Genomic studies on Strongyloides stercoralis in northern and western Thailand

Abstract

Background Strongyloidiasis is a soil borne helminthiasis, which in most cases is caused by Strongyloides stercoralis. Human infections with S. fuelleborni fuelleborni and S. fuelleborni kellyi also occur. Although up to 370 million people are currently estimated to be infected with S. stercoralis, this parasite is frequently overlooked. Strongyloides stercoralis is prevalent among humans in Thailand; however, S. fuelleborni fuelleborni has also been reported. Three recent genomic studies of individual S. stercoralis worms found genetically diverse populations of S. stercoralis, with comparably low heterozygosity in Cambodia and Myanmar, and less diverse populations with high heterozygosity in Japan and southern China that presumably reproduce asexually. Methods We isolated individual Strongyloides spp. from different localities in northern and western Thailand and determined their nuclear small ribosomal subunit rDNA (18S rDNA, SSU), in particular the hypervariable regions I and IV (HVR-I and HVR-IV), mitochondrial cytochrome c oxidase subunit 1 (cox1) and for a subset whole genome sequences. These sequences were then compared with each other and with published sequences from different geographical locations. Results All 237 worms isolated from 16 different human hosts were S. stercoralis, no S. fuelleborni was found. All worms had the common S. stercoralis SSU HVR IV haplotype A. Two different SSU HVR I haplotypes (I and II), both previously described in S. stercoralis, were found. No animal heterozygous for the two haplotypes was identified. Among the twelve cox1 haplotypes found, five had not been previously described. Based upon the mitochondrial cox1 and the nuclear whole genome sequences, S. stercoralis in Thailand was phylogenetically intermixed with the samples from other Southeast Asian countries and did not form its own branch. The genomic heterozygosity was even slightly lower than in the samples from the neighboring countries. Conclusions In our sample from humans, all Strongyloides spp. were S. stercoralis. The S. stercoralis from northern and western Thailand appear to be part of a diverse, intermixing continental Southeast Asian population. No obvious indication for genetic sub-structuring of S. stercoralis within Thailand or within the Southeast Asian peninsula was detected.

Prevalence of intestinal parasitic infections and genetic differentiation of Strongyloides stercoralis among migrant workers from Myanmar, Lao PDR and Cambodia in northeastern Thailand

“…Our results from the pairwise F ST values found that sequences of worms isolated from migrants from Lao PDR, Cambodia and Myanmar were similar to those from Thailand, indicating close genetic relationship and high gene flow. This is consistent with a previous report, based on 18S rDNA and cox1 sequences, that S. stercoralis populations were not very differentiated between countries within the Southeast Asian peninsula [26]. Parasite gene flow is typically strongly influenced by host migration [29].…”

“…Molecular identification of Strongyloides spp. is largely based on DNA sequences of mitochondrial (cytochrome C oxidase subunit 1 (cox1)) and nuclear ribosomal RNA regions (18S rDNA) [25,26]. Infection with S. stercoralis is more common than with S. fuelleborni and can have serious consequences, causing death in immunocompromised patients, those infected with human T-lymphotropic virus 1 (HTLV-1), organ-transplant patients, and those undergoing corticosteroid therapy [27].…”

Strongyloides genotyping: a review of methods and application in public health and population genetics

“…While the two HVR-IV haplotypes and cox1 clades appeared to support genetically separate and isolated populations with differing host specificity, the HVR-I haplotype within these groups did not appear to correspond to these differing lineages (Jaleta et al, 2017;Nagayasu et al, 2017). Later work in northern Thailand identified two isolates from one patient which were almost identical by WGS but had distinct HVR-I haplotypes I and II, while another two worms from a different patient were very distinct on WGS but shared HVR-I haplotype II (Aupalee et al, 2020). In simple terms, while cox1 and HVR-IV sequences are viable markers of differing populations of S. stercoralis, HVR-I haplotypes do not appear to represent reproductively isolated populations and may not be applicable for this purpose (Aupalee et al, 2020).…”

“…Later work in northern Thailand identified two isolates from one patient which were almost identical by WGS but had distinct HVR-I haplotypes I and II, while another two worms from a different patient were very distinct on WGS but shared HVR-I haplotype II (Aupalee et al, 2020). In simple terms, while cox1 and HVR-IV sequences are viable markers of differing populations of S. stercoralis, HVR-I haplotypes do not appear to represent reproductively isolated populations and may not be applicable for this purpose (Aupalee et al, 2020).…”

“…Sanpool et al (2019) sequenced one freeliving adult each from 23 human hosts and five dogs in northern Thailand, which were also all found to be cox1 lineage A and HVR-IV haplotype A. Aupalee et al (2020) sequenced 18S rRNA of 144 S. stercoralis isolates and a 552 bp region of cox1 of 237 S. stercoralis isolates from 16 human hosts in northern Thailand (four hosts from a village and 12 from a local hospital). All these larval isolates belonged to cox1 lineage A and HVR-I haplotype I or II.…”