Journal article
Phylodynamic Inference of Bacterial Outbreak Parameters Using Nanopore Sequencing
E Steinig, S Duchêne, I Aglua, A Greenhill, R Ford, M Yoannes, J Jaworski, J Drekore, B Urakoko, H Poka, C Wurr, E Ebos, D Nangen, L Manning, M Laman, C Firth, S Smith, W Pomat, SYC Tong, L Coin Show all
Molecular Biology and Evolution | OXFORD UNIV PRESS | Published : 2022
Abstract
Nanopore sequencing and phylodynamic modeling have been used to reconstruct the transmission dynamics of viral epidemics, but their application to bacterial pathogens has remained challenging. Cost-effective bacterial genome sequencing and variant calling on nanopore platforms would greatly enhance surveillance and outbreak response in communities without access to sequencing infrastructure. Here, we adapt random forest models for single nucleotide polymorphism (SNP) polishing developed by Sanderson and colleagues (2020. High precision Neisseria gonorrhoeae variant and antimicrobial resistance calling from metagenomic nanopore sequencing. Genome Res. 30(9):1354-1363) to estimate divergence a..
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Awarded by Australian National Health and Medical Research Council
Awarded by Improving Health Outcomes in the Tropical North fellowship by the Australian National Health and Medical Research Council
Awarded by European Union
Awarded by National Health and Medical Research Council
Awarded by Linkage Infrastructure, Equipment and Facilities (LIEF) at the highperformance computing facility
Awarded by National Health and Medical Research Council of Australia
Funding Acknowledgements
This work was supported by a joint Policy Relevant Infectious Disease Simulation and Mathematical Modelling & Improving Health Outcomes in the Tropical North pilot grant (Williams et al. 2021) by the Australian National Health and Medical Research Council (1131932 to E.S. and E.M.), an Improving Health Outcomes in the Tropical North fellowship by the Australian National Health and Medical Research Council (1131932 to C.F.), an Australian National Health and Medical Research Council fellowship (1145033 to S.Y.C.T.), a joint Australian National Health and Medical Research Council and European Union collaborative research grant (GNT1195743 to L.C.), a Queensland Genomics project grant (Vidgen et al. 2021) and a National Health and Medical Research Council Ideas grant (2012286 to P.H., I.A., A.G., C.F., R.F., S.S., E.S., L.C., S.Y.C.T., E.M., and W.P.). Models were run on graphical processing units supported by the Linkage Infrastructure, Equipment and Facilities (LIEF) at the highperformance computing facility hosted at the University of Melbourne (LE170100200; Lafayette et al. 2016).