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Michelacci V, Asséré A, Cacciò S, Cavaiuolo M, Mooijman K, Morabito S, Pedersen SK, Sayeb M, Segerman B, Simonsson M, Skarin H, Tozzoli R, van Hoek A, Hendriksen RS. European Union Reference Laboratories support the National food, feed and veterinary Reference Laboratories with rolling out whole genome sequencing in Europe. Microb Genom 2023; 9. [PMID: 37489877 PMCID: PMC10438819 DOI: 10.1099/mgen.0.001074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/26/2023] Open
Abstract
The Inter European Union Reference Laboratories (EURLs) Working Group on Next Generation Sequencing (NGS) involves eight EURLs for microbiological food and feed hazards and has been working since 2017 to promote the adoption of NGS by the National Reference Laboratories (NRLs) in the European Union. This work illustrates the results of the first 5 years of activity. By working together, the EURLs involved have released guidance documents for assisting NRLs in all the steps of NGS, helping the transition from classical molecular methods towards whole genome sequencing while ensuring harmonization, with the final aim of improving preparedness in the use of NGS to characterize microbial hazards and trace the sources of infection.
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Affiliation(s)
- Valeria Michelacci
- European Union Reference Laboratory for Escherichia coli including Shiga toxin-producing E. coli, Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Adrien Asséré
- European Union Reference Laboratory for Listeria monocytogenes, Laboratory for Food Safety, Anses, Maisons-Alfort, France
| | - Simone Cacciò
- European Union Reference Laboratory for Parasites, Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Marina Cavaiuolo
- European Union Reference Laboratory for Coagulase Positive Staphylococci, Laboratory for Food Safety, Anses, Maisons-Alfort, France
| | - Kirsten Mooijman
- European Union Reference Laboratory for Salmonella, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Stefano Morabito
- European Union Reference Laboratory for Escherichia coli including Shiga toxin-producing E. coli, Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Susanne Karlsmose Pedersen
- European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
| | - Maroua Sayeb
- European Union Reference Laboratory for Listeria monocytogenes, Laboratory for Food Safety, Anses, Maisons-Alfort, France
| | - Bo Segerman
- European Union Reference Laboratory for Campylobacter, National Veterinary Institute, Uppsala, Sweden
| | - Magnus Simonsson
- European Union Reference Laboratory for Foodborne Viruses, Swedish Food Agency, Uppsala, Sweden
| | - Hanna Skarin
- European Union Reference Laboratory for Campylobacter, National Veterinary Institute, Uppsala, Sweden
| | - Rosangela Tozzoli
- European Union Reference Laboratory for Escherichia coli including Shiga toxin-producing E. coli, Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Angela van Hoek
- European Union Reference Laboratory for Salmonella, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Rene Sjøgren Hendriksen
- European Union Reference Laboratory for Antimicrobial Resistance, Technical University of Denmark, National Food Institute, WHO Collaborating Center for Antimicrobial Resistance in Food borne Pathogens and Genomics, FAO Reference Laboratory for Antimicrobial Resistance, Kgs. Lyngby, Denmark
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Feldsine PT, Lienau AH, Leung SC, Mui LA, Humbert F, Bohnert M, Mooijman K, Schulten S, Veld PI, Rollier P, Leuschner R, Capps K, Agin J, Allaert C, Asmundson R, Asperger H, Bohnert M, Bound A, Dixon L, Donda S, Espersen M, Foster K, Gangar V, Hammack T, Humbert F, Humes L, in’t Veld P, James L, Jost-Keating K, Kalinowski R, Kwan J, Lamb J, Leung S, Lienau A, Littell A, Mooijman K, Mui L, Ott M, Qvist S, Roberts D, Ruby R, Rude R, Santos C, Schulten S, Sellers R, Smith M, Solis D, Stecchini ML, Stegeman H, Steneryd A, Suktankar V, Wiberg C, Young V. Detection of Salmonella in Fresh Cheese, Poultry Products, and Dried Egg Products by the ISO 6579 Salmonella Culture Procedure and the AOAC Official Method: Collaborative Study. J AOAC Int 2019. [DOI: 10.1093/jaoac/86.2.275] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Three food types were analyzed for the presence of Salmonella by the AOAC culture method and by the International Organization for Standardization (ISO 6579:2002) culture method. Paired test portions of each food type were simultaneously analyzed by both methods. A total of 21 laboratories representing federal government agencies and private industry, in the United States and Europe, participated in this interlaboratory study. Foods were artificially contaminated with Salmonella and competing microflora if naturally contaminated sources were not available. No statistical differences (p < 0.05) were observed between the AOAC and ISO culture methods for fresh cheese and dried egg products. A statistically significant difference was observed for one of the 2 lots of poultry from the first trial. The poultry meat used in this run was radiation sterilized, artificially contaminated with Salmonella and competitive flora, and then lyophilized. A second trial was conducted with 2 separate lots of raw ground chicken that were naturally contaminated. The results from the second trial showed no statistical difference between the 2 culture methods. A third trial involving 4 laboratories was conducted on 2 separate lots of naturally contaminated raw poultry. Again, no statistically significant differences occurred. It is recommended that ISO 6579:2002 culture method for Salmonella be adopted Official First Action for the analysis of fresh cheese, fresh chilled and frozen poultry, and dried egg products.
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Affiliation(s)
| | - Andrew H Lienau
- BioControl Systems, Inc., 12822 SE 32nd St, Bellevue, WA 98005
| | | | - Linda A Mui
- BioControl Systems, Inc., 12822 SE 32nd St, Bellevue, WA 98005
| | - Florence Humbert
- Agence Française de Sécurité Sanitaire des Aliments, Laboratoire d'Étude et de Recherches Avicoles et Porcines, BP 53, 22440, Ploufragan, France
| | - Marylène Bohnert
- Agence Française de Sécurité Sanitaire des Aliments, Laboratoire d'Étude et de Recherches Avicoles et Porcines, BP 53, 22440, Ploufragan, France
| | - Kirsten Mooijman
- National Institut of Public Health and Environment, Microbiological Laboratory for Health Protection, PO Box 1, 3720 BA Bilthoven, The Netherlands
| | - Saskia Schulten
- National Institut of Public Health and Environment, Microbiological Laboratory for Health Protection, PO Box 1, 3720 BA Bilthoven, The Netherlands
| | - Paul In’t Veld
- Regional Inspectorate South, PO Box 2280, 5202 CG's-Hertogenbosch, Rijzertlaan 19, 's-Hertogenbosch, The Netherlands
| | - Patricia Rollier
- Centre d'Étude et de Controle des Analyses en Industrie Laitière, BP 89, 39801 Poligny, France
| | - Renata Leuschner
- Ministry of Agriculture, Fisheries, and Food, Control Science Laboratory, Sand Hutton, Y041 1LZ York, United Kingdom
| | - Katherine Capps
- Ministry of Agriculture, Fisheries, and Food, Control Science Laboratory, Sand Hutton, Y041 1LZ York, United Kingdom
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Pijnacker R, Dallman TJ, Tijsma ASL, Hawkins G, Larkin L, Kotila SM, Amore G, Amato E, Suzuki PM, Denayer S, Klamer S, Pászti J, McCormick J, Hartman H, Hughes GJ, Brandal LCT, Brown D, Mossong J, Jernberg C, Müller L, Palm D, Severi E, Gołębiowska J, Hunjak B, Owczarek S, Le Hello S, Garvey P, Mooijman K, Friesema IHM, van der Weijden C, van der Voort M, Rizzi V, Franz E. An international outbreak of Salmonella enterica serotype Enteritidis linked to eggs from Poland: a microbiological and epidemiological study. Lancet Infect Dis 2019; 19:778-786. [PMID: 31133519 DOI: 10.1016/s1473-3099(19)30047-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Revised: 01/17/2019] [Accepted: 01/17/2019] [Indexed: 10/26/2022]
Abstract
BACKGROUND Salmonella spp are a major cause of food-borne outbreaks in Europe. We investigated a large multi-country outbreak of Salmonella enterica serotype Enteritidis in the EU and European Economic Area (EEA). METHODS A confirmed case was defined as a laboratory-confirmed infection with the outbreak strains of S Enteritidis based on whole-genome sequencing (WGS), occurring between May 1, 2015, and Oct 31, 2018. A probable case was defined as laboratory-confirmed infection with S Enteritidis with the multiple-locus variable-number tandem repeat analysis outbreak profile. Multi-country epidemiological, trace-back, trace-forward, and environmental investigations were done. We did a case-control study including confirmed and probable cases and controls randomly sampled from the population registry (frequency matched by age, sex, and postal code). Odds ratios (ORs) for exposure rates between cases and controls were calculated with unmatched univariable and multivariable logistic regression. FINDINGS 18 EU and EEA countries reported 838 confirmed and 371 probable cases. 509 (42%) cases were reported in 2016, after which the number of cases steadily increased. The case-control study results showed that cases more often ate in food establishments than did controls (OR 3·4 [95% CI 1·6-7·3]), but no specific food item was identified. Recipe-based food trace-back investigations among cases who ate in food establishments identified eggs from Poland as the vehicle of infection in October, 2016. Phylogenetic analysis identified two strains of S Enteritidis in human cases that were subsequently identified in salmonella-positive eggs and primary production premises in Poland, confirming the source of the outbreak. After control measures were implemented, the number of cases decreased, but increased again in March, 2017, and the increase continued into 2018. INTERPRETATION This outbreak highlights the public health value of multi-country sharing of epidemiological, trace-back, and microbiological data. The re-emergence of cases suggests that outbreak strains have continued to enter the food chain, although changes in strain population dynamics and fewer cases indicate that control measures had some effect. Routine use of WGS in salmonella surveillance and outbreak response promises to identify and stop outbreaks in the future. FUNDING European Centre for Disease Prevention and Control; Directorate General for Health and Food Safety, European Commission; and National Public Health and Food Safety Institutes of the authors' countries (see Acknowledgments for full list).
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Affiliation(s)
- Roan Pijnacker
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Bilthoven, Netherlands.
| | | | - Aloys S L Tijsma
- Netherlands Food and Consumer Product Safety Authority (NVWA), Utrecht, Netherlands
| | | | | | - Saara M Kotila
- European Centre for Disease Prevention and Control, Solna, Sweden
| | - Giusi Amore
- European Food Safety Authority, Parma, Italy
| | - Ettore Amato
- Rapid Alert System for Food and Feed, Directorate-General for Health and Food Safety, European Commission, Brussels, Belgium
| | - Pamina M Suzuki
- Crisis Management in Food, Directorate-General for Health and Food Safety, European Commission, Brussels, Belgium
| | - Sarah Denayer
- National Institute for Public Health (Sciensano), Elsene, Belgium
| | - Sofieke Klamer
- National Institute for Public Health (Sciensano), Elsene, Belgium
| | - Judit Pászti
- National Centre for Epidemiology, Budapest, Hungary
| | | | | | | | | | - Derek Brown
- Scottish Salmonella, Shigella, and Clostridium difficile Reference Laboratory, Glasgow, UK
| | - Joël Mossong
- National Health Laboratory, Dudelange, Luxembourg
| | | | | | - Daniel Palm
- European Centre for Disease Prevention and Control, Solna, Sweden
| | - Ettore Severi
- European Centre for Disease Prevention and Control, Solna, Sweden
| | | | | | | | | | | | - Kirsten Mooijman
- European Union Reference Laboratory for Salmonella, Bilthoven, Netherlands
| | - Ingrid H M Friesema
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Bilthoven, Netherlands
| | - Coen van der Weijden
- Netherlands Food and Consumer Product Safety Authority (NVWA), Utrecht, Netherlands
| | - Menno van der Voort
- Netherlands Food and Consumer Product Safety Authority (NVWA), Utrecht, Netherlands
| | | | - Eelco Franz
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Bilthoven, Netherlands
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Kinross P, van Alphen L, Martinez Urtaza J, Struelens M, Takkinen J, Coulombier D, Mäkelä P, Bertrand S, Mattheus W, Schmid D, Kanitz E, Rücker V, Krisztalovics K, Pászti J, Szögyényi Z, Lancz Z, Rabsch W, Pfefferkorn B, Hiller P, Mooijman K, Gossner C. Multidisciplinary investigation of a multicountry outbreak of Salmonella Stanley infections associated with turkey meat in the European Union, August 2011 to January 2013. Euro Surveill 2014; 19. [DOI: 10.2807/1560-7917.es2014.19.19.20801] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Binary file ES_Abstracts_Final_ECDC.txt matches
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Affiliation(s)
- P Kinross
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
- These authors contributed equally to this article
- European Programme for Intervention Epidemiology Training (EPIET), ECDC, Sweden
| | - L van Alphen
- European Programme for Public Health Microbiology Training (EUPHEM), ECDC, Sweden
- These authors contributed equally to this article
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - J Martinez Urtaza
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - M Struelens
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - J Takkinen
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - D Coulombier
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - P Mäkelä
- European Food Safety Authority (EFSA), Parma, Italy
| | - S Bertrand
- Wetenschappelijk Instituut Volksgezondheid/Institut scientifique de Santé-Publique, Brussels, Belgium
| | - W Mattheus
- Wetenschappelijk Instituut Volksgezondheid/Institut scientifique de Santé-Publique, Brussels, Belgium
| | - D Schmid
- Österreichische Agentur für Gesundheit und Ernährungssicherheit (AGES), Vienna, Austria
| | - E Kanitz
- Österreichische Agentur für Gesundheit und Ernährungssicherheit (AGES), Vienna, Austria
| | - V Rücker
- Bundesministerium für Gesundheit (BMG), Bereich Verbrauchergesundheit, Vienna, Austria
| | | | - J Pászti
- Országos Epidemiológiai Központ (OEK), Budapest, Hungary
| | - Z Szögyényi
- National Food Chain Safety Office, Ministry of Rural Development, Budapest, Hungary
| | - Z Lancz
- National Food Chain Safety Office, Ministry of Rural Development, Budapest, Hungary
| | - W Rabsch
- National Reference Centre for Salmonella and other Bacterial Enteric Pathogens, Robert Koch-Institute (RKI), Wernigerode, Germany
| | - B Pfefferkorn
- Bundesamt für Verbraucherschutz und Lebensmittelsicherheit, Berlin, Germany
| | - P Hiller
- Bundesinstitut für Risikobewertung (BfR), Berlin, Germany
| | - K Mooijman
- European Union Reference Laboratory for Salmonella, Bilthoven, the Netherlands
| | - C Gossner
- School of Public Health and Primary Care (CAPHRI), Maastricht University Medical Center (MUMC+), Maastricht, the Netherlands
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
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Feldsine PT, Lienau AH, Leung SC, Mui LA, Humbert F, Bohnert M, Mooijman K, Schulten S, Veld PI, Rollier P, Leuschner R, Capps K. Detection of Salmonella in fresh cheese, poultry products, and dried egg products by the ISO 6579 Salmonella culture procedure and the AOAC official method: collaborative study. J AOAC Int 2003; 86:275-95. [PMID: 12723915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Three food types were analyzed for the presence of Salmonella by the AOAC culture method and by the International Organization for Standardization (ISO 6579:2002) culture method. Paired test portions of each food type were simultaneously analyzed by both methods. A total of 21 laboratories representing federal government agencies and private industry, in the United States and Europe, participated in this interlaboratory study. Foods were artificially contaminated with Salmonella and competing microflora if naturally contaminated sources were not available. No statistical differences (p < 0.05) were observed between the AOAC and ISO culture methods for fresh cheese and dried egg products. A statistically significant difference was observed for one of the 2 lots of poultry from the first trial. The poultry meat used in this run was radiation sterilized, artificially contaminated with Salmonella and competitive flora, and then lyophilized. A second trial was conducted with 2 separate lots of raw ground chicken that were naturally contaminated. The results from the second trial showed no statistical difference between the 2 culture methods. A third trial involving 4 laboratories was conducted on 2 separate lots of naturally contaminated raw poultry. Again, no statistically significant differences occurred. It is recommended that ISO 6579:2002 culture method for Salmonella be adopted Official First Action for the analysis of fresh cheese, fresh chilled and frozen poultry, and dried egg products.
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Affiliation(s)
- Philip T Feldsine
- BioControl Systems, Inc., 12822 SE 32nd St, Bellevue, WA 98005, USA.
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Mendez J, Jofre J, Lucena F, Contreras N, Mooijman K, Araujo R. Conservation of phage reference materials and water samples containing bacteriophages of enteric bacteria. J Virol Methods 2002; 106:215-24. [PMID: 12393152 DOI: 10.1016/s0166-0934(02)00163-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The survival was determined in different conservation conditions of: somatic coliphages, F-specific RNA bacteriophages and phages infecting Bacteroides fragilis proposed as model micro-organisms for water quality control. Titres of phages of all groups either in pure culture phage suspensions or in naturally occurring phage suspensions were stable at (-70+/-10) degrees C and at (-20+/-5) degrees C when protected with glycerol. Moreover, phage analysis of stored suspensions demonstrated that their numbers were homogeneous, both between vials and within vials, and consequently they can be used as reference materials. Furthermore, changes in the storage temperature of the vials cause unpredictable changes in the numbers of bacteriophages. Consequently, phage reference materials and samples containing a quantitative number of phages must be maintained and dispatched at a constant temperature. Consequently, the results indicate that bacteriophages should be packed in dry ice during transport and storage. Finally, the number of phages in water samples stored at (5+/-3) degrees C in the dark does not decrease significantly during the first 72 h of storage. In addition, phage concentrates from natural samples obtained by adsorption-elution to cellulose nitrate filters and mixed with 10% glycerol were stable at least for 2 months at (-70+/-10) degrees C and at (-20+/-5) degrees C.
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Affiliation(s)
- J Mendez
- Departament de Microbiologia, Facultat de Biologia, Universitat de Barcelona, Av Diagonal 645, Barcelona 08028, Spain
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Contreras-Coll N, Lucena F, Mooijman K, Havelaar A, Pierz V, Boque M, Gawler A, Höller C, Lambiri M, Mirolo G, Moreno B, Niemi M, Sommer R, Valentin B, Wiedenmann A, Young V, Jofre J. Occurrence and levels of indicator bacteriophages in bathing waters throughout Europe. Water Res 2002; 36:4963-4974. [PMID: 12448544 DOI: 10.1016/s0043-1354(02)00229-4] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Somatic coliphages, F-specific RNA bacteriophages, bacteriophages infecting Bacteroides fragilis, Escherichia coli and enterococci were counted in bathing waters in the late spring and summer. We tested fresh and marine bathing waters from North, South, East and West Europe expected to contain between 100 and 500 E. coli per 100 ml, although wider ranges were sometimes found. Bacteriophages were counted after concentration, since a preliminary study proved that this step was necessary to obtain positive counts. During monitoring, a first-line quality control with reference materials for bacteria and bacteriophages was performed by all the laboratories participating in the study. The same microbes were also counted in raw sewage samples from various areas in Europe, where the bacterial indicators and the three groups of bacteriophages were detected in roughly the same numbers. All groups of bacteriophages were detected in both fresh and marine bathing waters throughout Europe. Reliable and complete results from 147 samples showed that for log-transformed values, E. coli and bacteriophages were slightly correlated. However, the slope of the regression line changed according to E. coli concentration and the correlation diminished when this concentration was close to zero per 100 ml. The ratios between E. coli and phages in bathing waters differed significantly from those in sewage. The relative amounts of bacteriophages, mainly somatic coliphages and phages infecting Bact. fragilis RYC2056, increased in bathing waters with low E. coli concentration, especially in seawater samples containing < 100 E. coli per 100 ml. The relationship of bacteriophages with respect to enterococci paralleled that of bacteriophages with respect to E. coli. Somatic coliphages and bacteriophages infecting Bact. fragilis are useful to predict the presence of some pathogens with the same origin as present bacterial indicators but with higher survival rates.
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Affiliation(s)
- N Contreras-Coll
- Department de Microbiologia, Facultat de Biologia, Universitat de Barcelona, Spain
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Maier EA, Griepink B, in't Veld PH, Mooijman K, Havelaar AH. Reference materials and certified reference materials for water and food microbiology. ACTA ACUST UNITED AC 1993. [DOI: 10.1007/bf00322574] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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