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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; 39:6529399. [PMID: 35171290 PMCID: PMC8963328 DOI: 10.1093/molbev/msac040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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.
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Affiliation(s)
- Eike Steinig
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Australian Institute of Tropical Health and Medicine, James Cook University, Townsville and Cairns, Australia
| | - Sebastián Duchêne
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Izzard Aglua
- Joseph Nombri Memorial-Kundiawa General Hospital, Kundiawa, Simbu Province, Sir, Papua New Guinea
| | - Andrew Greenhill
- New Guinea Institute of Medical Research, Eastern Highlands Province, Goroka, Papua, Papua New Guinea
| | - Rebecca Ford
- New Guinea Institute of Medical Research, Eastern Highlands Province, Goroka, Papua, Papua New Guinea
| | - Mition Yoannes
- New Guinea Institute of Medical Research, Eastern Highlands Province, Goroka, Papua, Papua New Guinea
| | - Jan Jaworski
- Joseph Nombri Memorial-Kundiawa General Hospital, Kundiawa, Simbu Province, Sir, Papua New Guinea
| | - Jimmy Drekore
- Simbu Children's Foundation, Kundiawa, Simbu Province, Papua New Guinea
| | - Bohu Urakoko
- Joseph Nombri Memorial-Kundiawa General Hospital, Kundiawa, Simbu Province, Sir, Papua New Guinea
| | - Harry Poka
- Joseph Nombri Memorial-Kundiawa General Hospital, Kundiawa, Simbu Province, Sir, Papua New Guinea
| | - Clive Wurr
- Surgical Department, Goroka General Hospital, Eastern Highlands Province Goroka
| | - Eri Ebos
- Surgical Department, Goroka General Hospital, Eastern Highlands Province Goroka
| | - David Nangen
- Surgical Department, Goroka General Hospital, Eastern Highlands Province Goroka
| | - Laurens Manning
- Department of Infectious Diseases, Fiona Stanley Hospital, Murdoch, Western Australia.,Medical School, University of Western Australia, Harry Perkins Research Institute, Fiona Stanley Hospital, Murdoch, Western Australia
| | - Moses Laman
- New Guinea Institute of Medical Research, Eastern Highlands Province, Goroka, Papua, Papua New Guinea
| | - Cadhla Firth
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville and Cairns, Australia
| | - Simon Smith
- Cairns Hospital and Hinterland Health Service, Queensland Health, Cairns, Australia
| | - William Pomat
- New Guinea Institute of Medical Research, Eastern Highlands Province, Goroka, Papua, Papua New Guinea
| | - Steven Y C Tong
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.,Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Lachlan Coin
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Emma McBryde
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville and Cairns, Australia
| | - Paul Horwood
- New Guinea Institute of Medical Research, Eastern Highlands Province, Goroka, Papua, Papua New Guinea.,College of Public Health, Medical & Veterinary Sciences, James Cook University, Townsville, Australia
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