Table 1.
PCR primers and reaction conditions.
Fig 1.
Schematic of the Strongyloides spp. genotyping scheme.
A graphical representation of the Strongyloides spp. genotyping scheme described previously [21], expanded to include additional genotypes from S. stercoralis and S. fuelleborni. This scheme includes novel sequences identified in this study and 18S sequences available in GenBank (GB), where the appropriate 18S HVR-I and/or HVR-IV regions were captured. Sequences from GB possessing Ns or ambiguous bases were excluded from the scheme. For additional details on the hosts in which these Strongyloides spp. haplotypes were detected, refer to Tables 2 and 3.
Table 2.
HVR-I haplotypes assigned to Strongyloides spp. as part of this typing scheme.
Table 3.
HVR-IV haplotypes assigned to Strongyloides spp. as part of this typing scheme.
Table 4.
Human, primate and dog Strongyloides spp. specimens analyzed in this study and their genotype.
Fig 2.
Dendrogram of clustered cox1 sequences.
This dendrogram represents 787 cox1 sequences, including those generated in this study (branches tipped in a black dot) and all published cox1 sequences from GB that overlap completely with our 217 base cox1 amplicon (to our knowledge). Peripheral bars are colored according to their site of origin, which corresponds to the colored countries on the map. Branches are color coded separately, according to their identity; either a species assignment, a genus, or their S. stercoralis genotype. The dog image with a black star indicates a sequence from an Australian dog generated by us previously [21], that is distinct from other Strongyloides spp. and clusters between the S. stercoralis and S. fuelleborni groups. The dog image with a black circle highlights a published sequence [21] that clusters close to, yet is distinct from Strongyloides spp. detected previously in lorises [27]. Animal images reflect the mammalian hosts that the sequences were associated with. The miniaturized image of Australia next to a human silhouette shows the location of a unique S. fuelleborni cox1 sequence. Two sequences of Strongyloides planiceps (orange branches) from Japanese raccoon dogs serve as an outgroup. The identity of each sequence is provided in S1 Fig, which is a searchable PDF of the same dendrogram with all GB accession numbers, the countries of origin, and host species provided. The GB accession numbers for sequences in this dendrogram that were generated as part of this study (branches tipped in a black dot) are provided in S1 File. The sequences used to construct this dendrogram are provided in S2 File.
Fig 3.
Global frequency of Strongyloides spp. 18S genotypes.
Histogram bars are colored according to their origin, corresponding to the colors on the map. A dash (-) in the horizontal axis labels indicates a missing 18S haplotype (either HVR-I or HVR-IV). The colored branches below the horizontal axis correspond to the colored branches in Fig 2, where red represents S. stercoralis types infecting both dogs and humans (lineage A), the green/purple clade represents S. stercoralis types infecting only dogs (lineage B), the gray clade represents S. fuelleborni types from African great apes and humans, the light pink clade represents S. fuelleborni from a baboon and the magenta/light blue clade represents types found in humans and macaques. The absence of a colored branch under a given group indicates that an associated cox1 sequence is presently unavailable for these 18S haplotypes. The miniaturized map of Australia under the horizontal axis represents the type associated with a cox1 sequence that clustered alongside S. fuelleborni from central Africa, yet is sufficiently distinct to be considered unique.
Fig 4.
Dendrogram of cox1 sequences from Strongyloides spp. and hookworms.
This figure demonstrates that the cox1 assay described here is broadly specific for Strongyloides spp. and some strongylids. Fragments of cox1 from Ancylostoma spp., Oesophogostomum and Necator americanus have been amplified and sequenced using this assay. Additionally, we previously detected cox1 sequences from Metastrongylus sp., a rotifer, and some unknown nematodes using this approach [21]. The sequences generated in this study are shaded in colors according to their country of origin and those generated by us in a previous study are marked with a black dot on the associated branch tip. The sequences used to construct this dendrogram are included in S3 File.
Table 5.
Human, primate and dog Strongyloides spp. specimens analyzed in previous studies and their genotype.