles of phage filaments linked to the bacterial cell walls. We propose that MDAΦ by increasing bacterial colonization in the mucosa at the site-of-entry, increase the occurrence of diseases. Bacteriophages are bacterial viruses, which in some cases encode for virulence factors and increase bacterial virulence. Comparative genomic of several strains of Neisseria meningitidis, a major human pathogen, identified the presence of an 8kb prophage in strains belonging to invasive clonal complexes. The analysis of this filamentous bacteriophage, designated MDA for Meningococcal Disease Associated (MDAΦ) did not reveal any obvious virulence factors responsible for an increase invasiveness of strains carrying this prophage. Using our animal model mimicking the septicemic phase of the neisserial invasive diseases, we demonstrate that the presence of the MDAΦ is not associated with a higher virulence, but we show that the bacteriophage particles, by promoting bacteria-bacteria interactions, increase the biomass of bacteria colonizing a monolayer of epithelial cells. These data suggest that the increased invasiveness mediated by the MDAΦ bacteriophage is likely to be due to a better ability of the bacteria to colonize the nasopharyngeal mucosa.
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Affiliation(s)
- Emmanuelle Bille
- Institut Necker-Enfants Malades, INSERM U1151, CNRS UMR 8253, Paris, France
- Université Paris Descartes, Paris, France
- Service de Microbiologie, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
- * E-mail:
| | - Julie Meyer
- Institut Necker-Enfants Malades, INSERM U1151, CNRS UMR 8253, Paris, France
- Université Paris Descartes, Paris, France
| | - Anne Jamet
- Institut Necker-Enfants Malades, INSERM U1151, CNRS UMR 8253, Paris, France
- Université Paris Descartes, Paris, France
- Service de Microbiologie, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Daniel Euphrasie
- Institut Necker-Enfants Malades, INSERM U1151, CNRS UMR 8253, Paris, France
- Université Paris Descartes, Paris, France
| | - Jean-Philippe Barnier
- Institut Necker-Enfants Malades, INSERM U1151, CNRS UMR 8253, Paris, France
- Université Paris Descartes, Paris, France
- Service de Microbiologie, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Terry Brissac
- Institut Necker-Enfants Malades, INSERM U1151, CNRS UMR 8253, Paris, France
- Université Paris Descartes, Paris, France
| | - Anna Larsen
- Institut Necker-Enfants Malades, INSERM U1151, CNRS UMR 8253, Paris, France
- Université Paris Descartes, Paris, France
| | - Philippe Pelissier
- Service de Chirurgie Reconstructrice et Plastique, Fondation Hôpital Saint Joseph, Paris, France
| | - Xavier Nassif
- Institut Necker-Enfants Malades, INSERM U1151, CNRS UMR 8253, Paris, France
- Université Paris Descartes, Paris, France
- Service de Microbiologie, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, Paris, France
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31
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Houot L, Navarro R, Nouailler M, Duché D, Guerlesquin F, Lloubes R. Electrostatic interactions between the CTX phage minor coat protein and the bacterial host receptor TolA drive the pathogenic conversion of Vibrio cholerae. J Biol Chem 2017. [PMID: 28642371 DOI: 10.1074/jbc.m117.786061] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Vibrio cholerae is a natural inhabitant of aquatic environments and converts to a pathogen upon infection by a filamentous phage, CTXΦ, that transmits the cholera toxin-encoding genes. This toxigenic conversion of V. cholerae has evident implication in both genome plasticity and epidemic risk, but the early stages of the infection have not been thoroughly studied. CTXΦ transit across the bacterial periplasm requires binding between the minor coat protein named pIII and a bacterial inner-membrane receptor, TolA, which is part of the conserved Tol-Pal molecular motor. To gain insight into the TolA-pIII complex, we developed a bacterial two-hybrid approach, named Oxi-BTH, suited for studying the interactions between disulfide bond-folded proteins in the bacterial cytoplasm of an Escherichia coli reporter strain. We found that two of the four disulfide bonds of pIII are required for its interaction with TolA. By combining Oxi-BTH assays, NMR, and genetic studies, we also demonstrate that two intermolecular salt bridges between TolA and pIII provide the driving forces of the complex interaction. Moreover, we show that TolA residue Arg-325 involved in one of the two salt bridges is critical for proper functioning of the Tol-Pal system. Our results imply that to prevent host evasion, CTXΦ uses an infection strategy that targets a highly conserved protein of Gram-negative bacteria essential for the fitness of V. cholerae in its natural environment.
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Affiliation(s)
- Laetitia Houot
- From the Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Romain Navarro
- From the Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Matthieu Nouailler
- From the Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Denis Duché
- From the Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Françoise Guerlesquin
- From the Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
| | - Roland Lloubes
- From the Laboratoire d'Ingénierie des Systèmes Macromoléculaires, UMR7255, Institut de Microbiologie de la Méditerranée, Aix-Marseille Université-CNRS, 31 Chemin Joseph Aiguier, 13402 Marseille Cedex 20, France
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Tommassen J, Arenas J. Biological Functions of the Secretome of Neisseria meningitidis. Front Cell Infect Microbiol 2017; 7:256. [PMID: 28670572 PMCID: PMC5472700 DOI: 10.3389/fcimb.2017.00256] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 05/29/2017] [Indexed: 11/13/2022] Open
Abstract
Neisseria meningitidis is a Gram-negative bacterial pathogen that normally resides as a commensal in the human nasopharynx but occasionally causes disease with high mortality and morbidity. To interact with its environment, it transports many proteins across the outer membrane to the bacterial cell surface and into the extracellular medium for which it deploys the common and well-characterized autotransporter, two-partner and type I secretion mechanisms, as well as a recently discovered pathway for the surface exposure of lipoproteins. The surface-exposed and secreted proteins serve roles in host-pathogen interactions, including adhesion to host cells and extracellular matrix proteins, evasion of nutritional immunity imposed by iron-binding proteins of the host, prevention of complement activation, neutralization of antimicrobial peptides, degradation of immunoglobulins, and permeabilization of epithelial layers. Furthermore, they have roles in interbacterial interactions, including the formation and dispersal of biofilms and the suppression of the growth of bacteria competing for the same niche. Here, we will review the protein secretion systems of N. meningitidis and focus on the functions of the secreted proteins.
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Affiliation(s)
- Jan Tommassen
- Department of Molecular Microbiology and Institute of Biomembranes, Utrecht UniversityUtrecht, Netherlands
| | - Jesús Arenas
- Department of Molecular Microbiology and Institute of Biomembranes, Utrecht UniversityUtrecht, Netherlands
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Diallo K, Gamougam K, Daugla DM, Harrison OB, Bray JE, Caugant DA, Lucidarme J, Trotter CL, Hassan-King M, Stuart JM, Manigart O, Greenwood BM, Maiden MCJ. Hierarchical genomic analysis of carried and invasive serogroup A Neisseria meningitidis during the 2011 epidemic in Chad. BMC Genomics 2017; 18:398. [PMID: 28532434 PMCID: PMC5441073 DOI: 10.1186/s12864-017-3789-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 05/12/2017] [Indexed: 12/12/2022] Open
Abstract
Background Serogroup A Neisseria meningitidis (NmA) was the cause of the 2011 meningitis epidemics in Chad. This bacterium, often carried asymptomatically, is considered to be an “accidental pathogen”; however, the transition from carriage to disease phenotype remains poorly understood. This study examined the role genetic diversity might play in this transition by comparing genomes from geographically and temporally matched invasive and carried NmA isolates. Results All 23 NmA isolates belonged to the ST-5 clonal complex (cc5). Ribosomal MLST comparison with other publically available NmA:cc5 showed that isolates were closely related, although those from Chad formed two distinct branches and did not cluster with other NmA, based on their MLST profile, geographical and temporal location. Whole genome MLST (wgMLST) comparison identified 242 variable genes among all Chadian isolates and clustered them into three distinct phylogenetic groups (Clusters 1, 2, and 3): no systematic clustering by disease or carriage source was observed. There was a significant difference (p = 0.0070) between the mean age of the individuals from which isolates from Cluster 1 and Cluster 2 were obtained, irrespective of whether the person was a case or a carrier. Conclusions Whole genome sequencing provided high-resolution characterization of the genetic diversity of these closely related NmA isolates. The invasive meningococcal isolates obtained during the epidemic were not homogeneous; rather, a variety of closely related but distinct clones were circulating in the human population with some clones preferentially colonizing specific age groups, reflecting a potential age-related niche adaptation. Systematic genetic differences were not identified between carriage and disease isolates consistent with invasive meningococcal disease being a multi-factorial event resulting from changes in host-pathogen interactions along with the bacterium. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3789-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kanny Diallo
- Centre pour les Vaccins en Développement, Bamako, Mali. .,Department of Zoology, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, OX1 3SY, Oxford, UK.
| | | | | | - Odile B Harrison
- Department of Zoology, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, OX1 3SY, Oxford, UK
| | - James E Bray
- Department of Zoology, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, OX1 3SY, Oxford, UK
| | | | - Jay Lucidarme
- Vaccine Evaluation Unit, Public Health England, Manchester, UK
| | - Caroline L Trotter
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - James M Stuart
- London School of Hygiene & Tropical Medicine, London, UK
| | | | | | - Martin C J Maiden
- Department of Zoology, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, OX1 3SY, Oxford, UK
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Marin MA, Fonseca E, Encinas F, Freitas F, Camargo DA, Coimbra RS, de Filippis I, Vicente AC. The invasive Neisseria meningitidis MenC CC103 from Brazil is characterized by an accessory gene repertoire. Sci Rep 2017; 7:1617. [PMID: 28487566 PMCID: PMC5431661 DOI: 10.1038/s41598-017-01671-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 03/30/2017] [Indexed: 12/21/2022] Open
Abstract
Neisseria meningitidis infections are a major issue for global health. The invasive MenC ST-103 clonal complex (CC103) has been the most prevalent in meningococcal outbreaks in Brazil, occurring also in several countries worldwide. Here we have analysed the population structure and accessory genome of MenC CC103 strains from a global perspective. An in-depth phylogenomic analysis revealed a lineage of N. meningitidis causing meningitis in Brazil and the United Kingdom. This lineage was also characterized as harbouring a particular accessory genome composed of CRISPR/Cas and restriction modification systems. This lineage was also characterized by a genomic island resembling an integrative and conjugative element. This island carried genes potentially associated with virulence and fitness. We propose this accessory gene repertoire could be contributing to the spatial-temporal persistence of the invasive MenC CC103 lineage.
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Affiliation(s)
- Michel Abanto Marin
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz (IOC) - Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brazil.
| | - Erica Fonseca
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz (IOC) - Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brazil
| | - Fernando Encinas
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz (IOC) - Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brazil
| | - Fernanda Freitas
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz (IOC) - Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brazil
| | | | - Roney Santos Coimbra
- Neurogenômica, Centro de Pesquisas René Rachou (CPqRR), Fundação Oswaldo Cruz (FIOCRUZ), Belo Horizonte, MG, Brazil
| | - Ivano de Filippis
- Instituto Nacional de Controle de Qualidade em Saúde (INCQS), Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, RJ, Brazil
| | - Ana Carolina Vicente
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz (IOC) - Fundação Oswaldo Cruz (FIOCRUZ), Av. Brasil, 4365, Rio de Janeiro, Brazil
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Rakonjac J, Russel M, Khanum S, Brooke SJ, Rajič M. Filamentous Phage: Structure and Biology. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1053:1-20. [PMID: 29549632 DOI: 10.1007/978-3-319-72077-7_1] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Ff filamentous phage (fd, M13 and f1) of Escherichia coli have been the workhorse of phage display technology for the past 30 years. Dominance of Ff over other bacteriophage in display technology stems from the titres that are about 100-fold higher than any other known phage, efficacious transformation ensuring large library size and superior stability of the virion at high temperatures, detergents and pH extremes, allowing broad range of biopanning conditions in screening phage display libraries. Due to the excellent understanding of infection and assembly requirements, Ff phage have also been at the core of phage-assisted continual protein evolution strategies (PACE). This chapter will give an overview of the Ff filamentous phage structure and biology, emphasizing those properties of the Ff phage life cycle and virion that are pertinent to phage display applications.
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Affiliation(s)
- Jasna Rakonjac
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand.
| | | | - Sofia Khanum
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Sam J Brooke
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
| | - Marina Rajič
- Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, University of Auckland, Auckland, New Zealand
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Abstract
Antigenic variation is a strategy used by a broad diversity of microbial pathogens to persist within the mammalian host. Whereas viruses make use of a minimal proofreading capacity combined with large amounts of progeny to use random mutation for variant generation, antigenically variant bacteria have evolved mechanisms which use a stable genome, which aids in protecting the fitness of the progeny. Here, three well-characterized and highly antigenically variant bacterial pathogens are discussed: Anaplasma, Borrelia, and Neisseria. These three pathogens display a variety of mechanisms used to create the structural and antigenic variation needed for immune escape and long-term persistence. Intrahost antigenic variation is the focus; however, the role of these immune escape mechanisms at the population level is also presented.
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Pelton SI. The Global Evolution of Meningococcal Epidemiology Following the Introduction of Meningococcal Vaccines. J Adolesc Health 2016; 59:S3-S11. [PMID: 27449148 DOI: 10.1016/j.jadohealth.2016.04.012] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 03/11/2016] [Accepted: 04/08/2016] [Indexed: 12/13/2022]
Abstract
Invasive meningococcal disease (IMD) caused by Neisseria meningitidis is associated with high morbidity and mortality. Although IMD incidence is highest in infants, a second peak occurs in adolescents/young adults. The incidence of IMD and the predominant disease-causing meningococcal serogroups vary worldwide. Epidemiologic data have guided the development of meningococcal vaccines to reduce the IMD burden. In Europe, serogroup C IMD has been substantially reduced since the introduction of a serogroup C conjugate vaccine. Serogroup B predominates in Europe, although cases of serogroup Y IMD have been increasing in recent years. In the United States, declines in serogroup C and Y disease have been observed in association with the introduction of quadrivalent (serogroups ACWY) meningococcal conjugate vaccines; serogroup B persists and is now the most common cause of outbreak associated disease. In the African meningitis belt, a conjugate vaccine for serogroup A has been effective in decreasing meningitis associated with that serogroup. Outbreaks of the previously rare serogroup X disease have been reported in this region since 2006. In recent years, outbreaks of serogroup B IMD, for which vaccines have only recently been approved by the U.S. Food and Drug Administration and the European Medicines Agency, have occurred in Europe and the United States. Targeting meningococcal vaccination to adolescents/young adults may reduce the morbidity and mortality associated with IMD and has the potential to impact the larger community through herd benefits.
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Affiliation(s)
- Stephen I Pelton
- Maxwell Finland Laboratory for Infectious Diseases, Boston, Massachusetts.
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40
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Distribution of the type III DNA methyltransferases modA, modB and modD among Neisseria meningitidis genotypes: implications for gene regulation and virulence. Sci Rep 2016; 6:21015. [PMID: 26867950 PMCID: PMC4751487 DOI: 10.1038/srep21015] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 01/14/2016] [Indexed: 12/03/2022] Open
Abstract
Neisseria meningitidis is a human-specific bacterium that varies in invasive potential. All meningococci are carried in the nasopharynx, and most genotypes are very infrequently associated with invasive meningococcal disease; however, those belonging to the ‘hyperinvasive lineages’ are more frequently associated with sepsis or meningitis. Genome content is highly conserved between carriage and disease isolates, and differential gene expression has been proposed as a major determinant of the hyperinvasive phenotype. Three phase variable DNA methyltransferases (ModA, ModB and ModD), which mediate epigenetic regulation of distinct phase variable regulons (phasevarions), have been identified in N. meningitidis. Each mod gene has distinct alleles, defined by their Mod DNA recognition domain, and these target and methylate different DNA sequences, thereby regulating distinct gene sets. Here 211 meningococcal carriage and >1,400 disease isolates were surveyed for the distribution of meningococcal mod alleles. While modA11-12 and modB1-2 were found in most isolates, rarer alleles (e.g., modA15, modB4, modD1-6) were specific to particular genotypes as defined by clonal complex. This suggests that phase variable Mod proteins may be associated with distinct phenotypes and hence invasive potential of N. meningitidis strains.
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Székely AJ, Breitbart M. Single-stranded DNA phages: from early molecular biology tools to recent revolutions in environmental microbiology. FEMS Microbiol Lett 2016; 363:fnw027. [DOI: 10.1093/femsle/fnw027] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2016] [Indexed: 01/22/2023] Open
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Uncovering Listeria monocytogenes hypervirulence by harnessing its biodiversity. Nat Genet 2016; 48:308-313. [PMID: 26829754 PMCID: PMC4768348 DOI: 10.1038/ng.3501] [Citation(s) in RCA: 431] [Impact Index Per Article: 53.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 01/06/2016] [Indexed: 12/17/2022]
Abstract
Microbial pathogenesis studies are typically performed with reference strains, thereby overlooking microbial intra-species virulence heterogeneity. Here we integrated human epidemiological and clinical data with bacterial population genomics to harness the biodiversity of the model foodborne pathogen Listeria monocytogenes and decipher the basis of its neural and placental tropisms. Taking advantage of the clonal structure of this bacterial species, we identify clones epidemiologically associated with either food or human central nervous system (CNS) and maternal-neonatal (MN) listeriosis. The latter are also most prevalent in patients without immunosuppressive comorbidities. Strikingly, CNS and MN clones are hypervirulent in a humanized mouse model of listeriosis. By integrating epidemiological data and comparative genomics, we uncovered multiple novel putative virulence factors and demonstrated experimentally the contribution of the first gene cluster mediating Listeria monocytogenes neural and placental tropisms. This study illustrates the exceptional power of harnessing microbial biodiversity to identify clinically relevant microbial virulence attributes.
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Meyer J, Brissac T, Frapy E, Omer H, Euphrasie D, Bonavita A, Nassif X, Bille E. Characterization of MDAΦ, a temperate filamentous bacteriophage of Neisseria meningitidis. MICROBIOLOGY-SGM 2015; 162:268-282. [PMID: 26602366 DOI: 10.1099/mic.0.000215] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The mechanism by which Neisseria meningitidis becomes invasive is not well understood. Comparative genomics identified the presence of an 8 kb island in strains belonging to invasive clonal complexes. This island was designated MDA for meningococcal disease associated. MDA is highly conserved among meningococcal isolates and its analysis revealed a genomic organization similar to that of a filamentous prophage such as CTXΦ of Vibrio cholerae. Subsequent molecular investigations showed that the MDA island has indeed the characteristics of a filamentous prophage, which can enter into a productive cycle and is secreted using the type IV pilus (tfp) secretin PilQ. At least three genes of the prophage are necessary for the formation of the replicative cytoplasmic form (orf1, orf2 and orf9). Immunolabelling of the phage with antibodies against the major capsid protein, ORF4, confirmed that filamentous particles, about 1200 nm long, covered with ORF4 are present at the bacterial surface forming bundles in some places and interacting with pili. The MDA bacteriophage is able to infect different N. meningitidis strains, using the type IV pili as a receptor via an interaction with the adsorption protein ORF6. Altogether, these data demonstrate that the MDA island encodes a functional prophage able to produce infectious filamentous phage particles.
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Affiliation(s)
- Julie Meyer
- Institut Necker-Enfants Malades, 14 Rue Maria Helena Vieira Da Silva, CS 61431, 75014, Paris, France.,CNRS UMR 8253, Paris, France.,INSERM U1151, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Terry Brissac
- Institut Necker-Enfants Malades, 14 Rue Maria Helena Vieira Da Silva, CS 61431, 75014, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,INSERM U1151, Paris, France.,CNRS UMR 8253, Paris, France
| | - Eric Frapy
- Institut Necker-Enfants Malades, 14 Rue Maria Helena Vieira Da Silva, CS 61431, 75014, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,INSERM U1151, Paris, France.,CNRS UMR 8253, Paris, France
| | - Hélène Omer
- Institut Necker-Enfants Malades, 14 Rue Maria Helena Vieira Da Silva, CS 61431, 75014, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,INSERM U1151, Paris, France.,CNRS UMR 8253, Paris, France
| | - Daniel Euphrasie
- Institut Necker-Enfants Malades, 14 Rue Maria Helena Vieira Da Silva, CS 61431, 75014, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,INSERM U1151, Paris, France.,CNRS UMR 8253, Paris, France
| | - Adrien Bonavita
- CNRS UMR 8253, Paris, France.,Institut Necker-Enfants Malades, 14 Rue Maria Helena Vieira Da Silva, CS 61431, 75014, Paris, France.,INSERM U1151, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Xavier Nassif
- INSERM U1151, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France.,Service de Microbiologie, Hôpital Necker-Enfants Malades, AP-HP, Paris, France.,CNRS UMR 8253, Paris, France.,Institut Necker-Enfants Malades, 14 Rue Maria Helena Vieira Da Silva, CS 61431, 75014, Paris, France
| | - Emmanuelle Bille
- Service de Microbiologie, Hôpital Necker-Enfants Malades, AP-HP, Paris, France.,CNRS UMR 8253, Paris, France.,Institut Necker-Enfants Malades, 14 Rue Maria Helena Vieira Da Silva, CS 61431, 75014, Paris, France.,INSERM U1151, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
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Hill DMC, Lucidarme J, Gray SJ, Newbold LS, Ure R, Brehony C, Harrison OB, Bray JE, Jolley KA, Bratcher HB, Parkhill J, Tang CM, Borrow R, Maiden MCJ. Genomic epidemiology of age-associated meningococcal lineages in national surveillance: an observational cohort study. THE LANCET. INFECTIOUS DISEASES 2015; 15:1420-8. [PMID: 26515523 PMCID: PMC4655307 DOI: 10.1016/s1473-3099(15)00267-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 08/09/2015] [Accepted: 08/11/2015] [Indexed: 11/24/2022]
Abstract
Background Invasive meningococcal disease (IMD) is a worldwide health issue that is potentially preventable with vaccination. In view of its sporadic nature and the high diversity of Neisseria meningitidis, epidemiological surveillance incorporating detailed isolate characterisation is crucial for effective control and understanding the evolving epidemiology of IMD. The Meningitis Research Foundation Meningococcus Genome Library (MRF-MGL) exploits whole-genome sequencing (WGS) for this purpose and presents data on a comprehensive and coherent IMD isolate collection from England and Wales via the internet. We assessed the contribution of these data to investigating IMD epidemiology. Methods WGS data were obtained for all 899 IMD isolates available for England and Wales in epidemiological years 2010–11 and 2011–12. The data had been annotated at 1720 loci, analysed, and disseminated online. Information was also available on meningococcal population structure and vaccine (Bexsero, GlaxoSmithKline, Brentford, Middlesex, UK) antigen variants, which enabled the investigation of IMD-associated genotypes over time and by patients' age groups. Population genomic analyses were done with a hierarchical gene-by-gene approach. Findings The methods used by MRF-MGL efficiently characterised IMD isolates and information was provided in plain language. At least 20 meningococcal lineages were identified, three of which (hyperinvasive clonal complexes 41/44 [lineage 3], 269 [lineage 2], and 23 [lineage 23]) were responsible for 528 (59%) of IMD isolates. Lineages were highly diverse and showed evidence of extensive recombination. Specific lineages were associated with IMD in particular age groups, with notable diversity in the youngest and oldest individuals. The increased incidence of IMD from 1984 to 2010 in England and Wales was due to successive and concurrent epidemics of different lineages. Genetically, 74% of isolates were characterised as encoding group B capsules: 16% group Y, 6% group W, and 3% group C. Exact peptide matches for individual Bexsero vaccine antigens were present in up to 26% of isolates. Interpretation The MRF-MGL represents an effective, broadly applicable model for the storage, analysis, and dissemination of WGS data that can facilitate real-time genomic pathogen surveillance. The data revealed information crucial to effective deployment and assessment of vaccines against N meningitidis. Funding Meningitis Research Foundation, Wellcome Trust, Public Health England, European Union.
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Affiliation(s)
| | - Jay Lucidarme
- Meningococcal Reference Unit, Public Health England, Manchester Royal Infirmary, Manchester, UK
| | - Stephen J Gray
- Meningococcal Reference Unit, Public Health England, Manchester Royal Infirmary, Manchester, UK
| | - Lynne S Newbold
- Meningococcal Reference Unit, Public Health England, Manchester Royal Infirmary, Manchester, UK
| | - Roisin Ure
- Scottish Haemophilus, Legionella, Meningococcus and Pneumococcus Reference Laboratory, Glasgow Royal Infirmary, Glasgow, UK
| | | | | | - James E Bray
- Department of Zoology, University of Oxford, Oxford, UK
| | | | | | | | - Christoph M Tang
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Ray Borrow
- Meningococcal Reference Unit, Public Health England, Manchester Royal Infirmary, Manchester, UK
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Henry KA, Arbabi-Ghahroudi M, Scott JK. Beyond phage display: non-traditional applications of the filamentous bacteriophage as a vaccine carrier, therapeutic biologic, and bioconjugation scaffold. Front Microbiol 2015; 6:755. [PMID: 26300850 PMCID: PMC4523942 DOI: 10.3389/fmicb.2015.00755] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 07/10/2015] [Indexed: 12/23/2022] Open
Abstract
For the past 25 years, phage display technology has been an invaluable tool for studies of protein-protein interactions. However, the inherent biological, biochemical, and biophysical properties of filamentous bacteriophage, as well as the ease of its genetic manipulation, also make it an attractive platform outside the traditional phage display canon. This review will focus on the unique properties of the filamentous bacteriophage and highlight its diverse applications in current research. Particular emphases are placed on: (i) the advantages of the phage as a vaccine carrier, including its high immunogenicity, relative antigenic simplicity and ability to activate a range of immune responses, (ii) the phage's potential as a prophylactic and therapeutic agent for infectious and chronic diseases, (iii) the regularity of the virion major coat protein lattice, which enables a variety of bioconjugation and surface chemistry applications, particularly in nanomaterials, and (iv) the phage's large population sizes and fast generation times, which make it an excellent model system for directed protein evolution. Despite their ubiquity in the biosphere, metagenomics work is just beginning to explore the ecology of filamentous and non-filamentous phage, and their role in the evolution of bacterial populations. Thus, the filamentous phage represents a robust, inexpensive, and versatile microorganism whose bioengineering applications continue to expand in new directions, although its limitations in some spheres impose obstacles to its widespread adoption and use.
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Affiliation(s)
- Kevin A. Henry
- Human Health Therapeutics Portfolio, National Research Council Canada, OttawaON, Canada
| | - Mehdi Arbabi-Ghahroudi
- Human Health Therapeutics Portfolio, National Research Council Canada, OttawaON, Canada
- School of Environmental Sciences, University of Guelph, GuelphON, Canada
- Department of Biology, Carleton University, OttawaON, Canada
| | - Jamie K. Scott
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BCCanada
- Faculty of Health Sciences, Simon Fraser University, BurnabyBC, Canada
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Messad N, Prajsnar TK, Lina G, O'Callaghan D, Foster SJ, Renshaw SA, Skaar EP, Bes M, Dunyach-Remy C, Vandenesch F, Sotto A, Lavigne JP. Existence of a Colonizing Staphylococcus aureus Strain Isolated in Diabetic Foot Ulcers. Diabetes 2015; 64:2991-5. [PMID: 25901094 PMCID: PMC4512213 DOI: 10.2337/db15-0031] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 04/09/2015] [Indexed: 12/17/2022]
Abstract
Staphylococcus aureus is an opportunistic bacterium capable of causing a wide range of severe diseases when it gains access to underlying tissues. Paradoxically, S. aureus is a common inhabitant of the skin microflora and colonizes the nares and other human mucosa. The purpose of this study was to determine the genetic basis for the differences in the pathogenic versus colonizing potential of S. aureus isolated from diabetic foot ulcers (DFUs). By performing optical map comparisons of a collection of S. aureus strains isolated from DFUs, we brought to light a prophage present in noninfecting bacteria. The phage, namely ROSA-like, was localized in a hotspot region ΦNM2 near the locus isd, the iron surface determinant system. The integrated phage significantly reduces the virulence of the strain and increases the biofilm formation. DFUs seem to be a specific niche of this colonizing strain. The ROSA-like phage represents the first description of a mobile element present mainly in S. aureus isolated from DFUs, which modulates the relationship of the bacteria with its human host. This phage appears to attenuate bacterial virulence and promote colonization.
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Affiliation(s)
- Nourreddine Messad
- National Institute of Health and Medical Research, Faculty of Medicine, University of Montpellier, Nîmes, France
| | - Tomasz K Prajsnar
- The Bateson Centre, University of Sheffield, Western Bank, Sheffield, U.K. Krebs Institute, University of Sheffield, Western Bank, Sheffield, U.K
| | - Gerard Lina
- CIRI, International Center for Infectiology Research, LabEx Ecofect, University of Lyon 1, INSERM U1111, Ecole Normale Supérieure de Lyon, CNRS UMR5308, Lyon, France Referent National Center of Staphylococci, Center of Biology and Pathology East, University Hospital Lyon, Bron, France
| | - David O'Callaghan
- National Institute of Health and Medical Research, Faculty of Medicine, University of Montpellier, Nîmes, France
| | - Simon J Foster
- Krebs Institute, University of Sheffield, Western Bank, Sheffield, U.K
| | - Steve A Renshaw
- The Bateson Centre, University of Sheffield, Western Bank, Sheffield, U.K. Krebs Institute, University of Sheffield, Western Bank, Sheffield, U.K
| | - Eric P Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University School of Medicine, Nashville, TN
| | - Michèle Bes
- CIRI, International Center for Infectiology Research, LabEx Ecofect, University of Lyon 1, INSERM U1111, Ecole Normale Supérieure de Lyon, CNRS UMR5308, Lyon, France Referent National Center of Staphylococci, Center of Biology and Pathology East, University Hospital Lyon, Bron, France
| | - Catherine Dunyach-Remy
- National Institute of Health and Medical Research, Faculty of Medicine, University of Montpellier, Nîmes, France Department of Microbiology, University Hospital Carémeau, Nîmes, France
| | - François Vandenesch
- CIRI, International Center for Infectiology Research, LabEx Ecofect, University of Lyon 1, INSERM U1111, Ecole Normale Supérieure de Lyon, CNRS UMR5308, Lyon, France Referent National Center of Staphylococci, Center of Biology and Pathology East, University Hospital Lyon, Bron, France
| | - Albert Sotto
- National Institute of Health and Medical Research, Faculty of Medicine, University of Montpellier, Nîmes, France Department of Infectious Diseases, University Hospital Carémeau, Nîmes, France
| | - Jean-Philippe Lavigne
- National Institute of Health and Medical Research, Faculty of Medicine, University of Montpellier, Nîmes, France Department of Microbiology, University Hospital Carémeau, Nîmes, France
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47
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Askora A, Yamada T. Two different evolutionary lines of filamentous phages in Ralstonia solanacearum: their effects on bacterial virulence. Front Genet 2015; 6:217. [PMID: 26150828 PMCID: PMC4471427 DOI: 10.3389/fgene.2015.00217] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 06/03/2015] [Indexed: 12/18/2022] Open
Abstract
The integration and excision of various filamentous phage genomes into and out of their host chromosomes occurs by site-specific recombination. The mechanisms proposed for these events include reactions mediated by phage-encoded recombinases and host recombination systems. Site-specific integration of filamentous phages plays a vital role in a variety of biological functions of the host, such as phase variation of certain pathogenic bacterial virulence factors. The importance of these filamentous phages in bacterial evolution is rapidly increasing with the discovery of new phages that are involved in pathogenicity. Studies of the diversity of two different filamentous phages infecting the phytopathogen Ralstonia solanacearum provide us with novel insights into the dynamics of phage genomes, biological roles of prophages, and the regulation and importance of phage-host interactions.
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Affiliation(s)
- Ahmed Askora
- Department of Microbiology and Botany, Faculty of Science, Zagazig University, Zagazig Egypt
| | - Takashi Yamada
- Department of Molecular Biotechnology, Graduate School of Advanced Sciences of Matter, Hiroshima University, Higashi-Hiroshima Japan
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48
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Quemin ERJ, Quax TEF. Archaeal viruses at the cell envelope: entry and egress. Front Microbiol 2015; 6:552. [PMID: 26097469 PMCID: PMC4456609 DOI: 10.3389/fmicb.2015.00552] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Accepted: 05/19/2015] [Indexed: 11/13/2022] Open
Abstract
The cell envelope represents the main line of host defense that viruses encounter on their way from one cell to another. The cytoplasmic membrane in general is a physical barrier that needs to be crossed both upon viral entry and exit. Therefore, viruses from the three domains of life employ a wide range of strategies for perforation of the cell membrane, each adapted to the cell surface environment of their host. Here, we review recent insights on entry and egress mechanisms of viruses infecting archaea. Due to the unique nature of the archaeal cell envelope, these particular viruses exhibit novel and unexpected mechanisms to traverse the cellular membrane.
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Affiliation(s)
| | - Tessa E F Quax
- Molecular Biology of Archaea, Institute for Biology II - Microbiology, University of Freiburg , Freiburg, Germany
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49
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Knezevic P, Voet M, Lavigne R. Prevalence of Pf1-like (pro)phage genetic elements among Pseudomonas aeruginosa isolates. Virology 2015; 483:64-71. [PMID: 25965796 DOI: 10.1016/j.virol.2015.04.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 04/06/2015] [Accepted: 04/07/2015] [Indexed: 12/14/2022]
Abstract
Pf1-like bacteriophages (family Inoviridae) of Pseudomonas aeruginosa can contribute to bacterial short term evolution and virulence. Here we examine Pf1-like (pro)phage diversity and prevalence among different P. aeruginosa isolates. Pf1-like prophages in sequenced genomes of P. aeruginosa were analyzed and grouped into four clades: Pf4, Pf5, Pf7 and Pf-LES. P. aeruginosa strains (n=241) were screened for the presence of universal (primers PfUa and PfUb) and specific Pf1-like genetic elements (Pf1, Pf4 and Pf5). More than half of the strains contained at least one Pf1-like genetic element (60%); universal elements were detected in 56% of the strains, Pf4 in 22%, Pf1 in 18% and Pf5 in 7%. Infectivity experiments confirmed that strains yielding PCR products with either universal or Pf4 specific primers can release infective virions. Based on the high prevalence of Pf1-like (pro)phages, it is necessary to further examine their involvement in P. aeruginosa virulence.
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Affiliation(s)
- Petar Knezevic
- Department of Biology and Ecology, Faculty of Sciences, University of Novi Sad, Trg Dositeja Obradovica 2, 21000 Novi Sad, Vojvodina, Serbia.
| | - Marleen Voet
- Laboratory of Gene Technology, Department Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, B-3001 Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department Biosystems, KU Leuven, Kasteelpark Arenberg 21 box 2462, B-3001 Leuven, Belgium
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50
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Farrugia DN, Elbourne LDH, Mabbutt BC, Paulsen IT. A novel family of integrases associated with prophages and genomic islands integrated within the tRNA-dihydrouridine synthase A (dusA) gene. Nucleic Acids Res 2015; 43:4547-57. [PMID: 25883135 PMCID: PMC4482086 DOI: 10.1093/nar/gkv337] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Accepted: 04/01/2015] [Indexed: 12/12/2022] Open
Abstract
Genomic islands play a key role in prokaryotic genome plasticity. Genomic islands integrate into chromosomal loci such as transfer RNA genes and protein coding genes, whilst retaining various cargo genes that potentially bestow novel functions on the host organism. A gene encoding a putative integrase was identified at a single site within the 5′ end of the dusA gene in the genomes of over 200 bacteria. This integrase was discovered to be a component of numerous genomic islands, which appear to share a target site within the dusA gene. dusA encodes the tRNA-dihydrouridine synthase A enzyme, which catalyses the post-transcriptional reduction of uridine to dihydrouridine in tRNA. Genomic islands encoding homologous dusA-associated integrases were found at a much lower frequency within the related dusB and dusC genes, and non-dus genes. Excision of these dusA-associated islands from the chromosome as circularized intermediates was confirmed by polymerase chain reaction. Analysis of the dusA-associated islands indicated that they were highly diverse, with the integrase gene representing the only universal common feature.
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Affiliation(s)
- Daniel N Farrugia
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Liam D H Elbourne
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Bridget C Mabbutt
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
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