Truyen, U. | Search bioRxiv

bioRxiv2026

Comparative Performance of Portable DNA Extraction Protocols and Bioinformatics Workflows for Rapid Detection of Pathogens and Antimicrobial Resistance Using Oxford Nanopore Sequencing.

Oxford Nanopore technology (ONT) enables rapid, portable pathogen identification and detection of antimicrobial resistance (AMR). Still, the reliability of downstream genomic analyses is highly dependent on DNA extraction quality, particularly in resource-limited settings. This study comparatively evaluated four portable bacterial DNA extraction protocols, derived from three commercial kits, to determine their impact on nanopore sequencing performance, bioinformatics workflow completion, and field deployability. Six Gram-negative bacterial isolates (Escherichia coli, n= 4; Pseudomonas sp., n= 1; and Salmonella sp., n= 1) were processed using four extraction protocols: SwiftX DNA, SwiftX DNA with proteinase K (ProtK), SwiftX ParaBact, and NucleoSpin Microbial. Twenty-four DNA extracts (6 isolates x 4 protocols) were sequenced on a single multiplexed MinION R10.4.1 flow cell. Sequencing data were analysed using validated Galaxy-based generic and species-specific pipelines, with workflow completion defined as successful progression through quality control, assembly, virulence, plasmid and AMR detection modules. DNA purity varied substantially by extraction protocol and was strongly associated with workflow success. NucleoSpin Microbial achieved 100% workflow completion, SwiftX ParaBact achieved 83%, while both SwiftX DNA-based protocols failed to complete full workflows. Higher A260/A280 ratios were strongly correlated with successful workflow completion (Spearmans {rho} = 0.767, p < 0.0001). Importantly, key AMR genes required to classify isolates as multidrug resistant were consistently detected using both NucleoSpin Microbial and SwiftX ParaBact extractions. However, NucleoSpin Microbial assemblies showed significantly higher contiguity and enabled broader and more complete detection of virulence factors, pathogenicity islands, plasmid replicons, and accessory AMR genes, reflecting enhanced genomic resolution. IMPORTANCERapid whole-genome sequencing is increasingly used to detect antimicrobial resistance and guide public health responses, but its reliability depends strongly on how bacterial DNA is extracted. In this study, we show that DNA extraction method choice has a major impact on Oxford Nanopore sequencing performance across clinically relevant bacteria. While silica-column-based extraction maximised genomic completeness and analytical depth, paramagnetic bead-based reverse purification offered superior portability with sufficient resolution for frontline AMR surveillance. These findings highlight a practical trade-off between field deployability and high-resolution genomic characterisation in low-resource settings.

genomics↗

bioRxiv2025

Distinct evolutionary patterns of endemic and emerging parvoviruses, and the origin of a new pandemic virus.

Emergence of epidemic viruses in new hosts threatens both human and animal populations, and often involves virus evolution to overcome barriers that normally prevent efficient infection and spread in that host. After transfer the separated viruses will evolve in parallel as they spread within the original and new hosts. Here we examine the details of a virus involved in such a host-jumping event, where we define the natural evolution of feline panleukopenia virus (FPV) over 60 years, clarify the origins of the new pandemic canine parvovirus (CPV) that arose in the 1970s, and compare the separate evolution of those viruses over 47 years in cats or dogs. Several live-attenuated FPV vaccine viruses originated from early 1960s isolates or were a recombinant of an early virus, and many sequences in databases proved to be vaccine-derived. The sequences of wild viruses showed that FPV-like strains evolved at [~]25% the rate seen for CPV in dogs, and the higher rate of CPV evolution was consistent since 1979 when a genetic variant became widespread. The common ancestor of the CPV lineage was related to FPVs from Europe, and contained several unique host-adaptive capsid changes associated with canine transferrin receptor type-1 binding. Although the FPV vaccine strains are around 60 years old, little selection for antigenic variation was observed. The distinct evolutionary patterns of these closely related viruses circulating for decades in different hosts emphasizes the complex evolution associated with viral epidemic emergence and spread in endemic and new hosts. SIGNIFICANCE STATEMENTComparing the evolution of a virus in its reservoir host with that seen in a new host will reveal the special circumstances that allow epidemic emergence. A feline parvovirus (FPV) jumping to dogs in the mid-1970s formed canine parvovirus (CPV), which has circulated world-wide until today. The evolutionary rate of FPV in its original hosts was much lower than that of CPV in dogs, and the mutational patterns seen in the different hosts were also distinct. Early CPV isolates differed from the ancestral FPV clade in several key host range mutations. These results highlight the complex biology associated with epidemic emergence, including host-specific rates of lineage evolution and complex origins of host-adaptive mutations. (113/120)

evolutionary biology↗