The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events
Open accessAbstract
The emergence of multidrug-resistant (MDR) typhoid is a major global health threat affecting many countries where the disease is endemic. Here whole-genome sequence analysis of 1,832 Salmonella enterica serovar Typhi (S. Typhi) identifies a single dominant MDR lineage, H58, that has emerged and spread throughout Asia and Africa over the last 30 years. Our analysis identifies numerous transmissions of H58, including multiple transfers from Asia to Africa and an ongoing, unrecognized MDR epidemic within Africa itself. Notably, our analysis indicates that H58 lineages are displacing antibiotic-sensitive isolates, transforming the global population structure of this pathogen. H58 isolates can harbor a complex MDR element residing either on transmissible IncHI1 plasmids or within multiple chromosomal integration sites. We also identify new mutations that define the H58 lineage. This phylogeographical analysis provides a framework to facilitate global management of MDR typhoid and is applicable to similar MDR lineages emerging in other bacterial species.
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The Sequence Alignment/Map format and SAMtools
Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G., Durbin, R., & 1000 Genome Project Data Processing Subgroup (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp352 · Cited by 62,041
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Stamatakis, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl446 · Cited by 15,582
Versatile and open software for comparing large genomes
Kurtz, S., Phillippy, A., Delcher, A. L., Smoot, M., Shumway, M., Antonescu, C., & Salzberg, S. L. (2004) · Genome Biology · doi:10.1186/gb-2004-5-2-r12 · Cited by 5,254
Parry, C. M., Hien, T. T., Dougan, G., White, N. J., & Farrar, J. J. (2002) · New England Journal of Medicine · doi:10.1056/nejmra020201 · Cited by 1,112
Self-citationBreiman, R. F., Cosmas, L., Njuguna, H., Audi, A., Olack, B., Ochieng, J. B., Wamola, N., Bigogo, G. M., Awiti, G., Tabu, C. W., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0029119 · Cited by 204
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Argimón, S., Abudahab, K., Goater, R. J. E., Fedosejev, A., Bhai, J., Glasner, C., Feil, E. J., Holden, M. T. G., Yeats, C. A., Grundmann, H., et al. (2016) · Microbial Genomics · doi:10.1099/mgen.0.000093 · Cited by 732
Jin, C., Gibani, M. M., Moore, M., Juel, H. B., Jones, E., Meiring, J., Harris, V., Gardner, J., Nebykova, A., Kerridge, S. A., et al. (2017) · The Lancet · doi:10.1016/s0140-6736(17)32149-9 · Cited by 313
Antimicrobial Resistance Rates and Surveillance in Sub-Saharan Africa: Where Are We Now?
Kariuki, S., Kering, K., Wairimu, C., Onsare, R., & Mbae, C. (2022) · Infection and Drug Resistance · doi:10.2147/idr.s342753 · Cited by 245
Self-citationGenetics of primary sclerosing cholangitis and pathophysiological implications
Jiang, X., & Karlsen, T. H. (2017) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/nrgastro.2016.154 · Cited by 155
The phylogeography and incidence of multi-drug resistant typhoid fever in sub-Saharan Africa
Park, S. E., Pham, D. T., Boinett, C., Wong, V. K., Pak, G. D., Panzner, U., Espinoza, L. M. C., von Kalckreuth, V., Im, J., Schütt-Gerowitt, H., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-07370-z · Cited by 120
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Metadata
- Authors
- Wong, V. K., Baker, S., Pickard, D. J., Parkhill, J., Page, A. J., Feasey, N. A., Kingsley, R. A., Thomson, N. R., Keane, J. A., Weill, F.-X., Edwards, D. J., Hawkey, J., Harris, S. R., Mather, A. E., Cain, A. K., Hadfield, J., Hart, P. J., Thieu, N. T. V., Klemm, E. J., Glinos, D. A., Breiman, R. F., Watson, C. H., Kariuki, S., Gordon, M. A., Heyderman, R. S., Okoro, C., Jacobs, J., Lunguya, O., Edmunds, W. J., Msefula, C., Chabalgoity, J. A., Kama, M., Jenkins, K., Dutta, S., Marks, F., Campos, J., Thompson, C., Obaro, S., MacLennan, C. A., Dolecek, C., Keddy, K. H., Smith, A. M., Parry, C. M., Karkey, A., Mulholland, E. K., Campbell, J. I., Dongol, S., Basnyat, B., Dufour, M., Bandaranayake, D., Naseri, T. T., Singh, S. P., Hatta, M., Newton, P., Onsare, R. S., Isaia, L., Dance, D., Davong, V., Thwaites, G., Wijedoru, L., Crump, J. A., De Pinna, E., Nair, S., Nilles, E. J., Thanh, D. P., Turner, P., Soeng, S., Valcanis, M., Powling, J., Dimovski, K., Hogg, G., Farrar, J., Holt, K. E., & Dougan, G.
- Venue
- Nature Genetics
- Published
- 2015-05-11
- Volume
- 47
- Issue
- 6
- Pages
- 632-639
- ISSN
- 1061-4036 (ISSN-L)
- 1546-1718
- OpenAlex
- W1779315825
- Cited by
- 471
- References
- 6
- FWCI
- 65.23
- Type
- journal article
- Language
- en
- Open access
- green
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- Wong, V. K., Baker, S., Pickard, D. J., Parkhill, J., Page, A. J., Feasey, N. A., Kingsley, R. A., Thomson, N. R., Keane, J. A., Weill, F.-X., Edwards, D. J., Hawkey, J., Harris, S. R., Mather, A. E., Cain, A. K., Hadfield, J., Hart, P. J., Thieu, N. T. V., Klemm, E. J., . . . Dougan, G. (2015). Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events. Nature Genetics. https://doi.org/10.1038/ng.3281
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
