The genome of the sparganosis tapeworm Spirometra erinaceieuropaei isolated from the biopsy of a migrating brain lesion

Abstract

Background: Sparganosis is an infection with a larval Diphyllobothriidea tapeworm. From a rare cerebral case presented at a clinic in the UK, DNA was recovered from a biopsy sample and used to determine the causative species as Spirometra erinaceieuropaei through sequencing of the cox1 gene. From the same DNA, we have produced a draft genome, the first of its kind for this species, and used it to perform a comparative genomics analysis and to investigate known and potential tapeworm drug targets in this tapeworm. Results: The 1.26 Gb draft genome of S. erinaceieuropaei is currently the largest reported for any flatworm. Through investigation of β-tubulin genes, we predict that S. erinaceieuropaei larvae are insensitive to the tapeworm drug albendazole. We find that many putative tapeworm drug targets are also present in S. erinaceieuropaei, allowing possible cross application of new drugs. In comparison to other sequenced tapeworm species we observe expansion of protease classes, and of Kuntiz-type protease inhibitors. Expanded gene families in this tapeworm also include those that are involved in processes that add post-translational diversity to the protein landscape, intracellular transport, transcriptional regulation and detoxification.

Genome Analysis of the Fatal Tapeworm Sparganum Proliferum Uncovers the Cryptic Life Cycle and Mechanisms Underlying Aberrant Larval Proliferation

“…In this study, we sequenced the S. proliferum genome and performed comparative genomics with other tapeworm species, including the newly-sequenced S. erinaceieuropaei genome. The S. erinaceieuropaei genome was sequenced previously [12], with an estimated genome size of more than 1.2 Gb, but because the source material was from a biopsy the assembled sequence was highly fragmented. Hence, the S. erinaceieuropaei genome To determine phylogenetic relationships, we confirmed that the genetic sequence of S. proliferum is distinct from that of S. erinaceieuropaei, despite the close relationship between these species.…”

De novoassembly of two Swedish genomes reveals missing segments from the human GRCh38 reference and improves variant calling of population-scale sequencing data

“…Since it is highly unlikely that the two Swedish individuals indeed have DNA from these parasites present in their blood, a more plausible explanation is that the worm genome assemblies contain a fraction of human sequence. The initial worm assemblies were based on short-read sequencing of samples extracted from human patients 20 , and contigs not aligning to GRCh38 may have been mis-annotated as worm sequence, thus explaining the overlap with our NS. Notably, the Swe2 sample also contained a complete human papilloma virus 35 (HPV35).…”

Human infectious diseases in the genomics era: where do we go from here?

“…They have also enabled researchers to retrospectively analyse where and why the outbreak of a particular disease occurred; examples of such an approach include studies of Legionnaires’ disease [ 5 ], severe acute respiratory syndrome [ 6 ], bird influenza [ 7 ], and global epidemics - including the current Ebola outbreak that is ravaging West Africa [ 8 ]. Sequencing technologies themselves also have incredible potential for diagnosing previously uncharacterised pathogens, as shown in the Genome Biology article on a rare brain tapeworm [ 9 ]. Genomics therefore has an important and multifaceted role in the future control of infectious diseases.…”