Comparative genomics and transcriptomics of 4 Paragonimus species provide insights into lung fluke parasitism and pathogenesis.

Bruce A Rosa,Paul J Brindley,David Blair,Hiromu Sugiyama,Hyeim Jung,Wanchai Maleewong,Takeshi Agatsuma,Samantha N McNulty,Young-Jun Choi,Thanh Hoa Le,Makedonka Mitreva,Peter U Fischer,Pham Ngoc Doanh,John Martin

doi:10.1093/gigascience/giaa073

Abstract

Background Paragonimus spp. (lung flukes) are among the most injurious foodborne helminths, infecting ∼23 million people and subjecting ∼292 million to infection risk. Paragonimiasis is acquired from infected undercooked crustaceans and primarily affects the lungs but often causes lesions elsewhere including the brain. The disease is easily mistaken for tuberculosis owing to similar pulmonary symptoms, and accordingly, diagnostics are in demand.ResultsWe assembled, annotated, and compared draft genomes of 4 prevalent and distinct Paragonimus species: Paragonimus miyazakii, Paragonimus westermani, Paragonimus kellicotti, and Paragonimus heterotremus. Genomes ranged from 697 to 923 Mb, included 12,072–12,853 genes, and were 71.6–90.1% complete according to BUSCO. Orthologous group analysis spanning 21 species (lung, liver, and blood flukes, additional platyhelminths, and hosts) provided insights into lung fluke biology. We identified 256 lung fluke–specific and conserved orthologous groups with consistent transcriptional adult-stage Paragonimus expression profiles and enriched for iron acquisition, immune modulation, and other parasite functions. Previously identified Paragonimus diagnostic antigens were matched to genes, providing an opportunity to optimize and ensure pan-Paragonimus reactivity for diagnostic assays.ConclusionsThis report provides advances in molecular understanding of Paragonimus and underpins future studies into the biology, evolution, and pathogenesis of Paragonimus and related foodborne flukes. We anticipate that these novel genomic and transcriptomic resources will be invaluable for future lung fluke research.

Highlights

Paragonimus spp. are among the most injurious foodborne helminths, infecting ∼23 million people and subjecting ∼292 million to infection risk
The sizes of the 4 newly generated Paragonimus genomes range from 697 to 923 Mb, containing between 12,072 and 12,853 genes. These draft genomes are estimated to be between 71.6% and 90.1% complete, according to the number of complete Benchmarking Universal Single-Copy Orthologs (BUSCO) eukaryote genes [19], with the new P. westermani genome produced from a sample collected from Japan being more complete than the previously sequenced genome produced from a sample collected from India [11] (90.1% vs 70.2%, respectively; Table 2)
We performed Basic Local Alignment Search Tool (BLAST) sequence similarity searches of previously identified Paragonimus diagnostic antigen targets among the 4 species (Fig. 10). These included (i) P. westermani and Paragonimus pseudoheterotremus cysteine proteases identified in 2 previous studies [65, 66], 1 of which had high adult-stage expression levels in all 4 species [65]; (ii) 3 different tyrosine kinases (1 of which was identified in 2 different studies, in Clonorchis sinensis and in P. westermani [67, 68]), all of which had relatively low gene expression levels in adult stages; (iii) a previously unannotated P. heterotremus enzyme-linked immunosorbent assay (ELISA) antigen [69] with low expression across life cycle stages, which we annotate as a saposin protein; and (iv) eggshell proteins of P. westermani [70], for which we provide full-length sequences. We observed that this gene was conserved across and specific to the lung flukes, with lower gene expression in the young adult stage (P. heterotremus) but higher expression in the adult stages of all species; (v) among serodiagnostic P. kellicotti antigens based on a transcriptome assembly and proteomic evidence [16], we identified the top 10 of the 25 prioritized transcripts that best matched between the transcript sequence and the newly annotated draft genome of P. kellicotti

Summary

Introduction

Paragonimus spp. (lung flukes) are among the most injurious foodborne helminths, infecting ∼23 million people and subjecting ∼292 million to infection risk. Paragonimiasis is acquired from infected undercooked crustaceans and primarily affects the lungs but often causes lesions elsewhere including the brain. Primarily affecting the lungs, lesions can occur at other sites, including the brain, and pulmonary paragonimiasis is frequently mistaken for tuberculosis owing to similar respiratory symptoms [4]. For example, the most noticeable clinical symptom of an infected individual is a chronic cough with gelatinous, rusty brown, pneumonia-like, blood-streaked sputum [6]. The symptoms of extra-pulmonary paragonimiasis vary depending on the location of the fluke, including cerebral [5] and abdominal paragonimiasis [6]

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Results

Conclusion