Pool sequencing maps genomic variation in Swedish Haemonchus contortus

Haemonchus contortus, the barber’s pole worm, is one of the most damaging gastrointestinal parasites of sheep and goats worldwide. A new genomic study from Sweden has now delivered the first genome-wide baseline of this blood-feeding nematode across multiple Swedish sheep farms, using pooled whole genome sequencing of field-derived isolates from 12 farms. The research, published in BMC Genomics by Nanxing Liu, Paulius Baltrušis, Åsa Ohlsson, Johan Höglund and Sofia Mikko of the Swedish University of Agricultural Sciences, reveals a striking pattern: very high genetic diversity within parasite populations but relatively low differentiation between them, with a handful of notable exceptions that hint at localized evolutionary pressures.

The team turned to pooled-sample whole genome sequencing, or Pool-seq, a cost-effective strategy in which DNA from many individual worms is sequenced together and allele frequencies are estimated from the pooled read depths. This approach is particularly well suited to organisms like H. contortus, whose enormous effective population sizes, extraordinary fecundity and extensive standing genetic variation fuel rapid adaptation and the spread of anthelmintic resistance. While earlier studies relied on reduced-representation sequencing or targeted marker panels to probe population structure, only whole genome sequencing can fully characterize genome-wide differentiation and pinpoint where divergent selection acts.

The results paint a picture of a parasite population that is, for the most part, genomically well mixed across the country. Nucleotide diversity within populations ranged from 0.0211 to 0.0253, values that reflect the tremendous standing variation harbored within each farm’s worm community. Meanwhile, the fixation index, F_ST, remained below 0.1 for most population pairs, indicating relatively low genomic differentiation among most Swedish isolates. In practical terms, the worms on any given farm carry most of the genetic variation found anywhere in the sampled region, a pattern consistent with extensive gene flow among parasite populations.

Yet the study was not without its surprises. Three population pairs stood out with markedly higher genomic differentiation, with F_ST values between 0.144 and 0.157, combined with lower within-population nucleotide diversity of 0.0211 to 0.0227. Intriguingly, this divergence was not spread evenly across the genome but concentrated on chromosomes 4, 5 and X. Such localized divergence can signal regions under divergent selection, or areas where recombination and demographic history have shaped patterns of variation differently from the rest of the genome.

When the researchers examined significantly differentiated single nucleotide polymorphisms, they found them linked to a limited set of annotated genes involved in regulatory processes, signalling pathways and nervous system-related functions. These functional categories are provocative in the context of parasite biology, since nervous system genes have previously been implicated in anthelmintic drug responses. However, the authors are careful to note that the biological basis of these differentiation patterns remains unclear and will require further investigation using phenotype-linked data and farm-management metadata before any resistance-associated interpretation can be made.

The methodological pipeline behind the study reflects standard practice in modern parasite genomics. Raw sequencing reads in FASTQ format were aligned to the reference genome using the Burrows-Wheeler Aligner with maximal exact matches seeding, producing SAM and then compressed BAM files. Variant calling generated BCF and VCF files from which single nucleotide polymorphisms were extracted. Statistical analyses included principal component analysis to visualize population structure, calculation of pairwise F_ST and nucleotide diversity, and Fisher’s exact tests to identify significantly differentiated SNPs, with gene ontology annotations used to interpret the functions of genes harboring differentiated variants.

Pool-seq offers clear advantages for surveillance-oriented genomics. By sequencing pools rather than individuals, researchers can characterize broad population-genomic patterns at a fraction of the cost, making it feasible to sample many farms and track variant distributions over time and space. For H. contortus, where anthelmintic resistance is a growing concern for sheep farmers, this kind of genome-wide baseline is a valuable foundation for future research on parasite adaptation, resistance surveillance and control strategies. The approach does, however, have limitations: pooling obscures individual-level haplotypes and can complicate the detection of rare variants, which is why the authors position Pool-seq as a tool for describing broad patterns rather than a substitute for individual-level studies when fine-scale resolution is needed.

The study material consisted of anonymised residual biobanked samples obtained through routine diagnostic laboratory activities, with technical assistance in sample collection and parasite identification provided by Vidilab AB in Enköping, Sweden. Sequencing was carried out by the SNP&SEQ Technology Platform in Uppsala, part of the National Genomics Infrastructure Sweden and Science for Life Laboratory. Computational resources were provided by the National Academic Infrastructure for Supercomputing in Sweden, and the work was funded by FORMAS with open access funding from the Swedish University of Agricultural Sciences.

What makes these findings broadly significant is the demonstration that Swedish H. contortus populations harbor most of their variation within, rather than between, farms. This pattern has implications for how resistance alleles might spread: if gene flow among parasite populations is extensive, a resistance variant emerging on one farm could, in principle, disseminate widely through the national parasite population. Conversely, the three highly differentiated population pairs, with divergence concentrated on specific chromosomes, suggest that localized selective pressures or demographic isolation can still carve out distinctive genomic regions worth monitoring.

As the first genome-wide characterization of field-derived H. contortus across multiple Swedish sheep farms, this study establishes a reference point against which future genomic variation can be measured. The authors emphasize that Pool-seq is a useful method for describing broad population-genomic patterns in this species and that their findings provide a valuable foundation for future research on parasite adaptation, resistance, surveillance and control. With anthelmintic resistance an escalating challenge for small ruminant production worldwide, genome-wide baselines of this kind are an essential first step toward tracking how parasite populations evolve under drug pressure and informing the parasite control strategies of tomorrow.

Subject of Research: Whole genome pool sequencing reveals genomic variation in field Haemonchus contortus isolates in Sweden

Article Title: Whole genome pool sequencing reveals genomic variation in field Haemonchus contortus isolates in Sweden

Article References: Liu, N., Baltrušis, P., Ohlsson, Å., Höglund, J., & Mikko, S. (2026). Whole genome pool sequencing reveals genomic variation in field Haemonchus contortus isolates in Sweden. BMC Genomics. https://doi.org/10.1186/s12864-026-13449-5

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13449-5

Keywords: Haemonchus contortus, Pool-seq, population genomics, genomic variation, nematode, sheep, parasite genomics, anthelmintic resistance, nucleotide diversity, fixation index, Sweden, whole genome sequencing