Publikasi Scopus 2024 per tanggal 30 September 2024 (820 artikel)

Krisna M.A.; Jolley K.A.; Monteith W.; Boubour A.; Hamers R.L.; Brueggemann A.B.; Harrison O.B.; Maiden M.C.J.
Krisna, Made Ananda (59160718700); Jolley, Keith A. (7003265292); Monteith, William (57078797400); Boubour, Alexandra (57191446582); Hamers, Raph L. (23034345900); Brueggemann, Angela B. (6701589391); Harrison, Odile B. (24329113200); Maiden, Martin C. J. (7006019693)
59160718700; 7003265292; 57078797400; 57191446582; 23034345900; 6701589391; 24329113200; 7006019693
Development and implementation of a core genome multilocus sequence typing scheme for Haemophilus influenzae
2024
Microbial Genomics
10
8
001281
0
Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom; Department of Biology, University of Oxford, Oxford, United Kingdom; Oxford University Clinical Research Unit Indonesia, Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia; Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom; Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
Krisna M.A., Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom, Department of Biology, University of Oxford, Oxford, United Kingdom, Oxford University Clinical Research Unit Indonesia, Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia; Jolley K.A., Department of Biology, University of Oxford, Oxford, United Kingdom; Monteith W., Department of Biology, University of Oxford, Oxford, United Kingdom, Department of Biology and Biochemistry, University of Bath, Bath, United Kingdom; Boubour A., Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Hamers R.L., Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom, Oxford University Clinical Research Unit Indonesia, Faculty of Medicine Universitas Indonesia, Jakarta, Indonesia; Brueggemann A.B., Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Harrison O.B., Department of Biology, University of Oxford, Oxford, United Kingdom, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom; Maiden M.C.J., Department of Biology, University of Oxford, Oxford, United Kingdom
Haemophilus influenzae is part of the human nasopharyngeal microbiota and a pathogen causing invasive disease. The extensive genetic diversity observed in H. influenzae necessitates discriminatory analytical approaches to evaluate its population structure. This study developed a core genome multilocus sequence typing (cgMLST) scheme for H. influenzae using pangenome analysis tools and validated the cgMLST scheme using datasets consisting of complete reference genomes (N = 14) and high-quality draft H. influenzae genomes (N = 2297). The draft genome dataset was divided into a development dataset (N = 921) and a validation dataset (N = 1376). The development dataset was used to identify potential core genes, and the validation dataset was used to refine the final core gene list to ensure the reliability of the proposed cgMLST scheme. Functional classifications were made for all the resulting core genes. Phylogenetic analyses were performed using both allelic profiles and nucleotide sequence alignments of the core genome to test congruence, as assessed by Spearman’s correlation and ordinary least square linear regression tests. Preliminary analyses using the development dataset identified 1067 core genes, which were refined to 1037 with the validation dataset. More than 70% of core genes were predicted to encode proteins essential for metabolism or genetic information processing. Phylogenetic and statistical analyses indicated that the core genome allelic profile accurately represented phylogenetic relatedness among the isolates (R2 = 0.945). We used this cgMLST scheme to define a high-resolution population structure for H. influenzae, which enhances the genomic analysis of this clinically relevant human pathogen. © 2024 The Authors.
cgMLST; core genome; Haemophilus influenzae; population genetics; typing scheme
Genetic Variation; Genome, Bacterial; Haemophilus Infections; Haemophilus influenzae; Humans; Multilocus Sequence Typing; Phylogeny; ornithine decarboxylase; RNA 16S; algorithm; Article; bacteremia; bloodstream infection; cluster analysis; core genome; data base; decision making; development; DNA extraction; epidemic; gene cluster; gene expression; gene identification; gene mapping; gene ontology; gene sequence; genetic variability; genetic variation; genome analysis; genome size; genotype; Haemophilus influenzae; hospital infection; implementation science; KEGG; linear regression analysis; microflora; molecular genetics; multilocus sequence typing; nasopharynx; nonhuman; nucleotide sequence; pangenome; phylogeny; polymerase chain reaction; population genetics; population structure; reliab
National Institute for Health and Care Research, NIHR; Ministry of Education Indonesia; Wellcome Trust, WT, (218205/Z/19/Z)
This study was funded by a Wellcome Trust Biomedical Resource Grant to M.J.C.M., A.B.B. and K.A.J. (grant number 218205/Z/19/Z) and a National Institute for Health and Care Research (NIHR) Grant called MEVacP to M.J.C.M., A.B.B. and O.B.H. Studentship for M.A.K. was funded by the Ministry of Education Indonesia in collaboration with the Medical Science Division, University of Oxford.
Microbiology Society
20575858
39120932
Article
Q1
1338
2720