Geographical distribution of samples
Genus distribution by WHO region
Species identification was peformed with KmerFinder(1,2,3) and rMLST(4). Identification of resistance-conferring genes was performed with ResFinder 4.1(5).
(1) Rapid whole-genome sequencing for detection and characterization of microorganisms directly from clinical samples. Hasman H, Saputra D, Sicheritz-Pontén T, Lund O, Svendsen CA, Frimodt-Møller N, Aarestrup FM. J Clin Microbiol. 2014 Jan;52(1):139-46. View the abstract
(2) Benchmarking of methods for genomic taxonomy. Larsen MV, Cosentino S, Lukjancenko O, Saputra D, Rasmussen S, Hasman H, Sicheritz-Pontén T, Aarestrup FM, Ussery DW, Lund O. J Clin Microbiol. 2014 May;52(5):1529-39. View the abstract
(3) Rapid and precise alignment of raw reads against redundant databases with KMA Philip T.L.C. Clausen, Frank M. Aarestrup, Ole Lund.
(4) Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C, Colles FM, Wimalarathna H, Harrison OB, Sheppard SK, Cody AJ, Maiden MCJ.
Timeline for sample collection
In relation to sharing your insights from analysing the data, please cite “The TWIW partnership on AMR and bacterial burden of disease, Nag et al ongoing, twiw.genomicepidemiology.org (last date accessed)”.