Phylodynamic Inference of Bacterial Outbreak Parameters Using Nanopore Sequencing

Steinig, Eike, Duchene, Sebastian, 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, and Horwood, Paul (2022) Phylodynamic Inference of Bacterial Outbreak Parameters Using Nanopore Sequencing. Molecular Biology and Evolution, 39 (3). msac040.

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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 and effective reproduction numbers (Re) of two methicillin-resistant Staphylococcus aureus (MRSA) outbreaks from remote communities in Far North Queensland and Papua New Guinea (PNG; n = 159). Successive barcoded panels of S. aureus isolates (2 × 12 per MinION) sequenced at low coverage (>5× to 10×) 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 PNG.

Item ID: 74896
Item Type: Article (Research - C1)
ISSN: 1537-1719
Keywords: nanopore, phylodynamics, bacteria, outbreaks, reproduction number, BEAST
Copyright Information: © The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
Funders: Australian National Health and Medical Research Council (NHMRC)
Projects and Grants: NHMRC 1131932, NHMRC 1145033, NHMRC GNT1195743, NHMRC 2012286
Research Data: https:// www.ncbi.nlm.nih.gov/bioproject, https://github.com/esteinig/ca-mrsa
Date Deposited: 15 Sep 2022 04:13
FoR Codes: 32 BIOMEDICAL AND CLINICAL SCIENCES > 3202 Clinical sciences > 320211 Infectious diseases @ 100%
SEO Codes: 20 HEALTH > 2004 Public health (excl. specific population health) > 200404 Disease distribution and transmission (incl. surveillance and response) @ 100%
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