A comparison of short- and long-read whole-genome sequencing for microbial pathogen epidemiology.

Whole-genome sequencing provides the highest resolution for characterizing pathogen evolution, epidemiology, and diagnostics. Genome assemblies contain information on the identity and potential phenotypes of a pathogen. Likewise, variant calling can inform on transmission patterns and evolutionary relationships. Recent improvements in Oxford Nanopore long-read sequencing have made its use attractive for genomic epidemiology. However, the accuracy and optimal strategy for analysis of Nanopore reads remain to be determined. We compared the use of Illumina short reads and Oxford Nanopore long reads for genome assembly and variant calling of phytopathogenic bacteria. We generated short- and long-read data sets for diverse phytopathogenic IMPORTANCE: Genome assembly and variant calling are important steps in microbial population studies and epidemiology. Most variant calling and genotyping pipelines are designed for Illumina short sequencing reads. Oxford Nanopore Technology long-read sequencing results in more complete genome assemblies but has historically been of lower quality. Here, we show that Nanopore long reads are now of sufficient quality for bacterial whole-genome assembly and epidemiology. We benchmarked the accuracy of multiple variant calling pipelines with short and long reads. Using an optimized variant calling approach, variant calls and genotypes inferred from long reads are as accurate as those inferred from short reads. Importantly, we found that gold-standard variant calling pipelines designed for short reads are also accurate with long reads when long reads are first fragmented into shorter sequences. This finding allows researchers to incorporate the advantages of Nanopore sequencing for genome assembly while maintaining high accuracy in epidemiology and population analyses.