The results of our project, the case-control study for the determination of gastroenteritis etiology in children, were presented at the congress of Slovenian biochemical society with international participation. The implementation and practical use of novel molecular methods (Next generation sequencing) was presented. This method is not broadly used in daily diagnostics, yet. However, it can present useful upgrade with added value of diagnostic procedure for cases with unknown etiology when standard diagnostic procedure is not sufficient.
F.18 Transfer of new know-how to direct users (seminars, fora, conferences)
COBISS.SI-ID: 31024089With the advent and the rapid evolution of next-generation sequencing (NGS) platforms, the possibilities of discovering new viruses and viral strains and of performing high scale virus population studies have broadened dramatically. Despite NGS can produce massive amounts of sequence data, viral sequences are often present in minor quantities within a vast background of host ones. With our study, we presented an alternative approach to the removal of host nucleic acids and simultaneous enrichment of viruses in different environments, cell culture and stool suspension. CIM monoliths are chromatographic supports that due to their structure and physical properties allow binding, concentrating and purification of viruses out of complex samples. The inclusion of a CIM purification step using a gradient elution resulted in an increase of the virus specific reads linked to a decrease in background nucleic acids, which facilitated the post sequencing data analysis. Such virus enriching strategy using CIM monoliths proved to have the potential of improving virus oriented NGS applications and could be used in various NGS platforms. The developed method was presented at the congress of Slovenian biochemical society with international participation.
F.10 Improvements to an existing technological process or technology
COBISS.SI-ID: 30826969At the annual meeting of the European Society of Clinical Virology, results of the case-control study in childhood gastroenteritis was presented. We have narrowed the diagnostic gap using Real-time (RT-) PCR detecting a broad spectrum of enteric pathogens (bacteria, parasites, viruses). At least one pathogen was found in 90.8% of cases and 20.2% of controls with viruses being the most prevalent pathogen (rotaviruses in 55.5%, adenoviruses 19.5% and genogroup II noroviruses 13.7%). Bacteria were detected with lower prevalence (E. coli 7.9%, Salmonella sp. 5.8% and Campylobacter spp. 5.1%). A relatively high percentage of C. difficile in cases (8. 6%) (25/292) was found, but it was detected mostly as a co-pathogen with rotaviruses, adenoviruses and noroviruses. From the results of the study, it was proposed that rotaviruses, adenoviruses and noroviruses GII should be included in the first choice of testing, combined with bacterial pathogens, especially Campylobacter spp., Salmonella sp., and pathogenic E. coli. Other enteric pathogens did not show significant difference between the studied groups and thus, presented probably just minor factor in gastroenteritis in the studied age group.
B.03 Paper at an international scientific conference
COBISS.SI-ID: 31025881