1
|
Zarske M, Luu HQ, Deneke C, Knüver MT, Thieck M, Hoang HTT, Bretschneider N, Pham NT, Huber I, Stingl K. Identification of knowledge gaps in whole-genome sequence analysis of multi-resistant thermotolerant Campylobacter spp. BMC Genomics 2024; 25:156. [PMID: 38331708 PMCID: PMC10851486 DOI: 10.1186/s12864-024-10014-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 01/14/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Campylobacter spp. is the most frequent cause of bacterial food-borne gastroenteritis and a high priority antibiotic resistant bacterium according to the World Health Organization (WHO). European monitoring of thermotolerant Campylobacter spp. does not reflect the global burden of resistances already circulating within the bacterial population worldwide. METHODS We systematically compared whole genome sequencing with comprehensive phenotypic antimicrobial susceptibility, analyzing 494 thermotolerant Campylobacter poultry isolates from Vietnam and Germany. Any discrepancy was checked by repeating the wet lab and improving the dry lab part. Selected isolates were additionally analyzed via long-read Oxford Nanopore technology, leading to closed chromosomes and plasmids. RESULTS Overall, 22 different resistance genes and gene variants (e. g. erm(B), aph(3')-IIIa, aph(2'')-If, catA, lnu(C), blaOXA, sat4) and point mutations in three distinct genes (gyrA, 23S rRNA, rpsL) associated with AMR were present in the Campylobacter isolates. Two AMR genes were missing in the database and one falsely associated with resistance. Bioinformatic analysis based on short-read data partly failed to identify tet(O) and aadE, when the genes were present as duplicate or homologous gene variants. Intriguingly, isolates also contained different determinants, redundantly conferring resistance to chloramphenicol, gentamicin, kanamycin, lincomycin and streptomycin. We found a novel tet(W) in tetracycline sensitive strains, harboring point mutations. Furthermore, analysis based on assemblies from short-read data was impaired to identify full length phase variable aad9, due to variations of the poly-C tract within the gene. The genetic determinant responsible for gentamicin resistance of one isolate from Germany could not be identified. GyrT86I, presenting the main determinant for (fluoro-)quinolone resistance led to a rare atypical phenotype of ciprofloxacin resistance but nalidixic acid sensitivity. Long-read sequencing predicted AMR genes were mainly located on the chromosome, and rarely on plasmids. Predictions from long- and short-read sequencing, respectively, often differed. AMR genes were often organized in multidrug resistance islands (MDRI) and partially located in proximity to transposase genes, suggesting main mobilization of resistance determinants is via natural transformation and transposition in Campylobacter. CONCLUSIONS The results of this study suggest that there is frequent resistance gene duplication, mosaicism, and mutation leading to gene variation and truncation in Campylobacter strains that have not been reported in previous studies and are missing from databases. Furthermore, there is a need for deciphering yet unknown resistance mechanisms and resistance spread in thermotolerant Campylobacter spp. that may pose a challenge to global food safety.
Collapse
Affiliation(s)
- Michael Zarske
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, Berlin, D-12277, Germany
| | - Huong Quynh Luu
- National Institute of Veterinary Research (NIVR), 86 Truong Chinh Street, Hanoi, Dong Da District, Vietnam
| | - Carlus Deneke
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, Berlin, D-12277, Germany
| | - Marie-Theres Knüver
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, Berlin, D-12277, Germany
| | - Maja Thieck
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, Berlin, D-12277, Germany
| | - Ha Thi Thu Hoang
- Department of Bacteriology, National Institute of Hygiene and Epidemiology (NIHE), 1 Yersin Street, Hanoi, Trung District, Vietnam
| | - Nancy Bretschneider
- Department of Molecular Biology and Gene Technology, Bavarian Health and Food Safety Authority, Oberschleissheim, D-85764, Germany
| | - Ngoc Thi Pham
- National Institute of Veterinary Research (NIVR), 86 Truong Chinh Street, Hanoi, Dong Da District, Vietnam
| | - Ingrid Huber
- Department of Molecular Biology and Gene Technology, Bavarian Health and Food Safety Authority, Oberschleissheim, D-85764, Germany
| | - Kerstin Stingl
- Department of Biological Safety, Federal Institute for Risk Assessment (BfR), Diedersdorfer Weg 1, Berlin, D-12277, Germany.
| |
Collapse
|
2
|
Zeller-Péronnet V, Bretschneider N, Lausch J, Hanifi N, Pavlovic M, Zarske M, Luu HQ, Busch U, Stingl K, Huber I. Multiplex Real-Time PCR for the Detection of Tetracycline, Ciprofloxacin, and Erythromycin Resistance Determinants from Human and Foodborne Campylobacter jejuni and Campylobacter coli. Microorganisms 2023; 11:2927. [PMID: 38138071 PMCID: PMC10745765 DOI: 10.3390/microorganisms11122927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 12/24/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- Véronique Zeller-Péronnet
- Department for Food and Food Hygiene, Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany; (V.Z.-P.); (N.B.); (N.H.); (M.P.); (U.B.)
| | - Nancy Bretschneider
- Department for Food and Food Hygiene, Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany; (V.Z.-P.); (N.B.); (N.H.); (M.P.); (U.B.)
| | - Johanna Lausch
- Department for Food and Food Hygiene, Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany; (V.Z.-P.); (N.B.); (N.H.); (M.P.); (U.B.)
| | - Nadera Hanifi
- Department for Food and Food Hygiene, Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany; (V.Z.-P.); (N.B.); (N.H.); (M.P.); (U.B.)
| | - Melanie Pavlovic
- Department for Food and Food Hygiene, Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany; (V.Z.-P.); (N.B.); (N.H.); (M.P.); (U.B.)
| | - Michael Zarske
- National Reference Laboratory for Campylobacter, Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), 10589 Berlin, Germany; (M.Z.); (K.S.)
| | - Huong Quynh Luu
- National Institute of Veterinary Research (NIVR), Hanoi 100000, Vietnam;
| | - Ulrich Busch
- Department for Food and Food Hygiene, Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany; (V.Z.-P.); (N.B.); (N.H.); (M.P.); (U.B.)
| | - Kerstin Stingl
- National Reference Laboratory for Campylobacter, Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), 10589 Berlin, Germany; (M.Z.); (K.S.)
| | - Ingrid Huber
- Department for Food and Food Hygiene, Bavarian Health and Food Safety Authority (LGL), 85764 Oberschleissheim, Germany; (V.Z.-P.); (N.B.); (N.H.); (M.P.); (U.B.)
| |
Collapse
|
3
|
Stingl K, Heise J, Thieck M, Wulsten IF, Pacholewicz E, Iwobi AN, Govindaswamy J, Zeller-Péronnet V, Scheuring S, Luu HQ, Fridriksdottir V, Gölz G, Priller F, Gruntar I, Jorgensen F, Koene M, Kovac J, Lick S, Répérant E, Rohlfing A, Zawilak-Pawlik A, Rossow M, Schlierf A, Frost K, Simon K, Uhlig S, Huber I. Challenging the "gold standard" of colony-forming units - Validation of a multiplex real-time PCR for quantification of viable Campylobacter spp. in meat rinses. Int J Food Microbiol 2021; 359:109417. [PMID: 34624596 DOI: 10.1016/j.ijfoodmicro.2021.109417] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 08/01/2021] [Accepted: 09/18/2021] [Indexed: 11/26/2022]
Abstract
Campylobacter jejuni is the leading bacterial food-borne pathogen in Europe. Despite the accepted limits of cultural detection of the fastidious bacterium, the "gold standard" in food microbiology is still the determination of colony-forming units (CFU). As an alternative, a live/dead differentiating qPCR has been established, using propidium monoazide (PMA) as DNA-intercalating crosslink agent for inactivating DNA from dead, membrane-compromised cells. The PMA treatment was combined with the addition of an internal sample process control (ISPC), i.e. a known number of dead C. sputorum cells to the samples. The ISPC enables i), monitoring the effective reduction of dead cell signal by the light-activated DNA-intercalating dye PMA, and ii), compensation for potential DNA losses during processing. Here, we optimized the method for routine application and performed a full validation of the method according to ISO 16140-2:2016(E) for the quantification of live thermophilic Campylobacter spp. in meat rinses against the classical enumeration method ISO 10272-2:2017. In order to render the method applicable and cost-effective for practical application, the ISPC was lyophilized to be distributable to routine laboratories. In addition, a triplex qPCR was established to simultaneously quantify thermophilic Campylobacter, the ISPC and an internal amplification control (IAC). Its performance was statistically similar to the two duplex qPCRs up to a contamination level of 4.7 log10Campylobacter per ml of meat rinse. The limit of quantification (LOQ) of the alternative method was around 20 genomic equivalents per PCR reaction, i.e. 2.3 log10 live Campylobacter per ml of sample. The alternative method passed a relative trueness study, confirming the robustness against different meat rinses, and displayed sufficient accuracy within the limits set in ISO 16140-2:2016(E). Finally, the method was validated in an interlaboratory ring trial, confirming that the alternative method was fit for purpose with a tendency of improved repeatability and reproducibility compared to the reference method for CFU determination. Campylobacter served as a model organism, challenging CFU as "gold standard" and could help in guidance to the general acceptance of live/dead differentiating qPCR methods for the detection of food-borne pathogens.
Collapse
Affiliation(s)
- Kerstin Stingl
- German Federal Institute for Risk Assessment (BfR), Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany.
| | - Janine Heise
- German Federal Institute for Risk Assessment (BfR), Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Maja Thieck
- German Federal Institute for Risk Assessment (BfR), Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Imke F Wulsten
- German Federal Institute for Risk Assessment (BfR), Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Ewa Pacholewicz
- German Federal Institute for Risk Assessment (BfR), Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany; Wageningen Bioveterinary Research, Lelystad, the Netherlands
| | - Azuka N Iwobi
- Bavarian Health and Food Safety Authority (LGL), Oberschleissheim, Germany
| | | | | | - Sandra Scheuring
- Bavarian Health and Food Safety Authority (LGL), Oberschleissheim, Germany
| | - Huong Quynh Luu
- National Institute of Veterinary Research (NIVR), Hanoi, Viet Nam
| | | | - Greta Gölz
- Freie Universitaet Berlin, Institute of Food Safety and Food Hygiene, Berlin, Germany
| | | | - Igor Gruntar
- University of Ljubljana, Institute of Microbiology and Parasitology, Ljubljana, Slovenia
| | - Frieda Jorgensen
- Public Health England, Food, Water and Environmental Laboratory - Porton, Salisbury, United Kingdom
| | - Miriam Koene
- Wageningen Bioveterinary Research, Lelystad, the Netherlands
| | - Jasna Kovac
- The Pennsylvania State University, Department of Food Science, State College, PA, United States
| | - Sonja Lick
- Max Rubner-Institute (MRI), Department of Safety and Quality of Meat, Kulmbach, Germany
| | | | - Annika Rohlfing
- Impetus GmbH & Co. Bioscience KG, Microbiology, Bremerhaven, Germany
| | - Anna Zawilak-Pawlik
- Hirszfeld Institute of Immunology and Experimental Therapy, PAS, Microbiology Department, Wroclaw, Poland
| | - Marko Rossow
- State Office for Consumer Protection Saxony-Anhalt, Department of Food Safety, Halle (Saale), Germany
| | | | | | | | | | - Ingrid Huber
- Bavarian Health and Food Safety Authority (LGL), Oberschleissheim, Germany
| |
Collapse
|
4
|
Maizels L, Heller E, Landesberg M, Huber I, Arbel G, Gepstein A, Gepstein L, Maor E. Study and modulation of cardiac electroporation with a novel model utilizing human induced pluripotent stem cells. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.3215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Cardiac electroporation is a promising novel non-thermal ablation method, gaining significant interest with recent first-in-man data suggesting effective cardiac lesion generation with no collateral damage. Nevertheless, significant knowledge gaps exist regarding its electrophysiological consequences in cardiomyocytes, including; cell specificity, protocol optimization, irreversibility threshold, recovery time-constants, and the mechanistic nature of its cytolytic and anti-arrhythmic properties.
Purpose
Establishing an innovative in-vitro model for the study of cardiac electroporation-ablation, utilizing human induced pluripotent stem cells (hiPSCs).
Methods and results
Healthy-control hiPSC-derived cardiomyocytes were enzymatically dissociated and seeded as circular cell sheets (hiPSC-CCSs). Electroporation-ablation experiments were performed using a custom designed high-frequency electroporation (HF-EP) generator. Two needle-shaped electrodes were used for HF-EP delivery (Figure 1). Subsequently, detailed voltage- and Ca2+-mapping studies of the hiPSC-CCSs were conducted (Figure 2). HF-EP application resulted in the generation of electrically isolated lesions within the hiPSC-CCSs (Figure 3). Further characterization of the temporal changes and electrophysiological properties following electroporation revealed that; (1) lesions persisted over prolonged periods of time (days), indicating irreversible electroporation, (2) a temporal decrease in lesion dimensions was noted, consistent with a significant reversible electroporation component (Figures 3–5), (3) most tissue recovery had occurred within the first 15 minutes following electroporation, with little recovery beyond that time-frame, (4) increasing pulse-number augmented lesion area as well as the proportion of irreversible damage, and (5) electroporation sensitization was achieved by increasing extracellular Ca2+, indicating its crucial role in electroporation cytolysis, potentially via direct cellular toxicity and apoptosis facilitation (Figures 5–6). Finally, evaluating for HF-EP anti-arrhythmic properties, we targeted multiple rotors or focal triggered-activity generated in the hiPSC-CCSs. HF-EP application generated sustained line-blocks, isolating arrhythmogenic substrates within the hiPSC-CCSs while blocking the propagation of arrhythmic wavefronts (Figure 7).
Conclusion
Our results demonstrate the ability to study cardiac electroporation utilizing hiPSC-derived cardiomyocytes, provide novel insights into its temporal and electrophysiological characteristics, facilitate electroporation protocol optimization, screen for potential electroporation sensitizers, and to study its mechanistic nature and anti-arrhythmic properties.
Funding Acknowledgement
Type of funding sources: Public Institution(s). Main funding source(s): Division of Cardiology, and Tamman Cardiovascular Research Institute, Leviev Heart Center, Sheba Medical Center - Tel Hashomer, Ramat-Gan, Israel Figures 1–4Figures 5–7
Collapse
Affiliation(s)
- L Maizels
- Sheba Medical Center, Division of Cardiology, and Tamman Cardiovascular Research Institute, Leviev Heart Center, Ramat Gan, Israel
| | - E Heller
- Sheba Medical Center, Division of Cardiology, and Tamman Cardiovascular Research Institute, Leviev Heart Center, Ramat Gan, Israel
| | - M Landesberg
- Technion - Israel Institute of Technology, Laboratory for Cardiac Electrophysiology and Regenerative Medicine, Rappaport Faculty of Medicine, Haifa, Israel
| | - I Huber
- Technion - Israel Institute of Technology, Laboratory for Cardiac Electrophysiology and Regenerative Medicine, Rappaport Faculty of Medicine, Haifa, Israel
| | - G Arbel
- Technion - Israel Institute of Technology, Laboratory for Cardiac Electrophysiology and Regenerative Medicine, Rappaport Faculty of Medicine, Haifa, Israel
| | - A Gepstein
- Technion - Israel Institute of Technology, Laboratory for Cardiac Electrophysiology and Regenerative Medicine, Rappaport Faculty of Medicine, Haifa, Israel
| | - L Gepstein
- Technion - Israel Institute of Technology, Laboratory for Cardiac Electrophysiology and Regenerative Medicine, Rappaport Faculty of Medicine, Haifa, Israel
| | - E Maor
- Sheba Medical Center, Division of Cardiology, and Tamman Cardiovascular Research Institute, Leviev Heart Center, Ramat Gan, Israel
| |
Collapse
|
5
|
Ghiringhelli M, Gruber A, Abboud Y, Shiti A, Ballan N, Huber I, Arbel G, Gepstein L. Light-controllable recellularized ventricular and atrial tissues. Eur Heart J 2021. [DOI: 10.1093/eurheartj/ehab724.3235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Introduction
Construction of three-dimensional ventricular and atrial patches using decellularized extracellular matrix could allow the creation of “organ-like” structures for disease modeling, drug testing and regenerative medicine applications. To engineer functional artificial anatomical hearts several obstacles need to be overcome including generation of chamber-specific cells, prevention of immune reaction and donor/host tissue electrical coupling.
Purpose
In order to tackle these challenges we aimed to combine human induced pluripotent stem cell (hiPSC) technology, developmental biology inspired differentiation system to generate chamber-specific cardiomyocytes, decellularization/recellularization processes, and optogenetics utilizing light-sensitive ion channels to generate light-controllable atrial/ventricular tissue engineered patches.
Material and method
Atrial and ventricular patches of adult rats were decellularized using 1% SDS, 3% triton-X. The decellularized scaffolds were then recellularized with hiPSC- derived cardiomyocytes (2x107 atrial or ventricular cells). Adenoviral transduction was used to express the light-sensitive cationic channel ChR2 in the tissue engineered constructs.
Results and discussion
Eight days after cell seeding, we observed the development of spontaneous contraction of the atrial/ventricular tissues. Immunostaining for atrial (Cx40) or ventricular (MLC-2V) markers, gene expression, action-potential morphology, and the response to chamber-specific pharmacology confirmed the atrial/ventricular specific identity of the patches. Histological examination confirmed the preservation of the macro/micro- atrial/ventricular anatomical features in the generated chamber-specific recellularized patches. Optical mapping, using an EM-CCD camera, was used to characterize the conduction and repolarization properties of the generated tissues. The engineered patches could be paced and their electrical activity controlled by either electrical or optogenetic stimulation. Finally, arrhythmogenic reentrant arrhythmias could be induced in the tissue models and terminated by using optogenetic stimulation (“optogenetic-defibrillation”).
Conclusions
Three-dimensional light-sensitive chamber-specific engineered heart patches could be generated that could be controlled and manipulated through electrical and light pacing. These tissue could be used for several pathophysiological, drug testing, disease modeling and regenerative medicine applications.
Funding Acknowledgement
Type of funding sources: Public grant(s) – EU funding. Main funding source(s): H2020-ERC-COG
Collapse
Affiliation(s)
- M Ghiringhelli
- Technion - Israel Institute of Technology, Physiology, Haifa, Israel
| | - A Gruber
- Technion - Israel Institute of Technology, Physiology, Haifa, Israel
| | - Y Abboud
- Technion - Israel Institute of Technology, Physiology, Haifa, Israel
| | - A Shiti
- Technion - Israel Institute of Technology, Physiology, Haifa, Israel
| | - N Ballan
- Technion - Israel Institute of Technology, Physiology, Haifa, Israel
| | - I Huber
- Technion - Israel Institute of Technology, Physiology, Haifa, Israel
| | - G Arbel
- Technion - Israel Institute of Technology, Physiology, Haifa, Israel
| | - L Gepstein
- Rambam Health Care Campus, Cardiology, Haifa, Israel
| |
Collapse
|
6
|
Derz W, Pavlovic M, Huber I, Schalch B, Gerdes L. Food fraud in the Alps? — Detection of chamois (Rupicapra rupicapra) in firm raw sausages, ham, and meat via qualitative duplex real-time PCR. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107764] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
7
|
Uelze L, Becker N, Borowiak M, Busch U, Dangel A, Deneke C, Fischer J, Flieger A, Hepner S, Huber I, Methner U, Linde J, Pietsch M, Simon S, Sing A, Tausch SH, Szabo I, Malorny B. Toward an Integrated Genome-Based Surveillance of Salmonella enterica in Germany. Front Microbiol 2021; 12:626941. [PMID: 33643254 PMCID: PMC7902525 DOI: 10.3389/fmicb.2021.626941] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 01/21/2021] [Indexed: 02/03/2023] Open
Abstract
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.
Collapse
Affiliation(s)
- Laura Uelze
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Natalie Becker
- Department of Food, Feed and Commodities, Federal Office of Consumer Protection and Food Safety, Berlin, Germany
| | - Maria Borowiak
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Ulrich Busch
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Alexandra Dangel
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Carlus Deneke
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Jennie Fischer
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Antje Flieger
- Unit of Enteropathogenic Bacteria and Legionella (FG11) – National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Sabrina Hepner
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Ingrid Huber
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Ulrich Methner
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Jörg Linde
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Jena, Germany
| | - Michael Pietsch
- Unit of Enteropathogenic Bacteria and Legionella (FG11) – National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Sandra Simon
- Unit of Enteropathogenic Bacteria and Legionella (FG11) – National Reference Centre for Salmonella and Other Bacterial Enteric Pathogens, Robert Koch Institute, Wernigerode, Germany
| | - Andreas Sing
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Simon H. Tausch
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Istvan Szabo
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Burkhard Malorny
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| |
Collapse
|
8
|
Eberle U, Wimmer C, Huber I, Neubauer-Juric A, Valenza G, Ackermann N, Sing A. Comparison of nine different commercially available molecular assays for detection of SARS-CoV-2 RNA. Eur J Clin Microbiol Infect Dis 2021; 40:1303-1308. [PMID: 33512617 PMCID: PMC7845288 DOI: 10.1007/s10096-021-04159-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 12/17/2020] [Indexed: 12/01/2022]
Abstract
To face the COVID-19 pandemic, the need for fast and reliable diagnostic assays for the detection of SARS-CoV-2 is immense. We describe our laboratory experiences evaluating nine commercially available real-time RT-PCR assays. We found that assays differed considerably in performance and validation before routine use is mandatory.
Collapse
Affiliation(s)
- Ute Eberle
- Unit of Virology, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Clara Wimmer
- Public Health Microbiology Unit, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Ingrid Huber
- Molecular Biology Unit, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Antonie Neubauer-Juric
- Unit of Veterinary Virology, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Giuseppe Valenza
- Unit of Hospital Hygiene, Bavarian Health and Food Safety Authority, Erlangen, Germany
| | - Nikolaus Ackermann
- Unit of Virology, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Andreas Sing
- Public Health Microbiology Unit, Bavarian Health and Food Safety Authority, Oberschleißheim, Germany.
- Ludwig Maximilians-Universität München, Munich, Germany.
| |
Collapse
|
9
|
Mulder PA, van Balkom IDC, Landlust AM, Priolo M, Menke LA, Acero IH, Alkuraya FS, Arias P, Bernardini L, Bijlsma EK, Cole T, Coubes C, Dapia I, Davies S, Di Donato N, Elcioglu NH, Fahrner JA, Foster A, González NG, Huber I, Iascone M, Kaiser AS, Kamath A, Kooblall K, Lapunzina P, Liebelt J, Lynch SA, Maas SM, Mammì C, Mathijssen IB, McKee S, Mirzaa GM, Montgomery T, Neubauer D, Neumann TE, Pintomalli L, Pisanti MA, Plomp AS, Price S, Salter C, Santos-Simarro F, Sarda P, Schanze D, Segovia M, Shaw-Smith C, Smithson S, Suri M, Tatton-Brown K, Tenorio J, Thakker RV, Valdez RM, Van Haeringen A, Van Hagen JM, Zenker M, Zollino M, Dunn WW, Piening S, Hennekam RC. Development, behaviour and sensory processing in Marshall-Smith syndrome and Malan syndrome: phenotype comparison in two related syndromes. J Intellect Disabil Res 2020; 64:956-969. [PMID: 33034087 PMCID: PMC8957705 DOI: 10.1111/jir.12787] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 08/19/2020] [Accepted: 09/15/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Ultrarare Marshall-Smith and Malan syndromes, caused by changes of the gene nuclear factor I X (NFIX), are characterised by intellectual disability (ID) and behavioural problems, although questions remain. Here, development and behaviour are studied and compared in a cross-sectional study, and results are presented with genetic findings. METHODS Behavioural phenotypes are compared of eight individuals with Marshall-Smith syndrome (three male individuals) and seven with Malan syndrome (four male individuals). Long-term follow-up assessment of cognition and adaptive behaviour was possible in three individuals with Marshall-Smith syndrome. RESULTS Marshall-Smith syndrome individuals have more severe ID, less adaptive behaviour, more impaired speech and less reciprocal interaction compared with individuals with Malan syndrome. Sensory processing difficulties occur in both syndromes. Follow-up measurement of cognition and adaptive behaviour in Marshall-Smith syndrome shows different individual learning curves over time. CONCLUSIONS Results show significant between and within syndrome variability. Different NFIX variants underlie distinct clinical phenotypes leading to separate entities. Cognitive, adaptive and sensory impairments are common in both syndromes and increase the risk of challenging behaviour. This study highlights the value of considering behaviour within developmental and environmental context. To improve quality of life, adaptations to environment and treatment are suggested to create a better person-environment fit.
Collapse
Affiliation(s)
- P A Mulder
- Autism Team Northern-Netherlands, Jonx Department of (Youth) Mental Health and Autism, Lentis Psychiatric Institute, Groningen, Netherlands
| | - I D C van Balkom
- Autism Team Northern-Netherlands, Jonx Department of (Youth) Mental Health and Autism, Lentis Psychiatric Institute, Groningen, Netherlands
- Rob Giel Research Centre, Department of Psychiatry, University Medical Center Groningen, Groningen, Netherlands
| | - A M Landlust
- Autism Team Northern-Netherlands, Jonx Department of (Youth) Mental Health and Autism, Lentis Psychiatric Institute, Groningen, Netherlands
| | - M Priolo
- Unità Operativa di Genetica Medica, Grande Ospedale Metropolitano Bianchi-Melacrino-Morelli, Reggio Calabria, Italy
| | - L A Menke
- Department of Paediatrics, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - I H Acero
- Genetics Unit, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - F S Alkuraya
- Saudi Human Genome Project, King Abdulaziz City for Science and Technology, and Department of Genetics, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - P Arias
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, and CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - L Bernardini
- Cytogenetics Unit, Casa Sollievo della Sofferenza Foundation, San Giovanni Rotondo, Italy
| | - E K Bijlsma
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, Netherlands
| | - T Cole
- Department of Clinical Genetics, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - C Coubes
- Département de Génétique Médicale, Hôpital Arnaud de Villeneuve, CHRU Montpellier, Montpellier, France
| | - I Dapia
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, and CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - S Davies
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - N Di Donato
- Institute for Clinical Genetics, TU Dresden, Dresden, Germany
| | - N H Elcioglu
- Department of Pediatric Genetics, Marmara University Medical School, Istanbul and Eastern Mediterranean University, Mersin, Turkey
| | - J A Fahrner
- McKusick-Nathans Institute of Genetic Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - A Foster
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, UK
| | - N G González
- Unit Hospital Universitario Central de Asturias, Oviedo, Spain
| | - I Huber
- Sørland Hospital, Kristiansand, Norway
| | - M Iascone
- Medical Genetics Laboratory, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - A-S Kaiser
- Institute of Human Genetics, Heidelberg University, Heidelberg, Germany
| | - A Kamath
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, UK
| | - K Kooblall
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - P Lapunzina
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, and CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - J Liebelt
- South Australian Clinical Genetics Services, Women's and Children's Hospital, North Adelaide, Australia
| | - S A Lynch
- UCD Academic Centre on Rare Diseases, School of Medicine and Medical Sciences, University College Dublin, and Clinical Genetics, Temple Street Children's University Hospital, Dublin, Ireland
| | - S M Maas
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, Netherlands
| | - C Mammì
- Unità Operativa di Genetica Medica, Grande Ospedale Metropolitano Bianchi-Melacrino-Morelli, Reggio Calabria, Italy
| | - I B Mathijssen
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, Netherlands
| | - S McKee
- Northern Ireland Regional Genetics Service, Belfast Health and Social Care Trust, Belfast, UK
| | - G M Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, and Division of Genetic Medicine, University of Washington School of Medicine, Seattle, WA, USA
| | - T Montgomery
- Newcastle upon Tyne NHS Foundation Trust, Newcastle upon Tyne, UK
| | - D Neubauer
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - T E Neumann
- Mitteldeutscher Praxisverbund Humangenetik, Halle, Germany
| | - L Pintomalli
- Unità Operativa di Genetica Medica, Grande Ospedale Metropolitano Bianchi-Melacrino-Morelli, Reggio Calabria, Italy
| | - M A Pisanti
- Medical Genetic and Laboratory Unit, "Antonio Cardarelli" Hospital, Naples, Italy
| | - A S Plomp
- Department of Clinical Genetics, Academic Medical Center, Amsterdam, Netherlands
| | - S Price
- Department of Clinical Genetics, Northampton General Hospital NHS Trust, Northampton, UK
| | - C Salter
- Wessex Clinical Genetics Service, Princess Ann Hospital, Southampton, UK
| | - F Santos-Simarro
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, and CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - P Sarda
- Département de Génétique Médicale, Hôpital Arnaud de Villeneuve, CHRU Montpellier, Montpellier, France
| | - D Schanze
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - M Segovia
- CENAGEM, Centro Nacional de Genética, Buenos Aires, Argentina
| | - C Shaw-Smith
- Royal Devon and Exeter NHS Foundation Trust, Exeter, UK
| | - S Smithson
- University Hospitals Bristol NHS Trust, Bristol, UK
| | - M Suri
- Nottingham Clinical Genetics Service, Nottingham University Hospitals NHS Trust, Nottingham, UK
| | - K Tatton-Brown
- Division of Genetics and Epidemiology, Institute of Cancer Research, London and South West Thames Regional Genetics Service, St. George's University Hospitals NHS Foundation Trust, London, UK
| | - J Tenorio
- Institute of Medical and Molecular Genetics (INGEMM), Hospital Universitario La Paz, IdiPAZ, Universidad Autónoma de Madrid, and CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain
| | - R V Thakker
- Academic Endocrine Unit, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - R M Valdez
- Genetics Unit, Hospital Militar Central "Cirujano Mayor Dr. Cosme Argerich", Buenos Aires, Argentina
| | - A Van Haeringen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, Netherlands
| | - J M Van Hagen
- Department of Clinical Genetics, VU University Medical Centre, Amsterdam, Netherlands
| | - M Zenker
- Institute of Human Genetics, University Hospital Magdeburg, Magdeburg, Germany
| | - M Zollino
- Department of Laboratory Medicine, Institute of Medical Genetics, Catholic University, Rome, Italy
| | - W W Dunn
- Department of Occupational Therapy Education, School of Health Professions, University of Missouri, Columbia, MO, USA
| | - S Piening
- Autism Team Northern-Netherlands, Jonx Department of (Youth) Mental Health and Autism, Lentis Psychiatric Institute, Groningen, Netherlands
- Rob Giel Research Centre, Department of Psychiatry, University Medical Center Groningen, Groningen, Netherlands
| | - R C Hennekam
- Autism Team Northern-Netherlands, Jonx Department of (Youth) Mental Health and Autism, Lentis Psychiatric Institute, Groningen, Netherlands
- Department of Paediatrics, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| |
Collapse
|
10
|
Mautner L, Baillie CK, Herold HM, Volkwein W, Guertler P, Eberle U, Ackermann N, Sing A, Pavlovic M, Goerlich O, Busch U, Wassill L, Huber I, Baiker A. Rapid point-of-care detection of SARS-CoV-2 using reverse transcription loop-mediated isothermal amplification (RT-LAMP). Virol J 2020; 17:160. [PMID: 33087160 PMCID: PMC7576985 DOI: 10.1186/s12985-020-01435-6] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Lena Mautner
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Christin-Kirsty Baillie
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Heike Marie Herold
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Wolfram Volkwein
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Patrick Guertler
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Ute Eberle
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Nikolaus Ackermann
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Andreas Sing
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Melanie Pavlovic
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Ottmar Goerlich
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Ulrich Busch
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Lars Wassill
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Ingrid Huber
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany
| | - Armin Baiker
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, 85764, Oberschleißheim, Germany.
| |
Collapse
|
11
|
Spielmann G, Ziegler S, Haszprunar G, Busch U, Huber I, Pavlovic M. Using loop-mediated isothermal amplification for fast species delimitation in eels (genus Anguilla), with special reference to the European eel (Anguilla anguilla). Food Control 2019. [DOI: 10.1016/j.foodcont.2019.02.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
|
12
|
Spielmann G, Diedrich J, Haszprunar G, Busch U, Huber I. Comparison of three DNA marker regions for identification of food relevant crustaceans of the order Decapoda. Eur Food Res Technol 2018. [DOI: 10.1007/s00217-018-3199-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
13
|
Pacholewicz E, Buhler C, Wulsten IF, Kraushaar B, Luu HQ, Iwobi AN, Huber I, Stingl K. Internal sample process control improves cultivation-independent quantification of thermotolerant Campylobacter. Food Microbiol 2018; 78:53-61. [PMID: 30497608 DOI: 10.1016/j.fm.2018.09.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 08/30/2018] [Accepted: 09/26/2018] [Indexed: 11/26/2022]
Abstract
Quantification of Campylobacter is challenging and one major reason is the fact that bacteria lose cultivability due to cold or oxygen stress during storage at retail. Alternative live/dead discriminatory qPCR currently lacks standardization and might overestimate live cells in the presence of dead cells. In this study an internal sample process control (ISPC) was developed. The ISPC consists of a specified number of peroxide-killed C. sputorum cells to be added to each sample in order to monitor (i) the level of reduction of the signal from dead cells and (ii) DNA losses during sample processing. A species-specific fragment of the 16S rRNA gene of C. sputorum was selected as real-time PCR target, based on its similar size and gene copy number compared to the C. jejuni/coli/lari target and confirmed in an exclusivity study. Extension of the amplification oligonucleotides for the target of thermotolerant Campylobacter improved real-time PCR efficiency, rendering the method suitable for quantification according to international standards. Concordant PCR signal variation of both C. jejuni and C. sputorum targets in co-inoculated chicken rinses verified the suitability of the ISPC. This provides a crucial step towards implementation of cultivation-independent quantification for improved food safety of fastidious bacteria.
Collapse
Affiliation(s)
- Ewa Pacholewicz
- German Federal Institute for Risk Assessment (BfR), Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Christiane Buhler
- German Federal Institute for Risk Assessment (BfR), Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Imke F Wulsten
- German Federal Institute for Risk Assessment (BfR), Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Britta Kraushaar
- German Federal Institute for Risk Assessment (BfR), Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany
| | - Huong Quynh Luu
- National Institute of Veterinary Research (NIVR), Hanoi, Viet Nam
| | - Azuka N Iwobi
- Bavarian Health and Food Safety Authority (LGL), Oberschleissheim, Germany
| | - Ingrid Huber
- Bavarian Health and Food Safety Authority (LGL), Oberschleissheim, Germany
| | - Kerstin Stingl
- German Federal Institute for Risk Assessment (BfR), Department of Biological Safety, National Reference Laboratory for Campylobacter, Berlin, Germany.
| |
Collapse
|
14
|
Tijsen A, Shinnawi R, Arbel G, Gepstein A, Selig S, Huber I, Gepstein L. Abnormally persisting KCNQ1 imprinting interferes with disease modeling of hiPSC-derived cardiomyocytes. J Mol Cell Cardiol 2018. [DOI: 10.1016/j.yjmcc.2018.05.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
15
|
Dobnik D, Demšar T, Huber I, Gerdes L, Broeders S, Roosens N, Debode F, Berben G, Žel J. Inter-laboratory analysis of selected genetically modified plant reference materials with digital PCR. Anal Bioanal Chem 2018; 410:211-221. [PMID: 29071363 PMCID: PMC5748423 DOI: 10.1007/s00216-017-0711-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/12/2017] [Accepted: 10/16/2017] [Indexed: 12/25/2022]
Abstract
Digital PCR (dPCR), as a new technology in the field of genetically modified (GM) organism (GMO) testing, enables determination of absolute target copy numbers. The purpose of our study was to test the transferability of methods designed for quantitative PCR (qPCR) to dPCR and to carry out an inter-laboratory comparison of the performance of two different dPCR platforms when determining the absolute GM copy numbers and GM copy number ratio in reference materials certified for GM content in mass fraction. Overall results in terms of measured GM% were within acceptable variation limits for both tested dPCR systems. However, the determined absolute copy numbers for individual genes or events showed higher variability between laboratories in one third of the cases, most possibly due to variability in the technical work, droplet size variability, and analysis of the raw data. GMO quantification with dPCR and qPCR was comparable. As methods originally designed for qPCR performed well in dPCR systems, already validated qPCR assays can most generally be used for dPCR technology with the purpose of GMO detection. Graphical abstract The output of three different PCR-based platforms was assessed in an inter-laboratory comparison.
Collapse
Affiliation(s)
- David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), Večna pot 111, 1000, Ljubljana, Slovenia.
| | - Tina Demšar
- Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), Večna pot 111, 1000, Ljubljana, Slovenia
| | - Ingrid Huber
- Bavarian Health and Food Safety Authority (LGL), Veterinärstraße 2, 85764, Oberschleißheim, Germany
| | - Lars Gerdes
- Bavarian Health and Food Safety Authority (LGL), Veterinärstraße 2, 85764, Oberschleißheim, Germany
| | - Sylvia Broeders
- Scientific Institute of Public Health (WIV-ISP), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Nancy Roosens
- Scientific Institute of Public Health (WIV-ISP), J. Wytsmanstraat 14, 1050, Brussels, Belgium
| | - Frederic Debode
- Walloon Agricultural Research Centre (CRA-W), Chaussée de Namur 24, 5030, Gembloux, Belgium
| | - Gilbert Berben
- Walloon Agricultural Research Centre (CRA-W), Chaussée de Namur 24, 5030, Gembloux, Belgium
| | - Jana Žel
- Department of Biotechnology and Systems Biology, National Institute of Biology (NIB), Večna pot 111, 1000, Ljubljana, Slovenia
| |
Collapse
|
16
|
Spielmann G, Huber I, Maggipinto M, Haszprunar G, Busch U, Pavlovic M. Comparison of five preparatory protocols for fish species identification using MALDI-TOF MS. Eur Food Res Technol 2017. [DOI: 10.1007/s00217-017-2983-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
17
|
Briciu VT, Flonta M, Ţăţulescu DF, Meyer F, Sebah D, Cârstina D, Mihalca AD, Gherman CM, Hizo-Teufel C, Huber I, Fingerle V, Lupșe M. Clinical and serological one-year follow-up of patients after the bite of Ixodes ricinus ticks infected with Borrelia burgdorferi sensu lato. Infect Dis (Lond) 2016; 49:277-285. [PMID: 27866446 DOI: 10.1080/23744235.2016.1258488] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
BACKGROUND The risk of developing Lyme borreliosis (LB) after the bite of a Borrelia (B.) burgdorferi sensu lato (s.l.) infected tick in Romania is unknown. METHODS The present prospective study, performed in 2010-2011 in a hospital in Romania, has followed-up clinical and serological outcome of patients that presented with B. burgdorferi positive Ixodes (I.) ricinus bite. A second group of patients, including age, sex and residence-matched individuals bitten by B. burgdorferi negative ticks, was followed-up as a control group. The subjects' outcome was evaluated one year after the tick bite. RESULTS Forty-three out of 389 ticks detached from patients were positive by hbb Real-Time PCR (RT-PCR) for B. burgdorferi s.l. (mainly B. afzelii, but also B. garinii, B. burgdorferi sensu stricto, B. spielmanii/B. valaisiana and B. lusitaniae). Twenty patients bitten by B. burgdorferi positive ticks and twenty matched control patients returned for the one year follow-up. Two patients from the B. burgdorferi positive group developed clinical manifestations of acute LB (erythema migrans) and 5 patients seroconverted (two from the B. burgdorferi positive group and three from the B. burgdorferi negative group). Borrelia afzelii was identified in ticks collected from persons that developed erythema migrans (EM). Comparing the two groups of patients, no statistical significant differences were found regarding presence of clinical symptoms or seroconversion. CONCLUSIONS No outcome differences were found between the group of patients bitten by B. burgdorferi positive ticks and the group of patients bitten by B. burgdorferi negative ticks.
Collapse
Affiliation(s)
- Violeta T Briciu
- a Department of Infectious Diseases , Iuliu Haţieganu University of Medicine and Pharmacy , Cluj-Napoca , Romania.,b Clinical Hospital of Infectious Diseases , Cluj-Napoca , Romania.,c Department of Parasitology and Parasitic Diseases, Faculty of Veterinary Medicine , University of Agricultural Sciences and Veterinary Medicine , Cluj-Napoca , Romania.,d National Reference Centre for Borrelia, Bavarian Health and Food Safety Authority , Oberschleißheim , Germany
| | - Mirela Flonta
- b Clinical Hospital of Infectious Diseases , Cluj-Napoca , Romania
| | - Doina F Ţăţulescu
- a Department of Infectious Diseases , Iuliu Haţieganu University of Medicine and Pharmacy , Cluj-Napoca , Romania.,b Clinical Hospital of Infectious Diseases , Cluj-Napoca , Romania
| | - Fabian Meyer
- e Bavarian Health and Food Safety Authority , Oberschleißheim , Germany
| | - Daniela Sebah
- e Bavarian Health and Food Safety Authority , Oberschleißheim , Germany
| | - Dumitru Cârstina
- a Department of Infectious Diseases , Iuliu Haţieganu University of Medicine and Pharmacy , Cluj-Napoca , Romania
| | - Andrei D Mihalca
- c Department of Parasitology and Parasitic Diseases, Faculty of Veterinary Medicine , University of Agricultural Sciences and Veterinary Medicine , Cluj-Napoca , Romania
| | - Călin M Gherman
- c Department of Parasitology and Parasitic Diseases, Faculty of Veterinary Medicine , University of Agricultural Sciences and Veterinary Medicine , Cluj-Napoca , Romania
| | - Cecilia Hizo-Teufel
- d National Reference Centre for Borrelia, Bavarian Health and Food Safety Authority , Oberschleißheim , Germany
| | - Ingrid Huber
- e Bavarian Health and Food Safety Authority , Oberschleißheim , Germany
| | - Volker Fingerle
- d National Reference Centre for Borrelia, Bavarian Health and Food Safety Authority , Oberschleißheim , Germany
| | - Mihaela Lupșe
- a Department of Infectious Diseases , Iuliu Haţieganu University of Medicine and Pharmacy , Cluj-Napoca , Romania.,b Clinical Hospital of Infectious Diseases , Cluj-Napoca , Romania
| |
Collapse
|
18
|
Parra J, Mayor R, Huber I, Cuartas I, Arias A, Raventós C, Seoane J. Similarities between the Marfan syndrome and cancer: Implications of the Fibrillin-TGFβ axis on cancer biology and treatment. Eur J Cancer 2016. [DOI: 10.1016/s0959-8049(16)61676-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
19
|
Briciu VT, Sebah D, Coroiu G, Lupşe M, Cârstina D, Ţăţulescu DF, Mihalca AD, Gherman CM, Leucuţa D, Meyer F, Hizo-Teufel C, Fingerle V, Huber I. Immunohistochemistry and real-time PCR as diagnostic tools for detection of Borrelia burgdorferi sensu lato in ticks collected from humans. Exp Appl Acarol 2016; 69:49-60. [PMID: 26801157 DOI: 10.1007/s10493-016-0012-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 01/01/2016] [Indexed: 06/05/2023]
Abstract
The objective of this study was to evaluate different methods used for detection of Borrelia burgdorferi sensu lato (s.l.) in ticks: immunohistochemistry followed by focus floating microscopy (FFM) and real-time polymerase chain reaction (real-time PCR) targeting the ospA and hbb genes. Additionally, an optimized ospA real-time PCR assay was developed with an integrated internal amplification control (IAC) for the detection of inhibition in the PCR assay and was validated as an improved screening tool for B. burgdorferi. One hundred and thirty-six ticks collected from humans in a hospital from Cluj-Napoca, Romania, were investigated regarding genus, stage of development and sex, and then tested by all three assays. A poor quality of agreement was found between FFM and each of the two real-time PCR assays, as assessed by concordance analysis (Cohen's kappa), whereas the agreement between the two real-time PCR assays was moderate. The present study argues for a low sensitivity of FFM and underlines that discordant results of different assays used for detection of B. burgdorferi in ticks are frequent.
Collapse
Affiliation(s)
- Violeta T Briciu
- Department of Infectious Diseases, University of Medicine and Pharmacy "Iuliu Haţieganu", Street Iuliu Moldovan 23, Cluj-Napoca, Romania.
- Department of Parasitology and Parasitic Diseases, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine, Calea Mănăstur 3-5, Cluj-Napoca, Romania.
- National Reference Center for Borrelia, Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, Oberschleißheim, Germany.
| | - Daniela Sebah
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, Oberschleißheim, Germany
| | - Georgiana Coroiu
- Department of Pathology, Clinic of Infectious Diseases, Street Iuliu Moldovan 23, Cluj-Napoca, Romania
| | - Mihaela Lupşe
- Department of Infectious Diseases, University of Medicine and Pharmacy "Iuliu Haţieganu", Street Iuliu Moldovan 23, Cluj-Napoca, Romania
| | - Dumitru Cârstina
- Department of Infectious Diseases, University of Medicine and Pharmacy "Iuliu Haţieganu", Street Iuliu Moldovan 23, Cluj-Napoca, Romania
| | - Doina F Ţăţulescu
- Department of Infectious Diseases, University of Medicine and Pharmacy "Iuliu Haţieganu", Street Iuliu Moldovan 23, Cluj-Napoca, Romania
| | - Andrei D Mihalca
- Department of Parasitology and Parasitic Diseases, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine, Calea Mănăstur 3-5, Cluj-Napoca, Romania
| | - Călin M Gherman
- Department of Parasitology and Parasitic Diseases, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine, Calea Mănăstur 3-5, Cluj-Napoca, Romania
| | - Daniel Leucuţa
- Department of Medical Informatics and Biostatistics, University of Medicine and Pharmacy "Iuliu Haţieganu", Street Pasteur 6, Cluj-Napoca, Romania
| | - Fabian Meyer
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, Oberschleißheim, Germany
| | - Cecilia Hizo-Teufel
- National Reference Center for Borrelia, Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, Oberschleißheim, Germany
| | - Volker Fingerle
- National Reference Center for Borrelia, Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, Oberschleißheim, Germany
| | - Ingrid Huber
- Bavarian Health and Food Safety Authority, Veterinaerstrasse 2, Oberschleißheim, Germany
| |
Collapse
|
20
|
Anderson AC, Jonas D, Huber I, Karygianni L, Wölber J, Hellwig E, Arweiler N, Vach K, Wittmer A, Al-Ahmad A. Enterococcus faecalis from Food, Clinical Specimens, and Oral Sites: Prevalence of Virulence Factors in Association with Biofilm Formation. Front Microbiol 2016; 6:1534. [PMID: 26793174 PMCID: PMC4707231 DOI: 10.3389/fmicb.2015.01534] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/21/2015] [Indexed: 12/21/2022] Open
Abstract
Enterococci have gained significance as the cause of nosocomial infections; they occur as food contaminants and have also been linked to dental diseases. E. faecalis has a great potential to spread virulence as well as antibiotic resistance genes via horizontal gene transfer. The integration of food-borne enterococci into the oral biofilm in-vivo has been observed. Therefore, we investigated the virulence determinants and antibiotic resistance of 97 E. faecalis isolates from the oral cavity, food, and clinical specimens. In addition, phenotypic expression of gelatinase and cytolysin were tested, in-vitro biofilm formation was quantified and isolates were compared for strain relatedness via pulsed field gel electrophoresis (PFGE). Each isolate was found to possess two or more virulence genes, most frequently gelE, efaA, and asa1. Notably, plaque/saliva isolates possessed the highest abundance of virulence genes, the highest levels of phenotypic gelatinase and hemolysin activity and concurrently a high ability to form biofilm. The presence of asa1 was associated with biofilm formation. The biofilm formation capacity of clinical and plaque/saliva isolates was considerably higher than that of food isolates and they also showed similar antibiotic resistance patterns. These results indicate that the oral cavity can constitute a reservoir for virulent E. faecalis strains possessing antibiotic resistance traits and at the same time distinct biofilm formation capabilities facilitating exchange of genetic material.
Collapse
Affiliation(s)
- Annette C Anderson
- Department of Operative Dentistry and Periodontology, Center for Dental Medicine, Medical Center, University of Freiburg Freiburg, Germany
| | - Daniel Jonas
- Department of Infection Control and Hospital Epidemiology, Institute for Environmental Health Sciences and Hospital Infection Control, Medical Center, University of Freiburg Freiburg, Germany
| | - Ingrid Huber
- Bavarian Health and Food Safety Authority Oberschleissheim, Germany
| | - Lamprini Karygianni
- Department of Operative Dentistry and Periodontology, Center for Dental Medicine, Medical Center, University of Freiburg Freiburg, Germany
| | - Johan Wölber
- Department of Operative Dentistry and Periodontology, Center for Dental Medicine, Medical Center, University of Freiburg Freiburg, Germany
| | - Elmar Hellwig
- Department of Operative Dentistry and Periodontology, Center for Dental Medicine, Medical Center, University of Freiburg Freiburg, Germany
| | - Nicole Arweiler
- Department of Periodontology, Philipps-University of Marburg Marburg, Germany
| | - Kirstin Vach
- Department of Medical Biometry and Statistics, Center for Medical Biometry and Medical Informatics, Medical Center, University of Freiburg Freiburg, Germany
| | - Annette Wittmer
- Department of Medical Microbiology and Hygiene, Center for Microbiology and Hygiene, Medical Center, University of Freiburg Freiburg, Germany
| | - Ali Al-Ahmad
- Department of Operative Dentistry and Periodontology, Center for Dental Medicine, Medical Center, University of Freiburg Freiburg, Germany
| |
Collapse
|
21
|
Iwobi A, Sebah D, Kraemer I, Losher C, Fischer G, Busch U, Huber I. Corrigendum to “A multiplex real-time PCR method for the quantification of beef and pork fractions in minced meat” [Food Chem. 169 (2015) 305–313]. Food Chem 2015. [DOI: 10.1016/j.foodchem.2014.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
22
|
Iwobi A, Sebah D, Kraemer I, Losher C, Fischer G, Busch U, Huber I. A multiplex real-time PCR method for the quantification of beef and pork fractions in minced meat. Food Chem 2015; 169:305-13. [DOI: 10.1016/j.foodchem.2014.07.139] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 07/01/2014] [Accepted: 07/30/2014] [Indexed: 11/24/2022]
|
23
|
Pavlovic M, Wudy C, Zeller-Peronnet V, Maggipinto M, Zimmermann P, Straubinger A, Iwobi A, Märtlbauer E, Busch U, Huber I. Identification of bacteria isolated from veterinary clinical specimens using MALDI-TOF MS. Berl Munch Tierarztl Wochenschr 2015; 128:24-30. [PMID: 25876281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) has recently emerged as a rapid and accurate identification method for bacterial species. Although it has been successfully applied for the identification of human pathogens, it has so far not been well evaluated for routine identification of veterinary bacterial isolates. This study was performed to compare and evaluate the performance of MALDI-TOF MS based identification of veterinary bacterial isolates with commercially available conventional test systems. Discrepancies of both methods were resolved by sequencing 16S rDNA and, if necessary, the infB gene for Actinobacillus isolates. A total of 375 consecutively isolated veterinary samples were collected. Among the 357 isolates (95.2%) correctly identified at the genus level by MALDI-TOF MS, 338 of them (90.1% of the total isolates) were also correctly identified at the species level. Conventional methods offered correct species identification for 319 isolates (85.1%). MALDI-TOF identification therefore offered more accurate identification of veterinary bacterial isolates. An update of the in-house mass spectra database with additional reference spectra clearly improved the identification results. In conclusion, the presented data suggest that MALDI-TOF MS is an appropriate platform for classification and identification of veterinary bacterial isolates.
Collapse
|
24
|
Luber F, Demmel A, Herbert D, Hosken A, Hupfer C, Huber I, Busch U, Engel KH. Comparative assessment of DNA-based approaches for the quantification of food allergens. Food Chem 2014; 160:104-11. [DOI: 10.1016/j.foodchem.2014.03.077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 10/10/2013] [Accepted: 03/14/2014] [Indexed: 11/29/2022]
|
25
|
Pavlovic M, Mewes A, Maggipinto M, Schmidt W, Messelhäußer U, Balsliemke J, Hörmansdorfer S, Busch U, Huber I. MALDI-TOF MS based identification of food-borne yeast isolates. J Microbiol Methods 2014; 106:123-128. [PMID: 25193440 DOI: 10.1016/j.mimet.2014.08.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 08/04/2014] [Accepted: 08/26/2014] [Indexed: 10/24/2022]
Abstract
In this study, food-borne yeast isolates (n=96), comprising at least 33 species, were identified using MALDI-TOF MS and conventional methods (API ID 32 C and Phoenix Yeast ID). Discrepancies of both methods were resolved by sequencing the ITS1-5.8S-rRNA-ITS2 region. For ten isolates, mainly classified to Rhodotorula and Trichosporon species, no clear final species identification was possible. 62 isolates were correctly identified to species level using either MALDI-TOF MS or conventional tests. 15 isolates were misidentified when applying conventional assays. In contrary, no species misidentifications were observed after MALDI-TOF MS based classification. In return, 16 isolates were not identifiable after matching their protein fingerprints against MALDI Biotyper 4.0.0.1 library. MALDI TOF MS in-house database update clearly improved the identification. In conclusion, the presented data suggest that MALDI-TOF MS is an appropriate platform for reliable classification and identification of food-borne yeast isolates.
Collapse
Affiliation(s)
- Melanie Pavlovic
- Bavarian Health and Food Safety Authority, Veterinaerstr. 2, 85764 Oberschleißheim, Germany.
| | - Anne Mewes
- Bavarian Health and Food Safety Authority, Veterinaerstr. 2, 85764 Oberschleißheim, Germany
| | - Marzena Maggipinto
- Bavarian Health and Food Safety Authority, Veterinaerstr. 2, 85764 Oberschleißheim, Germany
| | - Wolfgang Schmidt
- Bavarian Health and Food Safety Authority, Veterinaerstr. 2, 85764 Oberschleißheim, Germany
| | - Ute Messelhäußer
- Bavarian Health and Food Safety Authority, Veterinaerstr. 2, 85764 Oberschleißheim, Germany
| | - Joachim Balsliemke
- Bavarian Health and Food Safety Authority, Eggenreuther Weg 43, 91058 Erlangen, Germany
| | - Stefan Hörmansdorfer
- Bavarian Health and Food Safety Authority, Veterinaerstr. 2, 85764 Oberschleißheim, Germany
| | - Ulrich Busch
- Bavarian Health and Food Safety Authority, Veterinaerstr. 2, 85764 Oberschleißheim, Germany
| | - Ingrid Huber
- Bavarian Health and Food Safety Authority, Veterinaerstr. 2, 85764 Oberschleißheim, Germany
| |
Collapse
|
26
|
Boschert V, Berger A, Konrad R, Huber I, Hörmansdorfer S, Zöls S, Eddicks M, Ritzmann M, Sing A. Corynebacterium species nasal carriage in pigs and their farmers in Bavaria, Germany: implications for public health. Vet Rec 2014; 175:248. [PMID: 25037890 DOI: 10.1136/vr.102634] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Reports on cases of human diphtheria caused by toxigenic Corynebacterium ulcerans that were linked to occupational swine contact as well as isolation of C ulcerans from wild boars have suggested that pigs might serve as reservoir for human infections. Therefore, a prevalence study on Corynebacterium species nasal carriage in pigs and their farmers was performed between August 1 and December 31, 2009, in 41 swine farms from Bavaria, Germany. All 411 asymptomatic pigs and 29 of 30 healthy farmers were colonised with Corynebacterium strains of up to 11 different species. No potentially toxigenic Corynebacterium strain was isolated either from the pigs or from their farmers, respectively. The patterns of the species composition in the pigs and the farmers were very similar, suggesting a potential transmission of strains between animals and humans.
Collapse
Affiliation(s)
- V Boschert
- Bavarian Health and Food Safety Authority, Oberschleißheim 85764, Germany Clinic for Swine, Ludwig-Maximilians-University Munich, Oberschleißheim 85764, Germany
| | - A Berger
- National Consiliary Laboratory for Diphtheria, Oberschleißheim 85764, Germany Bavarian Health and Food Safety Authority, Oberschleißheim 85764, Germany
| | - R Konrad
- National Consiliary Laboratory for Diphtheria, Oberschleißheim 85764, Germany Bavarian Health and Food Safety Authority, Oberschleißheim 85764, Germany
| | - I Huber
- Bavarian Health and Food Safety Authority, Oberschleißheim 85764, Germany
| | - S Hörmansdorfer
- Bavarian Health and Food Safety Authority, Oberschleißheim 85764, Germany
| | - S Zöls
- Clinic for Swine, Ludwig-Maximilians-University Munich, Oberschleißheim 85764, Germany
| | - M Eddicks
- Clinic for Swine, Ludwig-Maximilians-University Munich, Oberschleißheim 85764, Germany
| | - M Ritzmann
- Clinic for Swine, Ludwig-Maximilians-University Munich, Oberschleißheim 85764, Germany
| | - A Sing
- National Consiliary Laboratory for Diphtheria, Oberschleißheim 85764, Germany Bavarian Health and Food Safety Authority, Oberschleißheim 85764, Germany
| |
Collapse
|
27
|
Schabauer L, Wenning M, Huber I, Ehling-Schulz M. Novel physico-chemical diagnostic tools for high throughput identification of bovine mastitis associated gram-positive, catalase-negative cocci. BMC Vet Res 2014; 10:156. [PMID: 25015262 PMCID: PMC4105049 DOI: 10.1186/1746-6148-10-156] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Accepted: 07/03/2014] [Indexed: 01/14/2023] Open
Abstract
Background The routine diagnosis of Streptococcus spp. and other mastitis associated gram-positive, catalase-negative cocci is still based upon biochemical tests and serological methods, which frequently provide ambiguous identification results. We therefore aimed to establish an accurate identification system for differential diagnosis of mastitis associated Streptococcus spp. and related species using biophysical techniques such as Fourier-transform infrared (FTIR) spectroscopy and MALDI – TOF/MS. Results Based on a panel of 210 isolates from cases of bovine mastitis, an unsupervised FTIR spectral reference library was established and an artificial neural network (ANN) - assisted identification system was developed. All bacterial isolates were previously identified by species-specific PCR and/or 16S rRNA gene sequence analysis. An overall identification rate of 100% at species level for 173 strains unknown to the ANN and the library was achieved by combining ANN and the spectral database, thus demonstrating the suitability of our FTIR identification system for routine diagnosis. In addition, we investigated the potential of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of mastitis associated Streptococcus spp. and related bacteria. Using the Microflex LT System, MALDI Biotyper software™ (V3.3) we achieved an accuracy rate of 95.2%. A blind study, including 21 clinical samples from dairy cows, revealed a 100% correct species identification rate for FTIR and 90.5% for MALDI-TOF MS, indicating that these techniques are valuable tools for diagnosis. Conclusions This study clearly demonstrates that FTIR spectroscopy as well as MALDI-TOF MS can significantly improve and facilitate the identification and differentiation of mastitis associated Streptococcus spp. and related species. Although the FTIR identification system turned out being slightly superior to MALDI-TOF MS in terms of identification on species level, both methods offer interesting alternatives to conventional methods currently used in mastitis diagnosis as both of them provide high accuracy at low operating costs once the instrument is acquired.
Collapse
Affiliation(s)
| | | | | | - Monika Ehling-Schulz
- Functional Microbiology, IBMH, Department of Pathobiology, University of Veterinary Medicine, Veterinaerplatz 1, 1210 Vienna, Austria.
| |
Collapse
|
28
|
Briciu VT, Meyer F, Sebah D, Tăţulescu DF, Coroiu G, Lupşe M, Carstina D, Mihalca AD, Hizo-Teufel C, Klier C, Huber I, Fingerle V. Real-time PCR-based identification of Borrelia burgdorferi sensu lato species in ticks collected from humans in Romania. Ticks Tick Borne Dis 2014; 5:575-81. [PMID: 24986749 DOI: 10.1016/j.ttbdis.2014.04.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Revised: 04/08/2014] [Accepted: 04/10/2014] [Indexed: 11/26/2022]
Abstract
The aims of our study were to determine (i) which tick species bite humans in Romania and (ii) the prevalence of Borrelia (B.) burgdorferi genospecies in these ticks. All ticks collected from patients who presented to the Clinic of Infectious Diseases Cluj Napoca in spring/summer 2010 were morphologically identified by an entomologist and tested for B. burgdorferi genospecies prevalence by a real-time PCR assay targeting the hbb gene and melting curve analysis. Out of 532 ticks, 518 were Ixodes ricinus, 10 Dermacentor marginatus, and 3 Haemaphysalis spp. ticks, and one unidentified tick due to destruction. Since evaluation of the hbb PCR revealed that it was not possible to differentiate between B. spielmanii/B. valaisiana and B. garinii/B. bavariensis, sequencing of an 800-bp fragment of the ospA gene was performed in these cases. Out of 389 investigated ticks, 43 were positive by hbb PCR for B. burgdorferi sensu lato. The positive samples were 42 Ixodes ricinus (11.1% B. burgdorferi sensu lato prevalence) and the one unidentified tick. Species identification revealed the presence of mainly B. afzelii, but also of B. garinii, B. burgdorferi sensu stricto, B. valaisiana, and B. lusitaniae. In 4 samples, differentiation between B. spielmanii/B. valaisiana was impossible. Our study shows that the most relevant human pathogenic B. burgdorferi genospecies - predominantly B. afzelii - are present in ticks collected from Romanian patients.
Collapse
Affiliation(s)
- Violeta T Briciu
- Department of Infectious Diseases, University of Medicine and Pharmacy "Iuliu Hatieganu", Cluj Napoca, Romania; Department of Parasitology and Parasitic Diseases, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine, Cluj Napoca, Romania; National Reference Centre for Borrelia, Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | - Fabian Meyer
- Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | - Daniela Sebah
- Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | - Doina F Tăţulescu
- Department of Infectious Diseases, University of Medicine and Pharmacy "Iuliu Hatieganu", Cluj Napoca, Romania
| | - Georgiana Coroiu
- Department of Pathology, Clinic of Infectious Diseases, Cluj Napoca, Romania
| | - Mihaela Lupşe
- Department of Infectious Diseases, University of Medicine and Pharmacy "Iuliu Hatieganu", Cluj Napoca, Romania
| | - Dumitru Carstina
- Department of Infectious Diseases, University of Medicine and Pharmacy "Iuliu Hatieganu", Cluj Napoca, Romania
| | - Andrei D Mihalca
- Department of Parasitology and Parasitic Diseases, Faculty of Veterinary Medicine, University of Agricultural Sciences and Veterinary Medicine, Cluj Napoca, Romania
| | - Cecilia Hizo-Teufel
- National Reference Centre for Borrelia, Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | - Christiane Klier
- National Reference Centre for Borrelia, Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | - Ingrid Huber
- Bavarian Health and Food Safety Authority, Oberschleissheim, Germany
| | - Volker Fingerle
- National Reference Centre for Borrelia, Bavarian Health and Food Safety Authority, Oberschleissheim, Germany.
| |
Collapse
|
29
|
Broeders S, Huber I, Grohmann L, Berben G, Taverniers I, Mazzara M, Roosens N, Morisset D. Guidelines for validation of qualitative real-time PCR methods. Trends Food Sci Technol 2014. [DOI: 10.1016/j.tifs.2014.03.008] [Citation(s) in RCA: 239] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
30
|
Wenning M, Breitenwieser F, Konrad R, Huber I, Busch U, Scherer S. Identification and differentiation of food-related bacteria: A comparison of FTIR spectroscopy and MALDI-TOF mass spectrometry. J Microbiol Methods 2014; 103:44-52. [PMID: 24878140 DOI: 10.1016/j.mimet.2014.05.011] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Revised: 05/19/2014] [Accepted: 05/20/2014] [Indexed: 11/17/2022]
Abstract
The food industry requires easy, accurate, and cost-effective techniques for microbial identification to ensure safe products and identify microbial contaminations. In this work, FTIR spectroscopy and MALDI-TOF mass spectrometry were assessed for their suitability and applicability for routine microbial diagnostics of food-related microorganisms by analyzing their robustness according to changes in incubation time and medium, identification accuracy and their ability to differentiate isolates down to the strain level. Changes in the protocol lead to a significantly impaired performance of FTIR spectroscopy, whereas they had only little effects on MALDI-TOF MS. Identification accuracy was tested using 174 food-related bacteria (93 species) from an in-house strain collection and 40 fresh isolates from routine food analyses. For MALDI-TOF MS, weaknesses in the identification of bacilli and pseudomonads were observed; FTIR spectroscopy had most difficulties in identifying pseudomonads and enterobacteria. In general, MALDI-TOF MS obtained better results (52-85% correct at species level), since the analysis of mainly ribosomal proteins is more robust and seems to be more reliable. FTIR spectroscopy suffers from the fact that it generates a whole-cell fingerprint and intraspecies diversity may lead to overlapping species borders which complicates identification. In the present study values between 56% and 67% correct species identification were obtained. On the opposite, this high sensitivity offers the opportunity of typing below the species level which was not possible using MALDI-TOF MS. Using fresh isolates from routine diagnostics, both techniques performed well with 88% (MALDI-TOF) and 75% (FTIR) correct identifications at species level, respectively.
Collapse
Affiliation(s)
- Mareike Wenning
- Abteilung Mikrobiologie, Zentralinstitut für Ernährungs-und Lebensmittelforschung (ZIEL), Technische Universität München, Weihenstephaner Berg 3, 85350 Freising, Germany.
| | - Franziska Breitenwieser
- Abteilung Mikrobiologie, Zentralinstitut für Ernährungs-und Lebensmittelforschung (ZIEL), Technische Universität München, Weihenstephaner Berg 3, 85350 Freising, Germany; Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), Veterinärstraße 2, 85764 Oberschleißheim, Germany
| | - Regina Konrad
- Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), Veterinärstraße 2, 85764 Oberschleißheim, Germany
| | - Ingrid Huber
- Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), Veterinärstraße 2, 85764 Oberschleißheim, Germany
| | - Ulrich Busch
- Bayerisches Landesamt für Gesundheit und Lebensmittelsicherheit (LGL), Veterinärstraße 2, 85764 Oberschleißheim, Germany
| | - Siegfried Scherer
- Abteilung Mikrobiologie, Zentralinstitut für Ernährungs-und Lebensmittelforschung (ZIEL), Technische Universität München, Weihenstephaner Berg 3, 85350 Freising, Germany; Lehrstuhl für Mikrobielle Ökologie, Department of Biosciences, Technische Universität München, D-85350 Freising, Germany
| |
Collapse
|
31
|
Meyer C, Heurich M, Huber I, Krause G, Ullrich U, Fetsch A. [The importance of wildlife as reservoir of antibiotic-resistant bacteria in Bavaria--first results]. Berl Munch Tierarztl Wochenschr 2014; 127:129-134. [PMID: 24693658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The use of antimicrobial agents is responsible for the emergence and spread of antibiotic resistant bacteria. Nevertheless, multiresistant bacteria have been found in animals that have never been exposed to antimicrobial agents. Wild animals that are carriers of methicillin-resistant organisms represent a hazard since they can transmit their bacteria to other animals and to humans. In the hunting season 2009/2010 nasal swabs of 98 red deer and 109 wild boars were examined for the presence of methicillin-sensitive and methicillin-resistant staphylococci. From each wild boar methicillin-susceptible staphylococci (Staphylococcus aureus in 28% and Staphylococcus spp. in 72% of the animals) were isolated. In red deer the detection rate of Staphylococcus (S.) aureus and methicillin-susceptible staphylococci was 49% and 17%, respectively. The occurrence of S. aureus was significantly higher (p < 0.05) in red deer than in wild boars. Methicillin-resistant staphylococci were not found. However, in one third of the red deer, methicillin-resistant bacteria of the genus Enterococcus spp. and Bacillus spp. were isolated. The results of the present study indicate that wildlife, especially red deer are an important reservoir for S. aureus and that the upper respiratory tract of red deer is regularly colonised with methicillin-resistant bacteria such as Bacillus spp. and Enterococcus spp. Primarily, commensal bacteria are harmless to human health, however, red deer may be a reservoir for antibiotic-resistant bacteria.
Collapse
|
32
|
Abstract
We report the case of a 63-year-old patient suffering from a nasopharyngeal adenoid cystic carcinoma. She presented with increased oral secretion and pharyngeal irritation, Horner's syndrome, and trigeminal neuralgia. Magnetic resonance imaging scans revealed a tumor of the nasopharyngeal space invading the right cranial base. Lymph node metastases were clinically excluded. The histological sample confirmed an adenoid cystic carcinoma, which was therapeutically treated with adequate radiotherapy. Based on the presented case report and a review of the literature, we discuss the diagnosis and treatment of adenoid cystic carcinomas of the nasopharynx.
Collapse
Affiliation(s)
- I Karapantzos
- Klinik für Hals-, Nasen-, Ohrenheilkunde, Marienhospital, Böheimstrasse 37, 70199 Stuttgart
| | | | | | | | | |
Collapse
|
33
|
Krüger NJ, Buhler C, Iwobi AN, Huber I, Ellerbroek L, Appel B, Stingl K. "Limits of control"--crucial parameters for a reliable quantification of viable campylobacter by real-time PCR. PLoS One 2014; 9:e88108. [PMID: 24505398 PMCID: PMC3914927 DOI: 10.1371/journal.pone.0088108] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 01/07/2014] [Indexed: 11/19/2022] Open
Abstract
The unsuitability of the "CFU" parameter and the usefulness of cultivation-independent quantification of Campylobacter on chicken products, reflecting the actual risk for infection, is increasingly becoming obvious. Recently, real-time PCR methods in combination with the use of DNA intercalators, which block DNA amplification from dead bacteria, have seen wide application. However, much confusion exists in the correct interpretation of such assays. Campylobacter is confronted by oxidative and cold stress outside the intestine. Hence, damage caused by oxidative stress probably represents the most frequent natural death of Campylobacter on food products. Treatment of Campylobacter with peroxide led to complete loss of CFU and to significant entry of any tested DNA intercalator, indicating disruption of membrane integrity. When we transiently altered the metabolic state of Campylobacter by abolishing the proton-motive force or by inhibiting active efflux, CFU was constant but enhanced entry of ethidium bromide (EtBr) was observed. Consistently, ethidium monoazide (EMA) also entered viable Campylobacter, in particular when nutrients for bacterial energization were lacking (in PBS) or when the cells were less metabolically active (in stationary phase). In contrast, propidium iodide (PI) and propidium monoazide (PMA) were excluded from viable bacterial cells, irrespective of their metabolic state. As expected for a diffusion-limited process, the extent of signal reduction from dead cells depended on the temperature, incubation time and concentration of the dyes during staining, prior to crosslinking. Consistently, free protein and/or DNA present in varying amounts in the heterogeneous matrix lowered the concentration of the DNA dyes at the bacterial membrane and led to considerable variation of the residual signal from dead cells. In conclusion, we propose an improved approach, taking into account principles of method variability and recommend the implementation of process sample controls for reliable quantification of intact and potentially infectious units (IPIU) of Campylobacter by real-time PCR.
Collapse
Affiliation(s)
- Nora-Johanna Krüger
- National Reference Laboratory for Campylobacter, Federal Institute for Risk Assessment, Berlin, Germany
| | - Christiane Buhler
- National Reference Laboratory for Campylobacter, Federal Institute for Risk Assessment, Berlin, Germany
| | - Azuka N. Iwobi
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Ingrid Huber
- Bavarian Health and Food Safety Authority, Oberschleißheim, Germany
| | - Lüppo Ellerbroek
- National Reference Laboratory for Campylobacter, Federal Institute for Risk Assessment, Berlin, Germany
| | - Bernd Appel
- National Reference Laboratory for Campylobacter, Federal Institute for Risk Assessment, Berlin, Germany
| | - Kerstin Stingl
- National Reference Laboratory for Campylobacter, Federal Institute for Risk Assessment, Berlin, Germany
- * E-mail:
| |
Collapse
|
34
|
Pavlovic M, Huber I, Konrad R, Busch U. Application of MALDI-TOF MS for the Identification of Food Borne Bacteria. Open Microbiol J 2013; 7:135-41. [PMID: 24358065 PMCID: PMC3866695 DOI: 10.2174/1874285801307010135] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Revised: 10/21/2013] [Accepted: 10/21/2013] [Indexed: 12/03/2022] Open
Abstract
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.
Collapse
Affiliation(s)
- Melanie Pavlovic
- Bavarian Health and Food Safety Authority, 85354 Oberschleißheim, Germany
| | - Ingrid Huber
- Bavarian Health and Food Safety Authority, 85354 Oberschleißheim, Germany
| | - Regina Konrad
- Bavarian Health and Food Safety Authority, 85354 Oberschleißheim, Germany
| | - Ulrich Busch
- Bavarian Health and Food Safety Authority, 85354 Oberschleißheim, Germany
| |
Collapse
|
35
|
Huber I, Block A, Sebah D, Debode F, Morisset D, Grohmann L, Berben G, Stebih D, Milavec M, Zel J, Busch U. Development and validation of duplex, triplex, and pentaplex real-time PCR screening assays for the detection of genetically modified organisms in food and feed. J Agric Food Chem 2013; 61:10293-10301. [PMID: 23971699 DOI: 10.1021/jf402448y] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Worldwide, qualitative methods based on PCR are most commonly used as screening tools for genetically modified material in food and feed. However, the increasing number and diversity of genetically modified organisms (GMO) require effective methods for simultaneously detecting several genetic elements marking the presence of transgenic events. Herein we describe the development and validation of a pentaplex, as well as complementary triplex and duplex real-time PCR assays, for the detection of the most common screening elements found in commercialized GMOs: P-35S, T-nos, ctp2-cp4-epsps, bar, and pat. The use of these screening assays allows the coverage of many GMO events globally approved for commercialization. Each multiplex real-time PCR assay shows high specificity and sensitivity with an absolute limit of detection below 20 copies for the targeted sequences. We demonstrate by intra- and interlaboratory tests that the assays are robust as well as cost- and time-effective for GMO screening if applied in routine GMO analysis.
Collapse
Affiliation(s)
- Ingrid Huber
- Bavarian Health and Food Safety Authority (LGL) , Veterinärstrasse 2, D-85764 Oberschleissheim, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
36
|
Block A, Debode F, Grohmann L, Hulin J, Taverniers I, Kluga L, Barbau-Piednoir E, Broeders S, Huber I, Van den Bulcke M, Heinze P, Berben G, Busch U, Roosens N, Janssen E, Žel J, Gruden K, Morisset D. The GMOseek matrix: a decision support tool for optimizing the detection of genetically modified plants. BMC Bioinformatics 2013; 14:256. [PMID: 23965170 PMCID: PMC3765097 DOI: 10.1186/1471-2105-14-256] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2013] [Accepted: 08/06/2013] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Since their first commercialization, the diversity of taxa and the genetic composition of transgene sequences in genetically modified plants (GMOs) are constantly increasing. To date, the detection of GMOs and derived products is commonly performed by PCR-based methods targeting specific DNA sequences introduced into the host genome. Information available regarding the GMOs' molecular characterization is dispersed and not appropriately organized. For this reason, GMO testing is very challenging and requires more complex screening strategies and decision making schemes, demanding in return the use of efficient bioinformatics tools relying on reliable information. DESCRIPTION The GMOseek matrix was built as a comprehensive, online open-access tabulated database which provides a reliable, comprehensive and user-friendly overview of 328 GMO events and 247 different genetic elements (status: 18/07/2013). The GMOseek matrix is aiming to facilitate GMO detection from plant origin at different phases of the analysis. It assists in selecting the targets for a screening analysis, interpreting the screening results, checking the occurrence of a screening element in a group of selected GMOs, identifying gaps in the available pool of GMO detection methods, and designing a decision tree. The GMOseek matrix is an independent database with effective functionalities in a format facilitating transferability to other platforms. Data were collected from all available sources and experimentally tested where detection methods and certified reference materials (CRMs) were available. CONCLUSIONS The GMOseek matrix is currently a unique and very valuable tool with reliable information on GMOs from plant origin and their present genetic elements that enables further development of appropriate strategies for GMO detection. It is flexible enough to be further updated with new information and integrated in different applications and platforms.
Collapse
Affiliation(s)
- Annette Block
- Walloon Agricultural Research Centre (CRA-W), Gembloux, Belgium.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Aurnhammer C, Haase M, Muether N, Hausl M, Rauschhuber C, Huber I, Nitschko H, Busch U, Sing A, Ehrhardt A, Baiker A. Universal real-time PCR for the detection and quantification of adeno-associated virus serotype 2-derived inverted terminal repeat sequences. Hum Gene Ther Methods 2013; 23:18-28. [PMID: 22428977 DOI: 10.1089/hgtb.2011.034] [Citation(s) in RCA: 283] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Viral vectors based on various naturally occurring adeno-associated virus (AAV) serotypes are among the most promising tools in human gene therapy. For the production of recombinant AAV (rAAV) vectors, researchers are focusing predominantly on cross-packaging an artificial AAV genome based on serotype 2 (AAV2) into capsids derived from other serotypes. Within the packaged genome the inverted terminal repeats (ITRs) are the only cis-acting viral elements required for rAAV vector generation and depict the lowest common denominator of all AAV2-derived vector genomes. Up to now, no quantitative PCR (qPCR) for the detection and quantification of AAV2 ITRs could be established because of their extensive secondary hairpin structure formation. Current qPCR-based methods are therefore targeting vector-encoded transgenes or regulatory elements. Herein we establish a molecular biological method that allows accurate and reproducible quantification of AAV2 genomes on the basis of an AAV2 ITR sequence-specific qPCR. Primers and labeled probe are located within the ITR sequence and have been designed to detect both wild-type AAV2 and AAV2-based vectors. This method is suitable for detecting single-stranded DNA derived from AAV2 vector particles and double-stranded DNA derived from vector plasmids. The limit of detection has been determined as 50 ITR sequence copies per reaction, by comparison with a plasmid standard. In conclusion, this method describes the first qPCR system facilitating the detection and quantification of AAV2 ITR sequences. Because this method can be used universally for all AAV2 genome-based vectors, it will significantly simplify rAAV2 vector titrations in the future.
Collapse
|
38
|
Rettinger A, Krupka I, Grünwald K, Dyachenko V, Fingerle V, Konrad R, Raschel H, Busch U, Sing A, Straubinger RK, Huber I. Leptospira spp. strain identification by MALDI TOF MS is an equivalent tool to 16S rRNA gene sequencing and multi locus sequence typing (MLST). BMC Microbiol 2012; 12:185. [PMID: 22925589 PMCID: PMC3460781 DOI: 10.1186/1471-2180-12-185] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Accepted: 07/30/2012] [Indexed: 01/23/2023] Open
Abstract
Background In this study mass spectrometry was used for evaluating extracted leptospiral protein samples and results were compared with molecular typing methods. For this, an extraction protocol for Leptospira spp. was independently established in two separate laboratories. Reference spectra were created with 28 leptospiral strains, including pathogenic, non-pathogenic and intermediate strains. This set of spectra was then evaluated on the basis of measurements with well-defined, cultured leptospiral strains and with 16 field isolates of veterinary or human origin. To verify discriminating peaks for the applied pathogenic strains, statistical analysis of the protein spectra was performed using the software tool ClinProTools. In addition, a dendrogram of the reference spectra was compared with phylogenetic trees of the 16S rRNA gene sequences and multi locus sequence typing (MLST) analysis. Results Defined and reproducible protein spectra using MALDI-TOF MS were obtained for all leptospiral strains. Evaluation of the newly-built reference spectra database allowed reproducible identification at the species level for the defined leptospiral strains and the field isolates. Statistical analysis of three pathogenic genomospecies revealed peak differences at the species level and for certain serovars analyzed in this study. Specific peak patterns were reproducibly detected for the serovars Tarassovi, Saxkoebing, Pomona, Copenhageni, Australis, Icterohaemorrhagiae and Grippotyphosa. Analysis of the dendrograms of the MLST data, the 16S rRNA sequencing, and the MALDI-TOF MS reference spectra showed comparable clustering. Conclusions MALDI-TOF MS analysis is a fast and reliable method for species identification, although Leptospira organisms need to be produced in a time-consuming culture process. All leptospiral strains were identified, at least at the species level, using our described extraction protocol. Statistical analysis of the three genomospecies L. borgpetersenii, L. interrogans and L. kirschneri revealed distinctive, reproducible differentiating peaks for seven leptospiral strains which represent seven serovars. Results obtained by MALDI-TOF MS were confirmed by MLST and 16S rRNA gene sequencing.
Collapse
Affiliation(s)
- Anna Rettinger
- Bacteriology and Mycology, Institute for Infectious Diseases and Zoonoses, Department of Veterinary Sciences, Faculty of Veterinary Medicine, LMU Munich, Munich, Germany
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
39
|
Abstract
Diphtheria is caused by diphtheria toxin-producing Corynebacterium species. While classical respiratory diphtheria is transmitted by droplets, cutaneous diphtheria often results from minor trauma. This report concerns the first case of sexually transmitted diphtheria in a patient with non-gonococcal urethritis after orogenital contact.
Collapse
Affiliation(s)
- Anja Berger
- National Consiliary Laboratory for Diphtheria, Oberschleissheim, Germany
| | | | | | | | | | | |
Collapse
|
40
|
Berger A, Huber I, Merbecks SS, Ehrhard I, Konrad R, Hörmansdorfer S, Hogardt M, Sing A. Toxigenic Corynebacterium ulcerans in woman and cat. Emerg Infect Dis 2012; 17:1767-9. [PMID: 21888821 PMCID: PMC3322090 DOI: 10.3201/eid1709.110391] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
41
|
Pavlovic M, Konrad R, Iwobi AN, Sing A, Busch U, Huber I. A dual approach employing MALDI-TOF MS and real-time PCR for fast species identification within the Enterobacter cloacae complex. FEMS Microbiol Lett 2012; 328:46-53. [DOI: 10.1111/j.1574-6968.2011.02479.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 11/05/2011] [Accepted: 12/02/2011] [Indexed: 11/27/2022] Open
Affiliation(s)
- Melanie Pavlovic
- Bavarian Health and Food Safety Authority; Oberschleißheim; Germany
| | - Regina Konrad
- Bavarian Health and Food Safety Authority; Oberschleißheim; Germany
| | - Azuka N. Iwobi
- Bavarian Health and Food Safety Authority; Oberschleißheim; Germany
| | - Andreas Sing
- Bavarian Health and Food Safety Authority; Oberschleißheim; Germany
| | - Ulrich Busch
- Bavarian Health and Food Safety Authority; Oberschleißheim; Germany
| | - Ingrid Huber
- Bavarian Health and Food Safety Authority; Oberschleißheim; Germany
| |
Collapse
|
42
|
Guertler P, Huber I, Pecoraro S, Busch U. Development of an event-specific detection method for genetically modified rice Kefeng 6 by quantitative real-time PCR. J Verbrauch Lebensm 2011. [DOI: 10.1007/s00003-011-0748-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
43
|
|
44
|
Aurnhammer C, Haase M, Muether N, Hausl M, Rauschhuber C, Huber I, Nitschko H, Busch U, Sing A, Ehrhardt A, Baiker A. Universal Real-Time PCR for the Detection and Quantification of Adeno-Associated Virus Serotype 2-Derived Inverted Terminal Repeat Sequences. Hum Gene Ther 2011. [DOI: 10.1089/hum.2011.034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
45
|
Konrad R, Wolf S, Meindl K, Fräßdorf J, Lindermayer M, Huber I, Messelhäußer U, Hautmann W, Sing A, Busch U. Diagnostik von pathogenen Escherichia coli (EHEC/EPEC) am Bayerischen Landesamt für Gesundheit und Lebensmittelsicherheit. Gesundheitswesen 2011. [DOI: 10.1055/s-0031-1274475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
46
|
Huber I, Konrad R, Sebah D, Hartberger C, Bayer M, Sing A, Campe H. Eine Multiplex one-step RT- Real Time PCR für die Diagnostik von Influenzaviren. Gesundheitswesen 2011. [DOI: 10.1055/s-0031-1274465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
47
|
Pavlovic M, Grünwald K, Zeller-Péronnet V, Maggipinto M, Huber I, Konrad R, Berger A, Messelhäußer U, Zimmermann P, Hörmansdorfer S, Sing A, Busch U. Identifizierung von Bakterien mit dem MALDI Biotyper am Bayerischen Landesamt für Gesundheit und Lebensmittelsicherheit. Gesundheitswesen 2011. [DOI: 10.1055/s-0031-1274482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
48
|
Pavlovic M, Luze A, Konrad R, Berger A, Sing A, Busch U, Huber I. Development of a duplex real-time PCR for differentiation between E. coli and Shigella spp. J Appl Microbiol 2011; 110:1245-51. [DOI: 10.1111/j.1365-2672.2011.04973.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
49
|
Huber I, Campe H, Sebah D, Hartberger C, Konrad R, Bayer M, Busch U, Sing A. A multiplex one-step real-time RT-PCR assay for influenza surveillance. Euro Surveill 2011. [DOI: 10.2807/ese.16.07.19798-en] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
For surveillance purposes real-time PCR assays for influenza viruses had to be adapted to the pandemic influenza A(H1N1)2009 strain. We combined published primers and probes for influenza A, influenza B and an internal amplification control with a detection system for influenza A(H1N1)2009 to set up a rapid, reliable, simple and cost-effective high-throughput multiplex one-step real-time RT-PCR. The workflow also includes automated sample preparation for high-throughput screening. The lower limit of detection of the multiplex assay was 3.5x102 RNA copies per PCR reaction. The diagnostic sensitivity of the multiplex assay was 87.7%, but increased to 99.4% for influenza-positive samples yielding Ct values of less than 34 cycles in the respective diagnostic assay. High specificity was confirmed by sequencing and correct detection of 15 reference samples from two quality assurance studies. The multiplex PCR was introduced for surveillance of samples from a network of general practitioners and paediatricians in Bavaria, Germany during the influenza pandemic of 2009. Comparison with surveillance data from reported cases proved the reliability of the multiplex assay for influenza surveillance programmes.
Collapse
Affiliation(s)
- I Huber
- Bavarian Health and Food Safety Authority (LGL), Oberschleißheim, Germany
- These authors contributed equally to this work
| | - H Campe
- These authors contributed equally to this work
- Bavarian Health and Food Safety Authority (LGL), Oberschleißheim, Germany
| | - D Sebah
- Bavarian Health and Food Safety Authority (LGL), Oberschleißheim, Germany
| | - C Hartberger
- Bavarian Health and Food Safety Authority (LGL), Oberschleißheim, Germany
| | - R Konrad
- Bavarian Health and Food Safety Authority (LGL), Oberschleißheim, Germany
| | - M Bayer
- Bavarian Health and Food Safety Authority (LGL), Oberschleißheim, Germany
| | - U Busch
- Bavarian Health and Food Safety Authority (LGL), Oberschleißheim, Germany
| | - A Sing
- Bavarian Health and Food Safety Authority (LGL), Oberschleißheim, Germany
| |
Collapse
|
50
|
Huber I, Campe H, Sebah D, Hartberger C, Konrad R, Bayer M, Busch U, Sing A. A multiplex one-step real-time RT-PCR assay for influenza surveillance. Euro Surveill 2011; 16:19798. [PMID: 21345319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023] Open
Abstract
For surveillance purposes real-time PCR assays for influenza viruses had to be adapted to the pandemic influenza A(H1N1)2009 strain. We combined published primers and probes for influenza A, influenza B and an internal amplification control with a detection system for influenza A(H1N1)2009 to set up a rapid, reliable, simple and cost-effective high-throughput multiplex one-step real-time RT-PCR. The workflow also includes automated sample preparation for high-throughput screening. The lower limit of detection of the multiplex assay was 3.5x10(2) RNA copies per PCR reaction. The diagnostic sensitivity of the multiplex assay was 87.7%, but increased to 99.4% for influenza-positive samples yielding C(t) values of less than 34 cycles in the respective diagnostic assay. High specificity was confirmed by sequencing and correct detection of 15 reference samples from two quality assurance studies. The multiplex PCR was introduced for surveillance of samples from a network of general practitioners and paediatricians in Bavaria, Germany during the influenza pandemic of 2009. Comparison with surveillance data from reported cases proved the reliability of the multiplex assay for influenza surveillance programmes.
Collapse
Affiliation(s)
- I Huber
- Bavarian Health and Food Safety Authority, LGL, Oberschleibheim, Germany
| | | | | | | | | | | | | | | |
Collapse
|