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2015|16 Annual Report Fraunhofer IGB

66 NEXT-GENERATION DIAGNOSTICS OF SEPSIS Silke Grumaz, Philip Stevens, Kai Sohn Sepsis epsis whole-body inflammation due to infection presents one of the greatest challenges in intensive care medicine because it is associated with a high patient mortality of over percent espite medical advances, this figure has remained unchanged for nearly 20 years. One reason for this is the frequent lack of early diagnosis and prompt treatment with effective pathogen-specific antibiotics owever, the use of these kinds of antibiotics requires knowledge of the patho- gen. With blood cultures – the current gold standard – micro- bial diagnostics can take two to five days, yet no pathogen at all is cultured in up to a third of cases [2]. Molecular-level bio- logical techniques offer alternative diagnostic approaches that are not dependent upon prior cultivation of the pathogen, but instead identify it based on its nucleic acids (DNA and RNA). Researchers at Fraunhofer IGB are using the newest advances in the field of high-throughput se uencing in order to develop and make available rapid alternative diagnostic procedures to identify pathogens in under 30 hours. Circulating nucleic acids – a very promising class of molecules We use a special class of molecules for this technique at Fraunhofer IGB, known as circulating nucleic acids in plasma and serum P or specific physiological or pathological processes (e.g. with cancer, stroke, or pregnancy), the concen- trations of these molecules in the blood are increased due to elevated cell turnover. As a result, this class of molecule has been recently employed for diagnosing various oncological diseases as well as for prenatal diagnostics [3]. In contrast to diagnostic procedures used up to now, this new technique can be carried out non-invasively using a blood sample – and is therefore also called a “liquid biopsy”. This works for sepsis patients as well, because bacterial as well as human nucleic acids are present in their plasma, as researchers of Fraunhofer IGB have shown. New technique for sepsis diagnostics A novel technique was developed, tested, and validated at Fraunhofer IGB that can be used to search for microbial nucleic acid sequences in the CNAPS. It uses existing high- throughput sequencing with the help of data processing al- gorithms developed in-house, then matches these sequences to specific pathogens mathematically and uantifies them This is not trivial and a high level of sensitivity and specificity is required, since over 99 percent of the nucleic acids in this kind of sample are of human origin. In a joint retrospective study with Heidelberg University Hospital, CNAPS were isolated from the plasma of sepsis patients and the newly developed process then validated. Since laboratory results from clinical microbiology were available for the patient samples, a direct comparison between next-generation diagnostics and conven- tional clinical microbiology was possible. The study showed excellent correlation between next-generation diagnostics and blood cultures, as well as with cultures from localized centers of infection, for example. In comparison to blood cultures, the next-gen diagnostics in some cases provided even more plausible results from a medical point of view – that contami- nating pathogens from skin flora are often cultured as well In addition, simultaneous single-step detection of very different pathogens, such as viruses, bacteria, and fungi, becomes feasible with the new technique. Moreover, researchers at Fraunhofer IGB were able to demonstrate that given a suitably high coverage of the bacterial genome, even detection of the genes responsible for resistance to antibiotics is possible in the same analysis. This is of great importance in the clinical environment, since it facilitates a fast and effective decision by the attending physician on what treatment to employ. 1 MEDICINE