The DOI matches its Crossref record; 38 of the 38 references it cites were found in a registry or an index.
Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis
Abstract
M. tuberculosis is evolving antibiotic resistance, threatening attempts at tuberculosis epidemic control. Mechanisms of resistance, including genetic changes favored by selection in resistant isolates, are incompletely understood. Using 116 newly sequenced and 7 previously sequenced M. tuberculosis whole genomes, we identified genome-wide signatures of positive selection specific to the 47 drug-resistant strains. By searching for convergent evolution--the independent fixation of mutations in the same nucleotide position or gene--we recovered 100% of a set of known resistance markers. We also found evidence of positive selection in an additional 39 genomic regions in resistant isolates. These regions encode components in cell wall biosynthesis, transcriptional regulation and DNA repair pathways. Mutations in these regions could directly confer resistance or compensate for fitness costs associated with resistance. Functional genetic analysis of mutations in one gene, ponA1, demonstrated an in vitro growth advantage in the presence of the drug rifampicin.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M. A., & Huelsenbeck, J. P. (2012) · Systematic Biology · doi:10.1093/sysbio/sys029 · Cited by 27,843
Guindon, S., Dufayard, J.-F., Lefort, V., Anisimova, M., Hordijk, W., & Gascuel, O. (2010) · Systematic Biology · doi:10.1093/sysbio/syq010 · Cited by 18,376
PHYLIP-Phylogeny inference package (Version 3.2)
Felsenstein, J. (1989) · Cladistics · Cited by 17,682
Circos: An information aesthetic for comparative genomics
Krzywinski, M., Schein, J., Birol, İ., Connors, J., Gascoyne, R., Horsman, D., Jones, S. J., & Marra, M. A. (2009) · Genome Research · doi:10.1101/gr.092759.109 · Cited by 10,964
Mapping short DNA sequencing reads and calling variants using mapping quality scores
Li, H., Ruan, J., & Durbin, R. (2008) · Genome Research · doi:10.1101/gr.078212.108 · Cited by 2,638
Prevention of Drug Access to Bacterial Targets: Permeability Barriers and Active Efflux
Nikaido, H. (1994) · Science · doi:10.1126/science.8153625 · Cited by 1,540
The Population Genetics of dN/dS
Kryazhimskiy, S., & Plotkin, J. B. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000304 · Cited by 962
Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved
Comas, I., Chakravartti, J., Small, P. M., Galagan, J., Niemann, S., Kremer, K., Ernst, J. D., & Gagneux, S. (2010) · Nature Genetics · doi:10.1038/ng.590 · Cited by 707
Self-citationComas, I., Borrell, S., Roetzer, A., Rose, G., Malla, B., Kato-Maeda, M., Galagan, J., Niemann, S., & Gagneux, S. (2012) · Nature Genetics · doi:10.1038/ng.1038 · Cited by 572
Self-citationTuberculosis Drug Resistance Mutation Database
Sandgren, A., Strong, M., Muthukrishnan, P., Weiner, B. K., Church, G. M., & Murray, M. B. (2009) · PLoS Medicine · doi:10.1371/journal.pmed.1000002 · Cited by 523
Self-citation
Cited by
Dheda, K., Gumbo, T., Maartens, G., Dooley, K. E., McNerney, R., Murray, M., Furin, J., Nardell, E. A., London, L., Lessem, E., et al. (2017) · The Lancet Respiratory Medicine · doi:10.1016/s2213-2600(17)30079-6 · Cited by 684
Self-citationWalker, T. M., Kohl, T. A., Omar, S. V., Hedge, J., Del Ojo Elias, C., Bradley, P., Iqbal, Z., Feuerriegel, S., Niehaus, K. E., Wilson, D. J., et al. (2015) · The Lancet Infectious Diseases · doi:10.1016/s1473-3099(15)00062-6 · Cited by 638
Ellington, M. J., Ekelund, O., Aarestrup, F. M., Canton, R., Doumith, M., Giske, C., Grundman, H., Hasman, H., Holden, M. T. G., Hopkins, K. L., et al. (2017) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2016.11.012 · Cited by 603
Ecology and evolution of Mycobacterium tuberculosis
Gagneux, S. (2018) · Nature Reviews Microbiology · doi:10.1038/nrmicro.2018.8 · Cited by 599
Self-citationEvolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage
Merker, M., Blin, C., Mona, S., Duforet-Frebourg, N., Lecher, S., Willery, E., Blum, M. G. B., Rüsch-Gerdes, S., Mokrousov, I., Aleksic, E., et al. (2015) · Nature Genetics · doi:10.1038/ng.3195 · Cited by 543
Self-citation
Metadata
- Authors
- Farhat, M. R., Shapiro, B. J., Kieser, K. J., Sultana, R., Jacobson, K. R., Victor, T. C., Warren, R. M., Streicher, E. M., Calver, A., Sloutsky, A., Kaur, D., Posey, J. E., Plikaytis, B., Oggioni, M. R., Gardy, J. L., Johnston, J. C., Rodrigues, M., Tang, P. K. C., Kato-Maeda, M., Borowsky, M. L., Muddukrishna, B., Kreiswirth, B. N., Kurepina, N., Galagan, J., Gagneux, S., Birren, B., Rubin, E. J., Lander, E. S., Sabeti, P. C., & Murray, M.
- Venue
- Nature Genetics
- Published
- 2013-09-01
- Volume
- 45
- Issue
- 10
- Pages
- 1183-1189
- ISSN
- 1061-4036
- 1546-1718
- OpenAlex
- W2110150994
- Cited by
- 440
- References
- 38
- FWCI
- 29.17
- Type
- journal article
- Language
- en
- Open access
- closed
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. https://app.cochat.ai/papers/10.1038/ng.2747
- The paper
- Farhat, M. R., Shapiro, B. J., Kieser, K. J., Sultana, R., Jacobson, K. R., Victor, T. C., Warren, R. M., Streicher, E. M., Calver, A., Sloutsky, A., Kaur, D., Posey, J. E., Plikaytis, B., Oggioni, M. R., Gardy, J. L., Johnston, J. C., Rodrigues, M., Tang, P. K. C., Kato-Maeda, M., . . . Murray, M. (2013). Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis. Nature Genetics. https://doi.org/10.1038/ng.2747
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
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.
