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Lebeurre J, Dahyot S, Diene S, Paulay A, Aubourg M, Argemi X, Giard JC, Tournier I, François P, Pestel-Caron M. Comparative Genome Analysis of Staphylococcus lugdunensis Shows Clonal Complex-Dependent Diversity of the Putative Virulence Factor, ess/Type VII Locus. Front Microbiol 2019; 10:2479. [PMID: 31736914 PMCID: PMC6834553 DOI: 10.3389/fmicb.2019.02479] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/15/2019] [Indexed: 12/17/2022] Open
Abstract
Staphylococcus lugdunensis is a commensal bacterium of human skin that has emerged as a virulent Coagulase-Negative Staphylococcus in both community-acquired and healthcare associated infections. Genotyping methods have shown a clonal population structure of this pathogen but failed to identify hypervirulent lineages. Here, complete genomes of three pathogenic and three carriage S. lugdunensis strains were obtained by Single-Molecule sequencing (PacBio) and compared to 15 complete genomes available in GenBank database. The aim was to identify (i) genetic determinants specific to pathogenic or carriage strains or specific to clonal complexes (CCs) defined by MultiLocus Sequence Typing, and (ii) antibiotic resistance genes and new putative virulence factors encoded or not by mobile genetic elements (MGE). Comparative genomic analysis did not show a strict correlation between gene content and the ability of the six strains to cause infections in humans and in a Galleria mellonella infection model. However, this study identified new MGEs (five prophages, two genomic islands and one plasmid) and genetic variations of some putative virulence-associated loci, especially in CC3 strains. For a clonal population, high variability and eight CC-dependent genetic organizations were observed for the ess locus, which encodes a putative type VII secretion system (T7SS) homologous to that of S. aureus. Further phenotypic and functional studies are needed to characterize this particular CC3 and to evaluate the role of T7SS in the virulence of S. lugdunensis.
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Affiliation(s)
| | - Sandrine Dahyot
- UNIROUEN, GRAM EA2656, Rouen University Hospital, Normandie Université, Rouen, France
| | - Seydina Diene
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | | | - Marion Aubourg
- EA4655 U2RM (Équipe Antibio-Résistance), Université de Caen Basse-Normandie, Caen, France
| | - Xavier Argemi
- CHRU de Strasbourg, VBP EA7290, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Institut de Bactériologie, Université de Strasbourg, Strasbourg, France
| | - Jean-Christophe Giard
- EA4655 U2RM (Équipe Antibio-Résistance), Université de Caen Basse-Normandie, Caen, France
| | - Isabelle Tournier
- UNIROUEN, Inserm U1245, Normandy Centre for Genomic and Personalized Medicine, Rouen University Hospital, Normandie Université, Rouen, France
| | - Patrice François
- Genomic Research Laboratory, Service of Infectious Diseases, Geneva University Hospitals, Geneva, Switzerland
| | - Martine Pestel-Caron
- UNIROUEN, GRAM EA2656, Rouen University Hospital, Normandie Université, Rouen, France
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Bratcher HB, Brehony C, Heuberger S, Pieridou-Bagatzouni D, Křížová P, Hoffmann S, Toropainen M, Taha MK, Claus H, Tzanakaki G, Erdôsi T, Galajeva J, van der Ende A, Skoczyńska A, Pana M, Vaculíková A, Paragi M, Maiden MC, Caugant DA. Establishment of the European meningococcal strain collection genome library (EMSC-GL) for the 2011 to 2012 epidemiological year. ACTA ACUST UNITED AC 2019; 23. [PMID: 29790460 PMCID: PMC6152424 DOI: 10.2807/1560-7917.es.2018.23.20.17-00474] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Invasive meningococcal disease surveillance in Europe combines isolate characterisation and epidemiological data to support public health intervention. A representative European Meningococcal Strain Collection (EMSC) of IMD isolates was obtained, and whole genome sequenced to characterise 799 EMSC isolates from the epidemiological year July 2011-June 2012. To establish a genome library (GL), the isolate information was deposited in the pubMLST.org/neisseria database. Genomes were curated and annotated at 2,429 meningococcal loci, including those defining clonal complex, capsule, antigens, and antimicrobial resistance. Most genomes contained genes encoding B (n = 525; 65.7%) or C (n = 163; 20.4%) capsules; isolates were genetically highly diverse, with >20 genomic lineages, five of which comprising 60.7% (n = 485) of isolates. There were >350 antigenic fine-types: 307 were present once, the most frequent (P1.7-2,4:F5-1) comprised 8% (n = 64) of isolates. Each genome was characterised for Bexsero Antigen Sequence Typing (BAST): 25.5% (n = 204) of isolates contained alleles encoding the fHbp and/or the PorA VR1 vaccine component, but most genomes (n = 513; 64.2%) did not contain the NadA component. EMSC-GL will support an integrated surveillance of disease-associated genotypes in Europe, enabling the monitoring of hyperinvasive lineages, outbreak identification, and supporting vaccine programme implementation.
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Affiliation(s)
- Holly B Bratcher
- University of Oxford, Department of Zoology, Oxford, United Kingdom
| | - Carina Brehony
- Clinical Science Institute, National University of Ireland, Galway, Republic of Ireland.,University of Oxford, Department of Zoology, Oxford, United Kingdom
| | | | | | - Pavla Křížová
- National Institute of Public Health, Prague, Czech Republic
| | | | | | | | | | | | - Tímea Erdôsi
- National Center for Epidemiology, Budapest, Hungary
| | | | | | | | - Marina Pana
- National Institute of Research and Development for Microbiology and Immunology, Bucharest, Romania
| | - Alena Vaculíková
- Public Health Authority of the Slovak Republic, Bratislava, Slovakia
| | - Metka Paragi
- National Institute of Public Health, Ljubljana, Slovenia
| | - Martin Cj Maiden
- University of Oxford, Department of Zoology, Oxford, United Kingdom
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Abstract
Bacteria and archaea possess numerous defense systems to combat viral infections and other mobile genetic elements. Uniquely among these, CRISPR-Cas (clustered, regularly interspaced short palindromic repeats-CRISPR associated) provides adaptive genetic interference against foreign nucleic acids. Here we review recent advances on the CRISPR-Cas9 system in Neisseria spp, with a focus on its biological functions in genetic transfer, its mechanistic features that establish new paradigms and its technological applications in eukaryotic genome engineering.
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Batista RS, Gomes AP, Dutra Gazineo JL, Balbino Miguel PS, Santana LA, Oliveira L, Geller M. Meningococcal disease, a clinical and epidemiological review. ASIAN PAC J TROP MED 2017; 10:1019-1029. [PMID: 29203096 DOI: 10.1016/j.apjtm.2017.10.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 08/29/2017] [Accepted: 09/28/2017] [Indexed: 11/29/2022] Open
Abstract
Meningococcal disease is the acute infection caused by Neisseria meningitidis, which has humans as the only natural host. The disease is widespread around the globe and is known for its epidemical potential and high rates of lethality and morbidity. The highest number of cases of the disease is registered in the semi-arid regions of sub-Saharan Africa. In Brazil, it is endemic with occasional outbreaks, epidemics and sporadic cases occurring throughout the year, especially in the winter. The major epidemics of the disease occurred in Brazil in the 70's caused by serogroups A and C. Serogroups B, C and Y represent the majority of cases in Europe, the Americas and Australia. However, there has been a growing increase in serogroup W in some areas. The pathogen transmission happens for respiratory route (droplets) and clinically can lead to meningitis and sepsis (meningococcemia). The treatment is made with antimicrobial and supportive care. For successful prevention, we have some measures like vaccination, chemoprophylaxis and droplets' precautions. In this review, we have described and clarify clinical features of the disease caused by N. meningitidis regarding its relevance for healthcare professionals.
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Affiliation(s)
- Rodrigo Siqueira Batista
- Laboratório de Agentes Patogênicos, Departamento de Medicina e Enfermagem, Universidade Federal de Viçosa, Viçosa, MG, Brazil; Curso de Medicina, Faculdade Dinâmica do Vale do Piranga, Ponte Nova, MG, Brazil.
| | - Andréia Patrícia Gomes
- Laboratório de Agentes Patogênicos, Departamento de Medicina e Enfermagem, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Jorge Luiz Dutra Gazineo
- Hospital Universitário Clementino Fraga Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Paulo Sérgio Balbino Miguel
- Laboratório de Agentes Patogênicos, Departamento de Medicina e Enfermagem, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Luiz Alberto Santana
- Laboratório de Agentes Patogênicos, Departamento de Medicina e Enfermagem, Universidade Federal de Viçosa, Viçosa, MG, Brazil
| | - Lisa Oliveira
- Curso de Medicina, Centro Universitário Serra dos Órgãos (UNIFESO), Teresópolis, RJ, Brazil
| | - Mauro Geller
- School of Medicine, New York University - NYU, New York, USA; Departamento de Genética Médica, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
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Abstract
Whether prokaryotes (Bacteria and Archaea) are naturally organized into phenotypically and genetically cohesive units comparable to animal or plant species remains contested, frustrating attempts to estimate how many such units there might be, or to identify the ecological roles they play. Analyses of gene sequences in various closely related prokaryotic groups reveal that sequence diversity is typically organized into distinct clusters, and processes such as periodic selection and extensive recombination are understood to be drivers of cluster formation ("speciation"). However, observed patterns are rarely compared with those obtainable with simple null models of diversification under stochastic lineage birth and death and random genetic drift. Via a combination of simulations and analyses of core and phylogenetic marker genes, we show that patterns of diversity for the genera Escherichia, Neisseria, and Borrelia are generally indistinguishable from patterns arising under a null model. We suggest that caution should thus be taken in interpreting observed clustering as a result of selective evolutionary forces. Unknown forces do, however, appear to play a role in Helicobacter pylori, and some individual genes in all groups fail to conform to the null model. Taken together, we recommend the presented birth-death model as a null hypothesis in prokaryotic speciation studies. It is only when the real data are statistically different from the expectations under the null model that some speciation process should be invoked.
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Affiliation(s)
- Timothy J Straub
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755;
- Department of Computer Science, Dartmouth College, Hanover, NH 03755
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Nunes AMPB, Ribeiro GS, Ferreira ÍE, Moura ARSS, Felzemburgh RDM, de Lemos APS, Reis MG, de Moraes JC, Campos LC. Meningococcal Carriage among Adolescents after Mass Meningococcal C Conjugate Vaccination Campaigns in Salvador, Brazil. PLoS One 2016; 11:e0166475. [PMID: 27861618 PMCID: PMC5115742 DOI: 10.1371/journal.pone.0166475] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 10/28/2016] [Indexed: 11/21/2022] Open
Abstract
Neisseria meningitidis is a commensal bacterium of the human nasopharynx. In rare cases, it penetrates the mucosa, entering the blood stream and causing various forms of disease. Meningococcal conjugate vaccines can prevent invasive disease not only by direct effect in vaccinated individuals but also by herd protection, preventing acquisition of carriage, which interrupts transmission and leads to protection of unvaccinated persons. In 2010 in Salvador, Brazil, an outbreak of group C meningococcal disease led to a mass meningococcal serogroup C conjugate vaccination drive, targeting those <5 and 10–24 years of age. The present study aimed to estimate the prevalence of and identify factors associated with N. meningitidis carriage among adolescents from Salvador, Brazil, in the post-vaccination period. In spring 2014, we performed a cross-sectional study involving 1,200 public school students aged 11–19 years old. Oropharyngeal swabs were collected to identify N. meningitidis. Of the 59 colonized participants, 36 (61.0%) carried non-groupable N. meningitidis, while genogroup B (11.9%), Y (8.5%), E (6.8%), Z (5.1%), C (3.4%), and W (3.4%) were also detected. The overall prevalence of N. meningitidis carriage was 4.9% (95% confidence interval [CI], 3.6–6.1%); the prevalence of N. meningitidis genogroup C was 0.17% (95% CI, 0.0–0.40%). There was no difference by age. Factors associated with carriage were having only one, shared, bedroom in the household (PR, 2.02; 95% CI, 0.99–4.12, p = 0.05); the mother being the only smoker in the home (PR, 2.48; 95% CI, 1.16–5.29; p = 0.01); and going to pubs/parties more than 5 times/month (PR, 2.61; 95% CI, 1.38–4.92; p = 0.02). Our findings show that the N. meningitidis carriage rate in adolescents from Salvador, Bahia, is low and is potentially influenced by the low prevalence of N. meningitidis genogroup C. However, continued surveillance is important to identify changes in the dynamics of N. meningitidis, including the emergence of diseases due to a non-C serogroup.
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Affiliation(s)
| | - Guilherme Sousa Ribeiro
- Instituto Gonçalo Moniz, FIOCRUZ-BA, 40296–710, Salvador, Brazil
- Instituto de Saúde Coletiva, Universidade Federal da Bahia, 40110–040, Salvador, Brazil
| | | | | | | | | | | | - José Cassio de Moraes
- Faculdade de Ciências Médicas da Santa Casa de São Paulo, 01221–020, São Paulo, Brazil
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Brehony C, Hill DM, Lucidarme J, Borrow R, Maiden MC. Meningococcal vaccine antigen diversity in global databases. ACTA ACUST UNITED AC 2016; 20:30084. [PMID: 26676305 DOI: 10.2807/1560-7917.es.2015.20.49.30084] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Accepted: 07/09/2015] [Indexed: 11/20/2022]
Abstract
The lack of an anti-capsular vaccine against serogroup B meningococcal disease has necessitated the exploration of alternative vaccine candidates, mostly proteins exhibiting varying degrees of antigenic variation. Analysis of variants of antigen-encoding genes is facilitated by publicly accessible online sequence repositories, such as the Neisseria PubMLST database and the associated Meningitis Research Foundation Meningococcus Genome Library (MRF-MGL). We investigated six proposed meningococcal vaccine formulations by deducing the prevalence of their components in the isolates represented in these repositories. Despite high diversity, a limited number of antigenic variants of each of the vaccine antigens were prevalent, with strong associations of particular variant combinations with given serogroups and genotypes. In the MRF-MGL and globally, the highest levels of identical sequences were observed with multicomponent/multivariant vaccines. Our analyses further demonstrated that certain combinations of antigen variants were prevalent over periods of decades in widely differing locations, indicating that vaccine formulations containing a judicious choice of antigen variants have potential for long-term protection across geographic regions. The data further indicated that formulations with multiple variants would be especially relevant at times of low disease incidence, as relative diversity was higher. Continued surveillance is required to monitor the changing prevalence of these vaccine antigens.
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Affiliation(s)
- Carina Brehony
- Department of Zoology, University of Oxford, South Parks Road, Oxford, United Kingdom
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8
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Abstract
Rapid low-cost whole-genome sequencing (WGS) is revolutionizing microbiology; however, complementary advances in accessible, reproducible, and rapid analysis techniques are required to realize the potential of these data. Here, investigations of the genus Neisseria illustrated the gene-by-gene conceptual approach to the organization and analysis of WGS data. Using the gene and its link to phenotype as a starting point, the BIGSdb database, which powers the PubMLST databases, enables the assembly of large open-access collections of annotated genomes that provide insight into the evolution of the Neisseria, the epidemiology of meningococcal and gonococcal disease, and mechanisms of Neisseria pathogenicity.
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Levy M, Antunes A, Fiette L, Deghmane AE, Taha MK. Impact of corticosteroids on experimental meningococcal sepsis in mice. Steroids 2015; 101:96-102. [PMID: 26066898 DOI: 10.1016/j.steroids.2015.05.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 05/21/2015] [Accepted: 05/25/2015] [Indexed: 11/17/2022]
Abstract
Neisseria meningitidis is responsible for septicemia and meningitis with high fatality that is associated with an excessive inflammatory reaction particularly with hyperinvasive isolates of the clonal complex ST-11 (cc11). However, anti-inflammatory adjuvant treatment remains controversial and difficult to assess in patients. We addressed this topic in a well-defined experimental meningococcal infection in transgenic mice expressing the human transferrin. Mice were infected by intra-peritoneal challenge with bioluminescent serogroup C/cc11 strain. After 3h of infection mice were differentially treated every 6h by saline, amoxicillin alone or amoxicillin and dexamethasone (DXM). Infected mice were scored for clinical status, temperature and weight. Biological markers of inflammation were also quantified. Significant clinical improvement was observed in mice treated with amoxicillin and DXM compared to the two other groups. A significant reduction of the inflammatory reaction assessed by CRP and Lipocalin 2 (two acute phase proteins) was also observed with this treatment. DXM significantly increased blood levels of IL-10 at 6h post-infection. DXM/amoxicillin treated mice, compared to the two other groups, also showed lower levels of TNF-α and lower bacterial blood load assessed by serial dilutions of blood and bioluminescence dynamic imaging. Our results suggest that DXM, added to an appropriate antibiotic therapy, has a beneficial effect on experimental sepsis with a hyperinvasive meningococcal strain in transgenic mice expressing human transferrin. This is most likely due to the reduction of inflammatory response by an early induction of IL-10 cytokine. These data may allow better decision-making to use or not corticotherapy during meningococcal sepsis.
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Affiliation(s)
- Michaël Levy
- Institut Pasteur, Unité des Infections Bactériennes Invasives, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; Institut Pasteur, Université Paris Descartes, Sorbonne Paris, Cité, France
| | - Ana Antunes
- Institut Pasteur, Unité des Infections Bactériennes Invasives, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; Institut Pasteur, Université Paris Descartes, Sorbonne Paris, Cité, France
| | - Laurence Fiette
- Institut Pasteur, Unité Histopathologie Humaine et Modèles Animaux, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; Institut Pasteur, Université Paris Descartes, Sorbonne Paris, Cité, France
| | - Ala-Eddine Deghmane
- Institut Pasteur, Unité des Infections Bactériennes Invasives, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; Institut Pasteur, Université Paris Descartes, Sorbonne Paris, Cité, France
| | - Muhamed-Kheir Taha
- Institut Pasteur, Unité des Infections Bactériennes Invasives, 28 rue du Dr Roux, 75724 Paris Cedex 15, France; Institut Pasteur, Université Paris Descartes, Sorbonne Paris, Cité, France.
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Chen M, Guo Q, Wang Y, Zou Y, Wang G, Zhang X, Xu X, Zhao M, Hu F, Qu D, Chen M, Wang M. Shifts in the Antibiotic Susceptibility, Serogroups, and Clonal Complexes of Neisseria meningitidis in Shanghai, China: A Time Trend Analysis of the Pre-Quinolone and Quinolone Eras. PLoS Med 2015; 12:e1001838; discussion e1001838. [PMID: 26057853 PMCID: PMC4461234 DOI: 10.1371/journal.pmed.1001838] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 04/29/2015] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Fluoroquinolones have been used broadly since the end of the 1980s and have been recommended for Neisseria meningitidis prophylaxis since 2005 in China. The aim of this study was to determine whether and how N. meningitidis antimicrobial susceptibility, serogroup prevalence, and clonal complex (CC) prevalence shifted in association with the introduction and expanding use of quinolones in Shanghai, a region with a traditionally high incidence of invasive disease due to N. meningitidis. METHODS AND FINDINGS A total of 374 N. meningitidis isolates collected by the Shanghai Municipal Center for Disease Control and Prevention between 1965 and 2013 were studied. Shifts in the serogroups and CCs were observed, from predominantly serogroup A CC5 (84%) in 1965-1973 to serogroup A CC1 (58%) in 1974-1985, then to serogroup C or B CC4821 (62%) in 2005-2013. The rates of ciprofloxacin nonsusceptibility in N. meningitidis disease isolates increased from 0% in 1965-1985 to 84% (31/37) in 2005-2013 (p < 0.001). Among the ciprofloxacin-nonsusceptible isolates, 87% (27/31) were assigned to either CC4821 (n = 20) or CC5 (n = 7). The two predominant ciprofloxacin-resistant clones were designated ChinaCC4821-R1-C/B and ChinaCC5-R14-A. The ChinaCC4821-R1-C/B clone acquired ciprofloxacin resistance by a point mutation, and was present in 52% (16/31) of the ciprofloxacin-nonsusceptible disease isolates. The ChinaCC5-R14-A clone acquired ciprofloxacin resistance by horizontal gene transfer, and was found in 23% (7/31) of the ciprofloxacin-nonsusceptible disease isolates. The ciprofloxacin nonsusceptibility rate was 47% (7/15) among isolates from asymptomatic carriers, and nonsusceptibility was associated with diverse multi-locus sequence typing profiles and pulsed-field gel electrophoresis patterns. As detected after 2005, ciprofloxacin-nonsusceptible strains were shared between some of the patients and their close contacts. A limitation of this study is that isolates from 1986-2004 were not available and that only a small sample of convenience isolates from 1965-1985 were available. CONCLUSIONS The increasing prevalence of ciprofloxacin resistance since 2005 in Shanghai was associated with the spread of hypervirulent lineages CC4821 and CC5. Two resistant meningococcal clones ChinaCC4821-R1-C/B and ChinaCC5-R14-A have emerged in Shanghai during the quinolone era. Ciprofloxacin should be utilized with caution for the chemoprophylaxis of N. meningitidis in China.
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Affiliation(s)
- Mingliang Chen
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institute of Medical Microbiology and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Qinglan Guo
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Ye Wang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Ying Zou
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Intensive Care Unit, Shanghai Public Health Clinical Center Affiliated to Fudan University, Shanghai, China
| | - Gangyi Wang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xi Zhang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Miao Zhao
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Fupin Hu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Di Qu
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institute of Medical Microbiology and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Min Chen
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
| | - Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- * E-mail:
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11
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Jolley KA, Maiden MCJ. Using multilocus sequence typing to study bacterial variation: prospects in the genomic era. Future Microbiol 2015; 9:623-30. [PMID: 24957089 DOI: 10.2217/fmb.14.24] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Multilocus sequence typing (MLST) indexes the sequence variation present in a small number (usually seven) of housekeeping gene fragments located around the bacterial genome. Unique alleles at these loci are assigned arbitrary integer identifiers, which effectively summarizes the variation present in several thousand base pairs of genome sequence information as a series of numbers. Comparing bacterial isolates using allele-based methods efficiently corrects for the effects of lateral gene transfer present in many bacterial populations and is computationally efficient. This 'gene-by-gene' approach can be applied to larger collections of loci, such as the ribosomal protein genes used in ribosomal MLST (rMLST), up to and including the complete set of coding sequences present in a genome, whole-genome MLST (wgMLST), providing scalable, efficient and readily interpreted genome analysis.
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Affiliation(s)
- Keith A Jolley
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
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12
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Bratcher HB, Corton C, Jolley KA, Parkhill J, Maiden MCJ. A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes. BMC Genomics 2014; 15:1138. [PMID: 25523208 PMCID: PMC4377854 DOI: 10.1186/1471-2164-15-1138] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 12/04/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Highly parallel, 'second generation' sequencing technologies have rapidly expanded the number of bacterial whole genome sequences available for study, permitting the emergence of the discipline of population genomics. Most of these data are publically available as unassembled short-read sequence files that require extensive processing before they can be used for analysis. The provision of data in a uniform format, which can be easily assessed for quality, linked to provenance and phenotype and used for analysis, is therefore necessary. RESULTS The performance of de novo short-read assembly followed by automatic annotation using the pubMLST.org Neisseria database was assessed and evaluated for 108 diverse, representative, and well-characterised Neisseria meningitidis isolates. High-quality sequences were obtained for >99% of known meningococcal genes among the de novo assembled genomes and four resequenced genomes and less than 1% of reassembled genes had sequence discrepancies or misassembled sequences. A core genome of 1600 loci, present in at least 95% of the population, was determined using the Genome Comparator tool. Genealogical relationships compatible with, but at a higher resolution than, those identified by multilocus sequence typing were obtained with core genome comparisons and ribosomal protein gene analysis which revealed a genomic structure for a number of previously described phenotypes. This unified system for cataloguing Neisseria genetic variation in the genome was implemented and used for multiple analyses and the data are publically available in the PubMLST Neisseria database. CONCLUSIONS The de novo assembly, combined with automated gene-by-gene annotation, generates high quality draft genomes in which the majority of protein-encoding genes are present with high accuracy. The approach catalogues diversity efficiently, permits analyses of a single genome or multiple genome comparisons, and is a practical approach to interpreting WGS data for large bacterial population samples. The method generates novel insights into the biology of the meningococcus and improves our understanding of the whole population structure, not just disease causing lineages.
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Briassoulis G, Galani A. Prognostic markers of pediatric meningococcal sepsis. Expert Rev Anti Infect Ther 2014; 12:1017-20. [DOI: 10.1586/14787210.2014.945431] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- George Briassoulis
- Pediatric Intensive Care Unit, University Hospital, University of Crete,
71110 Heraklion, Crete, Greece
| | - Angeliki Galani
- Pediatric Intensive Care Unit, University Hospital, University of Crete,
71110 Heraklion, Crete, Greece
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Pinto VB, Burden R, Wagner A, Moran EE, Lee CH. The development of an experimental multiple serogroups vaccine for Neisseria meningitidis. PLoS One 2013; 8:e79304. [PMID: 24244473 PMCID: PMC3828347 DOI: 10.1371/journal.pone.0079304] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 09/20/2013] [Indexed: 11/18/2022] Open
Abstract
A native outer membrane vesicles (NOMV) vaccine was developed from three antigenically diverse strains of Neisseria meningitidis that express the L1,8, L2, and L3,7 lipooligosaccharide (LOS) immunotypes, and whose synX, and lpxL1 genes were deleted.. Immunogenicity studies in mice showed that the vaccine induced bactericidal antibody against serogroups B, C, W, Y and X N. meningitidis strains. However, this experimental NOMV vaccine was not effective against serogroup A N. meningitidis strains. N. meningitidis capsular polysaccharide (PS) from serogroups A, C, W and Y were effective at inducing bactericidal antibody when conjugated to either tetanus toxoid or the fHbp1-fHbp2 fusion protein fHbp(1+2). The combination of the NOMV vaccine and the N. meningitidis serogroup A capsular polysaccharide (MAPS) protein conjugate was capable of inducing bactericidal antibodies against a limited number of N. meningitidis strains from serogroups A, B, C, W, Y and X tested in this study.
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Affiliation(s)
- Valerian B. Pinto
- Division of Bacterial and Rickettsial Diseases, Walter Reed Army Institute of Research (WRAIR), Silver Springs, Maryland, United States of America
- * E-mail:
| | - Robert Burden
- Division of Bacterial and Rickettsial Diseases, Walter Reed Army Institute of Research (WRAIR), Silver Springs, Maryland, United States of America
| | - Allyn Wagner
- Division of Bacterial and Rickettsial Diseases, Walter Reed Army Institute of Research (WRAIR), Silver Springs, Maryland, United States of America
| | - Elizabeth E. Moran
- Division of Bacterial and Rickettsial Diseases, Walter Reed Army Institute of Research (WRAIR), Silver Springs, Maryland, United States of America
| | - Che-Hung Lee
- Center for Biologics Evaluation and Research, Food and Drug Administration (FDA), Bethesda, Maryland, United States of America
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Maiden MCJ, Jansen van Rensburg MJ, Bray JE, Earle SG, Ford SA, Jolley KA, McCarthy ND. MLST revisited: the gene-by-gene approach to bacterial genomics. Nat Rev Microbiol 2013; 11:728-36. [PMID: 23979428 PMCID: PMC3980634 DOI: 10.1038/nrmicro3093] [Citation(s) in RCA: 472] [Impact Index Per Article: 42.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Multilocus sequence typing (MLST) was proposed in 1998 as a portable sequence-based method for identifying clonal relationships among bacteria. Today, in the whole-genome era of microbiology, the need for systematic, standardized descriptions of bacterial genotypic variation remains a priority. Here, to meet this need, we draw on the successes of MLST and 16S rRNA gene sequencing to propose a hierarchical gene-by-gene approach that reflects functional and evolutionary relationships and catalogues bacteria 'from domain to strain'. Our gene-based typing approach using online platforms such as the Bacterial Isolate Genome Sequence Database (BIGSdb) allows the scalable organization and analysis of whole-genome sequence data.
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Affiliation(s)
- Martin C J Maiden
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
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16
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Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis. Mol Cell 2013; 50:488-503. [PMID: 23706818 DOI: 10.1016/j.molcel.2013.05.001] [Citation(s) in RCA: 205] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Revised: 04/11/2013] [Accepted: 04/29/2013] [Indexed: 12/26/2022]
Abstract
CRISPR interference confers adaptive, sequence-based immunity against viruses and plasmids and is specified by CRISPR RNAs (crRNAs) that are transcribed and processed from spacer-repeat units. Pre-crRNA processing is essential for CRISPR interference in all systems studied thus far. Here, our studies of crRNA biogenesis and CRISPR interference in naturally competent Neisseria spp. reveal a unique crRNA maturation pathway in which crRNAs are transcribed from promoters that are embedded within each repeat, yielding crRNA 5' ends formed by transcription and not by processing. Although crRNA 3' end formation involves RNase III and trans-encoded tracrRNA, as in other type II CRISPR systems, this processing is dispensable for interference. The meningococcal pathway is the most streamlined CRISPR/Cas system characterized to date. Endogenous CRISPR spacers limit natural transformation, which is the primary source of genetic variation that contributes to immune evasion, antibiotic resistance, and virulence in the human pathogen N. meningitidis.
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