Background Fast, reliable and easy to handle methods are required to facilitate urgently needed point-of-care testing (POCT) in the current coronavirus pandemic. Life-threatening severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread all over the world, infecting more than 33,500,000 people and killing over 1 million of them as of October 2020. Infected individuals without any symptoms might still transfer the virus to others underlining the extraordinary transmissibility of this new coronavirus. In order to identify early infections effectively, treat patients on time and control disease spreading, rapid, accurate and onsite testing methods are urgently required. Results Here we report the development of a loop-mediated isothermal amplification (LAMP) based method to detect SARS-CoV-2 genes ORF8 and N directly from pharyngeal swab samples. The established reverse transcription LAMP (RT-LAMP) assay detects SARS-CoV-2 directly from pharyngeal swab samples without previous time-consuming and laborious RNA extraction. The assay is sensitive and highly specific for SARS-CoV-2 detection, showing no cross reactivity when tested on 20 other respiratory pathogens. The assay is 12 times faster and 10 times cheaper than routine reverse transcription real-time polymerase chain reaction, depending on the assay used. Conclusion The fast and easy to handle RT-LAMP assay amplifying specifically the genomic regions ORF8 and N of SARS-CoV-2 is ideally suited for POCT at e.g. railway stations, airports or hospitals. Given the current pandemic situation, rapid, cost efficient and onsite methods like the here presented RT-LAMP assay are urgently needed to contain the viral spread.

Sourdough has played a significant role in human nutrition and culture for thousands of years and is still of eminent importance for human diet and the bakery industry. Lactobacillus sanfranciscensis is the predominant key bacterium in traditionally fermented sourdoughs.The genome of L. sanfranciscensis TMW 1.1304 isolated from an industrial sourdough fermentation was sequenced with a combined Sanger/454-pyrosequencing approach followed by gap closing by walking on fosmids. The sequencing data revealed a circular chromosomal sequence of 1,298,316 bp and two additional plasmids, pLS1 and pLS2, with sizes of 58,739 bp and 18,715 bp, which are predicted to encode 1,437, 63 and 19 orfs, respectively. The overall GC content of the chromosome is 34.71%. Several specific features appear to contribute to the ability of L. sanfranciscensis to outcompete other bacteria in the fermentation. L. sanfranciscensis contains the smallest genome within the lactobacilli and the highest density of ribosomal RNA operons per Mbp genome among all known genomes of free-living bacteria, which is important for the rapid growth characteristics of the organism. A high frequency of gene inactivation and elimination indicates a process of reductive evolution. The biosynthetic capacity for amino acids scarcely availably in cereals and exopolysaccharides reveal the molecular basis for an autochtonous sourdough organism with potential for further exploitation in functional foods. The presence of two CRISPR/cas loci versus a high number of transposable elements suggests recalcitrance to gene intrusion and high intrinsic genome plasticity.

Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has recently emerged as a powerful tool for the routine identification of clinical isolates. MALDI-TOF MS based identification of bacteria has been shown to be more rapid, accurate and cost-efficient than conventional phenotypic techniques or molecular methods. Rapid and reliable identification of food-associated bacteria is also of crucial importance for food processing and product quality. This review is concerned with the applicability of MALDI-TOF MS for routine identification of foodborne bacteria taking the specific requirements of food microbiological laboratories and the food industry into account. The current state of knowledge including recent findings and new approaches are discussed.

The effect was investigated of sucrose concentration on sucrose metabolism and on the formation of exopolysaccharide (EPS) by Lactobacillus sanfranciscensis LTH2590 in pH-controlled fermentations with sucrose concentrations ranging from 20 to 160 g liter ؊1 . The EPS production increased and the relative sucrose hydrolysis activity decreased by increasing the sucrose concentration in the medium. The carbon recovery decreased from 95% at a sucrose concentration of 30 g liter ؊1 to 58% at a sucrose concentration of 160 g liter ؊1 because of the production of an unknown metabolite by L. sanfranciscensis. This metabolite was characterized as a fructo-oligosaccharide. The oligosaccharide produced by L. sanfranciscensis was purified and characterized as a trisaccharide with a glucose/fructose ratio of 1:2. The comparison of the retention time of this oligosaccharide and that of pure oligosaccharide standards using two different chromatography methods revealed that the oligosaccharide produced by L. sanfranciscensis LTH2590 is 1-kestose. Kestose production increased concomitantly with the initial sucrose concentration in the medium.Polysaccharides of plant origin have being used for a long time in the food industry as biothickeners, texture stabilizers, or gelling agents. In the last decades several microbial exopolysaccharides (EPS) have been described as alternatives for plant polysaccharides. Microbial polysaccharides have rheological properties that match the industrial demands and can be produced in large amounts and at high purities. The interest of the food industry in developing multifunctional additives that not only provide the desired improvement of the texture but also have additional nutritional properties led to extensive search for polysaccharides with prebiotic attributes. Prebiotics are nondigestible food ingredients that affect the host beneficially by selectively stimulating the growth and/or activity of specific bacteria in the colon and thus improve host health (12). Fructo-oligosaccharides (FOS), xylo-oligosaccharide, and inulin are some of the prebiotics available for human consumption (5, 24). FOS with prebiotic properties (e.g., kestose and nystose) are polymers of D-fructose joined by ␤(231) linkages and terminated with a D-glucose molecule linked to fructose by an ␣(132) bond as in sucrose (22). The degree of polymerization can vary from 2 to 35. FOS with a degree of polymerization of 3 to 5 are called neosugars (30) and can be enzymatically synthesized from sucrose by using fructosyltransferase from Aspergillus niger (16,17). Mckellar and Modler (23) showed that the maximum activity of ␤-fructosidase, responsible for the hydrolysis of inulin-type polysaccharides by bifidobacteria, was observed with neosugars.Lactic acid bacteria (LAB) are widely used for the production of numerous fermented foods and are generally recognized as safe. Several EPS-producing LAB such as Lactobacillus delbrueckii subsp. bulgaricus, Lactococcus lactis, and Streptococcus thermophilus have been isolated from ferme...

Aims:  The aim of this study was to develop a real‐time PCR test for differentiation between Shigella spp. and E. coli, in particular enteroinvasive Escherichia coli (EIEC). Methods and Results:  A duplex real‐time PCR specific for the genes encoding for β‐glucuronidase (uidA) and lactose permease (lacY) was developed. Ninety‐six isolates including 11 EIEC isolates of different serotypes and at least three representatives of each Shigella species were used for selectivity testing. All isolates tested were positive for the uidA gene. Additionally, all E. coli isolates were positive for the lacY gene, whereas no Shigella isolate tested harboured lacY. Conclusions:  The duplex real‐time PCR assay was found to be simple, rapid, reliable and specific. Significance and Impact of the Study:  If possible at all, delineation of so‐called inactive EIEC from Shigella spp. is cumbersome. Biochemical and serological methods are limited to specific pheno‐ and serotypes. This assay clearly simplifies the differentiation of both.