Please use this identifier to cite or link to this item: https://dora.health.qld.gov.au/qldresearchjspui/handle/1/1666
Title: Phylodynamic inference of bacterial outbreak parameters using nanopore sequencing
Authors: Steinig, Eike
Duchêne, Sebastián
Aglua, Izzard
Greenhill, Andrew
Ford, Rebecca
Yoannes, Mition
Jaworski, Jan
Drekore, Jimmy
Urakoko, Bohu
Poka, Harry
Wurr, Clive
Ebos, Eri
Nangen, David
Manning, Laurens
Laman, Moses
Firth, Cadhla
Smith, Simon 
Pomat, William
Tong, Steven Y C 
Coin, Lachlan
McBryde, Emma 
Horwood, Paul
Issue Date: 2022
Source: Steinig E, Duchêne S, Aglua I, Greenhill A, Ford R, Yoannes M, Jaworski J, Drekore J, Urakoko B, Poka H, Wurr C, Ebos E, Nangen D, Manning L, Laman M, Firth C, Smith S, Pomat W, Tong SYC, Coin L, McBryde E, Horwood P. Phylodynamic inference of bacterial outbreak parameters using nanopore sequencing. Mol Biol Evol. 2022 Feb 16:msac040. doi: 10.1093/molbev/msac040. Epub ahead of print. PMID: 35171290.
Journal: Molecular biology and evolution
Abstract: Nanopore sequencing and phylodynamic modelling 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) to estimate divergence and effective reproduction numbers (Re) of two methicillin-resistant Staphylococcus aureus (MRSA) outbreaks from remote communities in Far North Queensland and Papua New Guinea (n = 159). Successive barcoded panels of S. aureus isolates (2 x 12 per MinION) sequenced at low-coverage (> 5x - 10x) provided sufficient data to accurately infer genotypes with high recall when compared with Illumina references. Random forest models achieved high resolution on ST93 outbreak sequence types (> 90% accuracy and precision) and enabled phylodynamic inference of epidemiological parameters using birth death skyline models. Our method reproduced phylogenetic topology, origin of the outbreaks, and indications of epidemic growth (Re > 1). Nextflow pipelines implement SNP polisher training, evaluation, and outbreak alignments, enabling reconstruction of within-lineage transmission dynamics for infection control of bacterial disease outbreaks on portable nanopore platforms. Our study shows that nanopore technology can be used for bacterial outbreak reconstruction at competitive costs, providing opportunities for infection control in hospitals and communities without access to sequencing infrastructure, such as in remote northern Australia and Papua New Guinea.
Description: Cairns & Hinterland Hospital and Health Service (CHHHS) affiliated author: Simon Smith
DOI: 10.1093/molbev/msac040
Type: Article
Appears in Sites:Cairns & Hinterland HHS Publications

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