Hookworm genomic diversity and population structure from accessible sample types: A validated approach to generate genome-wide polymorphism datasets from individual third-stage larvae

Abstract

Hookworm infection is a neglected tropical disease affecting hundreds of thousands of people annually in the tropics and sub-tropics. Population genomic approaches have the potential to improve our understanding of hookworm infection dynamics and control efficacy. Here, we validate an approach to generate genome-wide polymorphism datasets from accessible sample types in the zoonotic hookworm (Ancylostoma ceylanicum) then apply the validated approach in the human hookworm (Necator americanus) to compare laboratory- and field-derived samples. We first present an optimized method for purifying nucleic acid from individual third-stage hookworm larvae (L3s). We then measure the accuracy of variant call datasets generated through whole genome amplification (WGA) and next-generation sequencing (NGS). We demonstrate that WGA via multiple displacement amplification (MDA) introduces predictable biases that are exacerbated by low inputs and poor sample preservation but show that with sufficient input mass ([≥]0.1ng) we are still able to produce highly accurate variant call datasets from nucleic acid concentrations that reflect those of individual L3s. Using our validated approach, we infer laboratory- and field-collected samples of N. americanus as distinct populations, with higher levels of heterozygosity and nucleotide diversity identified in field-collected samples, suggesting signatures of inbreeding and/or drift are detectable in laboratory specimens within several years of initiation of infection. We also show that, despite expected reductions in heterozygosity, laboratory samples still possess numerous heterozygous sites, and we demonstrate that a reference genome generated from an adult worm from an early laboratory passage performs well for variant calling in both laboratory- and field-derived samples. Moving forward, our optimized method for nucleic acid purification can be broadly applied to generate input for any amplification-based approach where sequencing individual hookworm L3s, rather than a pool of specimens, is preferred. Our validated population genomics workflow can be used to characterize structure and connectivity of hookworm populations in endemic communities, with the goal of leveraging these insights to improve our approach to hookworm treatment and control. AUTHOR SUMMARYInfection with the human hookworm, Necator americanus, is a significant cause of morbidity in the global south. Population genomic techniques have the potential to improve our understanding of hookworm infection and control. However, third-stage larvae, or L3, which are the hookworm life-cycle stage we routinely have access to when screening infected people, are less than a millimeter long, and this small size makes generating genomic datasets from individual worms difficult. Here, we introduce an optimized approach for purifying DNA from individual L3s and validate its use with whole genome amplification (WGA) for population genomics. We found that WGA from L3s produces sequencing datasets that are biased in their breadth and depth of coverage across the hookworm genome. But by ensuring a minimum threshold for the mass of DNA input to WGA and setting strict criteria for variant filtration, these biases can be overcome to produce highly accurate variant calls genome-wide. We then use this approach to demonstrate reduced genetic diversity in a recently established laboratory hookworm strain as compared to field-collected samples. Our study outlines a specimen-through-analysis workflow that can be used with accessible sample types to measure population structure and diversity of hookworms in endemic communities.