The determination of infectious titers of samples containing virus particles is critical for clinical gene therapy applications. Currently available methods that determine the infectivity of viruses/viral vectors are time-consuming. In this study, we developed cell culture-based infection assays that rapidly detect wide ranges of DNA/RNA viruses/viral vectors. Viruses analyzed in this study included Adenovirus type 5, Adenovirus type 41, Vaccinia virus, Measles virus, Coxsackie virus B5, Respiratory Syncytial Virus, and Adenovirus-, Adeno-associated virus-, Retrovirus-, and Lentivirus-based vectors. Susceptible cells were infected for 3 h with samples containing infectious viruses/viral vectors. In developed assays, differences in Cq values (∆Cq) were measured between cells incubated with infectious virus for 3 h and the two controls, including 0 h and heat-inactivated controls. Controls were included to detect background signals. An infection assay with a ∆Cq greater than 3.3 was considered positive. The reproducible and repeatable infection assays were functioning based on virus entry into the cells. For all tested viruses/viral vectors, ∆Cq above 3.3 was detected between cells incubated with infectious virus for 3 h and at least one control, indicating the positive functioning of the assay. The 0 h and heat-inactivated controls that were crucial for the estimation of the background, were successfully applied to all viruses/viral vectors tested in this study. We have developed a rapid cell-culture-based assay for detection of infectious viruses. The assay could be applied to all tested viruses/viral vectors, and has the potential to become a valuable tool in clinical virology and infectious virus diagnostics.

The high commercial value and the increasing demand for caviar make it susceptible to illegal trade and fraudulent activities, while mislabelling can occur both deliberately and unintentionally. Therefore, reliable methods are urgently needed to distinguish even closely related sturgeon species for the authentication of declared species in caviar products. In this study, we explore the effectiveness of ONT sequencing combined with nanopore adaptive sampling (NAS) to recover mitochondrial genomes from genomic DNA extracted from two caviar samples. NAS yielded similar percentages of mitochondrial reads as sequencing experiments without using the NAS option. However, NAS substantially increased the percentage of bases that could be mapped against a mitochondrial reference genome, demonstrating its effectiveness in enriching ONT sequencing data for mitochondrial sequences. The percentage of mapped mitochondrial reads varied between two samples in our sequencing experiments, ranging between 2.37% and 10.46%, which is exceptionally high compared to previous studies focusing on the recovery of mitochondrial genomes from genomic DNA. This increase may be attributed to the extraction of genomic DNA from individual fish eggs. To determine the taxonomic identities of the two caviar samples, a phylogenetic analysis was performed that included all available acipenseriform mitochondrial genomes from GenBank, as well as the newly recovered mitochondrial genomes. During this process, four problematic mitochondrial genomes obtained from GenBank were identified, which were characterized by either suggestively low sequence quality, chimeric sequence information, or potential misidentification. This underscores the need for reviewing sequencing data before database submission to avoid negative impacts on research and DNA-based species authentication.

LebensmittelchemieVolume 77, Issue S1 p. S1-039-S1-039 Aritlce Screening auf Tropanalkaloid-bildende Pflanzen in Lebensmitteln mittels real-time PCR Melanie Pavlovic, Melanie Pavlovic Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, OberschleißheimSearch for more papers by this authorJulia Pauly, Julia Pauly Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, OberschleißheimSearch for more papers by this authorJennifer Mels, Jennifer Mels Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, ErlangenSearch for more papers by this authorUlrich Busch, Ulrich Busch Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, OberschleißheimSearch for more papers by this authorIngrid Huber, Ingrid Huber Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, OberschleißheimSearch for more papers by this author Melanie Pavlovic, Melanie Pavlovic Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, OberschleißheimSearch for more papers by this authorJulia Pauly, Julia Pauly Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, OberschleißheimSearch for more papers by this authorJennifer Mels, Jennifer Mels Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, ErlangenSearch for more papers by this authorUlrich Busch, Ulrich Busch Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, OberschleißheimSearch for more papers by this authorIngrid Huber, Ingrid Huber Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, OberschleißheimSearch for more papers by this author First published: 01 March 2023 https://doi.org/10.1002/lemi.202352029AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume77, IssueS1Supplement: Abstracts der Vorträge der Regionalverbände und die der Posterflashtalks der AG JLCMarch 2023Pages S1-039-S1-039 RelatedInformation

In Germany, genetically modified organisms (GMO) analysis of food samples collected within the official food control is performed by the laboratories of the Federal States. The present report shows GMO analysis results from food samples of the years 2017 to 2021, including contaminations by unauthorized GMO, as well as genetically modified (GM) plant events authorized in the European Union. In addition to previous publications, evaluation of the aggregated food samples analysed for GMO components is shown. During this timeframe, 1077 (7.1%) out of 15,145 samples contained genetic modification. In 43 samples, DNA sequences of unauthorized GM plants were found. Additionally, for food derived from soybean, evaluations according to different product categories and the agronomic production (conventional and organic farming) are shown. Whereas in products from organic farming and in conventional soybeans labelled "without genetic engineering" GM soybeans were detected in 6.1% and 8.9%, of all tested samples, respectively, nearly 30% of all conventional soy samples yielded positive results below 0.1%. However, only in 0.7% of the overall analysed 5424 soybean samples GMO percentages of more than 0.1% were obtained. Generally, authorized GM plants were only found at low contamination levels. The labelling threshold of 0.9% for GM ingredients was exceeded only in 0.2% (maize) and 0.1% (soybean) samples, respectively. For monitoring purposes and risk evaluation, the data collection shall be continued.

Background In recent years, whole genome sequencing (WGS) in combination with bioinformatic analyses has become state of the art in evaluating the pathogenicity/resistance potential and relatedness of bacteria. WGS analysis thus represents a central tool in the investigation of the resistance and virulence potential of pathogens, as well as their dissemination via outbreak clusters and transmission chains within the framework of molecular epidemiology. In order to gain an overview of the available genotypic and phenotypic methods used for pathogen typing of Salmonella and Shiga toxin-producing and enterohemorrhagic Escherichia coli (STEC/EHEC) in Germany at state and federal level, along with the availability of WGS-based typing and corresponding analytical methods, a survey of laboratories was conducted.Methods An electronic survey of laboratories working for public health protection and consumer health protection was conducted from February to June 2020.Results and conclusion The results of the survey showed that many of the participating laboratories provide a wide range of phenotypic and molecular methods. Molecular typing is most commonly used for species identification of Salmonella. In many cases, WGS-based methods have already been established at federal and state institutions or are in the process of being established. The Illumina sequencing technology is the most widely used technology. The survey confirms the importance of molecular biology and whole genome typing technologies for laboratories in the diagnosis of bacterial zoonotic pathogens.

LebensmittelchemieVolume 77, Issue S3 p. S3-031-S3-031 Vorträe „Zukunftslabor 2030“ - Analyse von Fleischverderb am aktuellen Beispiel von Hackfleisch C. Wimmer, C. Wimmer Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), OberschleißheimSearch for more papers by this authorN. Hanifi, N. Hanifi Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), OberschleißheimSearch for more papers by this authorK. Roth, K. Roth Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), OberschleißheimSearch for more papers by this authorM. Wenning, M. Wenning Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), OberschleißheimSearch for more papers by this authorM. Pavlovic, M. Pavlovic Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), OberschleißheimSearch for more papers by this authorN. Bretschneider, N. Bretschneider Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), OberschleißheimSearch for more papers by this authorI. Huber, I. Huber Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), OberschleißheimSearch for more papers by this authorU. Busch, U. Busch Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), OberschleißheimSearch for more papers by this author C. Wimmer, C. Wimmer Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), OberschleißheimSearch for more papers by this authorN. Hanifi, N. Hanifi Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), OberschleißheimSearch for more papers by this authorK. Roth, K. Roth Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), OberschleißheimSearch for more papers by this authorM. Wenning, M. Wenning Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), OberschleißheimSearch for more papers by this authorM. Pavlovic, M. Pavlovic Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), OberschleißheimSearch for more papers by this authorN. Bretschneider, N. Bretschneider Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), OberschleißheimSearch for more papers by this authorI. Huber, I. Huber Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), OberschleißheimSearch for more papers by this authorU. Busch, U. Busch Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), OberschleißheimSearch for more papers by this author First published: 01 August 2023 https://doi.org/10.1002/lemi.202359027AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onEmailFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume77, IssueS3Supplement: Abstracts der Vorträge, Posterflashtalks und Poster von den 51. Deutschen Lebensmittelchemietagen 2023August 2023Pages S3-031-S3-031 RelatedInformation

Campylobacter jejuni and Campylobacter coli are the predominant thermophilic species responsible for foodborne gastroenteritis worldwide. Elevated resistance to certain antibiotics was observed due to antimicrobial therapy in farm animals and humans, while reduced antimicrobial usage partially reduced antibiotic resistance. Monitoring the antimicrobial resistance demonstrated a substantial fraction of multi-resistant isolates, indicating the necessity of reliable tools for their detection. In this study, resistance determinants in 129 German and 21 Vietnamese isolates were selected to establish a novel multiplex real-time PCR (qPCR), facilitating the simultaneous detection of four resistance determinants. These comprised tet(O) gene variants associated with tetracycline resistance, point mutations GyrA_T86I and GyrA_T86V associated with ciprofloxacin resistance, and the erm(B) gene together with the point mutation A2075G in the 23S rRNA gene, associated with erythromycin resistance. Moreover, the performance of the qPCR assay was evaluated by comparing the results of qPCR to phenotypic antimicrobial resistance profiles, obtained with standardized EUCAMP3 microdilution panel, which showed 100% similarity (inclusivity and exclusivity). Variation in measurement methods, including qPCR machines and master mixes showed robustness, essential for laboratories. The assay can be used for the rapid detection of resistance determinants, and is beneficial for monitoring the spread of antibiotic resistance in C. jejuni and C. coli.

Murine leukemia virus (MLV) and murine stem cell virus (MSCV) and derived retroviral vectors are widely used to study retrovirus biology and as tools for gene delivery. The method described here represents a quantitative real time PCR (qPCR) with hydrolysis probe that can be applied within classical qPCR as well as in digital droplet PCR (ddPCR). The method targets a 60 bp long fragment located within the U5 region of the MLV/MSCV genome sequence. For the here described method a LOD95% of 25 copies per PCR reaction (DNA) and 80 copies per PCR reaction (RNA) was determined, and PCR efficiencies of 92.5 % and 98.5 %, respectively, were observed. This method enables the fast and simple titration of viral genomic RNA present in retroviral vector stocks for accurate and consistent transduction experiments. Furthermore, it enables the detection of proviral and transfer plasmid derived DNA sequences and can be modified to differentiate between retroviral RNA and DNA.

Zusammenfassung Hintergrund In den vergangenen Jahren hat sich die Gesamtgenomsequenzierung („whole genome sequencing“; WGS) in Kombination mit bioinformatischen Analysen zum Stand der Technik bei der Bewertung des Pathogenitäts- und Resistenzpotenzials sowie der Verwandtschaftsgrade zwischen Bakterien entwickelt. Die WGS-Analyse stellt somit ein zentrales Instrument bei der Typisierung von Erregern und der Untersuchung von Krankheits- und Ausbruchsclustern im Rahmen der molekularen Epidemiologie dar. Ziel der Studie war die Generierung eines Überblicks der in Deutschland auf Landes- und Bundesebene verfügbaren Erregertypisiermethoden von Salmonellen und Shiga-Toxin-bildenden bzw. enterohämorrhagischen Escherichia coli (STEC/EHEC) und den angewandten geno- und phänotypischen Methoden sowie über die Verfügbarkeit der genombasierten Typisierung und entsprechenden Analyseverfahren. Methoden Im Zeitraum vom Februar bis Juni 2020 wurde eine elektronische Umfrage bei Laboratorien durchgeführt, die für den öffentlichen Gesundheitsschutz und gesundheitlichen Verbraucherschutz tätig sind. Ergebnisse und Fazit Die Ergebnisse der Umfrage zeigten, dass viele der teilnehmenden Laboratorien über eine große Auswahl an phänotypischen und molekularbiologischen Methoden verfügen. Molekularbiologische Typisierungen werden am häufigsten für die Speziesidentifizierung von Salmonellen herangezogen. WGS-Verfahren sind vielfach schon bei Einrichtungen auf Bundes- und Landesebene etabliert oder befinden sich im Aufbau. Die Illumina-Sequenzierung ist dabei die am weitesten verbreitete Technologie. Die Umfrage bestätigt die Bedeutung von molekularbiologischen und genombasierten Typisierungstechnologien für die Laboratorien bei der Diagnostik von bakteriellen zoonotischen Erregern.

Mass Spectrometry imaging (MS imaging) provides spatial information for a wide range of compound classes in different sample matrices. We used MS imaging to investigate the distribution of components in fresh and processed food, including meat, dairy and bakery products. The MS imaging workflow was optimized to cater to the specific properties and challenges of the individual samples. We successfully detected highly nonpolar and polar constituents such as beta-carotene and anthocyanins, respectively. For the first time, the distributions of a contaminant and a food additive were visualized in processed food. We detected acrylamide in German gingerbread and investigated the penetration of the preservative natamycin into cheese. For this purpose, a new data analysis tool was developed to study the penetration of analytes from uneven surfaces. Our results show that MS imaging has great potential in food analysis to provide relevant information about components' distributions, particularly those underlying official regulations.

LebensmittelchemieVolume 76, Issue S1 p. S1-053-S1-053 Article Lebensmittelbetrug als Herausforderung der 21. Jahrhundert - aktuelle Aspekte und Analytik Ulrich Busch, Ulrich Busch Bayerisches Landesamt für Gesundheit und LebensmittelsicherheitSearch for more papers by this author Ulrich Busch, Ulrich Busch Bayerisches Landesamt für Gesundheit und LebensmittelsicherheitSearch for more papers by this author First published: 01 March 2022 https://doi.org/10.1002/lemi.202252007AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume76, IssueS1Supplement: Abstracts der Vorträge der Regionalverbände und die der Posterflashtalks der AG JLCMarch 2022Pages S1-053-S1-053 RelatedInformation

LebensmittelchemieVolume 76, Issue S2 p. S2-179-S2-179 Authentizität (AUT) Metabarcoding zur Überprüfung der Lebensmittelauthentizität und -sicherheit Larissa Murr, Larissa Murr Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, Veterinärstraße 2, D-85764 OberschleißheimSearch for more papers by this authorMelanie Pavlovic, Melanie Pavlovic Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, Veterinärstraße 2, D-85764 OberschleißheimSearch for more papers by this authorNancy Bretschneider, Nancy Bretschneider Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, Veterinärstraße 2, D-85764 OberschleißheimSearch for more papers by this authorMarzena Maggipinto, Marzena Maggipinto Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, Veterinärstraße 2, D-85764 OberschleißheimSearch for more papers by this authorLars Gerdes, Lars Gerdes Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, Veterinärstraße 2, D-85764 OberschleißheimSearch for more papers by this authorUlrich Busch, Ulrich Busch Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, Veterinärstraße 2, D-85764 OberschleißheimSearch for more papers by this authorIngrid Huber, Ingrid Huber Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, Veterinärstraße 2, D-85764 OberschleißheimSearch for more papers by this author Larissa Murr, Larissa Murr Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, Veterinärstraße 2, D-85764 OberschleißheimSearch for more papers by this authorMelanie Pavlovic, Melanie Pavlovic Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, Veterinärstraße 2, D-85764 OberschleißheimSearch for more papers by this authorNancy Bretschneider, Nancy Bretschneider Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, Veterinärstraße 2, D-85764 OberschleißheimSearch for more papers by this authorMarzena Maggipinto, Marzena Maggipinto Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, Veterinärstraße 2, D-85764 OberschleißheimSearch for more papers by this authorLars Gerdes, Lars Gerdes Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, Veterinärstraße 2, D-85764 OberschleißheimSearch for more papers by this authorUlrich Busch, Ulrich Busch Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, Veterinärstraße 2, D-85764 OberschleißheimSearch for more papers by this authorIngrid Huber, Ingrid Huber Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit, Veterinärstraße 2, D-85764 OberschleißheimSearch for more papers by this author First published: 01 September 2022 https://doi.org/10.1002/lemi.202259135AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinkedInRedditWechat No abstract is available for this article. Volume76, IssueS2September 2022Pages S2-179-S2-179 RelatedInformation

Interpretation of whole-genome sequencing (WGS) data for foodborne outbreak investigations is complex, as the genetic diversity within processing plants and transmission events need to be considered. In this study, we analyzed 92 food-associated Listeria monocytogenes isolates by WGS-based methods. We aimed to examine the genetic diversity within meat and fish production chains and to assess the applicability of suggested thresholds for clustering of potentially related isolates. Therefore, meat-associated isolates originating from the same samples or processing plants as well as fish-associated isolates were analyzed as distinct sets. In silico serogrouping, multilocus sequence typing (MLST), core genome MLST (cgMLST), and pangenome analysis were combined with screenings for prophages and genetic traits. Isolates of the same subtypes (cgMLST types (CTs) or MLST sequence types (STs)) were additionally compared by SNP calling. This revealed the occurrence of more than one CT within all three investigated plants and within two samples. Analysis of the fish set resulted in predominant assignment of isolates from pangasius catfish and salmon to ST2 and ST121, respectively, potentially indicating persistence within the respective production chains. The approach not only allowed the detection of distinct subtypes but also the determination of differences between closely related isolates, which need to be considered when interpreting WGS data for surveillance.

The EU commission established Regulation (2017/1495) in 2017 to reduce Campylobacter on chicken skin and to decrease the number of human cases of campylobacteriosis attributable to the consumption of poultry meat. A Process Hygiene Criterion based on colony-forming unit data was set to a maximum of 1000 CFU Campylobacter spp. per gram chicken neck skin at slaughterhouses. Confronted with stressors, including cold, oxidative stress or antibiotic treatment, live cells may enter into a viable but non-cultivable state (VBNC) and lose the ability to grow, in reference to the plate count ISO 10272-2:2017 method, but still possess the potential to recover and cause infections under favorable conditions. In this study, a droplet digital PCR combined with the intercalating dye propidium monoazide (PMA) was established for quantification of C. coli and C. jejuni in chicken meat rinses. The PMA was used to inactivate DNA from dead cells in this technique. This method was successfully validated against the reference method according to ISO 16140-2:2016 for accuracy and relative trueness. Additionally, it presented a 100% selectivity for Campylobacter jejuni and C. coli. Moreover, the technical measurement uncertainty was determined according to ISO 19036:2019, and the applicability of ddPCR for quantifying C. coli and C. jejuni in chicken meat rinses was investigated on naturally contaminated samples from slaughterhouses and supermarkets. Results obtained from this study demonstrated a strong correlation to qPCR as well as the classical microbiological reference method.

Previous studies reported on the broad-spectrum antiviral function of heparin. Here we investigated the antiviral function of magnesium-modified heparin and found that modified heparin displayed a significantly enhanced antiviral function against human adenovirus (HAdV) in immortalized and primary cells. Nuclear magnetic resonance analyses revealed a conformational change of heparin when complexed with magnesium. To broadly explore this discovery, we tested the antiviral function of modified heparin against herpes simplex virus type 1 (HSV-1) and found that the replication of HSV-1 was even further decreased compared to aciclovir. Moreover, we investigated the antiviral effect against the new severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) and measured a 55-fold decreased viral load in the supernatant of infected cells associated with a 38-fold decrease in virus growth. The advantage of our modified heparin is an increased antiviral effect compared to regular heparin.

Despite extensive monitoring programs and preventative measures, Salmonella spp. continue to cause tens of thousands human infections per year, as well as many regional and international food-borne outbreaks, that are of great importance for public health and cause significant socio-economic costs. In Germany, salmonellosis is the second most common cause of bacterial diarrhea in humans and is associated with high hospitalization rates. Whole-genome sequencing (WGS) combined with data analysis is a high throughput technology with an unprecedented discriminatory power, which is particularly well suited for targeted pathogen monitoring, rapid cluster detection and assignment of possible infection sources. However, an effective implementation of WGS methods for large-scale microbial pathogen detection and surveillance has been hampered by the lack of standardized methods, uniform quality criteria and strategies for data sharing, all of which are essential for a successful interpretation of sequencing data from different sources. To overcome these challenges, the national GenoSalmSurv project aims to establish a working model for an integrated genome-based surveillance system of Salmonella spp. in Germany, based on a decentralized data analysis. Backbone of the model is the harmonization of laboratory procedures and sequencing protocols, the implementation of open-source bioinformatics tools for data analysis at each institution and the establishment of routine practices for cross-sectoral data sharing for a uniform result interpretation. With this model, we present a working solution for cross-sector interpretation of sequencing data from different sources (such as human, veterinarian, food, feed and environmental) and outline how a decentralized data analysis can contribute to a uniform cluster detection and facilitate outbreak investigations.

The following chapter deals with applicability of MALDI-TOF MS protein profiling beyond microbiological issues for the authentication of food, such as seafood, meat, edible mushroom and insect. The non-targeted nature of MALDI-TOF MS profiling makes it a promising method in alternative to molecular biological methods for validating the biological authenticity of certain food components. The analytical requirements of the method for the food matrix, food processing and reference databases are addressed along with the various methods of sample preparation. In addition, current application trends in food microbiology are also described.

The adulteration of fresh turkey meat by the undeclared addition of protein hydrolysates is of interest for fraudsters due to the increase of the economic gain by substituting meat with low cost ingredients. The aim of this study was to compare the suitability of three different analytical techniques such as GC-MS and 1H-NMR with HPLC-UV/VIS as a targeted method, for the detection of with protein hydrolysates adulterated turkey meat. For this, turkey breast muscles were treated with different plant- (e.g., wheat) and animal-based (e.g., gelatin, casein) protein hydrolysates with different hydrolyzation degrees (15–53%: partial; 100%: total), which were produced by enzymatic and acidic hydrolysis. A water- and a nontreated sample (REF) served as controls. The data analyses revealed that the hydrolysate-treated samples had significantly higher levels of amino acids (e.g., leucine, phenylalanine, lysine) compared with REF observed with all three techniques concordantly. Furthermore, the nontargeted metabolic profiling (GC-MS and NMR) showed that sugars (glucose, maltose) and/or by-products (build and released during acidic hydrolyses, e.g., levulinic acid) could be used for the differentiation between control and hydrolysates (type, degrees). The combination of amino acid profiling and additional compounds gives stronger evidence for the detection and classification of adulteration in turkey breast meat.

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.