Author

S. D. Bentley

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Microbiology· 11 Evolutionary Biology· 7

Signature Assays, Organisms & Methods

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Approach:statistical model· 13 Assay:whole-genome sequencing· 13 Organism:human· 9 Organism:bacteria (other)· 6 Research Focus:chromatin & epigenetic regulation· 5 Research Focus:gene regulatory network inference· 5 Research Focus:phylogenetics / evolution· 5 Research Focus:variant calling· 4

Frequent Co-Authors

J. Corander· 5 shared N. J. Croucher· 4 shared A. von Gottberg· 3 shared L. Mcgee· 3 shared M. du Plessis· 3 shared R. A. Gladstone· 3 shared S. W. Lo· 3 shared W. P. Hanage· 3 shared

Activity by Year

2017-2023 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 24 mutual co-author links

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5 shared papersEvolutionary Biology

J. Corander

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18 papers

Recent·Most cited

Streptococcus pneumoniae serotype 33G: genetic, serological, and structural analysis of a new capsule type

S. Manna, J. P. Werren, B. D. Ortika, B. Bellich, C. L. Pell, E. Nikolaou, I. Gjuroski, S. W. Lo, J. Hinds, O. Tundev, E. M. Dunne, B. D. Gessner, S. D. Bentley, F. Russell, E. K. Mulholland, , C. Satzke

This study identifies and characterizes a new Streptococcus pneumoniae serotype, 33G, through genetic, serological, and structural analysis of isolates from Mongolia.

bioRxiv · Sep 11, 2023 · PreprintMicrobiology

Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis

O. Xie, J. M. Morris, A. J. Hayes, R. J. Towers, M. G. Jespersen, J. A. Lees, N. L. Ben Zakour, O. Berking, S. L. Baines, G. P. Carter, G. Tonkin-Hill, L. Schrieber, L. McIntyre, J. L. Lacey, T. B. James, , M. R. Davies

The paper shows extensive genomic overlap between Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis, including shared genes and recombination events, with implications for vaccine development.

bioRxiv · Aug 10, 2023Microbiology

The emergence and diversification of a zoonotic pathogen from within the microbiota of intensively farmed pigs

G. G. R. Murray, A. S. M. M. Hossain, E. L. Miller, S. Bruchmann, A. J. Balmer, M. Matuszewska, J. Herbert, N. F. Hadjirin, R. Mugabi, G. Li, M. L. Ferrando, I. M. Fernades de Oliveira, T. Nguyen, P. L. K. Yen, H. D. Phuc, , L. A. Weinert

This study traces the emergence and spread of Streptococcus suis pathogens in pigs, linking their evolution to changes in farming practices and identifying genomic factors associated with pathogenicity.

bioRxiv · May 17, 2023Evolutionary Biology

Geographic migration and vaccine-induced fitness changes of Streptococcus pneumoniae

S. Belman, N. Lefrancq, S. A. Nzenze, S. L. Downs, M. du Plessis, S. W. Lo, The Global Pneumococcal Sequencing Consortium, L. Mcgee, S. A. Madhi, A. von Gottberg, S. D. Bentley, H. Salje

The paper uses genomic data to study geographic spread and fitness changes in Streptococcus pneumoniae strains before and after vaccine implementation.

bioRxiv · Jan 18, 2023 · PreprintEvolutionary Biology

The population-level impact of Enterococcus faecalis genetics on intestinal colonisation and extraintestinal infection

C. Chaguza, A. K. Pöntinen, J. Top, S. Arredondo-Alonso, A. R. Freitas, C. Novais, C. Torres, S. D. Bentley, L. Peixe, T. M. Coque, R. J. L. Willems, J. Corander

This study investigates the genetic factors influencing E. faecalis intestinal colonization and extraintestinal infection using GWAS and heritability analysis across 750 isolates.

bioRxiv · Sep 26, 2022 · PreprintMicrobiology

Post-vaccine epidemiology of serotype 3 pneumococci identifies transformation inhibition through prophage-driven alteration of a non-coding RNA

M. J. Kwun, A. V. Ion, H.-C. Cheng, J. C. D'Aeth, S. Dougan, M. R. Oggioni, D. A. Goulding, S. D. Bentley, N. J. Croucher

The paper identifies prophage-driven modification of a non-coding RNA that inhibits transformation in pneumococci, explaining the persistence of serotype 3 despite vaccination.

bioRxiv · Sep 21, 2022Microbiology

Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe

G. Tonkin-Hill, R. A. Gladstone, A. K. Pontinen, S. Arredondo-Alonso, S. D. Bentley, J. Corander

The paper introduces Panstripe, a method to robustly analyze gene gain and loss rates in prokaryotic pangenomes, accounting for sampling bias and annotation errors.

bioRxiv · Apr 23, 2022Evolutionary Biology

Diverse regulatory pathways modulate bet hedging of competence induction in epigenetically-differentiated phase variants of Streptococcus pneumoniae

M. J. Kwun, A. V. Ion, M. R. Oggioni, S. D. Bentley, N. J. Croucher

The paper identifies diverse regulatory pathways affecting transformation efficiency in Streptococcus pneumoniae phase variants through differential gene expression and chromosomal island activity.

bioRxiv · Mar 7, 2022 · PreprintMicrobiology

Pneumococcal genetic variability influences age-dependent bacterial carriage

P. H. C. Kremer, B. Ferwerda, H. J. Bootsma, N. Y. Rots, A. J. Wijmega-Monsuur, L. A. M. Sanders, K. Trzcinski, A. L. Wyllie, P. Turner, A. van der Ende, M. C. Brouwer, S. D. Bentley, D. van de Beek, J. A. Lees

This study identifies pneumococcal genetic factors associated with age-dependent carriage, suggesting vaccine formulations should target serotypes rather than proteins.

bioRxiv · Mar 3, 2021 · PreprintMicrobiology

Identification of colonisation and virulence determinants of Streptococcus pneumoniae via experimental evolution in mouse infection models

A. E. Green, D. Howarth, C. Chaguza, H. Echlin, R. F. Langendonk, C. Munro, T. E. Barton, J. C. Hinton, S. D. Bentley, J. Rosch, D. R. Neill

This study uses experimental evolution in mouse models to identify genetic factors affecting Streptococcus pneumoniae colonization and virulence.

bioRxiv · Sep 8, 2020 · PreprintMicrobiology

The effect of recombination on the evolution of a population of Neisseria meningitidis

N. MacAlasdair, M. Pesonen, O. Brynildsrud, V. Eldholm, P. A. Kristiansen, J. Corander, D. A. Caugant, S. D. Bentley

This study analyzes 2,839 Neisseria meningitidis genomes to show recombination's role in genome dynamics and population structure, with implications for vaccine effectiveness and public health surveillance.

bioRxiv · Apr 8, 2020Evolutionary Biology

Predicting evolution using frequency-dependent selection in bacterial populations

T. Azarian, P. P. P. Martinez, B. J. Arnold, L. R. Grant, J. Corander, C. Fraser, N. Croucher, L. Hammitt, R. Reed, M. Santosham, R. R. Weatherholtz, S. D. Bentley, K. L. O'Brien, M. Lipsitch, W. P. Hanage

The paper predicts changes in pneumococcal populations after vaccination by analyzing accessory gene frequencies under negative frequency-dependent selection.

bioRxiv · Feb 25, 2020 · PreprintEvolutionary Biology

A novel mosaic tetracycline resistance gene tet(S/M) detected in a multidrug-resistant pneumococcal CC230 lineage that underwent capsular switching in South Africa

S. W. Lo, R. A. Gladstone, A. J. van Tonder, M. du Plessis, J. E. Cornick, P. A. Hawkins, S. A. Madhi, S. A. Nzenze, R. Kandasamy, K. Ravikumar, N. Elmdaghri, B. Kwambana-Adams, S. C. G. Almeida, A. Skoczynska, E. Egorova, , A. von Gottberg

The paper identifies a novel tetracycline resistance gene tet(S/M) in a multidrug-resistant pneumococcal lineage in South Africa and links its spread to HIV treatment and vaccine implementation.

bioRxiv · Jul 30, 2019 · PreprintMicrobiology

Horizontal gene transfer rate is not the primary determinant of observed antibiotic resistance frequencies in Streptococcus pneumoniae

S. J. Lehtinen, C. Chewapreecha, W. P. Hanage, M. J. Lipsitch, N. J. Croucher, S. D. Bentley, P. Turner, C. Fraser, R. J. Mostowy

The study examines antibiotic resistance frequencies in Streptococcus pneumoniae and finds that horizontal gene transfer rates are not the main factor influencing these frequencies.

bioRxiv · Jun 11, 2019Evolutionary Biology

Global emergence and population dynamics of divergent serotype 3 CC180 pneumococci

T. Azarian, P. Mitchell, M. Georgieva, C. M. Thompson, A. Ghoulia, A. J. Pollard, A. von Gottberg, M. du Plessis, M. Antonio, B. A. Kwambana-Adams, S. C. Clarke, D. Everett, J. Cornick, E. Sadowy, W. Hryniewicz, , W. P. Hanage

This study analyzes global serotype 3 pneumococcal isolates to show a recent emergence of Clade II with antibiotic resistance and antigenic diversity, not linked to PCV13 usage.

bioRxiv · Jun 27, 2018Evolutionary Biology

Pneumococcal vaccine impacts on the population genomics of non-typeable Haemophilus influenzae

D. W. Cleary, V. T. Devine, D. E. Morris, K. L. Osman, R. A. Gladstone, S. D. Bentley, S. N. Faust, S. C. Clarke

This study examines how the introduction of pneumococcal conjugate vaccine 13 affected the population genomics of non-typeable Haemophilus influenzae in children, showing increased carriage and lineage-specific associations with Streptococcus pneumoniae.

bioRxiv · Dec 4, 2017Microbiology

PANINI: Pangenome Neighbor Identification for Bacterial Populations

K. Abudahab, J. M. Prada, Z. Yang, S. D. Bentley, N. J. Croucher, J. Corander, D. M. Aanensen

PANINI identifies bacterial population neighbours using machine learning, integrating core and accessory genome data with metadata for epidemiological analysis.

bioRxiv · Aug 21, 2017Microbiology

Methicillin resistant Staphylococcus aureus emerged long before the introduction of methicillin in to clinical practice

C. P. Harkins, B. Pichon, M. Doumith, J. Parkhill, H. Westh, A. Tomasz, H. de Lencastre, S. D. Bentley, A. M. Kearns, M. T. Holden

This study shows that MRSA emerged in the mid-1940s, long before methicillin was introduced, due to prior use of first-generation beta-lactams.

bioRxiv · Mar 31, 2017Microbiology