• Choice of assembly software has a critical impact on virome characterisation

      Sutton, Thomas D S; Clooney, Adam G; Ryan, Feargal J; Ross, R Paul; Hill, Colin; Science Foundation Ireland; European Regional Development Fund; Janssen Biotech, Inc.; SFI/12/RC/2273; SFI/14/SP APC/B3032 (Biomed Central, 2019-01-28)
      Background The viral component of microbial communities plays a vital role in driving bacterial diversity, facilitating nutrient turnover and shaping community composition. Despite their importance, the vast majority of viral sequences are poorly annotated and share little or no homology to reference databases. As a result, investigation of the viral metagenome (virome) relies heavily on de novo assembly of short sequencing reads to recover compositional and functional information. Metagenomic assembly is particularly challenging for virome data, often resulting in fragmented assemblies and poor recovery of viral community members. Despite the essential role of assembly in virome analysis and difficulties posed by these data, current assembly comparisons have been limited to subsections of virome studies or bacterial datasets. Design This study presents the most comprehensive virome assembly comparison to date, featuring 16 metagenomic assembly approaches which have featured in human virome studies. Assemblers were assessed using four independent virome datasets, namely, simulated reads, two mock communities, viromes spiked with a known phage and human gut viromes. Results Assembly performance varied significantly across all test datasets, with SPAdes (meta) performing consistently well. Performance of MIRA and VICUNA varied, highlighting the importance of using a range of datasets when comparing assembly programs. It was also found that while some assemblers addressed the challenges of virome data better than others, all assemblers had limitations. Low read coverage and genomic repeats resulted in assemblies with poor genome recovery, high degrees of fragmentation and low-accuracy contigs across all assemblers. These limitations must be considered when setting thresholds for downstream analysis and when drawing conclusions from virome data.
    • Comparison of four commercially available ELISA kits for diagnosis of Fasciola hepatica in Irish cattle

      Munita, Maria P; Rea, Rosemary; Martinez-Ibeas, Ana M; Byrne, Noel; Kennedy, Aideen; Sekiya, Mary; Mulcahy, Grace; Sayers, Riona; Department of Agriculture, Food and the Marine; Dairy Research Ireland; et al. (Biomed Central, 2019-11-21)
      Background Fasciola hepatica is a liver parasite of mammals and it results in poor welfare outcomes and economic losses in ruminants. While faecal egg count is the test most commonly used for diagnosis, it does not indicate presence of migrating immature stages. Serological techniques increase sensitivity at all stages of the liver fluke infection. The aim of this study was to compare four commercially available ELISA tests for the diagnosis of F. hepatica. For this purpose, we tested three sample types; (i) known F. hepatica status sera from an experimental infection for the comparison of sensitivities and specificities, (ii) sera from pre- and post-flukicide-treated (albendazole, closantel, nitroxynil and triclabendazole) beef cattle to contrast the differences of seropositivity before and after treatment, and (iii) bulk tank milk samples from dairy herds sampled during high and low F. hepatica exposure periods for assessing seasonal variations with the four tests available. Samples were tested using ELISA kits supplied by four manufacturers (Ildana Biotech, IDEXX, Svanova, and Bio-X). Samples were analysed simultaneously and in duplicate. Results In the control population Ildana, IDEXX and Bio-X presented 100% sensitivity (Se) and specificity (Sp), Svanovir presented a Se of 59% and a Sp of 96%. In flukicide-treated beef cattle, kits highlighted decreasing antibody levels 90 days post-treatment in variable degrees. Finally, bulk milk showed a significant decrease in ELISA value between high and low fluke exposure periods with all tests studied. Conclusions Se and Sp found in the present study, confirm that Ildana, IDEXX and Bio-X are accurate for the detection of F. hepatica exposure in Irish cattle. Svanovir Se and Sp in this population, indicate that a larger study is necessary to confirm this test characteristic in Irish herds. In post-treatment use, Bio-X showed a consistent and significant decrease of ELISA value in all groups treated, denoting to be a reliable tool for assessing treatment effect at 90 days post-treatment. Finally, all tests showed to be a reliable tool for the F. hepatica monitoring of high and low exposure seasons, using bulk tank milk samples.