A global genotyping survey of Strongyloides stercoralis and Strongyloides fuelleborni using deep amplicon sequencing

Barratt, JLN; Lane, M; Talundzic, E; Richins, T; Robertson, G; Formenti, F; Pritt, B; Verocai, G; De Souza, JN; Soares, NM; Traub, R; Buonfrate, D; Bradbury, RS

A global genotyping survey of Strongyloides stercoralis and Strongyloides fuelleborni using deep amplicon sequencing

Lane, M Talundzic, E Richins, T Robertson, G Formenti, F Pritt, B Verocai, G De Souza, JN Soares, NM Traub, R Buonfrate, D Bradbury, RS

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Publication Type:: Journal Article
Citation:: PLoS Neglected Tropical Diseases, 2019, 13 (9)
Issue Date:: 2019-01-01

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Field	Value	Language
dc.contributor.author	Barratt, JLN https://orcid.org/0000-0001-8711-2408	en_US
dc.contributor.author	Lane, M	en_US
dc.contributor.author	Talundzic, E	en_US
dc.contributor.author	Richins, T	en_US
dc.contributor.author	Robertson, G	en_US
dc.contributor.author	Formenti, F	en_US
dc.contributor.author	Pritt, B	en_US
dc.contributor.author	Verocai, G	en_US
dc.contributor.author	De Souza, JN	en_US
dc.contributor.author	Soares, NM	en_US
dc.contributor.author	Traub, R	en_US
dc.contributor.author	Buonfrate, D	en_US
dc.contributor.author	Bradbury, RS	en_US
dc.date.available	2019-07-06	en_US
dc.date.issued	2019-01-01	en_US
dc.identifier.citation	PLoS Neglected Tropical Diseases, 2019, 13 (9)	en_US
dc.identifier.issn	1935-2727	en_US
dc.identifier.uri	http://hdl.handle.net/10453/138125
dc.description.abstract	© 2019 This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. Strongyloidiasis is a neglected tropical disease caused by the human infective nematodes Strongyloides stercoralis, Strongyloides fuelleborni fuelleborni and Strongyloides fuelleborni kellyi. Previous large-scale studies exploring the genetic diversity of this important genus have focused on Southeast Asia, with a small number of isolates from the USA, Switzerland, Australia and several African countries having been genotyped. Consequently, little is known about the global distribution of geographic sub-variants of these nematodes and the genetic diversity that exists within the genus Strongyloides generally. We extracted DNA from human, dog and primate feces containing Strongyloides, collected from several countries representing all inhabited continents. Using a genotyping assay adapted for deep amplicon sequencing on the Illumina MiSeq platform, we sequenced the hyper-variable I and hyper-variable IV regions of the Strongyloides 18S rRNA gene and a fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene from these specimens. We report several novel findings including unique S. stercoralis and S. fuelleborni genotypes, and the first identifications of a previously unknown S. fuelleborni infecting humans within Australia. We expand on an existing Strongyloides genotyping scheme to accommodate S. fuelleborni and these novel genotypes. In doing so, we compare our data to all 18S and cox1 sequences of S. fuelleborni and S. stercoralis available in GenBank (to our knowledge), that overlap with the sequences generated using our approach. As this analysis represents more than 1,000 sequences collected from diverse hosts and locations, representing all inhabited continents, it allows a truly global understanding of the population genetic structure of the Strongyloides species infecting humans, non-human primates, and domestic dogs.	en_US
dc.relation.ispartof	PLoS Neglected Tropical Diseases	en_US
dc.relation.isbasedon	10.1371/journal.pntd.0007609	en_US
dc.subject.classification	Tropical Medicine	en_US
dc.subject.mesh	Feces	en_US
dc.subject.mesh	Animals	en_US
dc.subject.mesh	Dogs	en_US
dc.subject.mesh	Primates	en_US
dc.subject.mesh	Humans	en_US
dc.subject.mesh	Strongyloides	en_US
dc.subject.mesh	Strongyloides stercoralis	en_US
dc.subject.mesh	Strongyloidiasis	en_US
dc.subject.mesh	RNA, Ribosomal, 18S	en_US
dc.subject.mesh	Sequence Analysis, DNA	en_US
dc.subject.mesh	Genotype	en_US
dc.subject.mesh	Cyclooxygenase 1	en_US
dc.subject.mesh	Genetic Variation	en_US
dc.subject.mesh	Neglected Diseases	en_US
dc.subject.mesh	High-Throughput Nucleotide Sequencing	en_US
dc.title	A global genotyping survey of Strongyloides stercoralis and Strongyloides fuelleborni using deep amplicon sequencing	en_US
dc.type	Journal Article
utslib.citation.volume	9	en_US
utslib.citation.volume	13	en_US
utslib.for	0605 Microbiology	en_US
utslib.for	06 Biological Sciences	en_US
utslib.for	11 Medical and Health Sciences	en_US
pubs.embargo.period	Not known	en_US
pubs.organisational-group	/University of Technology Sydney
pubs.organisational-group	/University of Technology Sydney/Faculty of Science
pubs.organisational-group	/University of Technology Sydney/Faculty of Science/School of Life Sciences
utslib.copyright.status	open_access
pubs.issue	9	en_US
pubs.publication-status	Published	en_US
pubs.volume	13	en_US

Abstract:

© 2019 This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. Strongyloidiasis is a neglected tropical disease caused by the human infective nematodes Strongyloides stercoralis, Strongyloides fuelleborni fuelleborni and Strongyloides fuelleborni kellyi. Previous large-scale studies exploring the genetic diversity of this important genus have focused on Southeast Asia, with a small number of isolates from the USA, Switzerland, Australia and several African countries having been genotyped. Consequently, little is known about the global distribution of geographic sub-variants of these nematodes and the genetic diversity that exists within the genus Strongyloides generally. We extracted DNA from human, dog and primate feces containing Strongyloides, collected from several countries representing all inhabited continents. Using a genotyping assay adapted for deep amplicon sequencing on the Illumina MiSeq platform, we sequenced the hyper-variable I and hyper-variable IV regions of the Strongyloides 18S rRNA gene and a fragment of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene from these specimens. We report several novel findings including unique S. stercoralis and S. fuelleborni genotypes, and the first identifications of a previously unknown S. fuelleborni infecting humans within Australia. We expand on an existing Strongyloides genotyping scheme to accommodate S. fuelleborni and these novel genotypes. In doing so, we compare our data to all 18S and cox1 sequences of S. fuelleborni and S. stercoralis available in GenBank (to our knowledge), that overlap with the sequences generated using our approach. As this analysis represents more than 1,000 sequences collected from diverse hosts and locations, representing all inhabited continents, it allows a truly global understanding of the population genetic structure of the Strongyloides species infecting humans, non-human primates, and domestic dogs.

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http://hdl.handle.net/10453/138125