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Beterams A, Kirse A, Kreienbrock L, Stingl K, Bandick N, Reich F. Application of hot water and cold air to reduce bacterial contamination on broiler carcasses. Front Microbiol 2024; 15:1429756. [PMID: 39376704 PMCID: PMC11457684 DOI: 10.3389/fmicb.2024.1429756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Accepted: 09/05/2024] [Indexed: 10/09/2024] Open
Abstract
Two physical treatments (heat via water bath and cold air) with various temperatures (20/70/75/80°C and - 80/-90°C) and exposure times (20, 30, 40 s) were carried out to identify a decontaminating effect on zoonotic pathogens on broiler carcasses. Subsequently, carcasses were analyzed for thermotolerant Campylobacter (C.), Salmonella, Escherichia (E.). coli and total colony count (TCC). Moreover, for the hot water treatment, qPCR with viable/dead differentiation (v-qPCR) was applied to detect viable but non-culturable cells (VBNC) of Campylobacter, referred to as intact but putatively infectious units (IPIU). Hot water immersion was tested on carcasses inoculated with C. jejuni and Salmonella, while cold air treatment was evaluated for naturally contaminated carcasses of broiler flocks colonized with Campylobacter. For hot water treatment, the statistically significant reducing effect was about 1 log10 CFU/ml for both Salmonella and Campylobacter for 70-80°C and 20/30 s treatments. The effect of heat treatment for Campylobacter was smaller when samples were analyzed with v-qPCR with reductions of 0.5-0.8 log10 IPIU/ml in mean. Cold air treatments at -90°C were effective in reducing the mean contamination level of Campylobacter by 0.4-0.5 log10 CFU/ml at all exposure times (p < 0.05). Hot water treatments showed a decreasing trend on TCC by 0.6-0.9 log10 CFU/ml (p < 0.05). TCC counts were not significantly affected by cold air treatment. For E. coli no statistically significant reductions were observed by hot water treatment. The cold air treatment at -90°C for 20 and 40 s led to a reduction of E. coli by 0.4 and 0.8 log10 CFU/ml (p < 0.05), respectively. Treatment of carcasses with higher bacterial levels tended to show higher reduction. The research demonstrated that the efficacy of physical treatments for decontamination of broiler carcasses was more pronounced for hot water immersion than for cold air exposure. In conclusion, the results shed light on the potential application of these physical treatments in practice to reduce the quantitative load of contaminating pathogens to enhance food safety in the broiler meat production.
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Affiliation(s)
- Anja Beterams
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Alina Kirse
- Institute of Biometry, Epidemiology and Information Processing (IBEI), WHO Collaborating Centre for Research and Training for Health at the Human-Animal-Environment Interface, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Lothar Kreienbrock
- Institute of Biometry, Epidemiology and Information Processing (IBEI), WHO Collaborating Centre for Research and Training for Health at the Human-Animal-Environment Interface, University of Veterinary Medicine Hannover, Hanover, Germany
| | - Kerstin Stingl
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Niels Bandick
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Felix Reich
- Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
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Costa-Ribeiro A, Lamas A, Mora A, Prado M, Garrido-Maestu A. Moving towards on-site detection of Shiga toxin-producing Escherichia coli in ready-to-eat leafy greens. Curr Res Food Sci 2024; 8:100716. [PMID: 38511154 PMCID: PMC10950744 DOI: 10.1016/j.crfs.2024.100716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 03/01/2024] [Accepted: 03/06/2024] [Indexed: 03/22/2024] Open
Abstract
Rapid identification of Shiga toxin-producing Escherichia coli, or STEC, is of utmost importance to assure the innocuousness of the foodstuffs. STEC have been implicated in outbreaks associated with different types of foods however, among them, ready-to-eat (RTE) vegetables are particularly problematic as they are consumed raw, and are rich in compounds that inhibit DNA-based detection methods such as qPCR. In the present study a novel method based on Loop-mediated isothermal amplification (LAMP) to overcome the limitations associated with current molecular methods for the detection of STEC in RTE vegetables targeting stx1 and stx2 genes. In this sense, LAMP demonstrated to be more robust against inhibitory substances in food. In this study, a comprehensive enrichment protocol was combined with four inexpensive DNA extraction protocols. The one based on silica purification enhanced the performance of the method, therefore it was selected for its implementation in the final method. Additionally, three different detection chemistries were compared, namely real-time fluorescence detection, and two end-point colorimetric strategies, one based on the addition of SYBR Green, and the other based on a commercial colorimetric master mix. After optimization, all three chemistries demonstrated suitable for the detection of STEC in spiked RTE salad samples, as it was possible to reach a LOD50 of 0.9, 1.4, and 7.0 CFU/25 g for the real-time, SYBR and CC LAMP assays respectively. All the performance parameters reached values higher than 90 %, when compared to a reference method based on multiplex qPCR. More specifically, the analytical sensitivity was 100, 90.0 and 100 % for real-time, SYBR and CC LAMP respectively, the specificity 100 % for all three assays, and accuracy 100, 96 and 100 %. Finally, a high degree of concordance was also obtained (1, 0.92 and 1 respectively). Considering the current technological advances, the method reported, using any of the three detection strategies, demonstrated suitable for their implementation in decentralized settings, with low equipment resources.
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Affiliation(s)
- Ana Costa-Ribeiro
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310, Vigo, Spain
| | - Alexandre Lamas
- Food Hygiene, Inspection and Control Laboratory (Lhica), Department of Analytical Chemistry, Nutrition, and Bromatology, Veterinary School, Campus Terra, Universidade de Santiago de Compostela (USC), 27002, Lugo, Spain
| | - Azucena Mora
- Laboratorio de Referencia de E. coli (LREC), Dpto. de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), Lugo, Spain
- Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Santiago, Spain
| | - Marta Prado
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
- Food Hygiene, Inspection and Control Laboratory (Lhica), Department of Analytical Chemistry, Nutrition, and Bromatology, Veterinary School, Campus Terra, Universidade de Santiago de Compostela (USC), 27002, Lugo, Spain
| | - Alejandro Garrido-Maestu
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
- Laboratory of Microbiology and Technology of Marine Products (MicroTEC), Instituto de Investigaciones Marinas (IIM), CSIC, Eduardo Cabello, 6, 36208, Vigo, Spain
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Kailany R, Presmont Y, Zapata R, Owusu-Kwarteng J, Fedio W. Validation of rapid detection methods for Salmonella enterica in green chile. Lett Appl Microbiol 2024; 77:ovae011. [PMID: 38364315 DOI: 10.1093/lambio/ovae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 01/04/2024] [Accepted: 02/12/2024] [Indexed: 02/18/2024]
Abstract
The objective of this study is to validate the US Food and Drug Administration (FDA) rea-time polymerase chain reaction (qPCR) assay, the Neogen Amplified Nucleic Single Temperature Reaction (ANSR) assay, and the Vitek ImmunoDiagnostic Assay System (VIDAS) SLM procedure against the FDA cultural procedure for Salmonella detection in green chile pepper. Green chile was artificially contaminated with Salmonella according to the FDA guidelines (FDA. Guidelines for the Validation of Microbiological Methods for the FDA Foods Program, 3rd Edition. 2019. www.fda.gov/media/83812/download?attachment (17 March 2024, date last accessed)) at a fractional recovery level (where 50%-25% tests positive and at a level +1 log greater for each organism tested). Enriched samples were tested directly by the ANSR Salmonella test and by qPCR, and were subcultured into Rappaport-Vassiliadis and tetrathionate brilliant green broth for cultural detection and qPCR. For the VIDAS-SLM assay, the selective enrichments were further cultured in M broth before testing. Presumptive salmonellae were confirmed with biochemical tests, serology, and qPCR. All three rapid assays were compared favorably with the FDA-BAM (Bacteriological Analytical Manual) method. No significant differences at P < .05 were found between the procedures using McNemar's χ2 test. The three procedures were found to be rapid and reliable alternatives to cultural detection of Salmonella enterica in green chile.
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Affiliation(s)
- Raghda Kailany
- New Mexico State University, Food Safety Laboratory, Las Cruces, NM 88003, USA
| | - Yatziri Presmont
- New Mexico State University, Food Safety Laboratory, Las Cruces, NM 88003, USA
| | - Ruben Zapata
- New Mexico State University, Food Safety Laboratory, Las Cruces, NM 88003, USA
| | - James Owusu-Kwarteng
- Department of Food Science and Technology, University of Energy and Natural Resources, PO Box 214, Sunyani, Ghana
| | - Willis Fedio
- New Mexico State University, Food Safety Laboratory, Las Cruces, NM 88003, USA
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Hinrichs JB, Kreitlow A, Plötz M, Schotte U, Becher P, Gremmel N, Stephan R, Kemper N, Abdulmawjood A. Development of a Sensitive and Specific Quantitative RT-qPCR Method for the Detection of Hepatitis E Virus Genotype 3 in Porcine Liver and Foodstuff. Foods 2024; 13:467. [PMID: 38338602 PMCID: PMC10855453 DOI: 10.3390/foods13030467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
As an international and zoonotic cause of hepatitis, hepatitis E virus (HEV) poses a significant risk to public health. However, the frequency of occurrence and the degree of contamination of food of animal origin require further research. The aim of this study was to develop and validate a highly sensitive quantitative RT-qPCR assay for the detection and quantification of HEV contamination in porcine liver and food. The focus was on genotype 3, which is most common as a food contaminant in developed countries and Europe. The selected assay has its target sequence in the open reading frame 1 (ORF1) of the HEV genome and showed good results in inclusivity testing, especially for HEV genotype 3. The developed assay seems to show high efficiency and a low intercept when compared to other assays, while having a comparable limit of detection (LOD). In addition, a standard curve was generated using artificially spiked liver to provide more accurate quantitative results for contamination assessment and tracking in this matrix. Application of the assay to test 67 pig livers from different origins resulted in a positivity rate of 7.5%, which is consistent with the results of numerous other prevalence studies. Quantitative detection of the viral genome in the food chain, particularly in pig livers, is essential for understanding the presence and evolution of HEV contamination and thus ensures consumer safety.
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Affiliation(s)
- Jan Bernd Hinrichs
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, 30173 Hannover, Germany; (J.B.H.); (A.K.); (M.P.)
| | - Antonia Kreitlow
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, 30173 Hannover, Germany; (J.B.H.); (A.K.); (M.P.)
| | - Madeleine Plötz
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, 30173 Hannover, Germany; (J.B.H.); (A.K.); (M.P.)
| | - Ulrich Schotte
- Department C Animal Health and Zoonoses, Central Institute of the Bundeswehr Medical Service Kiel, 24119 Kronshagen, Germany;
| | - Paul Becher
- Institute of Virology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (P.B.); (N.G.)
| | - Nele Gremmel
- Institute of Virology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (P.B.); (N.G.)
| | - Roger Stephan
- Vetsuisse Faculty, Institute for Food Safety and Hygiene, University of Zurich, 8057 Zurich, Switzerland;
| | - Nicole Kemper
- Institute for Animal Hygiene, Animal Welfare and Farm Animal Behaviors, University of Veterinary Medicine Hannover, 30173 Hannover, Germany;
| | - Amir Abdulmawjood
- Institute of Food Quality and Food Safety, University of Veterinary Medicine Hannover, 30173 Hannover, Germany; (J.B.H.); (A.K.); (M.P.)
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Costa-Ribeiro A, Lamas A, Prado M, Garrido-Maestu A. Evaluation of the Novel mTA10 Selective Broth, MSB, for the Co-Enrichment and Detection of Salmonella spp., Escherichia coli O157 and Listeria monocytogenes in Ready-to-Eat Salad Samples. Foods 2023; 13:63. [PMID: 38201091 PMCID: PMC10778508 DOI: 10.3390/foods13010063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/19/2023] [Accepted: 12/21/2023] [Indexed: 01/12/2024] Open
Abstract
Multiplex assays implementing DNA-based methods have been demonstrated as suitable alternatives to culture-based microbiological methods; however, in most cases, they still require a suitable enrichment step. Finding suitable enrichment conditions for different bacteria may result in challenges. In the present study, a novel selective broth named MSB (mTA10 selective broth) was formulated for the simultaneous recovery of Salmonella spp., E. coli O157:H7 and L. monocytogenes. Attention was paid to ensure the optimal enrichment of L. monocytogenes as its enrichment is more challenging. To this end, cellobiose was added to increase the growth of L. monocytogenes, and sodium pyruvate was also added to improve the recovery of stressed bacteria. Four selective agents were added, namely nalidixic acid, sodium cholate, lithium chloride and potassium tellurite, to control the growth of interfering microorganisms. It was concluded that the novel broth was suitable for the simultaneous enrichment of the target pathogens, allowing them to reach concentrations higher than 7 log CFU/mL for each bacterium in pure culture. Furthermore, all heavily contaminated ready-to-eat salad samples reached concentrations higher than 5 log CFU/g. Finally, after 24 h of enrichment of spiked salad, it was possible to detect concentrations below 10 CFU/25 g.
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Affiliation(s)
- Ana Costa-Ribeiro
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal; (A.C.-R.); (M.P.)
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Alexandre Lamas
- Food Hygiene, Inspection and Control Laboratory (Lhica), Department of Analytical Chemistry, Nutrition and Bromatology, Veterinary School, Campus Terra, University of Santiago de Compostela (USC), 27002 Lugo, Spain;
| | - Marta Prado
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal; (A.C.-R.); (M.P.)
- Food Hygiene, Inspection and Control Laboratory (Lhica), Department of Analytical Chemistry, Nutrition and Bromatology, Veterinary School, Campus Terra, University of Santiago de Compostela (USC), 27002 Lugo, Spain;
| | - Alejandro Garrido-Maestu
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal; (A.C.-R.); (M.P.)
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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] [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.
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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.)
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Reichelt B, Szott V, Stingl K, Roesler U, Friese A. Detection of Viable but Non-Culturable (VBNC)- Campylobacter in the Environment of Broiler Farms: Innovative Insights Delivered by Propidium Monoazide (PMA)-v-qPCR Analysis. Microorganisms 2023; 11:2492. [PMID: 37894150 PMCID: PMC10609165 DOI: 10.3390/microorganisms11102492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 09/30/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023] Open
Abstract
Campylobacteriosis cases in humans are of global concern, with high prevalence rates in the poultry reservoir considered the most important source of infection. Research findings show Campylobacters' ability to enter a viable but non-culturable (VBNC) state, remaining "viable" but unable to grow on culture media. We explored the persistence of VBNC states in specific environments, particularly at broiler farms, as this state may lead to an underestimation of the present Campylobacter prevalence. For VBNC detection, a propidium monoazide PMA-dye viability qPCR (v-qPCR) was used in combination with cultivation methods. We examined samples collected from broiler farm barns and their surroundings, as well as chicken manure from experimental pens. In addition, the tenacity of culturable and VBNC-Campylobacter was studied in vitro in soil and water. In a total of three visits, Campylobacter was not detected either culturally or by v-qPCR (no Campylobacter DNA) in the environment of the broiler farms. In four visits, however, VBNC-Campylobacter were detected both inside and outside the barns. The overall prevalence in environmental samples was 15.9% for VBNC-Campylobacter, 62.2% for Campylobacter DNA, and 1.2% for culturable C. jejuni. In the experimental pens, no cultivable C. jejuni was detected in chicken manure after 24 h. Strikingly, "VBNC-Campylobacter" persisted even after 72 h. "VBNC-Campylobacter" were confirmed in barn surroundings and naturally contaminated chicken manure. Laboratory studies revealed that VBNC-Campylobacter can remain intact in soil for up to 28 days and in water for at least 63 days, depending on environmental conditions.
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Affiliation(s)
- Benjamin Reichelt
- Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, 14163 Berlin, Germany; (B.R.)
| | - Vanessa Szott
- Institute of Food Safety and Food Hygiene, Freie Universität Berlin, 14163 Berlin, Germany;
| | - Kerstin Stingl
- Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), 10589 Berlin, Germany
| | - Uwe Roesler
- Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, 14163 Berlin, Germany; (B.R.)
| | - Anika Friese
- Institute for Animal Hygiene and Environmental Health, Freie Universität Berlin, 14163 Berlin, Germany; (B.R.)
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Lamas A, Santos SB, Prado M, Garrido-Maestu A. Phage amplification coupled with loop-mediated isothermal amplification (PA-LAMP) for same-day detection of viable Salmonella Enteritidis in raw poultry meat. Food Microbiol 2023; 115:104341. [PMID: 37567642 DOI: 10.1016/j.fm.2023.104341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 07/10/2023] [Accepted: 07/10/2023] [Indexed: 08/13/2023]
Abstract
Salmonella Enteritidis is the main serotype responsible for human salmonellosis in the European Union. One of the main sources of Salmonella spp. in the food chain are poultry products, such as eggs or chicken meat. In recent years, molecular methods have become an alternative to culture dependent methods for the rapid screening of Salmonella spp. In this work, the strain S. Enteritidis S1400, and previously isolated and characterized bacteriophage PVP-SE2, were used to develop and evaluate a same-day detection method combining Phage Amplification and Loop-mediated isothermal amplification (PA-LAMP) to specifically detect viable S. Enteritidis in chicken breast. This method is based on the detection of the phage DNA rather than bacterial DNA. The virus is added to the sample during pre-enrichment in buffered peptone water, where it replicates in the presence of viable S. Enteritidis. The detection of phage DNA allows, on the one hand to detect viable bacteria, since viruses only replicate in them, and on the other hand to increase the sensitivity of the method since for each infected S. Enteritidis cell, hundreds of new viruses are produced. Two different PA-LAMP detection strategies were evaluated, a real time fluorescence and a naked-eye detection. The present method could down to 0.2 fg/μL of pure phage DNA and a concentration of viral particles of 2.2 log PFU/mL. After a short Salmonella recovery step of 3 h and a co-culture of 4 h of the samples with phage particles, both real-time fluorescence and naked-eye method showed a LoD95 of 6.6 CFU/25 g and a LoD50 of 1.5/25 g in spiked chicken breast samples. The entire detection process, including DNA extraction and LAMP analysis, can be completed in around 8 h. In the current proof-of-concept, the novel PA-LAMP obtained comparable results to those of the reference method ISO 6579, to detect Salmonella Enteritidis in poultry meat.
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Affiliation(s)
- Alexandre Lamas
- Food Hygiene, Inspection and Control Laboratory, Department of Analytical Chemistry, Nutrition and Bromatology, University of Santiago de Compostela, Spain
| | - Sílvio B Santos
- Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal; LABBELS - Associate Laboratory, 4800-122, Braga, Guimarães, Portugal
| | - Marta Prado
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
| | - Alejandro Garrido-Maestu
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal.
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Azinheiro S, Rodríguez-López P, Lozano-León A, Guedes H, Regal P, Franco CM, Cepeda A, Teixeira P, Melo LD, Silva D, Fernández A, Faria M, Roumani F, Herrera J, Prado M, López-Cabo M, Garrido-Maestu A. Interlaboratory validation of a multiplex qPCR method for the detection of Listeria monocytogenes in a ready-to-eat seafood product. Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
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10
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Ferrari S, Ástvaldsson Á, Jernberg T, Stingl K, Messelhäußer U, Skarin H. Validation of PCR methods for confirmation and species identification of thermotolerant Campylobacter as part of EN ISO 10272 - Microbiology of the food chain - Horizontal method for detection and enumeration of Campylobacter spp. Int J Food Microbiol 2023; 388:110064. [PMID: 36610236 DOI: 10.1016/j.ijfoodmicro.2022.110064] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/29/2022]
Abstract
This article describes the outline and organisation of the validation of three multiplex PCR methods for species identification and/or confirmation of thermotolerant Campylobacter spp. The three PCR methods were validated against the reference method described in the EN ISO standard 10272:2017. The results of the PCR methods were compared against the reference method in a method comparison study and an interlaboratory study based on EN ISO 16140-6:2019. The performance, in terms of inclusivity and exclusivity, of each of the eight PCR targets were comparable to the performance of the reference method: close, equal, or better depending on the target. In total, all three PCR methods were concluded to be equally qualified as the reference method for molecular identification and/or confirmation of thermotolerant Campylobacter spp., C. jejuni, C. coli and C. lari isolated from the food chain and have been included in Amendment 1 of ISO 10272:2017.
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Affiliation(s)
| | | | | | - Kerstin Stingl
- German Federal Institute for Risk Assessment, Department of Biological Safety, National Reference Laboratory for Campylobacter, 12277 Berlin, Germany
| | - Ute Messelhäußer
- Bavarian Health and Food Safety Authority, 91058 Erlangen, Bavaria, Germany
| | - Hanna Skarin
- National Veterinary Institute, 751 89 Uppsala, Sweden.
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Roumani F, Barros-Velázquez J, Garrido-Maestu A, Prado M. Real-time PCR, and Recombinase Polymerase Amplification combined with SYBR Green I for naked-eye detection, along with Propidium Monoazide (PMA) for the detection of viable patulin-producing fungi in apples and by-products. Food Control 2023. [DOI: 10.1016/j.foodcont.2022.109347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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12
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Jaudou S, Deneke C, Tran ML, Schuh E, Goehler A, Vorimore F, Malorny B, Fach P, Grützke J, Delannoy S. A step forward for Shiga toxin-producing Escherichia coli identification and characterization in raw milk using long-read metagenomics. Microb Genom 2022; 8:mgen000911. [PMID: 36748417 PMCID: PMC9836091 DOI: 10.1099/mgen.0.000911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 10/12/2022] [Indexed: 11/25/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) are a cause of severe human illness and are frequently associated with haemolytic uraemic syndrome (HUS) in children. It remains difficult to identify virulence factors for STEC that absolutely predict the potential to cause human disease. In addition to the Shiga-toxin (stx genes), many additional factors have been reported, such as intimin (eae gene), which is clearly an aggravating factor for developing HUS. Current STEC detection methods classically rely on real-time PCR (qPCR) to detect the presence of the key virulence markers (stx and eae). Although qPCR gives an insight into the presence of these virulence markers, it is not appropriate for confirming their presence in the same strain. Therefore, isolation steps are necessary to confirm STEC viability and characterize STEC genomes. While STEC isolation is laborious and time-consuming, metagenomics has the potential to accelerate the STEC characterization process in an isolation-free manner. Recently, short-read sequencing metagenomics have been applied for this purpose, but assembly quality and contiguity suffer from the high proportion of mobile genetic elements occurring in STEC strains. To circumvent this problem, we used long-read sequencing metagenomics for identifying eae-positive STEC strains using raw cow's milk as a causative matrix for STEC food-borne outbreaks. By comparing enrichment conditions, optimizing library preparation for MinION sequencing and generating an easy-to-use STEC characterization pipeline, the direct identification of an eae-positive STEC strain was successful after enrichment of artificially contaminated raw cow's milk samples at a contamination level as low as 5 c.f.u. ml-1. Our newly developed method combines optimized enrichment conditions of STEC in raw milk in combination with a complete STEC analysis pipeline from long-read sequencing metagenomics data. This study shows the potential of the innovative methodology for characterizing STEC strains from complex matrices. Further developments will nonetheless be necessary for this method to be applied in STEC surveillance.
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Affiliation(s)
- Sandra Jaudou
- COLiPATH Unit, Laboratory for Food Safety, ANSES, Maisons-Alfort, France
- National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Carlus Deneke
- National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Mai-Lan Tran
- COLiPATH Unit, Laboratory for Food Safety, ANSES, Maisons-Alfort, France
- Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, Maisons-Alfort, France
| | - Elisabeth Schuh
- National Reference Laboratory for Escherichia coli including VTEC, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - André Goehler
- National Reference Laboratory for Escherichia coli including VTEC, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Fabien Vorimore
- Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, Maisons-Alfort, France
| | - Burkhard Malorny
- National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Patrick Fach
- COLiPATH Unit, Laboratory for Food Safety, ANSES, Maisons-Alfort, France
- Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, Maisons-Alfort, France
| | - Josephine Grützke
- National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Sabine Delannoy
- COLiPATH Unit, Laboratory for Food Safety, ANSES, Maisons-Alfort, France
- Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, Maisons-Alfort, France
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13
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Metreveli M, Bulia S, Tevzadze L, Tsanava S, Zarske M, Goenaga JC, Preuß S, Lomidze G, Koulouris S, Imnadze P, Stingl K. Comparison of Antimicrobial Susceptibility Profiles of Thermotolerant Campylobacter spp. Isolated from Human and Poultry Samples in Georgia (Caucasus). Antibiotics (Basel) 2022; 11:1419. [PMID: 36290077 PMCID: PMC9598889 DOI: 10.3390/antibiotics11101419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 11/27/2022] Open
Abstract
Antimicrobial resistance remains a public health concern globally. This study presents antimicrobial resistance by microdilution and genetic diversity by the whole-genome sequencing of Campylobacter spp. from human and poultry samples isolated in Georgia in 2020/2021. The major species in poultry samples was C. coli, while C. jejuni was preferentially isolated from human samples. Resistance against tetracycline was highest (100%) in C. coli from industrial chicken and lowest in C. jejuni from clinical isolates (36%), while resistance against ciprofloxacin varied from 80% in C. jejuni from backyard chicken to 100% in C. jejuni and C. coli from industrial chicken. The point mutations in gyrA (T86I) and tet (O) genes were detected as resistance determinants for (fluoro-)quinolone or tetracycline resistance, respectively. Ertapenem resistance is still enigmatic. All isolates displayed sensitivity towards erythromycin, gentamicin and chloramphenicol. Multi-resistance was more frequently observed in C. coli than in C. jejuni, irrespective of the isolation matrix, and in chicken isolates compared to human isolates, independent of the Campylobacter species. The Georgian strains showed high variability of multi-locus sequence types (ST), including novel STs. This study provides the first antibiotic resistance data from Campylobacter spp. in Georgia and addresses the need for follow-up monitoring programs.
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Affiliation(s)
- Maia Metreveli
- Faculty of Medicine, Ivane Javakhishvili Tbilisi State University, 0179 Tbilisi, Georgia
| | - Salome Bulia
- Department of Gastroenteric Infection Diseases, Tbilisi Children Infectious Diseases Clinical Hospital, 0171 Tbilisi, Georgia
| | - Liana Tevzadze
- National Center for Disease Control and Public Health, 0198 Tbilisi, Georgia
| | - Shota Tsanava
- National Center for Disease Control and Public Health, 0198 Tbilisi, Georgia
| | - Michael Zarske
- National Reference Laboratory for Campylobacter, Department of Biological Safety, German Federal Institute for Risk Assessment, 12277 Berlin, Germany
| | - Juan Cruz Goenaga
- National Reference Laboratory for Campylobacter, Department of Biological Safety, German Federal Institute for Risk Assessment, 12277 Berlin, Germany
| | - Sandra Preuß
- National Reference Laboratory for Campylobacter, Department of Biological Safety, German Federal Institute for Risk Assessment, 12277 Berlin, Germany
| | - Giorgi Lomidze
- Faculty of Medicine, European University, 0189 Tbilisi, Georgia
| | - Stylianos Koulouris
- European Commission, Directorate General for Health and Food Safety (DG-SANTE), 1049 Brussels, Belgium
| | - Paata Imnadze
- Faculty of Medicine, Ivane Javakhishvili Tbilisi State University, 0179 Tbilisi, Georgia
- National Center for Disease Control and Public Health, 0198 Tbilisi, Georgia
| | - Kerstin Stingl
- National Reference Laboratory for Campylobacter, Department of Biological Safety, German Federal Institute for Risk Assessment, 12277 Berlin, Germany
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14
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Change of Campylobacter, Escherichia coli and Salmonella counts in packaged broiler breast meat stored under modified atmosphere and vacuum conditions at 4 and 10 °C based on cultural and molecular biological quantification. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.109337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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15
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Chicken Skin Decontamination of Thermotolerant Campylobacter spp. and Hygiene Indicator Escherichia coli Assessed by Viability Real-Time PCR. Pathogens 2022; 11:pathogens11060706. [PMID: 35745559 PMCID: PMC9230925 DOI: 10.3390/pathogens11060706] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/31/2022] [Accepted: 06/10/2022] [Indexed: 11/17/2022] Open
Abstract
Thermotolerant Campylobacter spp. are fecal contaminants of chicken meat with serious implications for human health. E. coli is considered as hygiene indicator since, in contrast to Campylobacter. spp., the bacterium is generally present in the avian gut. Stress exposure may transiently cease bacterial division. Therefore, colony forming units (CFU) may underestimate the infection risk of pathogens. We developed a viability real-time PCR (v-qPCR) for the quantification of viable E. coli targeting the uidA gene, encoding β-glucuronidase, which is usually detected for phenotypic species identification. The short- and long-term effects of decontaminating chicken skin on the survival of both C. jejuni and an ESBL-producing E. coli were evaluated by CFU and v-qPCR. The results showed that freezing and storage in cool conditions are potentially underestimated by CFU but not by v-qPCR. The effect of treatment with peroxyacetic acid on survival was consistently detected by CFU and v-qPCR. v-qPCR analysis detected bacterial survival upon the application of lactic acid, which awaits further analysis. Interestingly, both bacteria showed similar kinetics of inactivation upon the application of reduction strategies, suggesting that E. coli might be a complementary hygiene indicator. We conclude that v-qPCR can improve food safety under the consideration of some limitations.
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16
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Digital Droplet-PCR for Quantification of Viable Campylobacter jejuni and Campylobacter coli in Chicken Meat Rinses. APPLIED SCIENCES-BASEL 2022. [DOI: 10.3390/app12115315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The EU commission established Regulation (2017/1495) in 2017 to reduce Campylobacter on chicken skin and to decrease the number of human cases of campylobacteriosis attributable to the consumption of poultry meat. A Process Hygiene Criterion based on colony-forming unit data was set to a maximum of 1000 CFU Campylobacter spp. per gram chicken neck skin at slaughterhouses. Confronted with stressors, including cold, oxidative stress or antibiotic treatment, live cells may enter into a viable but non-cultivable state (VBNC) and lose the ability to grow, in reference to the plate count ISO 10272-2:2017 method, but still possess the potential to recover and cause infections under favorable conditions. In this study, a droplet digital PCR combined with the intercalating dye propidium monoazide (PMA) was established for quantification of C. coli and C. jejuni in chicken meat rinses. The PMA was used to inactivate DNA from dead cells in this technique. This method was successfully validated against the reference method according to ISO 16140-2:2016 for accuracy and relative trueness. Additionally, it presented a 100% selectivity for Campylobacter jejuni and C. coli. Moreover, the technical measurement uncertainty was determined according to ISO 19036:2019, and the applicability of ddPCR for quantifying C. coli and C. jejuni in chicken meat rinses was investigated on naturally contaminated samples from slaughterhouses and supermarkets. Results obtained from this study demonstrated a strong correlation to qPCR as well as the classical microbiological reference method.
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17
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Iron deficient diets modify the gut microbiome and reduce the severity of enteric infection in a mouse model of S. Typhimurium-induced enterocolitis. J Nutr Biochem 2022; 107:109065. [DOI: 10.1016/j.jnutbio.2022.109065] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 04/20/2022] [Accepted: 04/25/2022] [Indexed: 01/04/2023]
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18
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Development and evaluation of a real-time fluorescence, and naked-eye colorimetric, loop-mediated isothermal amplification-based method for the rapid detection of spoilage fungi in fruit preparations. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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19
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Development of a real-time PCR assay with an internal amplification control for the detection of spoilage fungi in fruit preparations. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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20
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Roumani F, Rodrigues C, Barros-Velázquez J, Garrido-Maestu A, Prado M. Development of a Panfungal Recombinase Polymerase Amplification (RPA) Method Coupled with Lateral Flow Strips for the Detection of Spoilage Fungi. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-022-02242-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Campylobacteriosis, Shigellosis and Salmonellosis in Hospitalized Children with Acute Inflammatory Diarrhea in Georgia. Pathogens 2022; 11:pathogens11020232. [PMID: 35215176 PMCID: PMC8877102 DOI: 10.3390/pathogens11020232] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/24/2022] [Accepted: 02/01/2022] [Indexed: 02/01/2023] Open
Abstract
This is the first study on campylobacteriosis carried out in Georgia. It targeted 382 hospitalized children with acute inflammatory diarrhea. The study was conducted between July 2020 to July 2021 based on the main infection clinic of the capital city. Culture-based bacteriological methods were followed by phenotypic and Real-time PCR tests for bacterial confirmation and identification. The data revealed recent epidemiologic prevalences of the three main causative bacteria in the target population. Shigella sonnei with 19.1% (95% CI: 15.2%−23.4%) was the most frequently detected pathogen followed by Campylobacter spp. with 12.3% (95% CI: 9.2%−16.0%) and Salmonella spp. with 4.9% (95% CI: 3.0%−7.6%). However, in 63.6% of the samples, the causative agent remained unknown. Species differentiation of Campylobacter spp. revealed 81% Campylobacter jejuni and 19% Campylobacter coli. An epidemiological pyramid with estimated magnification factors may give more insights into the burden of campylobacteriosis among the studied population, resulting in a putative annual incidence of 6 per 1000 children in Tbilisi. Children with campylobacteriosis were younger (median age 40 months (interquartile range (IQR) 22−95)) than with shigellosis (median age 92 months (interquartile range (IQR) 52−140)). However, no statistically significant difference was found with the age range of patients with campylobacteriosis and salmonellosis as well as with salmonellosis and shigellosis. In conclusion, Campylobacter spp. may be suspected to be the second most frequent bacterial causative agent of acute inflammatory diarrhea in hospitalized children and the primary cause in the 0–3 age group in Georgia. In addition, Campylobacter CROMagar showed better selectivity in comparison to mCCDA selective agar of stool samples in our study.
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22
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Azinheiro S, Roumani F, Rodríguez-Lorenzo L, Carvalho J, Prado M, Garrido-Maestu A. Combination of Recombinase Polymerase Amplification with SYBR Green I for naked-eye, same-day detection of Escherichia coli O157:H7 in ground meat. Food Control 2022. [DOI: 10.1016/j.foodcont.2021.108494] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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Azinheiro S, Carvalho J, Fuciños P, Pastrana L, Prado M, Garrido-Maestu A. Short pre-enrichment and modified matrix lysis. A comparative study towards same-day detection of Listeria monocytogenes. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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24
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Linke RB, Zeki S, Mayer R, Keiblinger K, Savio D, Kirschner AKT, Reischer GH, Mach RL, Sommer R, Farnleitner AH. Identifying Inorganic Turbidity in Water Samples as Potential Loss Factor During Nucleic Acid Extraction: Implications for Molecular Fecal Pollution Diagnostics and Source Tracking. Front Microbiol 2021; 12:660566. [PMID: 34745021 PMCID: PMC8565874 DOI: 10.3389/fmicb.2021.660566] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 08/13/2021] [Indexed: 11/13/2022] Open
Abstract
Molecular diagnostic methods are increasingly applied for food and environmental analysis. Since several steps are involved in sample processing which can affect the outcome (e.g., adhesion of DNA to the sample matrix, inefficient precipitation of DNA, pipetting errors and (partial) loss of the DNA pellet during DNA isolation), quality control is essential at all processing levels. In soil microbiology, particular attention has been paid to the inorganic component of the sample matrix affecting DNA extractability. In water quality testing, however, this aspect has mostly been neglected so far, although it is conceivable that these mechanisms have a similar impact. The present study was therefore dedicated to investigate possible matrix effects on results of water quality analysis. Field testing in an aquatic environment with pronounced chemo-physical gradients [total suspended solids (TSS), inorganic turbidity, total organic carbon (TOC), and conductivity] indicated a negative association between DNA extractability (using a standard phenol/chloroform extraction procedure) and turbidity (spearman ρ = −0.72, p < 0.001, n = 21). Further detailed laboratory experiments on sediment suspensions confirmed the hypothesis of inorganic turbidity being the main driver for reduced DNA extractability. The observed effects, as known from soil samples, were also indicated to result from competitive effects for free charges on clay minerals, leading to adsorption of DNA to these inorganic particles. A protocol modification by supplementing the extraction buffer with salmon sperm DNA, to coat charged surfaces prior to cell lysis, was then applied on environmental water samples and compared to the standard protocol. At sites characterized by high inorganic turbidity, DNA extractability was significantly improved or made possible in the first place by applying the adapted protocol. This became apparent from intestinal enterococci and microbial source tracking (MST)-marker levels measured by quantitative polymerase chain reaction (qPCR) (100 to 10,000-fold median increase in target concentrations). The present study emphasizes the need to consider inorganic turbidity as a potential loss factor in DNA extraction from water-matrices. Negligence of these effects can lead to a massive bias, by up to several orders of magnitude, in the results of molecular MST and fecal pollution diagnostics.
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Affiliation(s)
- Rita B Linke
- Research Group Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Sibel Zeki
- Department of Marine Environment, Institute of Marine Sciences and Management, Istanbul University, Istanbul, Turkey
| | - René Mayer
- Research Group Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Katharina Keiblinger
- Department of Forest and Soil Sciences, Institute of Soil Research, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Domenico Savio
- Research Group Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.,Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
| | - Alexander K T Kirschner
- Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria.,Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria
| | - Georg H Reischer
- Research Group Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.,Research Area Molecular Diagnostics, Department IFA-Tulln, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Tulln, Austria
| | - Robert L Mach
- Research Division Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria
| | - Regina Sommer
- Unit of Water Microbiology, Institute for Hygiene and Applied Immunology, Medical University of Vienna, Vienna, Austria
| | - Andreas H Farnleitner
- Research Group Environmental Microbiology and Molecular Diagnostics 166/5/3, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, Vienna, Austria.,Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, Krems an der Donau, Austria
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25
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Azinheiro S, Roumani F, Carvalho J, Prado M, Garrido-Maestu A. Suitability of the MinION long read sequencer for semi-targeted detection of foodborne pathogens. Anal Chim Acta 2021; 1184:339051. [PMID: 34625270 DOI: 10.1016/j.aca.2021.339051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/07/2021] [Indexed: 12/20/2022]
Abstract
Foodborne pathogens are still a significant source of morbidity and mortality worldwide. In addition to this the current methodologies to track these microorganisms cannot cope with the current intensive production systems, thus novel methods are of outmost importance. DNA-based methods have already demonstrated suitable to address this issue, but most of them are targeted methods such as real-time PCR (qPCR), meaning that one will only find what is looking for, thus taking the risk of missing relevant pathogens in a given sample. To overcome this limitation we have developed an easy-to-implement methodology which enables the detection of several pathogens simultaneously by using long-read Next Generation Sequencing (NGS) with MinION. The method was named "semi-targeted" due to the combination of a non-targeted detection method, NGS, with the usage of selective media in order to partially eliminate non-pathogenic interfering bacteria. To this end, we included an enrichment step for the recovery of different pathogens, namely Salmonella Enteritidis and Typhimurium, Listeria monocytogenes and Escherichia coli O157:H7, after DNA extraction and library preparation, the samples were analyzed with MinION implementing the low-cost Flongle Flow Cells. The methodology was successfully evaluated in spiked milk samples with an excellent agreement with the results obtained by qPCR and culture-based methods. The method can provide accurate results after only 2 h of sequencing. Sample multiplexing, along with the lower cost of the Flongle Flow Cells and the reduced price of the MinION platform, make the assay cost-effective that is of importance for the food industry. Starting the method with a classical microbiological approach, the enrichment, the method is easy to implement in testing laboratories, it provides flexibility in terms of potential pathogens to be detected, and the positive results can be easily confirmed following culture-based, or other type, of confirmation procedures.
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Affiliation(s)
- Sarah Azinheiro
- Food Quality and Safety Research Group. International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga S/n, 4715-330 Braga, Portugal; College of Pharmacy/School of Veterinary Sciences. Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Spain
| | - Foteini Roumani
- Food Quality and Safety Research Group. International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga S/n, 4715-330 Braga, Portugal; College of Pharmacy/School of Veterinary Sciences. Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Spain
| | - Joana Carvalho
- Food Quality and Safety Research Group. International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga S/n, 4715-330 Braga, Portugal; College of Pharmacy/School of Veterinary Sciences. Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Spain
| | - Marta Prado
- Food Quality and Safety Research Group. International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga S/n, 4715-330 Braga, Portugal
| | - Alejandro Garrido-Maestu
- Food Quality and Safety Research Group. International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga S/n, 4715-330 Braga, Portugal.
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26
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Dhital R, Shen Z, Zhang S, Mustapha A. Detection of virulence and extended spectrum β-lactamase genes in Salmonella by multiplex high-resolution melt curve real-time PCR assay. J Appl Microbiol 2021; 132:2355-2367. [PMID: 34689400 DOI: 10.1111/jam.15334] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/29/2021] [Accepted: 10/17/2021] [Indexed: 11/29/2022]
Abstract
AIMS Develop and standardize multiplex high-resolution melt curve (HRM) real-time PCR assays for simultaneous detection of Salmonella virulence and extended spectrum β-lactamase (ESBL) genes in food. METHODS AND RESULTS Two sets of multiplex real-time PCR assays targeting six virulence and three ESBL genes with internal amplification control were standardized. The first assay detected hilA, fimH, sipA, blaTEM and blaSHV, and the second detected invA, fimA, stn and blaCMY . The PCR assays were validated with DNA samples from 77 different Salmonella strains. The assay specificity was tested with DNA from 47 non-Salmonella strains. Melt curve analyses showed distinct, well-separated melting peaks of each target gene detected by their respective melting temperatures (Tm ). Different food samples were spiked with 10, 102 and 103 CFU/ml of Salmonella. The optimized assays were able to detect all target genes in concentrations of as low as 10 CFU/ml in 25 g foods within 10 h of enrichment. CONCLUSIONS Multiplex HRM real-time PCR assays can be used as rapid detection methods for detecting Salmonella in foods. SIGNIFICANCE AND IMPACT OF STUDY The assays developed in this study will allow for accurate detection of virulence and ESBL genes in Salmonella that are present in low concentrations in food samples.
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Affiliation(s)
- Rajiv Dhital
- Food Science Program, University of Missouri, Columbia, Missouri, USA
| | - Zhenyu Shen
- Veterinary Diagnostic Laboratory, University of Missouri, Columbia, Missouri, USA
| | - Shuping Zhang
- Veterinary Diagnostic Laboratory, University of Missouri, Columbia, Missouri, USA
| | - Azlin Mustapha
- Food Science Program, University of Missouri, Columbia, Missouri, USA
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27
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Roumani F, Azinheiro S, Carvalho J, Prado M, Garrido-Maestu A. Loop-mediated isothermal amplification combined with immunomagnetic separation and propidium monoazide for the specific detection of viable Listeria monocytogenes in milk products, with an internal amplification control. Food Control 2021. [DOI: 10.1016/j.foodcont.2021.107975] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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28
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Goshu G, Koelmans AA, de Klein JJM. Performance of faecal indicator bacteria, microbial source tracking, and pollution risk mapping in tropical water. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 276:116693. [PMID: 33631685 DOI: 10.1016/j.envpol.2021.116693] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/25/2021] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
Faecal indicator bacteria (FIB) are used for the assessment of faecal pollution and possible water quality deterioration. There is growing evidence that FIB used in temperate regions are not adequate and reliable to detect faecal pollution in tropical regions. Hence, this study evaluated the adequacy of FIB, including total coliforms (TC), Escherichia coli (EC), Enterococci (IEC), and Clostridium perfringens (CP) in the high-altitude, tropical country of Ethiopia. In addition to FIB, for microbial source tracking (MST), a ruminant-associated molecular marker was applied at different water types and altitudes, and faecal pollution risk mapping was conducted based on consensus FIB. The performances of the indicators were evaluated at 22 sites from different water types. The results indicate that EC cell enumeration and CP spore determination perform well for faecal contamination monitoring. Most of the sub-basins of Lake Tana were found to be moderately to highly polluted, and the levels of pollution were demonstrated to be higher in the rainy season than in the post-rainy season. Markers associated with ruminants (BacR) were identified in more than three quarters of the sites. A bacterial pollution risk map was developed for sub-basins of Lake Tana, including the un-gauged sub-basins. We demonstrate how bacterial pollution risk mapping can aid in improvements to water quality testing and reduce risk to the general population from stream bacteria.
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Affiliation(s)
- Goraw Goshu
- Aquatic Ecology and Water Quality Management Group, Department of Environmental Sciences, Wageningen University &Research, P.O. Box, 47,6700AA, Wageningen, the Netherlands; College of Agriculture and Environmental Sciences and Blue Nile Water Institute, Bahir Dar University, P.O. Box 1701, Bahir Dar, Ethiopia.
| | - A A Koelmans
- Aquatic Ecology and Water Quality Management Group, Department of Environmental Sciences, Wageningen University &Research, P.O. Box, 47,6700AA, Wageningen, the Netherlands
| | - J J M de Klein
- Aquatic Ecology and Water Quality Management Group, Department of Environmental Sciences, Wageningen University &Research, P.O. Box, 47,6700AA, Wageningen, the Netherlands
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29
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Linke RB, Kebede G, Mushi D, Lakew A, Hayes DS, Graf W, Farnleitner AH. Assessing the faecal source sensitivity and specificity of ruminant and human genetic microbial source tracking markers in the central Ethiopian highlands. Lett Appl Microbiol 2020; 72:458-466. [PMID: 33300161 PMCID: PMC7986238 DOI: 10.1111/lam.13436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 12/04/2020] [Accepted: 12/04/2020] [Indexed: 12/21/2022]
Abstract
This study tested genetic microbial source tracking (MST) methods for identifying ruminant‐ (BacR) and human‐associated (HF183/BacR287, BacHum) bacterial faecal contaminants in Ethiopia in a newly created regional faecal sample bank (n = 173). BacR performed well, and its marker abundance was high (100% sensitivity (Sens), 95% specificity (Spec), median log10 8·1 marker equivalents (ME) g−1 ruminant faeces). Human‐associated markers tested were less abundant in individual human samples (median: log10 5·4 and 4·2 (ME + 1) g−1) and were not continuously detected (81% Sens, 91% Spec for BacHum; 77% Sens, 91% Spec for HF183/BacR287). Furthermore, the pig‐associated Pig2Bac assay was included and performed excellent (100% Sens, 100% Spec). To evaluate the presence of MST targets in the soil microbiome, representative soil samples were tested during a whole seasonal cycle (n = 60). Only BacR could be detected, but was limited to the dry season and to sites of higher anthropogenic influence (log10 3·0 to 4·9 (ME + 1) g−1 soil). In conclusion, the large differences in marker abundances between target and non‐target faecal samples (median distances between distributions ≥log10 3 to ≥log10 7) and their absence in pristine soil indicate that all tested assays are suitable candidates for diverse MST applications in the Ethiopian area.
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Affiliation(s)
- R B Linke
- Research Group of Environmental Microbiology and Molecular Diagnostics, Institute for Chemical, Biological and Environmental Engineering, Technical University Vienna, Vienna, Austria
| | - G Kebede
- Department of Biological Sciences, Ambo University, Ambo, Ethiopia.,Institute of Hydrobiology and Aquatic Ecosystem Management (IHG), University of Natural Resources and Life Sciences, Vienna, Austria
| | - D Mushi
- Department of Biosciences, Solomon Mahlangu College of Science and Education, Sokoine University of Agriculture, Morogoro, Tanzania
| | - A Lakew
- National Fishery and Aquatic Life Research Centre, Ethiopian Institute of Agricultural Research (EIAR), Sebeta, Ethiopia
| | - D S Hayes
- Institute of Hydrobiology and Aquatic Ecosystem Management (IHG), University of Natural Resources and Life Sciences, Vienna, Austria.,Centro de Estudos Florestais (CEF), Instituto Superior de Agronomia, University of Lisbon, Lisbon, Portugal
| | - W Graf
- Institute of Hydrobiology and Aquatic Ecosystem Management (IHG), University of Natural Resources and Life Sciences, Vienna, Austria
| | - A H Farnleitner
- Research Group of Environmental Microbiology and Molecular Diagnostics, Institute for Chemical, Biological and Environmental Engineering, Technical University Vienna, Vienna, Austria.,Research Division Water Quality and Health, Karl Landsteiner University for Health Sciences, Krems, Austria
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30
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Garrido-Maestu A, Azinheiro S, Roumani F, Carvalho J, Prado M. Application of Short Pre-enrichment, and Double Chemistry Real-Time PCR, Combining Fluorescent Probes and an Intercalating Dye, for Same-Day Detection and Confirmation of Salmonella spp. and Escherichia coli O157 in Ground Beef and Chicken Samples. Front Microbiol 2020; 11:591041. [PMID: 33162968 PMCID: PMC7581864 DOI: 10.3389/fmicb.2020.591041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/22/2020] [Indexed: 11/13/2022] Open
Abstract
Molecular methods, particularly those based on real-time PCR (qPCR), have become a popular approach to detect pathogens in food samples. This technique may take advantage of hydrolysis fluorescent probes for increased specificity. Even though suitable, this approach loses the capacity of performing result confirmation by melt curve analysis. In the current study, we developed an alternative approach, combining fluorescent probes along with an intercalating dye (SYBR Green) in order to simultaneously detect, and confirm the result, of two foodborne pathogens (Salmonella spp. and Escherichia coli O157). This new approach named double chemistry qPCR was combined with a short pre-enrichment in order to obtain a multiplex “same-day” detection method for the selected pathogens. The evaluation of the novel method in spiked food samples (ground beef and chicken breast) obtained values of relative sensitivity, specificity, and accuracy higher than 95%, and Cohen’s kappa of 0.92, with a Limit of Detection95 below 5 cfu/25 g, demonstrating its reliability. In addition to this, the method was challenged by inoculating heat-stressed bacteria as well as dead ones. It was observed that it was also possible to detect stressed bacteria with an initial inoculation level below 10 cfu/25 g. Also, it was noticed that high initial concentration of either pathogen (higher than 104 cfu/25 g) was needed in order to generate false positive results due to the presence of dead bacteria, thus the method presents potential for its application in the specific detection of live microorganisms.
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Affiliation(s)
- Alejandro Garrido-Maestu
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - Sarah Azinheiro
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal.,Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Foteini Roumani
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal.,Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Joana Carvalho
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal.,Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Marta Prado
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
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31
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Frick C, Vierheilig J, Nadiotis-Tsaka T, Ixenmaier S, Linke R, Reischer GH, Komma J, Kirschner AKT, Mach RL, Savio D, Seidl D, Blaschke AP, Sommer R, Derx J, Farnleitner AH. Elucidating fecal pollution patterns in alluvial water resources by linking standard fecal indicator bacteria to river connectivity and genetic microbial source tracking. WATER RESEARCH 2020; 184:116132. [PMID: 32777635 DOI: 10.1016/j.watres.2020.116132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 06/12/2020] [Accepted: 06/29/2020] [Indexed: 06/11/2023]
Abstract
A novel concept for fecal pollution analysis was applied at alluvial water resources to substantially extend the information provided by fecal indicator bacteria (FIB). FIB data were linked to river connectivity and genetic microbial source tracking (MST). The concept was demonstrated at the Danube River and its associated backwater area downstream of the city of Vienna, using a comprehensive 3-year data set (10 selected sites, n = 317 samples). Enumeration of Escherichia coli (ISO 16649-2), intestinal enterococci (ISO 7899-2) and Clostridium perfringens (ISO 14189) revealed a patchy distribution for the investigation area. Based on these parameters alone a clear interpretation of the observed fecal contamination patterns was not possible. Comparison of FIB concentrations to river connectivity allowed defining sites with dominating versus rare fecal pollution influence from the River Danube. A strong connectivity gradient at the selected backwater sites became obvious by 2D hydrodynamic surface water modeling, ranging from 278 days (25%) down to 5 days (<1%) of hydraulic connectivity to the River Danube within the 3-year study period. Human sewage pollution could be identified as the dominating fecal source at the highly connected sites by adding information from MST analysis. In contrast, animal fecal pollution proofed to be dominating in areas with low river connectivity. The selection of genetic MST markers was focusing on potentially important pollution sources in the backwater area, using human (BacHum, HF183II), ruminant (BacR) and pig (Pig2Bac) -associated quantitative PCR assays. The presented approach is assumed to be useful to characterize alluvial water resources for water safety management throughout the globe, by allocating fecal pollution to autochthonous, allochthonous, human or animal contamination components. The established river connectivity metric is not limited to bacterial fecal pollution, but can be applied to any type of chemical and microbiological contamination.
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Affiliation(s)
- Christina Frick
- Municipal Department 39, Rinnböckstraße 15/2, 1110, Vienna, Austria; Centre for Water Resource Systems (CWRS), TU Wien, Karlsplatz 13, 1040, Vienna, Austria.
| | - Julia Vierheilig
- Karl Landsteiner University of Health Sciences, Division Water Quality and Health, Dr.-Karl-Dorrek-Straße 30, 3500, Krems an der Donau, Austria; Interuniversity Cooperation Centre for Water and Health, Austria.
| | | | - Simone Ixenmaier
- Interuniversity Cooperation Centre for Water and Health, Austria; Institute of Chemical, Environmental and Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostics 166/5/3, TU Wien, Gumpendorfer Straße 1A/166, 1060, Vienna, Austria.
| | - Rita Linke
- Interuniversity Cooperation Centre for Water and Health, Austria; Institute of Chemical, Environmental and Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostics 166/5/3, TU Wien, Gumpendorfer Straße 1A/166, 1060, Vienna, Austria.
| | - Georg H Reischer
- Interuniversity Cooperation Centre for Water and Health, Austria; Institute of Chemical, Environmental and Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostics 166/5/3, TU Wien, Gumpendorfer Straße 1A/166, 1060, Vienna, Austria.
| | - Jürgen Komma
- Institute of Hydraulic Engineering and Water Resources Management, TU Wien, Karlsplatz 13, 1040, Vienna, Austria.
| | - Alexander K T Kirschner
- Karl Landsteiner University of Health Sciences, Division Water Quality and Health, Dr.-Karl-Dorrek-Straße 30, 3500, Krems an der Donau, Austria; Interuniversity Cooperation Centre for Water and Health, Austria; Unit of Water Microbiology, Institute for Hygiene and Applied Immunology, Medical University of Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria.
| | - Robert L Mach
- Research Division Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, 1060, Vienna, Austria.
| | - Domenico Savio
- Karl Landsteiner University of Health Sciences, Division Water Quality and Health, Dr.-Karl-Dorrek-Straße 30, 3500, Krems an der Donau, Austria; Interuniversity Cooperation Centre for Water and Health, Austria; Institute of Chemical, Environmental and Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostics 166/5/3, TU Wien, Gumpendorfer Straße 1A/166, 1060, Vienna, Austria.
| | - Dagmar Seidl
- Municipal Department 39, Rinnböckstraße 15/2, 1110, Vienna, Austria.
| | - Alfred P Blaschke
- Interuniversity Cooperation Centre for Water and Health, Austria; Institute of Hydraulic Engineering and Water Resources Management, TU Wien, Karlsplatz 13, 1040, Vienna, Austria.
| | - Regina Sommer
- Interuniversity Cooperation Centre for Water and Health, Austria; Unit of Water Hygiene, Institute for Hygiene and Applied Immunology, Medical University of Vienna, Kinderspitalgasse 15, 1090, Vienna, Austria.
| | - Julia Derx
- Interuniversity Cooperation Centre for Water and Health, Austria; Institute of Hydraulic Engineering and Water Resources Management, TU Wien, Karlsplatz 13, 1040, Vienna, Austria.
| | - Andreas H Farnleitner
- Karl Landsteiner University of Health Sciences, Division Water Quality and Health, Dr.-Karl-Dorrek-Straße 30, 3500, Krems an der Donau, Austria; Interuniversity Cooperation Centre for Water and Health, Austria; Institute of Chemical, Environmental and Bioscience Engineering, Research Group Environmental Microbiology and Molecular Diagnostics 166/5/3, TU Wien, Gumpendorfer Straße 1A/166, 1060, Vienna, Austria.
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32
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Azinheiro S, Carvalho J, Prado M, Garrido-Maestu A. Multiplex Detection of Salmonella spp., E. coli O157 and L. monocytogenes by qPCR Melt Curve Analysis in Spiked Infant Formula. Microorganisms 2020; 8:E1359. [PMID: 32899815 PMCID: PMC7564587 DOI: 10.3390/microorganisms8091359] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 09/02/2020] [Accepted: 09/03/2020] [Indexed: 01/23/2023] Open
Abstract
Food poisoning continue to be a threat in the food industry showing a need to improve the detection of the pathogen responsible for the hospitalization cases and death. DNA-based techniques represent a real advantage and allow the detection of several targets at the same time, reducing cost and time of analysis. The development of new methodology using SYBR Green qPCR for the detection of L. monocytogenes, Salmonella spp. and E. coli O157 simultaneously was developed and a non-competitive internal amplification control (NC-IAC) was implemented to detect reaction inhibition. The formulation and supplementation of the enrichment medium was also optimized to allow the growth of all pathogens. The limit of detection (LoD) 95% obtained was <1 CFU/25 g for E. coli O157, and 2 CFU/25 g for Salmonella spp. and L. monocytogenes and regarding the multiplex detection a LoD 95% of 1.7 CFU/25 g was observed. The specificity, relative sensitivity and accuracy of full methodology were 100% and the use of the NC-IAC allowed the reliability of the results without interfering with the sensitivity of the methodology. The described study proved to obtain results comparable to those of probe-based qPCR, and more economically than classical high resolution melting qPCR, being both important aspects for its implementation in the food industry.
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Affiliation(s)
- Sarah Azinheiro
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal; (S.A.); (J.C.); (M.P.)
- College of Pharmacy/School of Veterinary Sciences, University of Santiago de Compostela, Campus Vida, E-15782 Santiago de Compostela, Spain
| | - Joana Carvalho
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal; (S.A.); (J.C.); (M.P.)
- College of Pharmacy/School of Veterinary Sciences, University of Santiago de Compostela, Campus Vida, E-15782 Santiago de Compostela, Spain
| | - Marta Prado
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal; (S.A.); (J.C.); (M.P.)
| | - Alejandro Garrido-Maestu
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal; (S.A.); (J.C.); (M.P.)
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33
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Wulsten IF, Galeev A, Stingl K. Underestimated Survival of Campylobacter in Raw Milk Highlighted by Viability Real-Time PCR and Growth Recovery. Front Microbiol 2020; 11:1107. [PMID: 32625171 PMCID: PMC7311638 DOI: 10.3389/fmicb.2020.01107] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Accepted: 05/04/2020] [Indexed: 02/03/2023] Open
Abstract
Raw milk is a frequent vehicle for transmission of thermophilic Campylobacter, leading to reported outbreaks. Milk is a challenging food matrix for pathogen detection, due to its high protein and lipid content. Limited detection of Campylobacter colony-forming unit (CFU) in raw milk might underestimate the pathogen's infectious potential. We optimized a viability real-time PCR (qPCR) for application with raw milk. The procedure was robust against variations of milk lots and different Campylobacter strains. Various DNA-intercalating dyes were evaluated for their ability to reduce the PCR signal of dead cells. Only propidium monoazide (PMA) and PMAxx qualified for diagnostic use. Different sedimentation properties of viable and dead Campylobacter jejuni and Campylobacter coli strains in 10-fold diluted milk enhanced viable/dead differentiation. The new method enabled to review survival of Campylobacter spp. in raw milk based on viable cells harboring an intact cell membrane. The data were compared to culturability according to ISO10272-2:2017. A difference of up to 4.5 log10 between viable Campylobacter counts and CFU values became apparent. Relevance of viability qPCR values was corroborated by full recovery of CFU under extremely reduced oxygen concentration in the presence of hydrogen. Recovery of CFU was limited, however, upon prolonged exposure in raw milk. The data confirm that Campylobacter survival in raw milk can be largely underestimated when relying on CFU data only. We conclude that raw milk led to oxidative stress-induced growth arrest in thermophilic Campylobacter, which was reversible by reduction of the oxygen partial pressure in a time-limited way.
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Affiliation(s)
- Imke F. Wulsten
- National Reference Laboratory for Campylobacter, Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
| | - Alibek Galeev
- Institute of Medical Microbiology and Hospital Epidemiology, Hannover Medical School (MHH), Hannover, Germany
| | - Kerstin Stingl
- National Reference Laboratory for Campylobacter, Department of Biological Safety, German Federal Institute for Risk Assessment (BfR), Berlin, Germany
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34
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Garrido-Maestu A, Azinheiro S, Fuciños P, Carvalho J, Prado M. Comparative study of multiplex real-time recombinase polymerase amplification and ISO 11290-1 methods for the detection of Listeria monocytogenes in dairy products. Food Microbiol 2020; 92:103570. [PMID: 32950155 DOI: 10.1016/j.fm.2020.103570] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/09/2020] [Accepted: 06/09/2020] [Indexed: 01/12/2023]
Abstract
Dairy products have been implicated in foodborne infections caused by different bacterial pathogens. Among them, Listeria monocytogenes is of particular concern due to its ubiquity, resistance to sanitation processes and high mortality rates resulting from infection. These issues make the development of novel methods for the rapid detection of this bacterium of high interest. The evaluation of a novel multiplex real-time Recombinase Polymerase Amplification method including an internal amplification control is reported in the present work. The method performance was compared to that of the European reference method (ISO 11290-1) for the detection of the species in samples from 40 commercial products, including 14 UHT milk samples, 16 hard cheese samples, 6 infant dairy preparation samples and 4 fresh cheese samples. A limit of detection below 10 cfu/25 g or mL sample was achieved, and values higher than 90% were obtained for relative sensitivity, specificity, accuracy, positive and negative predictive values and the index (kappa) of concordance. Analysis was achieved within one working day, compared to the six days required using the ISO method. Moreover, slight modification of the ISO 11290-1 method to include secondary enrichment in half Fraser broth resulted in the confirmation of all positive samples.
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Affiliation(s)
- Alejandro Garrido-Maestu
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal.
| | - Sarah Azinheiro
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
| | - Pablo Fuciños
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
| | - Joana Carvalho
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
| | - Marta Prado
- International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
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35
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Garrido-Maestu A, Azinheiro S, Carvalho J, Espiña B, Prado M. Evaluation and implementation of commercial antibodies for improved nanoparticle-based immunomagnetic separation and real-time PCR for faster detection of Listeria monocytogenes. Journal of Food Science and Technology 2020; 57:4143-4151. [PMID: 33071335 DOI: 10.1007/s13197-020-04450-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 04/06/2020] [Accepted: 04/15/2020] [Indexed: 12/15/2022]
Abstract
L. monocytogenes continues to be a major health issue in Europe, as well as worldwide. Faster methods, not only for detection, but also for sample preparation are of great interest particularly for this slow-growing pathogen. Immunomagnetic separation has been previously reported to be an effective way to concentrate bacteria, and remove inhibitors. In the present study, different commercial antibodies were evaluated to select the most appropriate one, in order to develop a highly specific method. Additionally, magnetic nanoparticles, instead of microparticles, were selected due to their reported advantages (higher surface-volume ration and faster kinetics). Finally, the separation protocol, with a calculated capture efficiency of 95%, was combined with real-time PCR for highly sensitive detection of the concentrated bacteria. The optimized IMS-qPCR allowed to reduce hands-on time in the sample treatment, without affecting the overall performance of the method as a very low limit of detection was still obtained (9.7 CFU/ 25 g) with values for sensitivity, specificity, accuracy, positive and negative predictive values of 100%, resulting in a kappa index of concordance of 1.00. These results were obtained in spiked food samples of different types (chicken, fish, milk, hard and fresh cheese), further demonstrating the applicability of the optimized methodology presented.
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Affiliation(s)
- Alejandro Garrido-Maestu
- Department of Life Sciences, Nano4Food - Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal
| | - Sarah Azinheiro
- Department of Life Sciences, Nano4Food - Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal
| | - Joana Carvalho
- Department of Life Sciences, Nano4Food - Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal
| | - Begoña Espiña
- Department of Life Sciences, Nano4Food - Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal
| | - Marta Prado
- Department of Life Sciences, Nano4Food - Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga s/n, 4715-330 Braga, Portugal
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36
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Optimized sample treatment, combined with real-time PCR, for same-day detection of E. coli O157 in ground beef and leafy greens. Food Control 2020. [DOI: 10.1016/j.foodcont.2019.106790] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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37
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de Melo-Silva AJ, Lucena JP, Hueneburg T. The evolution of molecular diagnosis using digital polymerase chain reaction to detect cancer via cell-free DNA and circulating tumor cells. Cell Biol Int 2019; 44:735-743. [PMID: 31829466 DOI: 10.1002/cbin.11286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 12/10/2019] [Indexed: 01/05/2023]
Abstract
Cancer is one of the most important causes of death worldwide. The onset of cancer may be initiated due to a variety of factors such as environment, genetics or even due to personal lifestyle choices. To counteract this tremendous increase, the demand for a new technology has risen. By this means, the use of digital polymerase chain reaction (dPCR) has been shown to be a promising methodology in the early detection of many types of cancers. Furthermore, several researchers confirmed that the use of tumor cell-free DNA (cfDNA) and circulating tumor cells (CTC) in peripheral blood is essential in revealing an early prognosis of such diseases. Besides this, it was established that dPCR might be used in a much more efficient, accurate, and reliable manner to amplify a variety of genetic material up to the identification of mutations in hematological diseases. Therefore, this article demonstrates the differences between conventional PCR and dPCR as a molecular technique to detect the early onset of cancer. Furthermore, CTC and cfDNA were officially approved by the Food and Drug Administration as new biological biomarkers in cancer development and monitoring.
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Affiliation(s)
- Alex José de Melo-Silva
- Department of Immunology, Aggeu Magalhães Institute, IAM/FIOCRUZ-PE, Recife-PE, 50670-420, Brazil
| | - Jessica Paula Lucena
- Department of Immunology, Aggeu Magalhães Institute, IAM/FIOCRUZ-PE, Recife-PE, 50670-420, Brazil
| | - Thomas Hueneburg
- University of Technology Sydney, Sydney, 2007, Australia.,Department of Microbiology and Immunology, University of Melbourne, Melbourne-Vic, 3010 Parkeville VIC, Australia
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38
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Garrido-Maestu A, Azinheiro S, Carvalho J, Prado M. Combination of Immunomagnetic Separation and Real-Time Recombinase Polymerase Amplification (IMS-qRPA) for Specific Detection of Listeria monocytogenes in Smoked Salmon Samples. J Food Sci 2019; 84:1881-1887. [PMID: 31264719 DOI: 10.1111/1750-3841.14662] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/18/2019] [Accepted: 04/23/2019] [Indexed: 01/24/2023]
Abstract
Nowadays, Listeria monocytogenes continues to be a major health issue. Therefore, improvements in the speed and reliability of its detection are still needed. In the present study, the combination of real-time Recombinase Polymerase Amplification (qRPA) with immunomagnetic separation (IMS) is described. The proposed methodology was tested against a real-time PCR method, and was successfully applied to 50 smoked salmon samples spiked at levels ranging from 2 to 9.3 × 102 cfu/25 g. L. monocytogenes was detected after a 24 hr pre-enrichment, which represents a great improvement over other previously published RPA methods. Additionally, the evaluation of the method reported a Limit of dDetection 50 (LoD50 ) of 6.3 cfu/25 g, along with relative sensitivity, specificity and accuracy values higher than 90%. Finally, the index of kappa concordance was calculated to be 0.93 which is interpreted as "almost complete concordance" between the reference and alternative method. Overall, the described methodology proved to be faster, specific, and as sensitive as other methods based on RPA or real-time PCR. PRACTICAL APPLICATION: The methodology described in this study significantly reduces the detection time of L. monocytogenes, when compared with culture-based methods, and it requires fewer steps than other molecular methods, making it a reliable and more convenient method for routine testing. Finally, the evaluation of the methodology in spiked food samples, confirms its reliability.
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Affiliation(s)
- Alejandro Garrido-Maestu
- Dept. of Life Sciences, Food Quality and Safety Research Group, Intl. Iberian Nanotechnology Lab., Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
| | - Sarah Azinheiro
- Dept. of Life Sciences, Food Quality and Safety Research Group, Intl. Iberian Nanotechnology Lab., Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
| | - Joana Carvalho
- Dept. of Life Sciences, Food Quality and Safety Research Group, Intl. Iberian Nanotechnology Lab., Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
| | - Marta Prado
- Dept. of Life Sciences, Food Quality and Safety Research Group, Intl. Iberian Nanotechnology Lab., Av. Mestre José Veiga s/n, 4715-330, Braga, Portugal
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39
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Garrido-Maestu A, Fuciños P, Azinheiro S, Carvalho C, Carvalho J, Prado M. Specific detection of viable Salmonella Enteritidis by phage amplification combined with qPCR (PAA-qPCR) in spiked chicken meat samples. Food Control 2019. [DOI: 10.1016/j.foodcont.2018.12.038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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40
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Comparative evaluation of impedanciometry combined with chromogenic agars or RNA hybridization and real-time PCR methods for the detection of L. monocytogenes in dry-cured ham. Food Control 2018. [DOI: 10.1016/j.foodcont.2018.06.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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41
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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] [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.
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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.
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42
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Blanco G, Díaz de Tuesta JA. Culture- and molecular-based detection of swine-adapted Salmonella shed by avian scavengers. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 634:1513-1518. [PMID: 29710649 DOI: 10.1016/j.scitotenv.2018.04.089] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 04/05/2018] [Accepted: 04/06/2018] [Indexed: 06/08/2023]
Abstract
Salmonella can play an important role as a disease agent in wildlife, which can then act as carriers and reservoirs of sanitary importance at the livestock-human interface. Transmission from livestock to avian scavengers can occur when these species consume contaminated carcasses and meat remains in supplementary feeding stations and rubbish dumps. We compared the performance of PCR-based detection with conventional culture-based methods to detect Salmonella in the faeces of red kites (Milvus milvus) and griffon vultures (Gyps fulvus) in central Spain. The occurrence of culturable Salmonella was intermediate in red kites (1.9%, n=52) and high in griffon vultures (26.3%, n=99). These proportions were clearly higher with PCR-based detection (13.5% and 40.4%, respectively). Confirmation cultures failed to grow Salmonella in all faecal samples positive by the molecular assay but negative by the initial conventional culture in both scavenger species, indicating the occurrence of false (non-culturable) positives by PCR-based detection. This suggests that the molecular assay is highly sensitive to detecting viable Salmonella in cultures, but also partial genomes and dead or unviable bacteria from past infections or contamination. Thus, the actual occurrence of Salmonella in a particular sampling time period can be underestimated when using only culture detection. The serovars found in the scavenger faeces were among the most frequently isolated in pigs from Spain and other EU countries, especially those generally recognized as swine-adapted monophasic variants of S. Typhimurium. Because the studied species obtain much of their food from pig carcasses, this livestock may be the primary source of Salmonella via direct ingestion of infected carcasses and indirectly via contamination due to the unsanitary conditions found in supplementary feeding stations established for scavenger conservation. Combining culture- and molecular-based detection is encouraged to understand the epidemiology and impact of Salmonella in wildlife populations.
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Affiliation(s)
- Guillermo Blanco
- Department of Evolutionary Ecology, Museo Nacional de Ciencias Naturales (CSIC), José Gutiérrez Abascal 2, 28006 Madrid, Spain.
| | - Juan A Díaz de Tuesta
- Laboratorio Regional de Sanidad Animal, Consejería de Medio Ambiente, Administración Local y Ordenación del Territorio, Comunidad de Madrid, Colmenar Viejo, Madrid, Spain
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43
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Rapid and sensitive detection of viable Listeria monocytogenes in food products by a filtration-based protocol and qPCR. Food Microbiol 2018. [DOI: 10.1016/j.fm.2018.02.004] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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44
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Mayer R, Reischer GH, Ixenmaier SK, Derx J, Blaschke AP, Ebdon JE, Linke R, Egle L, Ahmed W, Blanch AR, Byamukama D, Savill M, Mushi D, Cristóbal HA, Edge TA, Schade MA, Aslan A, Brooks YM, Sommer R, Masago Y, Sato MI, Taylor HD, Rose JB, Wuertz S, Shanks OC, Piringer H, Mach RL, Savio D, Zessner M, Farnleitner AH. Global Distribution of Human-Associated Fecal Genetic Markers in Reference Samples from Six Continents. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:5076-5084. [PMID: 29570973 PMCID: PMC5932593 DOI: 10.1021/acs.est.7b04438] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 03/09/2018] [Accepted: 03/23/2018] [Indexed: 05/19/2023]
Abstract
Numerous bacterial genetic markers are available for the molecular detection of human sources of fecal pollution in environmental waters. However, widespread application is hindered by a lack of knowledge regarding geographical stability, limiting implementation to a small number of well-characterized regions. This study investigates the geographic distribution of five human-associated genetic markers (HF183/BFDrev, HF183/BacR287, BacHum-UCD, BacH, and Lachno2) in municipal wastewaters (raw and treated) from 29 urban and rural wastewater treatment plants (750-4 400 000 population equivalents) from 13 countries spanning six continents. In addition, genetic markers were tested against 280 human and nonhuman fecal samples from domesticated, agricultural and wild animal sources. Findings revealed that all genetic markers are present in consistently high concentrations in raw (median log10 7.2-8.0 marker equivalents (ME) 100 mL-1) and biologically treated wastewater samples (median log10 4.6-6.0 ME 100 mL-1) regardless of location and population. The false positive rates of the various markers in nonhuman fecal samples ranged from 5% to 47%. Results suggest that several genetic markers have considerable potential for measuring human-associated contamination in polluted environmental waters. This will be helpful in water quality monitoring, pollution modeling and health risk assessment (as demonstrated by QMRAcatch) to guide target-oriented water safety management across the globe.
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Affiliation(s)
- René
E. Mayer
- Research
Group Environmental Microbiology and Molecular
Diagnostics 166-5-3, Institute of Chemical, Environmental
and Bioscience Engineering, TU Wien, 1060 Vienna, Austria
- Interuniversity
Cooperation Centre Water & Health, Vienna, Austria
| | - Georg H. Reischer
- Research
Group Environmental Microbiology and Molecular
Diagnostics 166-5-3, Institute of Chemical, Environmental
and Bioscience Engineering, TU Wien, 1060 Vienna, Austria
- Molecular
Diagnostics Group, IFA-Tulln, Institute
of Chemical, Environmental and Bioscience Engineering, TU Wien, 3430 Tulln, Austria
| | - Simone K. Ixenmaier
- Research
Group Environmental Microbiology and Molecular
Diagnostics 166-5-3, Institute of Chemical, Environmental
and Bioscience Engineering, TU Wien, 1060 Vienna, Austria
- Interuniversity
Cooperation Centre Water & Health, Vienna, Austria
| | - Julia Derx
- Interuniversity
Cooperation Centre Water & Health, Vienna, Austria
- Institute of Hydraulic
Engineering and Water Resources Management, TU Wien, 1040 Vienna, Austria
| | - Alfred Paul Blaschke
- Interuniversity
Cooperation Centre Water & Health, Vienna, Austria
- Institute of Hydraulic
Engineering and Water Resources Management, TU Wien, 1040 Vienna, Austria
| | - James E. Ebdon
- Environment
& Public Health Research and Enterprise Group, School of Environment
and Technology, University of Brighton, BN2 4GJ Brighton, U.K.
| | - Rita Linke
- Research
Group Environmental Microbiology and Molecular
Diagnostics 166-5-3, Institute of Chemical, Environmental
and Bioscience Engineering, TU Wien, 1060 Vienna, Austria
- Interuniversity
Cooperation Centre Water & Health, Vienna, Austria
| | - Lukas Egle
- Institute for Water Quality
and Resource Management, TU Wien, 1040 Vienna, Austria
| | - Warish Ahmed
- CSIRO
Land and Water, Ecosciences Precinct, 41 Boggo Road, Qld 4102, Australia
| | - Anicet R. Blanch
- Department
of Genetics, Microbiology and Statistics, University of Barcelona, 08028 Barcelona, Spain
| | - Denis Byamukama
- Department
of Biochemistry, Makerere University, P.O. Box 27755 Kampala, Uganda
| | - Marion Savill
- Affordable Water Limited, 1011 Auckland, New Zealand
| | - Douglas Mushi
- Department
of Biosciences, Sokoine University of Agriculture, PO BOX 3038, Morogoro, Tanzania
| | - Héctor A. Cristóbal
- Laboratorio
de Aguas y Suelos, Instituto de Investigaciones para la Industria
Química (INIQUI), Consejo Nacional
de Investigaciones Científicas y Técnicas and Universidad
Nacional de Salta, CP 4400 Salta, Argentina
| | - Thomas A. Edge
- Environment and Climate Change Canada, Canada Centre for Inland Waters, Burlington, L7S 1A1, Ontario, Canada
| | | | - Asli Aslan
- Department
of Epidemiology and Environmental Health Sciences, Georgia Southern University, Statesboro, 30460 Georgia, United States
| | - Yolanda M. Brooks
- Department of Fisheries and Wildlife, Michigan State University East Lansing, 48824 Michigan, United States
| | - Regina Sommer
- Interuniversity
Cooperation Centre Water & Health, Vienna, Austria
- Institute
for Hygiene and Applied Immunology, Water Hygiene, Medical University of Vienna, 1090 Vienna, Austria
| | - Yoshifumi Masago
- New
Industry Creation Hatchery Center, Tohoku
University, 980-8579 Sendai, Japan
| | - Maria I. Sato
- Departamento
de Análises Ambientais, CETESB -
Cia. Ambiental do Estado de São Paulo, 05459-900 São
Paulo, Brasil
| | - Huw D. Taylor
- Environment
& Public Health Research and Enterprise Group, School of Environment
and Technology, University of Brighton, BN2 4GJ Brighton, U.K.
| | - Joan B. Rose
- Department of Fisheries and Wildlife, Michigan State University East Lansing, 48824 Michigan, United States
| | - Stefan Wuertz
- Singapore Centre
for Environmental Life Sciences Engineering and
School of Civil and Environmental Engineering, Nanyang Technological University, 637551 Singapore
| | - Orin C. Shanks
- U.S. Environmental Protection Agency, Office
of Research and Development, 45268 Cincinnati, Ohio, United States
| | | | - Robert L. Mach
- Research Division Biochemical Technology, Institute of Chemical, Environmental and Bioscience Engineering, TU Wien, 1060 Vienna, Austria
| | - Domenico Savio
- Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, 3500 Krems an der Donau, Austria
| | - Matthias Zessner
- Institute for Water Quality
and Resource Management, TU Wien, 1040 Vienna, Austria
| | - Andreas H. Farnleitner
- Research
Group Environmental Microbiology and Molecular
Diagnostics 166-5-3, Institute of Chemical, Environmental
and Bioscience Engineering, TU Wien, 1060 Vienna, Austria
- Interuniversity
Cooperation Centre Water & Health, Vienna, Austria
- Division Water Quality and Health, Department Pharmacology, Physiology and Microbiology, Karl Landsteiner University of Health Sciences, 3500 Krems an der Donau, Austria
- Phone: +43 664 605882244; e-mail:
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45
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Garrido-Maestu A, Azinheiro S, Carvalho J, Fuciños P, Prado M. Development and evaluation of loop-mediated isothermal amplification, and Recombinase Polymerase Amplification methodologies, for the detection of Listeria monocytogenes in ready-to-eat food samples. Food Control 2018. [DOI: 10.1016/j.foodcont.2017.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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46
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Azinheiro S, Carvalho J, Prado M, Garrido-Maestu A. Evaluation of Different Genetic Targets for Salmonella enterica Serovar Enteriditis and Typhimurium, Using Loop-Mediated Isothermal AMPlification for Detection in Food Samples. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2018. [DOI: 10.3389/fsufs.2018.00005] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
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47
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Siala M, Barbana A, Smaoui S, Hachicha S, Marouane C, Kammoun S, Gdoura R, Messadi-Akrout F. Screening and Detecting Salmonella in Different Food Matrices in Southern Tunisia Using a Combined Enrichment/Real-Time PCR Method: Correlation with Conventional Culture Method. Front Microbiol 2017; 8:2416. [PMID: 29270157 PMCID: PMC5725475 DOI: 10.3389/fmicb.2017.02416] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 11/22/2017] [Indexed: 11/13/2022] Open
Abstract
A combined enrichment/ newly developed invA TaqMan® real-time PCR (qPCR) method as a screening assay to detect Salmonella spp. in 500 naturally food matrices is evaluated. DNA template for qPCR was extracted from an overnight pre-enriched sample in buffered peptone water using lysis–guanidine isothiocyanate method. Heterologous internal amplification control (IAC) was incorporated during qPCR assays and co-amplified with the invA gene of the target pathogen. InvA qPCR exhibited 100% specificity when testing 94 Salmonella strains (inclusivity) and 32 non-Salmonella strains (exclusivity). The qPCR showed a consistent detection of two copies of the invA gene/PCR reaction, a good intra- and inter-run reproducibility with a good PCR efficiency (89.6%). QPCR was sensitive and showed Salmonella detection at 8.5 × 100 CFU mL-1 of artificially spiked poultry meat -BWP solution in less than 40 cycles. When analyzing 500 different food matrices and comparing the results with the ISO 6579:2002 conventional culture method, the sensitivity and specificity were 100 and 76.6%, respectively. QPCR showed Salmonella spp. DNA in raw poultry meat 27/45 (60%), milk 31/93 (33.3%), raw red meat 5/13 (38.5%), and fish 11/46 (23.9%) samples. The prevalence of Salmonella spp. in cakes, dairy, cooked meals, charcuterie products using qPCR was 11/14 (26.8%), 5/22 (22.7%), 32/150 (21.3%), and 5/20 (25%), respectively, compared to 0% as demonstrated by culture. S. Anatum was the most common serovar found associated with red meat compared to S. kentucky isolated from fish and poultry meat. In conclusion, our study is the first to use a combined enrichment/invA qPCR method as a screening assay to detect Salmonella DNA in different types of commercialized food in Southern Tunisia. QPCR results indicate that Salmonella contamination is common in milk and in other types of food samples.
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Affiliation(s)
- Mariam Siala
- Department of Biology, Preparatory Institute for Engineering Studies of Sfax, University of Sfax, Sfax, Tunisia.,Department of Life Sciences, Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences of Sfax, University of Sfax, Sfax, Tunisia
| | - Amina Barbana
- Department of Life Sciences, Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences of Sfax, University of Sfax, Sfax, Tunisia
| | - Salma Smaoui
- Regional Hygiene Care Laboratory, Department of Microbiology, Hedi-Chaker University Hospital, Sfax, Tunisia.,Department of Biology B, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Salma Hachicha
- Regional Hygiene Care Laboratory, Department of Microbiology, Hedi-Chaker University Hospital, Sfax, Tunisia.,Department of Biology B, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Chema Marouane
- Regional Hygiene Care Laboratory, Department of Microbiology, Hedi-Chaker University Hospital, Sfax, Tunisia.,Department of Biology B, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Sana Kammoun
- Regional Hygiene Care Laboratory, Department of Microbiology, Hedi-Chaker University Hospital, Sfax, Tunisia.,Department of Biology B, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
| | - Radhouane Gdoura
- Department of Life Sciences, Research Laboratory of Environmental Toxicology-Microbiology and Health (LR17ES06), Faculty of Sciences of Sfax, University of Sfax, Sfax, Tunisia
| | - Férièle Messadi-Akrout
- Regional Hygiene Care Laboratory, Department of Microbiology, Hedi-Chaker University Hospital, Sfax, Tunisia.,Department of Biology B, Faculty of Pharmacy of Monastir, University of Monastir, Monastir, Tunisia
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48
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Kirschner AKT, Reischer GH, Jakwerth S, Savio D, Ixenmaier S, Toth E, Sommer R, Mach RL, Linke R, Eiler A, Kolarevic S, Farnleitner AH. Multiparametric monitoring of microbial faecal pollution reveals the dominance of human contamination along the whole Danube River. WATER RESEARCH 2017; 124:543-555. [PMID: 28806705 PMCID: PMC5718294 DOI: 10.1016/j.watres.2017.07.052] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 07/19/2017] [Accepted: 07/20/2017] [Indexed: 05/22/2023]
Abstract
The microbial faecal pollution of rivers has wide-ranging impacts on a variety of human activities that rely on appropriate river water quality. Thus, detailed knowledge of the extent and origin of microbial faecal pollution is crucial for watershed management activities to maintain safe water use. In this study, the microbial faecal pollution levels were monitored by standard faecal indicator bacteria (SFIB) along a 2580 km stretch of the Danube, the world's most international river, as well as the Danube's most important tributaries. To track the origin of faecal pollution, host-associated Bacteroidetes genetic faecal marker qPCR assays for different host groups were applied in concert with SFIB. The spatial resolution analysis was followed by a time resolution analysis of faecal pollution patterns over 1 year at three selected sites. In this way, a comprehensive faecal pollution map of the total length of the Danube was created, combining substantiated information on both the extent and origin of microbial faecal pollution. Within the environmental data matrix for the river, microbial faecal pollution constituted an independent component and did not cluster with any other measured environmental parameters. Generally, midstream samples representatively depicted the microbial pollution levels at the respective river sites. However, at a few, somewhat unexpected sites, high pollution levels occurred in the lateral zones of the river while the midstream zone had good water quality. Human faecal pollution was demonstrated as the primary pollution source along the whole river, while animal faecal pollution was of minor importance. This study demonstrates that the application of host-associated genetic microbial source tracking markers in concert with the traditional concept of microbial faecal pollution monitoring based on SFIB significantly enhances the knowledge of the extent and origin of microbial faecal pollution patterns in large rivers. It constitutes a powerful tool to guide target-oriented water quality management in large river basins.
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Affiliation(s)
- A K T Kirschner
- Medical University of Vienna, Institute for Hygiene and Applied Immunology, Water Hygiene, Kinderspitalgasse 15, A-1090 Vienna, Austria; Interuniversity Cooperation Centre for Water & Health, Austria(1).
| | - G H Reischer
- Interuniversity Cooperation Centre for Water & Health, Austria(1); Technische Universität Wien, Institute for Chemical, Biological and Environmental Engineering, Research Group of Environmental Microbiology and Molecular Diagnostics 166/5/4, Gumpendorferstrasse 1A, A-1060 Vienna, Austria
| | - S Jakwerth
- Medical University of Vienna, Institute for Hygiene and Applied Immunology, Water Hygiene, Kinderspitalgasse 15, A-1090 Vienna, Austria; Interuniversity Cooperation Centre for Water & Health, Austria(1)
| | - D Savio
- Interuniversity Cooperation Centre for Water & Health, Austria(1); Technische Universität Wien, Institute for Chemical, Biological and Environmental Engineering, Research Group of Environmental Microbiology and Molecular Diagnostics 166/5/4, Gumpendorferstrasse 1A, A-1060 Vienna, Austria
| | - S Ixenmaier
- Technische Universität Wien, Institute for Chemical, Biological and Environmental Engineering, Research Group of Environmental Microbiology and Molecular Diagnostics 166/5/4, Gumpendorferstrasse 1A, A-1060 Vienna, Austria
| | - E Toth
- Eötvös Loránd University of Sciences, Department of Microbiology, Pázmány Postny 1/c, H-1117 Budapest, Hungary
| | - R Sommer
- Medical University of Vienna, Institute for Hygiene and Applied Immunology, Water Hygiene, Kinderspitalgasse 15, A-1090 Vienna, Austria; Interuniversity Cooperation Centre for Water & Health, Austria(1)
| | - R L Mach
- Technische Universität Wien, Institute for Chemical, Biological and Environmental Engineering, Research Group of Environmental Microbiology and Molecular Diagnostics 166/5/4, Gumpendorferstrasse 1A, A-1060 Vienna, Austria
| | - R Linke
- Interuniversity Cooperation Centre for Water & Health, Austria(1); Technische Universität Wien, Institute for Chemical, Biological and Environmental Engineering, Research Group of Environmental Microbiology and Molecular Diagnostics 166/5/4, Gumpendorferstrasse 1A, A-1060 Vienna, Austria
| | - A Eiler
- eDNA Solutions Ltd, Björkåsgatan 16, 43131 Mölndal, Sweden; University of Gothenburg, Department of Chemistry and Molecular Biology, Medicinaregatan 9C, 40530 Göteborg, Sweden
| | - S Kolarevic
- University of Belgrade, Chair of Microbiology, Studentski trg 16, SRB-11000 Belgrade, Serbia
| | - A H Farnleitner
- Interuniversity Cooperation Centre for Water & Health, Austria(1); Technische Universität Wien, Institute for Chemical, Biological and Environmental Engineering, Research Group of Environmental Microbiology and Molecular Diagnostics 166/5/4, Gumpendorferstrasse 1A, A-1060 Vienna, Austria; Karl Landsteiner University of Health Sciences, Dr.-Karl-Dorrek-Straße 30, 3500 Krems, Austria.
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49
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Garrido-Maestu A, Fuciños P, Azinheiro S, Carvalho J, Prado M. Systematic loop-mediated isothermal amplification assays for rapid detection and characterization of Salmonella spp., Enteritidis and Typhimurium in food samples. Food Control 2017. [DOI: 10.1016/j.foodcont.2017.05.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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50
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Dmitric M, Vidanovic D, Matovic K, Sekler M, Saric L, Arsic M, Karabasil N. In‐house validation of real‐time PCR methods for detecting the
INV A
and
TTR
genes of
Salmonella
spp. in food. J FOOD PROCESS PRES 2017. [DOI: 10.1111/jfpp.13455] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Marko Dmitric
- Department for Testing Raw Materials of Animal Origin, Food and Water, Veterinary Specialized Institute Kraljevo, Zicka 34 36000 Kraljevo Serbia
| | - Dejan Vidanovic
- Department for Laboratory DiagnosticVeterinary Specialized Institute Kraljevo Zicka 34, 36000 Kraljevo Serbia
| | - Kazimir Matovic
- Department for Laboratory DiagnosticVeterinary Specialized Institute Kraljevo Zicka 34, 36000 Kraljevo Serbia
| | - Milanko Sekler
- Department for Laboratory DiagnosticVeterinary Specialized Institute Kraljevo Zicka 34, 36000 Kraljevo Serbia
| | - Ljubisa Saric
- Institute of Food Technology, University of Novi SadBulevar cara Lazara 1 21000 Novi Sad Serbia
| | - Milos Arsic
- Service for Laboratory Testing of FoodVeterinary Specialized Institute Nis, Naselje Milka Protic 18106 Nis Serbia
| | - Nedjeljko Karabasil
- Department of Food Hygiene and TechnologyFaculty of Veterinary Medicine, University of Belgrade, Bulevar oslobodjenja 18 11000 Belgrade Serbia
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