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Phylodynamic Inference of Bacterial Outbreak Parameters Using Nanopore Sequencing.
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.
Afiliação
  • Steinig E; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
  • Duchêne S; Australian Institute of Tropical Health and Medicine, James Cook University, Townsville and Cairns, Australia.
  • Aglua I; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
  • Greenhill A; Joseph Nombri Memorial-Kundiawa General Hospital, Kundiawa, Papua New Guinea.
  • Ford R; Papua New Guinea Institute of Medical Research, Goroka, Papua, Papua New Guinea.
  • Yoannes M; Papua New Guinea Institute of Medical Research, Goroka, Papua, Papua New Guinea.
  • Jaworski J; Papua New Guinea Institute of Medical Research, Goroka, Papua, Papua New Guinea.
  • Drekore J; Joseph Nombri Memorial-Kundiawa General Hospital, Kundiawa, Papua New Guinea.
  • Urakoko B; Simbu Children's Foundation, Kundiawa, Papua New Guinea.
  • Poka H; Joseph Nombri Memorial-Kundiawa General Hospital, Kundiawa, Papua New Guinea.
  • Wurr C; Joseph Nombri Memorial-Kundiawa General Hospital, Kundiawa, Papua New Guinea.
  • Ebos E; Surgical Department, Goroka General Hospital, Goroka, Papua New Guinea.
  • Nangen D; Surgical Department, Goroka General Hospital, Goroka, Papua New Guinea.
  • Manning L; Surgical Department, Goroka General Hospital, Goroka, Papua New Guinea.
  • Laman M; Department of Infectious Diseases, Fiona Stanley Hospital, Murdoch, Australia.
  • Firth C; Medical School, University of Western Australia, Harry Perkins Research Institute, Fiona Stanley Hospital, Murdoch, Australia.
  • Smith S; Papua New Guinea Institute of Medical Research, Goroka, Papua, Papua New Guinea.
  • Pomat W; Australian Institute of Tropical Health and Medicine, James Cook University, Townsville and Cairns, Australia.
  • Tong SYC; Cairns Hospital and Hinterland Health Service, Queensland Health, Cairns, Australia.
  • Coin L; Papua New Guinea Institute of Medical Research, Goroka, Papua, Papua New Guinea.
  • McBryde E; Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
  • Horwood P; Victorian Infectious Diseases Service, The Royal Melbourne Hospital at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
Mol Biol Evol ; 39(3)2022 03 02.
Article em En | MEDLINE | ID: mdl-35171290
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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Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Staphylococcus aureus Resistente à Meticilina / Sequenciamento por Nanoporos Idioma: En Ano de publicação: 2022 Tipo de documento: Article

Texto completo: 1 Coleções: 01-internacional Base de dados: MEDLINE Assunto principal: Staphylococcus aureus Resistente à Meticilina / Sequenciamento por Nanoporos Idioma: En Ano de publicação: 2022 Tipo de documento: Article