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

Joel L.N. Barratt, Meredith Lane, Emir Talundzic, Travis Richins, Gemma Robertson, Fabio Formenti, Bobbi Pritt, Guilherme Verocai, Joelma Nascimento De Souza, Neci Mato Soares, Rebecca Traub, Dora Buonfrate, Richard S. Bradbury

Research output: Contribution to journalArticle

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Abstract

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.

Original languageEnglish (US)
Article numbere0007609
JournalPLoS Neglected Tropical Diseases
Volume13
Issue number9
DOIs
StatePublished - Jan 1 2019

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Strongyloides
Strongyloides stercoralis
High-Throughput Nucleotide Sequencing
Primates
Genotype
Dogs
Strongyloidiasis
Neglected Diseases
Southeastern Asia
Genetic Structures
Nucleic Acid Databases
Population Genetics
Electron Transport Complex IV
Surveys and Questionnaires
Switzerland
rRNA Genes
Feces
Oxidoreductases
DNA

ASJC Scopus subject areas

  • Public Health, Environmental and Occupational Health
  • Infectious Diseases

Cite this

Barratt, J. L. N., Lane, M., Talundzic, E., Richins, T., Robertson, G., Formenti, F., ... Bradbury, R. S. (2019). A global genotyping survey of Strongyloides stercoralis and Strongyloides fuelleborni using deep amplicon sequencing. PLoS Neglected Tropical Diseases, 13(9), [e0007609]. https://doi.org/10.1371/journal.pntd.0007609

A global genotyping survey of Strongyloides stercoralis and Strongyloides fuelleborni using deep amplicon sequencing. / Barratt, Joel L.N.; Lane, Meredith; Talundzic, Emir; Richins, Travis; Robertson, Gemma; Formenti, Fabio; Pritt, Bobbi; Verocai, Guilherme; De Souza, Joelma Nascimento; Soares, Neci Mato; Traub, Rebecca; Buonfrate, Dora; Bradbury, Richard S.

In: PLoS Neglected Tropical Diseases, Vol. 13, No. 9, e0007609, 01.01.2019.

Research output: Contribution to journalArticle

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 2019, 'A global genotyping survey of Strongyloides stercoralis and Strongyloides fuelleborni using deep amplicon sequencing', PLoS Neglected Tropical Diseases, vol. 13, no. 9, e0007609. https://doi.org/10.1371/journal.pntd.0007609
Barratt, Joel L.N. ; Lane, Meredith ; Talundzic, Emir ; Richins, Travis ; Robertson, Gemma ; Formenti, Fabio ; Pritt, Bobbi ; Verocai, Guilherme ; De Souza, Joelma Nascimento ; Soares, Neci Mato ; Traub, Rebecca ; Buonfrate, Dora ; Bradbury, Richard S. / A global genotyping survey of Strongyloides stercoralis and Strongyloides fuelleborni using deep amplicon sequencing. In: PLoS Neglected Tropical Diseases. 2019 ; Vol. 13, No. 9.
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