Projects / Programmes
Classical and modern approaches to etiology determination of gastroenteritis
| Code |
Science |
Field |
Subfield |
| 3.01.00 |
Medical sciences |
Microbiology and immunology |
|
| Code |
Science |
Field |
| B230 |
Biomedical sciences |
Microbiology, bacteriology, virology, mycology |
| Code |
Science |
Field |
| 3.02 |
Medical and Health Sciences |
Clinical medicine |
gastroenteritis, metagenomics, enteric pathogens, molecular methods
Researchers (22)
Organisations (5)
Abstract
Acute gastroenteritis (GE) is responsible for high mortality in children up to 6 years of age in developing countries and is the leading cause of hospitalization among infectious diseases in developed countries. Although extensive progress has been made in diagnostic methods in the last 30 years, the etiology of acute GE remains undetermined in a relatively high proportion of cases. According to published data from other European countries and statistics of infectious diseases in Slovenia, this proportion is higher than 30 percent. Viral enteric pathogens account for more than 70 percent of GE cases of known etiology. The recent use of metagenomic approaches has revolutionated the field of pathogen discovery and new, especially viral pathogens have been described in the last few years. The use of this approach in acute GE of unknown etiology is expected to enable the description of new, in particular viral causative agents.
Our project proposal describes a study design for the determination of GE etiology, focusing on the population in which GE is the most common cause of severe infectious disease. The study group will include children up to 6 years old with acute GE, who have been hospitalized at the Department of Infectious Diseases and Febrile Illnesses, University Medical Center, Ljubljana. Stool samples will be collected for microbiological investigations, in addition to blood samples for serological testing and for checking for probable viremia. Stool samples will be tested for the most common bacterial, viral and parasitic pathogens causing GE, using molecular and classical methods in microbiological diagnostics. A control group of children without GE, hospitalized at the Department of Paediatric Surgery and Intensive Care for elective surgical intervention, will also be included in the study. Both stool and blood samples will also be collected from the control group. We anticipate that the etiology will not be determined in at least 25 percent of GE cases tested for the most common pathogens. Those samples will be included in further testing using a metagenomic approach and some additional molecular testing for rare or uncommon bacterial and parasitic pathogens causing GE will be carried out.
Using such a systemic approach, with classical and modern methods in diagnostic microbiology, including also a control group, we expect to be able to explain the etiology of the majority of GE cases. Additionally, new viral causes of GE may be detected and characterized, together with an analysis of their etiological role in GE. The etiological determination of infectious disease is critical for successful disease suppression and patient management, identification of the source of infection and avoidance of new infections or even epidemic outbreaks. This results in lowering the disease burden in public health and reducing the high costs of healthcare. Working together with microbiologists, clinicians and epidemiologists, the management of acute GE cases will be evaluated and possible improvements and rationalizations will be suggested on the basis of the results obtained in our study. A further output of our study will be the transfer of knowledge in microbiological diagnostics, including combining new molecular techniques with some classical methods.
Significance for science
This study is one of the rare syndromic approach studies, including specific molecular tests as well as metagenomic analysis of undiagnosed cases in a prospective, hospital based case-control study. The rate of pathogen detection in this study is the highest reported in the literature. It was also shown that some potential pathogens detected in relatively high proportions (e.g. Parechoviruses in 16.2% and C. difficile in 8.1%) are probably not involved directly in diarrhoea in this early childhood period. Our project result trigger some additional questions regarding a high proportion of mixed infection and the role of individual pathogens in concurrent infections, requiring additional research on this topic. We have confirmed speculations in previous publications, that quantitative data, or relative abundance data on specific viral pathogen, is an important information in aetiology determination. In this sense we have indicated a possibility for introduction of a novel molecular methodology, digital PCR, in the molecular diagnostics. This could improve the reliability regarding the role of specific pathogen in the disease for such a complex samples. Our findings are important for the wider European region and could be implemented in microbiological diagnostics, as it indicates the prevalence of specific pathogens which should be included preferentially in a rapid and reliable diagnostics procedure for hospitalized children with diarrhoea up to 6 years of age. In addition, one of the main deliverables of our work is the innovative sample pre-treatment for NGS analysis, which introduces higher quality of NGS data in virus research using complex biological samples, like stool
Significance for the country
This is the first case-control study with a systematic approach to determine diarrhoea aetiology in hospitalized children in Slovenia. With our results, it is clearly shown, what are the most important pathogens in the study population, which potential pathogens are present in stool samples but have no major role in the disease and what is the optimal target combination to be tested in the frontline for the aetiology determination in diarrhoea cases. This should be considered in the future by infectologists. Till now, we have followed such data in studies performed in other European countries and worldwide, but this is the first time that we gathered such important data in our environment. This could be the basis for improving the quality of work and collaboration between infectologists, paediatricians and most important diagnostic laboratories in medical microbiology. This data could be also used as a baseline for further research in aetiology determination of outpatients, who visit only their local paediatrician. For the implementation of new sample pre-treatment method for NGS analysis a chromatographic method was used. The CIM monolith chromatography was developed and produced by the Slovenian biotechnological company. A successful application of this product into the NGS protocols is a good promotion of Slovenian knowledge, and contributes to a better recognition of Slovenian high technology products with added value.
Most important scientific results
Annual report
2011,
2012,
2013,
final report,
complete report on dLib.si
Most important socioeconomically and culturally relevant results
Annual report
2011,
2012,
2013,
final report,
complete report on dLib.si
