In food safety the detection of food contaminations with pathogenic microorganisms is a race against time and often outpaced by error-prone epidemiological approaches. For evidence-based outbreak investigations fast and reliable techniques and procedures are required to identify the source of infection. Metagenomics has the potential to become a powerful tool in the field of modern food safety, since it allows the detection, identification and characterization of a broad range of pathogens in a single experiment without pre-cultivation within a couple of days. Nevertheless, sample handling, sequencing and data analysis are challenging and can introduce errors and biases into the analysis. In order to evaluate the potential of metagenomics in food safety, we generated a mock community containing DNA of foodborne bacteria. Herewith, we compare the aptitude of the two prevalent approaches – 16S rDNA amplicon sequencing and whole genome shotgun sequencing – for the detection of foodborne bacteria using different parameters during sample preparation, sequencing and data analysis. 16S rDNA sequencing did not only result in high deviations from the expected sample composition on genus and species level, but more importantly lacked the detection of several pathogenic species. While shotgun sequencing is more suitable for species detection, abundance estimation, genome assembly and species characterization, the performance can vary depending on the library preparation kit, which was confirmed for a naturally Francisella tularensis contaminated game meat sample. The application of the Nextera XT DNA Library Preparation Kit for shotgun sequencing did not only result in lower reference genome recovery and coverage, but also in distortions of the mock community composition. For data analysis, we propose a publicly available workflow for pathogen detection and characterization and demonstrate its benefits on the usability of metagenomic sequencing in food safety by analyzing an authentic metagenomic sample.

Clostridium perfringens causes a plethora of devastating infections, with toxin production being the underlying mechanism of pathogenicity in various hosts. Genomic analyses of 206 public-available C. perfringens strains´ sequence data identified a substantial degree of genomic variability in respect to episome content, chromosome size and mobile elements. However, the position and order of the local collinear blocks on the chromosome showed a considerable degree of preservation. The strains were divided into five stable phylogroups (I–V). Phylogroup I contained human food poisoning strains with chromosomal enterotoxin (cpe) and a Darmbrand strain characterized by a high frequency of mobile elements, a relatively small genome size and a marked loss of chromosomal genes, including loss of genes encoding virulence traits. These features might correspond to the adaptation of these strains to a particular habitat, causing human foodborne illnesses. This contrasts strains that belong to phylogroup II where the genome size points to the acquisition of genetic material. Most strains of phylogroup II have been isolated from enteric lesions in horses and dogs. Phylogroups III, IV and V are heterogeneous groups containing a variety of different strains, with phylogroup III being the most abundant (65.5%). In conclusion, C. perfringens displays five stable phylogroups reflecting different disease involvements, prompting further studies on the evolution of this highly important pathogen.

Aggregation of huntingtin (htt) in neuronal inclusionsis associated with the development of Huntington's disease (HD). Previously, we have shown that mutant htt fragments with polyglutamine (polyQ) tracts in the pathological range (>37 glutamines) form SDS-resistant aggregates with a fibrillar morphology, whereas wildtype htt fragments with normal polyQ domains do not aggregate. In this study we have investigated the coaggregation of mutant and wild-type htt fragments. We found that mutant htt promotes the aggregation of wildtype htt, causing the formation of SDS-resistant co-aggregates with a fibrillar morphology. Conversely, mutant htt does not promote the fibrillogenesis of the polyQ-containing protein NOCT3 or the polyQ-binding protein PQBP1, although these proteins are recruited into inclusions containing mutant htt aggregates in mammalian cells. The formation of mixed htt fibrils is a highly selective process that not only depends on polyQ tract length but also on the surrounding amino acid sequence. Our data suggest that mutant and wild-type htt fragments may also co-aggregate in neurons of HD patients and that a loss of wild-type htt function may contribute to HD pathogenesis. Huntington's disease (HD)1 is an autosomal dominant neurodegenerative disorder characterized by uncontrolled movements, motor impairment, and dementia (1). The disease is associated with selective neuronal cell death occurring mainly in the cerebral cortex and the striatum (2). The mutation causing HD is an expanded CAG repeat located within exon 1 of the IT-15 gene encoding huntingtin (htt), a 350-kDa protein of unknown function (3). The CAG repeat is translated into a polyglutamine (polyQ) sequence, and the disease appears when the critical length of ϳ37 glutamines is exceeded (4).It is generally assumed that the expanded polyQ stretch confers a toxic gain of function to the htt protein. However, the current data do not exclude the possibility that loss of wild-type htt function may also contribute to the disease phenotype in post-mitotic neurons. htt function is essential for neurogenesis (5) and also important for neuron survival in adult brains (6, 7). Strikingly, deletion of the gene encoding the htt mouse homologue hdh resulted in a progressive neurological phenotype (8). Therefore, it is intriguing to speculate that the toxic gain of function of mutant htt may cause a loss of the essential function of wild-type htt and thereby induce selective neurotoxicity (9). However, the molecular basis for such a disease mechanism remains unclear. A characteristic feature of mutant htt proteins with elongated polyQ sequences is that they spontaneously self-assemble into SDS-resistant protein aggregates with a fibrillar morphology in vitro and in vivo (10,11). This suggests that HD is due to a toxic gain of function that leads to the formation of abnormal protein aggregates in a nucleation-dependent process.Indeed, the formation of neuronal inclusions (NIs) in affected brain regions of patients is a characteristic feature of HD (11,12),...

S U M M A R YA surface-enhanced laser desorption/ionization time of flight (SELDI-TOF)-based ProteinChip System was used as a tool for rapid discovery and identification of protein patterns in serum that discriminate between trisomy 21 and unaffected pregnancies. We analyzed 24 serum samples from women carrying a trisomy 21 pregnancy and 32 with an unaffected pregnancy, ranging from 10.0 to 14.0 weeks of gestation. The resulting protein profiles were submitted to a clustering algorithm, a rule extraction, a rating, and a rule base construction step. For the generated combined rule base, the specificity and sensitivity for the prediction of a trisomy 21 pregnancy reach 97% and 91%, respectively.