Fig 1.
The life cycle of S. stercoralis.
The life cycle of Strongyloides stercoralis. The numbers refer to the numbers of the developmental options in the description of the life cycle in the text.
Fig 2.
The different SSU HVR variants found.
The sequence of the portion of the SSU amplified for genotyping of the two HVRs. Arrows indicate the positions of the primers used for amplification, from top to bottom SSU18A, 18SP4F, SSU26R, 18SPCR (c.f. Table 1). Note that forward primers are above the sequence while reverse primers are below the sequence. HVR I and HVR IV as defined by Hasegawa and colleagues [35] are boxed. For sequencing results for both SSU HVR and cox1 for each individual worm see S1 Table.
Table 1.
Primers and PCR conditions.
Fig 3.
Gene tree of the mitochondrial gene cox1.
Maximum likelihood tree of the 17 different cox1 sequences we found and representative previously published sequences. The numbers are bootstrap values based on 1000 bootstraps. For haplotypes isolated in this study the labels have the following format: Haplotype number (accession number) host country (number of individuals this haplotype was found in). 1For sequences previously published by Hasegawa and colleagues [36] the label starts with Hasegawa. 2For sequences previously published by Laymanifong and colleagues [6] the label starts with the cox1 clade this reference assigned the particular sequence to. This is followed by: (accession number) host country (CAR = Central African Republic). The hosts are also highlighted by red circles (human) and blue squares (dog). Entries to the right of the tree indicate for each cox1 haplotype the SSU haplotypes it was found together in the same individual. If a given cox1 haplotype existed in the context of multiple SSU haplotypes, the number of worms with this particular combination is given in parentheses. Note: the cox1 haplotypes 2 and 3 were found in both hosts and are included twice in this tree. For the sequencing results for both SSU HVR and cox1 for each individual worm see S1 Table.
Fig 4.
Sample relatedness analysis on whole genome data.
A) Neighbor joining tree based on a genomic identity-by-state relationship matrix in cooperating 1326 SNPs (thresholds: LD = 0.05, MAF = 0.05). B) Neighbor joining tree based on pairwise similarities of the 23 individual genomes estimated using kWIP. The same samples in the two trees are connected with dotted lines colored in red for human derived worms and in blue for dog derived worms. ERX044031 indicates the reference genome short read data set [57], which has HVR I haplotype I and HVR IV haplotype A. The labels contain: [identifier of the worm] | [identifier of the host individual] | [HVR I haplotype, HVR IV haplotype], with each attribute separated by vertical lines.
Table 2.
SSU HVR IV haplotype distribution in S. stercoralis from humans and dogs.
Table 3.
SSU HVR I haplotypes of S. stercoralis with HVR IV haplotype A isolated from humans and dogs, 2013 and 2016.
Table 4.
Genotypes of free-living mothers and their progeny.
Table 5.
Genotypes of free-living parents and their progeny at ytP274.
Table 6.
SSU haplotypes found in individual gravid females.