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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.

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