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Podda M, Bonechi S, Palladino A, Scaramuzzino M, Brozzi A, Roma G, Muzzi A, Priami C, Sîrbu A, Bodini M. Classification of Neisseria meningitidis genomes with a bag-of-words approach and machine learning. iScience 2024; 27:109257. [PMID: 38439962 PMCID: PMC10910294 DOI: 10.1016/j.isci.2024.109257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 12/13/2023] [Accepted: 02/13/2024] [Indexed: 03/06/2024] Open
Abstract
Whole genome sequencing of bacteria is important to enable strain classification. Using entire genomes as an input to machine learning (ML) models would allow rapid classification of strains while using information from multiple genetic elements. We developed a "bag-of-words" approach to encode, using SentencePiece or k-mer tokenization, entire bacterial genomes and analyze these with ML. Initial model selection identified SentencePiece with 8,000 and 32,000 words as the best approach for genome tokenization. We then classified in Neisseria meningitidis genomes the capsule B group genotype with 99.6% accuracy and the multifactor invasive phenotype with 90.2% accuracy, in an independent test set. Subsequently, in silico knockouts of 2,808 genes confirmed that the ML model predictions aligned with our current understanding of the underlying biology. To our knowledge, this is the first ML method using entire bacterial genomes to classify strains and identify genes considered relevant by the classifier.
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Affiliation(s)
- Marco Podda
- Vaccines Discovery Data Sciences, GSK Vaccines, GSK, 53100 Siena, Italy
| | - Simone Bonechi
- Vaccines Discovery Data Sciences, GSK Vaccines, GSK, 53100 Siena, Italy
- Department of Computer Science, University of Pisa, 56127 Pisa, Italy
| | - Andrea Palladino
- Vaccines Discovery Data Sciences, GSK Vaccines, GSK, 53100 Siena, Italy
| | | | - Alessandro Brozzi
- Vaccines Discovery Data Sciences, GSK Vaccines, GSK, 53100 Siena, Italy
| | - Guglielmo Roma
- Vaccines Discovery Data Sciences, GSK Vaccines, GSK, 53100 Siena, Italy
| | - Alessandro Muzzi
- Vaccines Discovery Data Sciences, GSK Vaccines, GSK, 53100 Siena, Italy
| | - Corrado Priami
- Department of Computer Science, University of Pisa, 56127 Pisa, Italy
| | - Alina Sîrbu
- Department of Computer Science, University of Pisa, 56127 Pisa, Italy
| | - Margherita Bodini
- Vaccines Discovery Data Sciences, GSK Vaccines, GSK, 53100 Siena, Italy
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2
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Li J, Long D, Wu S, Wu X, Wei B, Chen D, Shao Y, Wang H, Cui L, Chen X, Yu L. Association of CFH polymorphism with susceptibility to sepsis caused by Pseudomonas aeruginosa in Chinese Han populations: A multi-center study. Gene 2019; 722:144127. [PMID: 31525397 DOI: 10.1016/j.gene.2019.144127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 09/11/2019] [Accepted: 09/12/2019] [Indexed: 10/26/2022]
Abstract
Complement factor H (CFH) serves as a major down-regulator in the complement system, often utilized by bacterial pathogens to evade complement attack. Yet, little is currently known about the genetic correlation of CFH polymorphisms with sepsis due to various microbial infections. A case-control method (488 septic patients and 527 healthy individuals) was carried out in this study to investigate the genetic relationship between CFH polymorphisms (rs3753394 C/T, rs1065489 G/T and rs1061170 C/T) and susceptibility to sepsis caused by bacterial infections in Chinese Han populations. Our findings indicated that the frequency of rs3753394 CT/TT genotype in the septic patients with P. aeruginosa was significantly higher than that in the control individuals (P = 0.033, OR = 2.668, 95%CI = 1.072-6.334). The rs3753394 T allele frequency in the P. aeruginosa-infected patients was significantly increased, compared to that in the healthy controls (P = 0.014, OR = 1.68, 95%CI = 1.118-2.538). Moreover, these significant differences of rs3753394 genotype and allele frequencies remained after multiple testing corrections [P (corr.) = 0.033 for genotype; P (corr.) = 0.033 for allele]. The current study highlighted the significance of CFH polymorphism rs3753394 as a potential biomarker for targeting P. aeruginosa infection in critically ill patients.
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Affiliation(s)
- Jia Li
- Department of Health Technology and Informatics, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong.
| | - Ding Long
- Intensive Care Units, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Sisi Wu
- Intensive Care Units, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Xiaoling Wu
- Intensive Care Units, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Bohua Wei
- Intensive Care Units, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Dan Chen
- Intensive Care Units, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yiming Shao
- Intensive Care Units, The Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Hongliang Wang
- Department of Critical Care Medicine, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Lili Cui
- Institute of Neurology, Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, The Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Xiangyan Chen
- Department of Health Technology and Informatics, the Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong
| | - Li Yu
- Intensive Care Units, The Central Hospital of Wuhan, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.
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3
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Wang B, Santoreneos R, Giles L, Haji Ali Afzali H, Marshall H. Case fatality rates of invasive meningococcal disease by serogroup and age: A systematic review and meta-analysis. Vaccine 2019; 37:2768-2782. [DOI: 10.1016/j.vaccine.2019.04.020] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 03/14/2019] [Accepted: 04/04/2019] [Indexed: 10/27/2022]
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Kahler CM, Nawrocki KL, Anandan A, Vrielink A, Shafer WM. Structure-Function Relationships of the Neisserial EptA Enzyme Responsible for Phosphoethanolamine Decoration of Lipid A: Rationale for Drug Targeting. Front Microbiol 2018; 9:1922. [PMID: 30186254 PMCID: PMC6111236 DOI: 10.3389/fmicb.2018.01922] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 07/30/2018] [Indexed: 11/13/2022] Open
Abstract
Bacteria cause disease by two general mechanisms: the action of their toxins on host cells and induction of a pro-inflammatory response that can lead to a deleterious cytokine/chemokine response (e.g., the so-called cytokine storm) often seen in bacteremia/septicemia. These major mechanisms may overlap due to the action of surface structures that can have direct and indirect actions on phagocytic or non-phagocytic cells. In this respect, the lipid A (endotoxin) component of lipopolysaccharide (LPS) possessed by Gram-negative bacteria has been the subject of literally thousands of studies over the past century that clearly identified it as a key virulence factor in endotoxic shock. In addition to its capacity to modulate inflammatory responses, endotoxin can also modulate bacterial susceptibility to host antimicrobials, such as the host defense peptides termed cationic antimicrobial peptides. This review concentrates on the phosphoethanolamine (PEA) decoration of lipid A in the pathogenic species of the genus Neisseria [N. gonorrhoeae and N. meningitidis]. PEA decoration of lipid A is mediated by the enzyme EptA (formerly termed LptA) and promotes resistance to innate defense systems, induces the pro-inflammatory response and can influence the in vivo fitness of bacteria during infection. These important biological properties have driven efforts dealing with the biochemistry and structural biology of EptA that will facilitate the development of potential inhibitors that block PEA addition to lipid A.
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Affiliation(s)
- Charlene M Kahler
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA, Australia.,Perth Children's Hospital, Telethon Kids Institute, Subiaco, WA, Australia
| | - K L Nawrocki
- Department of Microbiology and Immunology, The Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, United States.,Laboratories of Bacterial Pathogenesis, VA Medical Center, Decatur, GA, United States
| | - A Anandan
- School of Molecular Sciences, University of Western Australia, Crawley, WA, Australia
| | - Alice Vrielink
- The Marshall Center for Infectious Diseases Research and Training, School of Biomedical Sciences, University of Western Australia, Crawley, WA, Australia.,School of Molecular Sciences, University of Western Australia, Crawley, WA, Australia
| | - William M Shafer
- Department of Microbiology and Immunology, The Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, United States.,Laboratories of Bacterial Pathogenesis, VA Medical Center, Decatur, GA, United States
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Siena E, Bodini M, Medini D. Interplay Between Virulence and Variability Factors as a Potential Driver of Invasive Meningococcal Disease. Comput Struct Biotechnol J 2018; 16:61-69. [PMID: 29686800 PMCID: PMC5910500 DOI: 10.1016/j.csbj.2018.02.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Revised: 01/29/2018] [Accepted: 02/11/2018] [Indexed: 01/09/2023] Open
Abstract
Neisseria meningitidis (Nm) is frequently found in the upper respiratory tract of the human population. Despite its prevalence as a commensal organism, Nm can occasionally invade the pharyngeal mucosal epithelium causing septicemia and life-threatening disease. A number of studies have tried to identify factors that are responsible for the onset of a virulent phenotype. Despite this however, we still miss clear causative elements. Several factors have been identified to be associated to an increased susceptibility to meningococcal disease in humans. None of them, however, could unambiguously discriminate healthy carrier from infected individuals. Similarly, comparative studies of virulent and apathogenic strains failed to identify virulence factors that could explain the emergence of the pathogenic phenotype. In line with this, a recent study of within host evolution found that Nm accumulates genomic changes during the asymptomatic carriage phase and that these are likely to contribute to the shift to a pathogenic phenotype. These results suggest that the presence of virulence factors in the meningococcal genome is not a sufficient condition for developing virulent traits, but is rather the ability to promote phenotypic variation, through the stochastic assortment of the repertoire of such factors, which could explain the occasional and unpredictable onset of IMD. Here, we present a series of argumentations supporting the hypothesis that invasive meningococcal disease comes as a result of the coexistence of bacterial virulence and variability factors in a plot that can be further complicated by additional latent factors, like host pre-existing immune status and genetic predisposition.
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Abstract
The majority of rare diseases affect children, most of whom have an underlying genetic cause for their condition. However, making a molecular diagnosis with current technologies and knowledge is often still a challenge. Paediatric genomics is an immature but rapidly evolving field that tackles this issue by incorporating next-generation sequencing technologies, especially whole-exome sequencing and whole-genome sequencing, into research and clinical workflows. This complex multidisciplinary approach, coupled with the increasing availability of population genetic variation data, has already resulted in an increased discovery rate of causative genes and in improved diagnosis of rare paediatric disease. Importantly, for affected families, a better understanding of the genetic basis of rare disease translates to more accurate prognosis, management, surveillance and genetic advice; stimulates research into new therapies; and enables provision of better support.
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7
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Abstract
Bacteremia and sepsis are conditions associated with high mortality and are of great impact to health care operations. Among the top causes of mortality in the United States, these conditions cause over 600 fatalities each day. Empiric, broad-spectrum treatment is a common but often a costly approach that may fail to effectively target the correct microbe, may inadvertently harm patients via antimicrobial toxicity or downstream antimicrobial resistance. To meet the diagnostic challenges of bacteremia and sepsis, laboratories must understand the complexity of diagnosing and treating septic patients, in order to focus on creating algorithms that can help direct a more targeted approach to antimicrobial therapy and synergize with existing clinical practices defined in new Surviving Sepsis Guidelines. Significant advances have been made in improving blood culture media; as yet no molecular or antigen-based method has proven superior for the detection of bacteremia in terms of limit of detection. Several methods for rapid molecular identification of pathogens from blood cultures bottles are available and many more are on the diagnostic horizon. Ultimately, early intervention by molecular detection of bacteria and fungi directly from whole blood could provide the most patient benefit and contribute to tailored antibiotic coverage of the patient early on in the course of the disease. Although blood cultures remain as the best means of diagnosing bacteremia and candidemia, complementary testing with antigen tests, microbiologic investigations from other body sites, and histopathology can often aid in the diagnosis of disseminated disease, and application of emerging nucleic acid test methods and other new technology may greatly impact our ability to bacteremic and septic patients, particularly those who are immunocompromised.
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Klughammer J, Dittrich M, Blom J, Mitesser V, Vogel U, Frosch M, Goesmann A, Müller T, Schoen C. Comparative Genome Sequencing Reveals Within-Host Genetic Changes in Neisseria meningitidis during Invasive Disease. PLoS One 2017; 12:e0169892. [PMID: 28081260 PMCID: PMC5231331 DOI: 10.1371/journal.pone.0169892] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 12/22/2016] [Indexed: 11/29/2022] Open
Abstract
Some members of the physiological human microbiome occasionally cause life-threatening disease even in immunocompetent individuals. A prime example of such a commensal pathogen is Neisseria meningitidis, which normally resides in the human nasopharynx but is also a leading cause of sepsis and epidemic meningitis. Using N. meningitidis as model organism, we tested the hypothesis that virulence of commensal pathogens is a consequence of within host evolution and selection of invasive variants due to mutations at contingency genes, a mechanism called phase variation. In line with the hypothesis that phase variation evolved as an adaptation to colonize diverse hosts, computational comparisons of all 27 to date completely sequenced and annotated meningococcal genomes retrieved from public databases showed that contingency genes are indeed enriched for genes involved in host interactions. To assess within-host genetic changes in meningococci, we further used ultra-deep whole-genome sequencing of throat-blood strain pairs isolated from four patients suffering from invasive meningococcal disease. We detected up to three mutations per strain pair, affecting predominantly contingency genes involved in type IV pilus biogenesis. However, there was not a single (set) of mutation(s) that could invariably be found in all four pairs of strains. Phenotypic assays further showed that these genetic changes were generally not associated with increased serum resistance, higher fitness in human blood ex vivo or differences in the interaction with human epithelial and endothelial cells in vitro. In conclusion, we hypothesize that virulence of meningococci results from accidental emergence of invasive variants during carriage and without within host evolution of invasive phenotypes during disease progression in vivo.
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Affiliation(s)
- Johanna Klughammer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Marcus Dittrich
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
- Institute of Human Genetics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Jochen Blom
- Institute for Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Vera Mitesser
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Ulrich Vogel
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
- Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany
- German Reference Laboratory for Meningococci and Haemophilus influenzae, Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Matthias Frosch
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
- Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany
- German Reference Laboratory for Meningococci and Haemophilus influenzae, Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
| | - Alexander Goesmann
- Institute for Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Tobias Müller
- Department of Bioinformatics, Biocenter, University of Würzburg, Würzburg, Germany
| | - Christoph Schoen
- Institute for Hygiene and Microbiology, University of Würzburg, Würzburg, Germany
- Research Center for Infectious Diseases, University of Würzburg, Würzburg, Germany
- * E-mail:
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9
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Gianchecchi E, Torelli A, Piccini G, Piccirella S, Montomoli E. N. meningitidis and TLR Polymorphisms: A Fascinating Immunomodulatory Network. Vaccines (Basel) 2016; 4:vaccines4020020. [PMID: 27240411 PMCID: PMC4931637 DOI: 10.3390/vaccines4020020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 04/29/2016] [Accepted: 05/20/2016] [Indexed: 12/21/2022] Open
Abstract
N. meningitidis infections represent a global health problem that can lead to the development of serious permanent sequelae. Although the use of antibiotics and prevention via vaccination have reduced the incidence of meningococcal disease, our understanding regarding N. meningitidis pathogenesis is still limited, especially of those mechanisms responsible for IMD and fulminant or deadly septic shock. These severe clinical presentations occur in a limited number of subjects, whereas about 10% of healthy individuals are estimated to carry the bacteria as a commensal. Since TLR activation is involved in the defense against N. meningitidis, several studies have highlighted the association between host TLR SNPs and a higher susceptibility and severity of N. meningitidis infections. Moreover, TLR SNPs induced variations in immunological responses and in their persistence upon vaccination against meningococcal disease. In the absence of mass vaccination programs, the early identification of risk factors for meningococcal disease would be recommended in order to start immunization strategies and antibiotic treatment in those subjects carrying the risk variants. In addition, it could allow us to identify individuals with a higher risk for severe disease and sequelae in order to develop a personalized healthcare of high-risk subjects based on their genomic profile. In this review, we have illustrated important preliminary correlations between TLR variants and meningococcal susceptibility/severity and with vaccine-induced immune responses.
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Affiliation(s)
| | - Alessandro Torelli
- Strada del Petriccio e Belriguardo, 53100 Siena, Italy.
- Department of Life Sciences, University of Siena, 53100 Siena, Italy.
| | | | | | - Emanuele Montomoli
- Strada del Petriccio e Belriguardo, 53100 Siena, Italy.
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy.
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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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11
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Bradley DT, Bourke TW, Fairley DJ, Borrow R, Shields MD, Zipfel PF, Hughes AE. Susceptibility to invasive meningococcal disease: polymorphism of complement system genes and Neisseria meningitidis factor H binding protein. PLoS One 2015; 10:e0120757. [PMID: 25798599 PMCID: PMC4370764 DOI: 10.1371/journal.pone.0120757] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Accepted: 01/05/2015] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Neisseria meningitidis can cause severe infection in humans. Polymorphism of Complement Factor H (CFH) is associated with altered risk of invasive meningococcal disease (IMD). We aimed to find whether polymorphism of other complement genes altered risk and whether variation of N. meningitidis factor H binding protein (fHBP) affected the risk association. METHODS We undertook a case-control study with 309 European cases and 5,200 1958 Birth Cohort and National Blood Service cohort controls. We used additive model logistic regression, accepting P<0.05 as significant after correction for multiple testing. The effects of fHBP subfamily on the age at infection and severity of disease was tested using the independent samples median test and Student's T test. The effect of CFH polymorphism on the N. meningitidis fHBP subfamily was investigated by logistic regression and Chi squared test. RESULTS Rs12085435 A in C8B was associated with odds ratio (OR) of IMD (0.35 [95% CI 0.19-0.67]; P = 0.03 after correction). A CFH haplotype tagged by rs3753396 G was associated with IMD (OR 0.56 [95% CI 0.42-0.76], P = 1.6x10⁻⁴). There was no bacterial load (CtrA cycle threshold) difference associated with carriage of this haplotype. Host CFH haplotype and meningococcal fHBP subfamily were not associated. Individuals infected with meningococci expressing subfamily A fHBP were younger than those with subfamily B fHBP meningococci (median 1 vs 2 years; P = 0.025). DISCUSSION The protective CFH haplotype alters odds of IMD without affecting bacterial load for affected heterozygotes. CFH haplotype did not affect the likelihood of infecting meningococci having either fHBP subfamily. The association between C8B rs12085435 and IMD requires independent replication. The CFH association is of interest because it is independent of known functional polymorphisms in CFH. As fHBP-containing vaccines are now in use, relationships between CFH polymorphism and vaccine effectiveness and side-effects may become important.
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Affiliation(s)
- Declan T. Bradley
- Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, United Kingdom
- Public Health Agency, Belfast, United Kingdom
- * E-mail:
| | - Thomas W. Bourke
- Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Derek J. Fairley
- Regional Virus Laboratory, Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Raymond Borrow
- Vaccine Evaluation Unit, Public Health England, Manchester, United Kingdom
- Inflammation Sciences Research Group, School of Translational Medicine, University of Manchester, Manchester, United Kingdom
| | - Michael D. Shields
- Centre for Infection and Immunity, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, United Kingdom
| | - Peter F. Zipfel
- Department of Infection Biology, Leibniz Institute for Natural Product Research and Infection Biology—Hans Knöll Institute, Jena, Germany
- Friedrich Schiller University, Jena, Germany
| | - Anne E. Hughes
- Formerly of Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, Belfast, United Kingdom
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12
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Ladhani SN, Cordery R, Mandal S, Christensen H, Campbell H, Borrow R, Ramsay ME. Preventing secondary cases of invasive meningococcal capsular group B (MenB) disease using a recently-licensed, multi-component, protein-based vaccine (Bexsero(®)). J Infect 2014; 69:470-80. [PMID: 25043395 DOI: 10.1016/j.jinf.2014.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2014] [Revised: 07/10/2014] [Accepted: 07/12/2014] [Indexed: 11/18/2022]
Abstract
OBJECTIVES To assess the potential use of a protein-based meningococcal group B (MenB) vaccine (Bexsero(®)) in addition to antibiotic chemoprophylaxis for preventing secondary cases. METHODS Published studies on the risk of secondary meningococcal infections were used to estimate the numbers needed to vaccinate (NNV) with Bexsero(®) to prevent a secondary case in household and educational settings. RESULTS Most secondary cases occur within a few days of diagnosis in the index case. Unlike conjugate vaccines, early protection offered after a single dose of Bexsero(®) is likely to be low, particularly in young children, who are at higher risk of secondary infection. NNV was dependent on predicted meningococcal strain coverage, estimated onset of protection after one Bexsero(®) dose and estimated vaccine efficacy. Even in the most favourable scenario where we assume the vaccine is administered within 4 days of the index case and prevents 90% of cases occurring after 14 days, the NNV for household contacts was >1000. NNV in educational settings was much higher. CONCLUSIONS The estimated NNV should be taken into account when deciding policy to recommend Bexsero(®) for close contacts of single cases in household or educational settings. Bexsero(®) may have a protective role in clusters and outbreaks.
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Affiliation(s)
- Shamez N Ladhani
- Immunisation Department, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom; Paediatric Infectious Diseases Research Group, St. George's University of London, Cranmer Terrace, London SW17 0RE, United Kingdom.
| | - Rebecca Cordery
- South East London Health Protection Team, Public Health England, 1 Lower Marsh, London SE1 7NT, United Kingdom
| | - Sema Mandal
- Immunisation Department, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom
| | - Hannah Christensen
- School of Social and Community Medicine, Canynge Hall, 39 Whatley Road, Bristol BS8 2PS, United Kingdom
| | - Helen Campbell
- Immunisation Department, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom
| | - Ray Borrow
- Vaccine Evaluation Unit, Public Health England, Manchester Royal Infirmary, Manchester M13 9WZ, United Kingdom
| | - Mary E Ramsay
- Immunisation Department, Public Health England, 61 Colindale Avenue, London NW9 5EQ, United Kingdom
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Abstract
BACKGROUND Due to its extraordinarily fast economic and social transition, virtually closed borders before 1940 and, moreover, that 85% of the population has the distinctive genetics of the Inuit, Greenland is a very interesting country to study cervical cancer from a historical perspective. Nevertheless, little has been reported about long-term cancer trends in Greenland. Our aim was to describe and interpret the incidence of cervical cancer from 1950 to 2009. MATERIAL AND METHODS We systematically searched PubMed for articles reporting the incidence of cervical cancer in Greenland. We supplemented this with data for 1980-2009 obtained from the Chief Medical Officer of Greenland. RESULTS Incidence of cervical cancer was around 10 per 100 000 women (age-standardised, world population, ASW) in the 1950s, 30 per 100 000 in the 1960s, and in the 1980s around 60 per 100 000. From 1985 onwards, the incidence of cervical cancer started decreasing to the current level of 25 per 100 000. CONCLUSION The steep increase in the incidence of cervical cancer from the 1950s onwards is unlikely to be explained by increasing completeness of data. In parallel with the economic development, however, out-of-wedlock births (proxy for sexual behaviour) increased dramatically from 1935 onwards while tobacco use increased from the 1950s onwards. From the late 1960s to around 1990, data suggested rather stable but high levels of sexual habits. The decrease in the incidence of cervical cancer since 1985 is consistent with the introduction of screening. The data strongly suggested that the increased burden of cervical cancer in Greenlandic women was real and followed earlier changes in sexual behaviour; these changes were likely a consequence of the tremendous societal changes.
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Affiliation(s)
- Bente B. Sander
- Department of Public Health, University of Copenhagen,
Copenhagen K, Denmark
| | - Matejka Rebolj
- Department of Public Health, University of Copenhagen,
Copenhagen K, Denmark
| | - Elsebeth Lynge
- Department of Public Health, University of Copenhagen,
Copenhagen K, Denmark
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Boyd JH, Russell JA, Fjell CD. The meta-genome of sepsis: host genetics, pathogens and the acute immune response. J Innate Immun 2014; 6:272-83. [PMID: 24525633 DOI: 10.1159/000358835] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Accepted: 01/20/2014] [Indexed: 12/22/2022] Open
Abstract
Severe infection and the patient response constitute sepsis. Here, we review the meta-genome (patient genetics, pathogen communities and host response) and its impact upon the outcome of severe sepsis. Patient genetics, both predisposition for infection and the subsequent response to infection are reviewed. The pathogen is discussed with particular emphasis upon the modern era of microbiome analysis and nucleic acid diagnostics. Finally, we discuss the host clinical and immune responses and present new data to suggest that the immune response is the key to understanding sepsis and improving a death rate of nearly 30%.
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Affiliation(s)
- John H Boyd
- Division of Critical Care Medicine, St. Paul's Hospital, Vancouver, B.C., Canada
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Abstract
Despite considerable advances in the understanding of the pathogenesis of meningococcal disease, this infection remains a major cause of morbidity and mortality globally. The role of the complement system in innate immune defenses against invasive meningococcal disease is well established. Individuals deficient in components of the alternative and terminal complement pathways are highly predisposed to invasive, often recurrent meningococcal infections. Genome-wide analysis studies also point to a central role for complement in disease pathogenesis. Here we review the pathophysiologic events pertinent to the complement system that accompany meningococcal sepsis in humans. Meningococci use several often redundant mechanisms to evade killing by human complement. Capsular polysaccharide and lipooligosaccharide glycan composition play critical roles in complement evasion. Some of the newly described protein vaccine antigens interact with complement components and have sparked considerable research interest.
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Affiliation(s)
- Lisa A Lewis
- Division of Infectious Diseases and Immunology; University of Massachusetts Medical School; Worcester, MA USA
| | - Sanjay Ram
- Division of Infectious Diseases and Immunology; University of Massachusetts Medical School; Worcester, MA USA
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