2024
Population genomics of Streptococcus mitis in UK and Ireland bloodstream infection and infective endocarditis cases
Kalizang’oma A, Richard D, Kwambana-Adams B, Coelho J, Broughton K, Pichon B, Hopkins K, Chalker V, Beleza S, Bentley S, Chaguza C, Heyderman R. Population genomics of Streptococcus mitis in UK and Ireland bloodstream infection and infective endocarditis cases. Nature Communications 2024, 15: 7812. PMID: 39242612, PMCID: PMC11379897, DOI: 10.1038/s41467-024-52120-z.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedAnti-Bacterial AgentsBacteremiaDrug Resistance, BacterialEndocarditisEndocarditis, BacterialFemaleGenetic VariationGenome, BacterialGenomicsHumansIrelandMaleMiddle AgedPhylogenyStreptococcal InfectionsStreptococcus mitisUnited KingdomVirulenceVirulence FactorsWhole Genome SequencingConceptsGenetic diversityBloodstream infectionsInvestigate genetic diversityInfective endocarditisStreptococcus mitisPneumococcal virulence genesS. mitisPopulation genomicsInfective endocarditis casesGenome sequenceVirulence genesGenomic epidemiologyCarriage strainsResistant lineagesPathogenic natureIE casesAntimicrobial resistanceEndocarditis casesIE incidenceLineagesGenomeIsolatesPathogensClinicPatientsGenomic insights into the 2022–2023Vibrio cholerae outbreak in Malawi
Chaguza C, Chibwe I, Chaima D, Musicha P, Ndeketa L, Kasambara W, Mhango C, Mseka U, Bitilinyu-Bangoh J, Mvula B, Kipandula W, Bonongwe P, Munthali R, Ngwira S, Mwendera C, Kalizang’oma A, Jambo K, Kambalame D, Kamng’ona A, Steele A, Chauma-Mwale A, Hungerford D, Kagoli M, Nyaga M, Dube Q, French N, Msefula C, Cunliffe N, Jere K. Genomic insights into the 2022–2023Vibrio cholerae outbreak in Malawi. Nature Communications 2024, 15: 6291. PMID: 39060226, PMCID: PMC11282309, DOI: 10.1038/s41467-024-50484-w.Peer-Reviewed Original ResearchConceptsSerogroup O1 strainsIntegrative conjugative elementsPhylogenetic reconstructionPopulation genomicsGenomic insightsOutbreak isolatesVirulence elementsConjugative elementsO1 strainsVibrio choleraeOutbreak strainEl TorAntimicrobial resistanceCholera outbreaksO1 OgawaIsolatesCholeraStrainCtxB7 genotypesProphageGenomeVirulenceCtxB7SublineagesLineages
2021
RCandy: an R package for visualizing homologous recombinations in bacterial genomes
Chaguza C, Tonkin-Hill G, Lo S, Hadfield J, Croucher N, Harris S, Bentley S. RCandy: an R package for visualizing homologous recombinations in bacterial genomes. Bioinformatics 2021, 38: 1450-1451. PMID: 34864895, PMCID: PMC8826011, DOI: 10.1093/bioinformatics/btab814.Peer-Reviewed Original ResearchConceptsBacterial genomesHomologous recombinationRecombination eventsImportant evolutionary processPlatform-independent R packageGenomic sequence diversityValuable biological insightsSuch recombination eventsR packageGenomic regionsSequence diversityBiological insightsEvolutionary processesGenomeSupplementary dataRecombinationMIT licenseProkaryotesBioinformaticsDiversityBacteriaMacOSXAdaptation
2015
Mechanisms and impact of genetic recombination in the evolution of Streptococcus pneumoniae
Chaguza C, Cornick JE, Everett DB. Mechanisms and impact of genetic recombination in the evolution of Streptococcus pneumoniae. Computational And Structural Biotechnology Journal 2015, 13: 241-247. PMID: 25904996, PMCID: PMC4404416, DOI: 10.1016/j.csbj.2015.03.007.Peer-Reviewed Original ResearchGenetic recombinationWhole-genome sequence dataKey evolutionary mechanismGenome sequence dataPopulation geneticsEvolutionary mechanismsGenetic variationSequence dataExogenous DNASelective pressureSpontaneous mutationsHuman diseasesEvolution studiesPneumococcal adaptationRecombinationAdaptive immune responsesComputational toolsGenomeEvolutionGeneticsOrganismsImmune responseRapid influxDNABacterium