Author

N. R. Thomson

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

Signature Assays, Organisms & Methods

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Assay:whole-genome sequencing· 10 Approach:statistical model· 8 Organism:bacteria (other)· 4 Research Focus:chromatin & epigenetic regulation· 4 Research Focus:clustering· 4 Approach:experimental assay· 4 Research Focus:cell type annotation· 3 Research Focus:gene regulatory network inference· 3

Frequent Co-Authors

F.-X. Weill· 3 shared G. A. Blackwell· 3 shared K. E. Holt· 3 shared M. A. Beale· 3 shared C. Chewapreecha· 2 shared E. Heinz· 2 shared J. M. Lewis· 2 shared J. Mallewa· 2 shared

Activity by Year

2017-2023 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 12 mutual co-author links

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3 shared papersMicrobiology

F.-X. Weill

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11 papers

Recent·Most cited

Genetic diversity, determinants, and dissemination of Burkholderia pseudomallei lineages implicated in melioidosis in northeast Thailand

R. Seng, C. Chomkatekaew, S. Tandhavanant, N. Saiprom, R. Phunpang, J. Thaipadungpanit, E. M. Batty, N. P. Day, W. Chantratita, T. E. West, N. R. Thomson, J. Parkhill, C. Chewapreecha, N. Chantratita

This study identifies three dominant B. pseudomallei lineages in northeast Thailand, their environmental persistence, and factors driving their geographic spread.

bioRxiv · Jun 2, 2023 · PreprintMicrobiology

Genomic epidemiology of the cholera outbreak in Yemen reveals the spread of a multi-drug resistance plasmid between diverse lineages of Vibrio cholerae

F. Lassalle, S. Al-Shalali, M. Al-Hakimi, E. Njamkepo, I. M. Bashir, M. J. Dorman, J. Rauzier, G. A. Blackwell, A. Taylor-Brown, M. A. Beale, A. A. Al-Somainy, A. Al-Mahbashi, K. Almoayed, M. Aldawla, A. Al-Harazi, , N. R. Thomson

The paper analyzes genomic data from a Yemen cholera outbreak to show the spread of a multi-drug resistance plasmid among Vibrio cholerae strains.

bioRxiv · Aug 24, 2022 · PreprintMicrobiology

Genomic and antigenic diversity of carried Klebsiella pneumoniae isolates mirrors that of invasive isolates in Blantyre, Malawi

J. M. Lewis, M. Mphasa, R. Banda, M. A. Beale, J. Mallewa, E. Heinz, N. R. Thomson, N. A. Feasey

This study compares genomic and antigenic diversity of colonizing and invasive Klebsiella pneumoniae isolates in Blantyre, Malawi, finding similar population structures and highlighting the potential of colonizing isolates for vaccine development.

bioRxiv · Oct 7, 2021Microbiology

Genomic analysis of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli colonising adults in Blantyre, Malawi reveals previously undescribed diversity.

J. M. Lewis, M. Mphasa, R. Banda, M. A. Beale, J. Mallewa, C. Anscombe, A. Zuza, A. P. Roberts, E. Heinz, N. R. Thomson, N. A. Feasey

This study sequenced ESBL-producing E. coli from Malawi to assess genetic diversity and AMR determinants, revealing locally circulating subclades and carbapenemase genes.

bioRxiv · Oct 7, 2021Microbiology

Exploring bacterial diversity via a curated and searchable snapshot of archived DNA sequences

G. A. Blackwell, M. Hunt, K. M. Malone, L. Lima, G. Horesh, B. T. F. Alako, N. R. Thomson, Z. Iqbal

The paper curates and analyzes 661,405 bacterial genomes from ENA, revealing biases in species representation and highlighting common human pathogens as overrepresented.

bioRxiv · Mar 2, 2021 · PreprintMicrobiology

gbpA and chiA genes are not uniformly distributed amongst diverse Vibrio cholerae

T. G. Fennell, G. A. Blackwell, N. R. Thomson, M. J. Dorman

The paper examines the distribution of chitin metabolism genes in 195 diverse Vibrio cholerae isolates, revealing non-uniformity in gene presence and identifying a novel chitinase.

bioRxiv · Feb 11, 2021Microbiology

Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei

J. Hawkey, K. Paranagama, K. S. Baker, R. J. Bengtsson, F.-X. Weill, N. R. Thomson, S. Baker, L. Cerdeira, Z. Iqbal, M. Hunt, D. J. Ingle, T. J. Dallman, C. Jenkins, D. A. Williamson, K. E. Holt

The paper develops a genomic framework and genotyping scheme for Shigella sonnei to identify resistance determinants from WGS data, revealing common genotypes linked to antimicrobial resistance and global spread.

bioRxiv · Oct 29, 2020Microbiology

Co-evolutionary signals from Burkholderia pseudomallei genomics identify its survival strategies and highlight improving environmental health as prevention policy

C. Chewapreecha, J. Pensar, S. Chattagul, M. Pesonen, A. Sangphukieo, P. Boonklang, C. Potisap, S. Koosakulnirand, E. J. Feil, S. Dunachie, N. Chantratita, D. Limmathurotsakul, S. J. Peacock, N. P. J. Day, J. Parkhill, , J. Corander

This study identifies co-selected gene pairs in Burkholderia pseudomallei genomes that enhance survival under nutrient stress, linking environmental factors to melioidosis prevalence.

bioRxiv · Aug 11, 2020 · PreprintMicrobiology

Genomic surveillance for hypervirulence and multi-drug resistance in invasive Klebsiella pneumoniae from south and southeast Asia.

K. L. Wyres, T. N. Nguyen, M. M. Lam, L. M. Judd, N. van Vinh Chau, D. A. Dance, M. Ip, A. Karkey, C. L. Ling, T. Miliya, P. Newton, L. Nguyen, A. Sengduangphachanh, P. Turner, B. Veeraraghavan, , K. E. Holt

This study identifies diverse antimicrobial resistant and hypervirulent Klebsiella pneumoniae strains in South and Southeast Asia, highlighting the convergence of AMR and virulence genes.

bioRxiv · Feb 26, 2019Microbiology

Antimicrobial resistant Klebsiella pneumoniae carriage and infection in specialized geriatric care wards linked to acquisition in the referring hospital

C. L. Gorrie, M. Mirceta, R. R. Wick, L. M. Judd, K. L. Wyres, N. R. Thomson, R. A. Strugnell, N. F. Pratt, J. F. Garlick, K. M. Watson, P. C. Hunter, S. A. McGloughlin, D. W. Spelman, A. W. J. Jenney, K. E. Holt

The paper investigates K. pneumoniae carriage and infection in geriatric wards, finding that most isolates originated from patients' gut microbiomes, while ESBL strains were acquired in the referring hospital.

bioRxiv · Nov 13, 2017Microbiology

Millennia of genomic stability within the invasive Para C Lineage of Salmonella enterica

Z. Zhou, I. Lundstrom, A. Tran-Dien, S. Duchene, N.-F. Alikhan, M. J. Sergeant, G. Langridge, A. K. Fotakis, S. Nair, H. K. Stenoien, S. S. Hamre, S. Casjens, A. Christophersen, C. Quince, N. R. Thomson, , M. Achtman

The study analyzes an 800-year-old Paratyphi C genome to show its origin from swine pathogens and its long history as a human pathogen.

bioRxiv · Feb 14, 2017Microbiology