From the feces to the genome: a guideline for the isolation and preservation of Strongyloides stercoralis in the field for genetic and genomic analysis of individual worms

Parasit Vectors. 2019 Oct 22;12(1):496. doi: 10.1186/s13071-019-3748-5.


Strongyloidiasis is a soil-borne helminthiasis, which, in spite of the up to 370 million people currently estimated to be infected with its causing agent, the nematode Strongyloides stercoralis, is frequently overlooked. Recent molecular taxonomic studies conducted in Southeast Asia and Australia, showed that dogs can carry the same genotypes of S. stercoralis that also infect humans, in addition to a presumably dog-specific Strongyloides species. This suggests a potential for zoonotic transmission of S. stercoralis from dogs to humans. Although natural S. stercoralis infections have not been reported in any host other than humans, non-human primates and dogs, other as yet unidentified animal reservoirs cannot be excluded. Molecular studies also showed that humans carry rather different genotypes of S. stercoralis. As a result, their taxonomic status and the question of whether they differ in their pathogenic potential remains open. It would therefore be very important to obtain molecular genetic/genomic information about S. stercoralis populations from around the world. One way of achieving this (with little additional sampling effort) would be that people encountering S. stercoralis in the process of their diagnostic work preserve some specimens for molecular analysis. Here we provide a guideline for the isolation, preservation, genotyping at the nuclear 18S rDNA and the mitochondrial cox1 loci, and for whole genome sequencing of single S. stercoralis worms. Since in many cases the full analysis is not possible or desired at the place and time where S. stercoralis are found, we emphasize when and how samples can be preserved, stored and shipped for later analysis. We hope this will benefit and encourage researchers conducting field studies or diagnostics to collect and preserve S. stercoralis for molecular genetic/genomic analyses and either analyze them themselves or make them available to others for further analysis.

Keywords: Phylogeny; Single worm whole genome sequencing; Strongyloides stercoralis; Strongyloidiasis.

MeSH terms

  • Animals
  • Cyclooxygenase 1 / genetics
  • DNA, Helminth / chemistry
  • DNA, Helminth / isolation & purification
  • Dog Diseases / parasitology
  • Dog Diseases / transmission
  • Dogs
  • Feces / parasitology
  • Female
  • Genome*
  • Genotyping Techniques
  • Humans
  • Larva / physiology
  • Male
  • Microspheres
  • Polymerase Chain Reaction
  • Preservation, Biological / methods*
  • RNA, Ribosomal, 18S / genetics
  • Soil / parasitology
  • Strongyloides stercoralis / anatomy & histology
  • Strongyloides stercoralis / genetics*
  • Strongyloides stercoralis / isolation & purification*
  • Strongyloides stercoralis / physiology
  • Strongyloidiasis / parasitology*
  • Strongyloidiasis / transmission
  • Time Factors
  • Whole Genome Sequencing


  • DNA, Helminth
  • RNA, Ribosomal, 18S
  • Soil
  • Cyclooxygenase 1