Journal article
Short read sequence typing (SRST): multi-locus sequence types from short reads
M Inouye, TC Conway, J Zobel, KE Holt
BMC Genomics | BMC | Published : 2012
Open access
Abstract
Background: Multi-locus sequence typing (MLST) has become the gold standard for population analyses of bacterial pathogens. This method focuses on the sequences of a small number of loci (usually seven) to divide the population and is simple, robust and facilitates comparison of results between laboratories and over time. Over the last decade, researchers and population health specialists have invested substantial effort in building up public MLST databases for nearly 100 different bacterial species, and these databases contain a wealth of important information linked to MLST sequence types such as time and place of isolation, host or niche, serotype and even clinical or drug resistance prof..
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Awarded by Australian Research Council
Funding Acknowledgements
This work utilised publicly available MLST databases for Salmonella and E. coli (http://mlst.ucc.ie, supported by a grant from the Science Foundation of Ireland (05/FE1/B882)), for S. aureus and S. pneumoniae (http://www.mlst.net, supported by the Wellcome Trust), and for plasmids (http://pubmlst.org/plasmid/). Data for all schemes was retrieved from the collation at http://pubmlst.org (University of Oxford), the development of which has been funded by the Wellcome Trust. KEH, MI were supported by fellowships #628930, #637400 from the NHMRC of Australia; National ICT Australia (NICTA) is funded by the Australian Government's Department of Communications, Information Technology and the Arts, Australian Research Council through Backing Australia's Ability, ICT Centre of Excellence programs. This research was supported by a Victorian Life Sciences Computation Initiative (VLSCI) grant #VR0082.