Citing mykrobe

Please cite us if you use Mykrobe in a publication.

The citation to use is:

Hunt M, Bradley P, Lapierre SG et al. Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe [version 1; peer review: 2 approved, 1 approved with reservations]. Wellcome Open Res 2019, 4:191 (https://doi.org/10.12688/wellcomeopenres.15603.1)

An addition to the above citation, if you use one of the following panels please cite the relevant publications.

Species	Panel	Citation(s)
tb	202309 (default)	[4],[5],[10]
tb	202206.	[4],[5]
tb	202010	[1],[2]
tb	202001	[1],[2]
tb	walker-2015	[2]
tb	bradley-2015	[3]
staph	20170217	[3]
sonnei	20201012	[6]
typhi	20240407	[11]
typhi	20221207	[7],[8],[9]
typhi	20210323	[7],[8]
paratyphiB	20230627	TBC

[1] The CRyPTIC Consortium and the 100,000 Genomes Project. Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing. N Engl J Med 2018; 379:1403-1415. https://www.nejm.org/doi/full/10.1056/NEJMoa1800474.

[2] Walker, Timothy M et al. “Whole-genome sequencing for prediction of Mycobacterium tuberculosis drug susceptibility and resistance: a retrospective cohort study.” The Lancet. Infectious diseases vol. 15,10 (2015): 1193-1202. https://dx.doi.org/10.1016%2FS1473-3099(15)00062-6

[3] Bradley, P., Gordon, N., Walker, T. et al. Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis. Nat Commun 6, 10063 (2015). https://doi.org/10.1038/ncomms10063

[4] Walker, T. M. et al. The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: a genotypic analysis. Lancet Microbe (2022) doi:10.1016/s2666-5247(21)00301-3.

[5] Hall, M. B. & Coin, L. J. M. Assessment of the 2021 WHO Mycobacterium tuberculosis drug resistance mutation catalogue on an independent dataset. Lancet Microbe (2022) doi:10.1016/s2666-5247(22)00151-3.

[6] Hawkey, J., Paranagama, K., Baker, K.S. et al. Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei. Nat Commun 12, 2684 (2021). https://doi.org/10.1038/s41467-021-22700-4.

[7] Wong, V., Baker, S., Connor, T. et al. An extended genotyping framework for Salmonella enterica serovar Typhi, the cause of human typhoid. Nat Commun 7, 12827 (2016). https://doi.org/10.1038/ncomms12827

[8] Zoe A Dyson, Kathryn E Holt, Five Years of GenoTyphi: Updates to the Global Salmonella Typhi Genotyping Framework, The Journal of Infectious Diseases, Volume 224, Issue Supplement_7, 15 December 2021, Pages S775–S780, https://doi.org/10.1093/infdis/jiab414

[9] Sikorski et al. Persistence of Rare Salmonella Typhi Genotypes Susceptible to First-Line Antibiotics in the Remote Islands of Samoa. mBio, Volume 13, Number 5, 26 October 2022. https://doi.org/10.1128/mbio.01920-22

[10] Donovan H Parks, Maria Chuvochina, Christian Rinke, Aaron J Mussig, Pierre-Alain Chaumeil, Philip Hugenholtz, GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy, Nucleic Acids Research, Volume 50, Issue D1, 7 January 2022, Pages D785–D794, https://doi.org/10.1093/nar/gkab776

[11] Danielle J. Ingle et al. Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi. bioRxiv 2024.09.30.613582; doi: https://doi.org/10.1101/2024.09.30.613582