Genetic characterisation of Malawian pneumococci prior to the roll-out of the PCV13 vaccine using a high-throughput whole genome sequencing approach.

PubWeight™: 1.03‹?› | Rank: Top 15%

🔗 View Article (PMC 3438182)

Published in PLoS One on September 10, 2012

Authors

Dean B Everett1, Jennifer Cornick, Brigitte Denis, Claire Chewapreecha, Nicholas Croucher, Simon Harris, Julian Parkhill, Stephen Gordon, Enitan D Carrol, Neil French, Robert S Heyderman, Stephen D Bentley

Author Affiliations

1: Malawi-Liverpool-Wellcome Clinical Research Programme, Chichiri, Blantyre 3, Malawi. Dean.Everett@liverpool.ac.uk

Articles citing this

Pneumococcal Capsules and Their Types: Past, Present, and Future. Clin Microbiol Rev (2015) 1.45

Mechanisms of genome evolution of Streptococcus. Infect Genet Evol (2014) 0.92

High multiple carriage and emergence of Streptococcus pneumoniae vaccine serotype variants in Malawian children. BMC Infect Dis (2015) 0.90

Recombination in Streptococcus pneumoniae Lineages Increase with Carriage Duration and Size of the Polysaccharide Capsule. MBio (2016) 0.83

Whole genome sequencing of Streptococcus pneumoniae: development, evaluation and verification of targets for serogroup and serotype prediction using an automated pipeline. PeerJ (2016) 0.82

Reducing deaths from severe pneumonia in children in Malawi by improving delivery of pneumonia case management. PLoS One (2014) 0.82

Genomic identification of a novel co-trimoxazole resistance genotype and its prevalence amongst Streptococcus pneumoniae in Malawi. J Antimicrob Chemother (2013) 0.81

Virulence Factors of Streptococcus pneumoniae. Comparison between African and French Invasive Isolates and Implication for Future Vaccines. PLoS One (2015) 0.80

Application of a target enrichment-based next-generation sequencing protocol for identification and sequence-based prediction of pneumococcal serotypes. BMC Microbiol (2014) 0.79

Potentially Modifiable Factors Associated with Death of Infants and Children with Severe Pneumonia Routinely Managed in District Hospitals in Malawi. PLoS One (2015) 0.77

Genomic pneumococcal load and CSF cytokines are not related to outcome in Malawian adults with meningitis. J Infect (2014) 0.76

Piliation of invasive Streptococcus pneumoniae isolates in the era before pneumococcal conjugate vaccine introduction in Malawi. Clin Vaccine Immunol (2013) 0.76

Understanding pneumococcal serotype 1 biology through population genomic analysis. BMC Infect Dis (2016) 0.75

A novel streptococcal cell-cell communication peptide promotes pneumococcal virulence and biofilm formation. Mol Microbiol (2017) 0.75

Trends in antimicrobial resistance in bloodstream infection isolates at a large urban hospital in Malawi (1998-2016): a surveillance study. Lancet Infect Dis (2017) 0.75

Pre-vaccine serotype composition within a lineage signposts its serotype replacement - a carriage study over 7 years following pneumococcal conjugate vaccine use in the UK. Microb Genom (2017) 0.75

Articles cited by this

MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89

Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res (2008) 151.16

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics (2006) 87.59

SSAHA: a fast search method for large DNA databases. Genome Res (2001) 48.64

A multilocus sequence typing scheme for Streptococcus pneumoniae: identification of clones associated with serious invasive disease. Microbiology (1998) 17.05

Burden of disease caused by Streptococcus pneumoniae in children younger than 5 years: global estimates. Lancet (2009) 15.31

Evolution of MRSA during hospital transmission and intercontinental spread. Science (2010) 13.34

Antimicrobial resistance in Streptococcus pneumoniae: an overview. Clin Infect Dis (1992) 11.24

Rapid pneumococcal evolution in response to clinical interventions. Science (2011) 9.09

Efficacy of nine-valent pneumococcal conjugate vaccine against pneumonia and invasive pneumococcal disease in The Gambia: randomised, double-blind, placebo-controlled trial. Lancet (2005) 7.99

A trial of a 9-valent pneumococcal conjugate vaccine in children with and those without HIV infection. N Engl J Med (2003) 7.39

Intercontinental spread of a multiresistant clone of serotype 23F Streptococcus pneumoniae. J Infect Dis (1991) 6.69

Nomenclature of major antimicrobial-resistant clones of Streptococcus pneumoniae defined by the pneumococcal molecular epidemiology network. J Clin Microbiol (2001) 6.66

Incidence of pneumococcal disease due to non-pneumococcal conjugate vaccine (PCV7) serotypes in the United States during the era of widespread PCV7 vaccination, 1998-2004. J Infect Dis (2007) 6.45

ABACAS: algorithm-based automatic contiguation of assembled sequences. Bioinformatics (2009) 4.98

Dexamethasone treatment in childhood bacterial meningitis in Malawi: a randomised controlled trial. Lancet (2002) 4.57

Typing of pneumococci by using 12 pooled antisera. J Clin Microbiol (1993) 3.85

Laboratory diagnosis of Pneumococcus infections. Bull World Health Organ (1960) 3.47

Identification of three major clones of multiply antibiotic-resistant Streptococcus pneumoniae in Taiwanese hospitals by multilocus sequence typing. J Clin Microbiol (1998) 3.36

Systematic evaluation of serotypes causing invasive pneumococcal disease among children under five: the pneumococcal global serotype project. PLoS Med (2010) 3.25

Evolutionary dynamics of Clostridium difficile over short and long time scales. Proc Natl Acad Sci U S A (2010) 3.18

Invasive pneumococcal disease in children 5 years after conjugate vaccine introduction--eight states, 1998-2005. MMWR Morb Mortal Wkly Rep (2008) 3.03

Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species. Genome Biol (2010) 2.60

Role of conjugative elements in the evolution of the multidrug-resistant pandemic clone Streptococcus pneumoniaeSpain23F ST81. J Bacteriol (2008) 2.51

Burden of invasive pneumococcal disease and serotype distribution among Streptococcus pneumoniae isolates in young children in Europe: impact of the 7-valent pneumococcal conjugate vaccine and considerations for future conjugate vaccines. Int J Infect Dis (2009) 2.33

Bacterial meningitis in Malawian adults: pneumococcal disease is common, severe, and seasonal. Clin Infect Dis (2000) 2.14

High pneumococcal DNA loads are associated with mortality in Malawian children with invasive pneumococcal disease. Pediatr Infect Dis J (2007) 2.10

Ten years of surveillance for invasive Streptococcus pneumoniae during the era of antiretroviral scale-up and cotrimoxazole prophylaxis in Malawi. PLoS One (2011) 1.39

Serotyping of Streptococcus pneumoniae by agglutination assays: a cost-effective technique for developing countries. Bull World Health Organ (1996) 1.22

Global prevailing and emerging pediatric pneumococcal serotypes. Expert Rev Vaccines (2011) 1.14

Poor potential coverage for 7-valent pneumococcal conjugate vaccine, Malawi. Emerg Infect Dis (2003) 1.10

Quellung test for pneumonia. N Engl J Med (1973) 0.77

Articles by these authors

A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63

The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol (2008) 31.04

Enterotypes of the human gut microbiome. Nature (2011) 24.36

High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nat Genet (2008) 19.97

ACT: the Artemis Comparison Tool. Bioinformatics (2005) 17.91

Evolution of MRSA during hospital transmission and intercontinental spread. Science (2010) 13.34

Prepublication data sharing. Nature (2009) 12.24

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Bioinformatics (2008) 9.17

Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat Genet (2003) 9.13

Rapid pneumococcal evolution in response to clinical interventions. Science (2011) 9.09

Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc Natl Acad Sci U S A (2004) 8.95

The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat Genet (2006) 8.02

Salmonella enterica serovar typhimurium exploits inflammation to compete with the intestinal microbiota. PLoS Biol (2007) 7.58

Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei. Proc Natl Acad Sci U S A (2004) 7.30

Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. Lancet Infect Dis (2012) 7.18

The complete genome sequence of Mycobacterium bovis. Proc Natl Acad Sci U S A (2003) 6.79

Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study. Lancet Infect Dis (2012) 6.64

Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes. PLoS Genet (2006) 6.43

Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak. N Engl J Med (2012) 6.36

GeneDB: a resource for prokaryotic and eukaryotic organisms. Nucleic Acids Res (2004) 6.30

Meticillin-resistant Staphylococcus aureus with a novel mecA homologue in human and bovine populations in the UK and Denmark: a descriptive study. Lancet Infect Dis (2011) 6.08

The genome of the blood fluke Schistosoma mansoni. Nature (2009) 5.94

Multidrug-resistant Salmonella enterica serovar paratyphi A harbors IncHI1 plasmids similar to those found in serovar typhi. J Bacteriol (2007) 5.88

Evidence for several waves of global transmission in the seventh cholera pandemic. Nature (2011) 5.62

DNAPlotter: circular and linear interactive genome visualization. Bioinformatics (2008) 5.49

Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J (2010) 5.43

Microevolution and history of the plague bacillus, Yersinia pestis. Proc Natl Acad Sci U S A (2004) 5.04

Microbiology in the post-genomic era. Nat Rev Microbiol (2008) 4.88

Whole-genome sequencing to identify transmission of Mycobacterium abscessus between patients with cystic fibrosis: a retrospective cohort study. Lancet (2013) 4.75

Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog (2012) 4.69

Corticosteroids for bacterial meningitis in adults in sub-Saharan Africa. N Engl J Med (2007) 4.56

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol (2014) 4.39

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Bioinformatics (2011) 4.31

Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands. Bioinformatics (2006) 4.27

Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Res (2009) 4.12

Emergence and global spread of epidemic healthcare-associated Clostridium difficile. Nat Genet (2012) 4.10

Invasive non-typhoidal salmonella disease: an emerging and neglected tropical disease in Africa. Lancet (2012) 4.02

Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype. Genome Res (2009) 3.99

Epidemics of invasive Salmonella enterica serovar enteritidis and S. enterica Serovar typhimurium infection associated with multidrug resistance among adults and children in Malawi. Clin Infect Dis (2008) 3.89

Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans. Nat Genet (2013) 3.89

The complete genome, comparative and functional analysis of Stenotrophomonas maltophilia reveals an organism heavily shielded by drug resistance determinants. Genome Biol (2008) 3.85

Targeted restoration of the intestinal microbiota with a simple, defined bacteriotherapy resolves relapsing Clostridium difficile disease in mice. PLoS Pathog (2012) 3.81

Genome plasticity of BCG and impact on vaccine efficacy. Proc Natl Acad Sci U S A (2007) 3.73

Comparative genome and phenotypic analysis of Clostridium difficile 027 strains provides insight into the evolution of a hypervirulent bacterium. Genome Biol (2009) 3.66

Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biol (2009) 3.63

Comparative genomic analyses of seventeen Streptococcus pneumoniae strains: insights into the pneumococcal supragenome. J Bacteriol (2007) 3.62

Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways. Genome Res (2008) 3.54

Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer. Genome Res (2007) 3.45

Antibiotic treatment of clostridium difficile carrier mice triggers a supershedder state, spore-mediated transmission, and severe disease in immunocompromised hosts. Infect Immun (2009) 3.36

Comparative genomic structure of prokaryotes. Annu Rev Genet (2004) 3.34

The complete genome sequence and comparative genome analysis of the high pathogenicity Yersinia enterocolitica strain 8081. PLoS Genet (2006) 3.33

Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei. Lancet (2003) 3.30

Insights from the complete genome sequence of Mycobacterium marinum on the evolution of Mycobacterium tuberculosis. Genome Res (2008) 3.26

The uptake and accuracy of oral kits for HIV self-testing in high HIV prevalence setting: a cross-sectional feasibility study in Blantyre, Malawi. PLoS Med (2011) 3.25

BamView: viewing mapped read alignment data in the context of the reference sequence. Bioinformatics (2010) 3.24

Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe. Nat Genet (2012) 3.22

Evolutionary dynamics of Clostridium difficile over short and long time scales. Proc Natl Acad Sci U S A (2010) 3.18

High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease. BMC Microbiol (2011) 3.11

Complete genome sequence and comparative genome analysis of enteropathogenic Escherichia coli O127:H6 strain E2348/69. J Bacteriol (2008) 3.10

Extensive DNA inversions in the B. fragilis genome control variable gene expression. Science (2005) 3.08

Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa. Genome Res (2008) 3.03

Sequencing ancient calcified dental plaque shows changes in oral microbiota with dietary shifts of the Neolithic and Industrial revolutions. Nat Genet (2013) 3.03

The genome of Rhizobium leguminosarum has recognizable core and accessory components. Genome Biol (2006) 2.93

A strand-specific RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genet (2009) 2.87

Intracontinental spread of human invasive Salmonella Typhimurium pathovariants in sub-Saharan Africa. Nat Genet (2012) 2.86

Complete genome sequence and lytic phase transcription profile of a Coccolithovirus. Science (2005) 2.86

Genome sequence of a recently emerged, highly transmissible, multi-antibiotic- and antiseptic-resistant variant of methicillin-resistant Staphylococcus aureus, sequence type 239 (TW). J Bacteriol (2009) 2.81

Microevolution of extensively drug-resistant tuberculosis in Russia. Genome Res (2012) 2.81

The genome of Burkholderia cenocepacia J2315, an epidemic pathogen of cystic fibrosis patients. J Bacteriol (2008) 2.71

Genome sequence of a proteolytic (Group I) Clostridium botulinum strain Hall A and comparative analysis of the clostridial genomes. Genome Res (2007) 2.67

Predicted functions and linkage specificities of the products of the Streptococcus pneumoniae capsular biosynthetic loci. J Bacteriol (2007) 2.67

Whole-genome sequencing for rapid susceptibility testing of M. tuberculosis. N Engl J Med (2013) 2.63

Population genomics of post-vaccine changes in pneumococcal epidemiology. Nat Genet (2013) 2.63

A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: convergence or divergence by homologous recombination? Genome Res (2006) 2.62

Reverse transcriptase-mediated tropism switching in Bordetella bacteriophage. Science (2002) 2.62

Structure and dynamics of the pan-genome of Streptococcus pneumoniae and closely related species. Genome Biol (2010) 2.60

A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic. Genome Res (2013) 2.59