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Esteves E, Whyte P, Mills J, Brightwell G, Gupta TB, Bolton D. An investigation into the anaerobic spoilage microbiota of beef carcass and rump steak cuts using high- throughput sequencing. FEMS Microbiol Lett 2021; 368:6362601. [PMID: 34472614 DOI: 10.1093/femsle/fnab109] [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: 02/18/2021] [Accepted: 08/31/2021] [Indexed: 11/14/2022] Open
Abstract
The presence of anaerobic microflora on fresh beef carcass and rump steaks, which may contribute to meat spoilage, was explored in this study. A total of 120 carcass and 120 rump steak swabs were collected immediately after slaughtering and boning, respectively from five meat plants, anaerobically incubated and enriched at 4°C for 3 weeks. This was followed by DNA extraction and 16S rRNA amplicon sequencing using the Illumina MiSeq, with subsequent bioinformatics analysis. The enriched microbiota of the samples was classified and grouped into 149 operational taxonomic units (OTUs). The microbiota recovered from both sample types consisted mainly of Carnobacterium, with an average relative abundance of 28.4% and 32.8% in beef carcasses and beef rump steaks, respectively. This was followed by Streptococcus, Serratia, Lactococcus, Enterococcus, Escherichia-Shigella, Raoultella and Aeromonas ranging from 1.5 to 20% and 0.1 to 29.8% in enriched carcasses and rump steak swabs, respectively. Trichococcus, Bacteroides, Dysgomonas, Providencia, Paraclostridium and Proteus were also present ranging from 0 to 0.8% on carcass and 0 to 1.8% on rump steak swabs, respectively. Alpha and beta diversity measurements showed limited diversity between the two sample types, but some differences between samples from the beef plants investigated were evident. This study highlights the presence of potential spoilage bacteria, mainly anaerobic genera on and between carcass and rump steaks, as an indication of contamination on and between these samples.
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Affiliation(s)
- Eden Esteves
- Department of Food Safety, Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland.,School of Veterinary Medicine, UCD, Belfield, Dublin 4, Ireland.,Food Assurance Team, AgResearch Limited, Hopkirk Research Institute, Massey University, Palmerston North 4472, New Zealand
| | - Paul Whyte
- School of Veterinary Medicine, UCD, Belfield, Dublin 4, Ireland
| | - John Mills
- Food Assurance Team, AgResearch Limited, Hopkirk Research Institute, Massey University, Palmerston North 4472, New Zealand
| | - Gale Brightwell
- Food Assurance Team, AgResearch Limited, Hopkirk Research Institute, Massey University, Palmerston North 4472, New Zealand
| | - Tanushree B Gupta
- Food Assurance Team, AgResearch Limited, Hopkirk Research Institute, Massey University, Palmerston North 4472, New Zealand
| | - Declan Bolton
- Department of Food Safety, Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland
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Esteves E, Gupta TB, Whyte P, Brightwell G, Bolton D. An investigation of the environmental niches of blown pack spoilage causing Clostridium estertheticum and Clostridium gasigenes on New Zealand beef and sheep farms. Food Microbiol 2021; 98:103769. [PMID: 33875205 DOI: 10.1016/j.fm.2021.103769] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 02/17/2021] [Accepted: 02/18/2021] [Indexed: 11/19/2022]
Abstract
The transfer of blown pack spoilage causing Clostridium spores from the farm to the meat plant is of growing concern to the meat industry. This study investigated the environmental niches of these Clostridium spp., specifically Clostridium estertheticum and Clostridium gasigenes in the beef and sheep farm environments in New Zealand. Faecal, soil, grass, drinking water, puddle water and feed (fodder beet, hay, bailage and silage, where available) samples were collected on five beef and sheep farms during Winter and Spring in 2018, in North and South Island, respectively. Beef and sheep farm samples were tested for C. estertheticum and C. gasigenes using enrichment plus PCR, qPCR and direct plating. C. estertheticum was detected in bovine faecal (4%), soil (2-18%) and grass (0-12%) samples at concentration of up to 2.0 log10 cfu/g. C. gasigenes were found in 18-46% of faecal, 16-82% of soil, 12-44% of grass, 0-44.4% of drinking water and 0-58.3% of puddle water samples tested and the direct counts ranged from 2.4 log10 cfu/ml in puddle water to 3.4 log10 cfu/g in soil. C. estertheticum were detected by qPCR in sheep farms in ovine feces (2.3%), soil (2.3%) and fodder beet (10%). All other sample types (grass, drinking water, puddle water, baleage, hay, silage and fodder beet) were negative using direct and enrichment plus PCR methods. In contrast C. gasigenes was detected in of faecal (22.7-38.6%), soil (22.7-84.1%), grass (17.5-34.1%) drinking water (35.7-78.6%), puddle water (33.3-40%), hay baleage (57%), silage (2%) and fodder beet (10%) at concentrations of up to 3.7 log10 cfu/g/ml. It was concluded that C. estertheticum and C. gasigenes were common on beef and sheep farms with the latter having higher incidence and mean concentration.
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Affiliation(s)
- Eden Esteves
- Department of Food Safety, Teagasc Food Research Centre, Ashtown, Dublin, 15, Ireland; School of Veterinary Medicine, UCD, Belfield, Dublin, 4, Ireland; Food Assurance Team, Hopkirk Research Institute, AgResearch Ltd, Massey University, Palmerston North, 4472, New Zealand
| | - Tanushree B Gupta
- Food Assurance Team, Hopkirk Research Institute, AgResearch Ltd, Massey University, Palmerston North, 4472, New Zealand.
| | - Paul Whyte
- School of Veterinary Medicine, UCD, Belfield, Dublin, 4, Ireland
| | - Gale Brightwell
- Food Assurance Team, Hopkirk Research Institute, AgResearch Ltd, Massey University, Palmerston North, 4472, New Zealand; New Zealand Food Safety and Science Centre, Massey University, Palmerston North, 4472, New Zealand
| | - Declan Bolton
- Department of Food Safety, Teagasc Food Research Centre, Ashtown, Dublin, 15, Ireland
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Comparative genomics of Clostridium species associated with vacuum-packed meat spoilage. Food Microbiol 2020; 95:103687. [PMID: 33397617 DOI: 10.1016/j.fm.2020.103687] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/23/2022]
Abstract
Bacterial species belonging to the genus Clostridium have been recognized as causative agents of blown pack spoilage (BPS) in vacuum packed meat products. Whole-genome sequencing of six New Zealand psychrotolerant clostridia isolates derived from three meat production animal types and their environments was performed to examine their roles in BPS. Comparative genome analyses have provided insight into the genomic diversity and physiology of these bacteria and divides clostridia into two separate species clusters. BPS-associated clostridia encode a large and diverse spectrum of degradative carbohydrate-active enzymes (CAZymes) that enable them to utilize the intramuscular carbohydrate stores and facilitate sporulation. In total, 516 glycoside hydrolases (GHs), 93 carbohydrate esterases (CEs), 21 polysaccharide lyases (PLs), 434 glycosyl transferases (GTs) and 211 carbohydrate-binding protein modules (CBM) with predicted activities involved in the breakdown and transport of carbohydrates were identified. Clostridia genomes have different patterns of CAZyme families and vary greatly in the number of genes within each CAZy category, suggesting some level of functional redundancy. These results suggest that BPS-associated clostridia occupy similar environmental niches but apply different carbohydrate metabolism strategies to be able to co-exist and cause meat spoilage.
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Brightwell G, Horváth KM. Molecular discrimination of New Zealand sourced meat spoilage associated psychrotolerant Clostridium species by ARDRA and its comparison with 16s RNA gene sequencing. Meat Sci 2018; 138:23-27. [DOI: 10.1016/j.meatsci.2017.12.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/18/2017] [Accepted: 12/19/2017] [Indexed: 10/18/2022]
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5
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Húngaro HM, Caturla MY, Horita CN, Furtado MM, Sant'Ana AS. Blown pack spoilage in vacuum-packaged meat: A review on clostridia as causative agents, sources, detection methods, contributing factors and mitigation strategies. Trends Food Sci Technol 2016. [DOI: 10.1016/j.tifs.2016.04.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Bonke R, Drees N, Gareis M. Detection of psychrophilic and psychrotolerantClostridiumspp. in chilled fresh vacuum-packed meat using different PCR methods. FEMS Microbiol Lett 2015; 363:fnv218. [DOI: 10.1093/femsle/fnv218] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2015] [Indexed: 11/14/2022] Open
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Bacterial populations and the volatilome associated to meat spoilage. Food Microbiol 2015; 45:83-102. [DOI: 10.1016/j.fm.2014.02.002] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 01/27/2014] [Accepted: 02/08/2014] [Indexed: 11/18/2022]
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Panelli S, Brambati E, Bonacina C, Feligini M. Detection of Clostridium tyrobutyricum in milk to prevent late blowing in cheese by automated ribosomal intergenic spacer analysis. J Food Sci 2014; 78:M1569-M1574. [PMID: 24106762 DOI: 10.1111/1750-3841.12229] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 06/24/2013] [Indexed: 11/28/2022]
Abstract
Clostridium tyrobutyricum has been identified as the main causal agent of the late blowing defect in cheese, with major effects on quality and commercial value. In this work, for the first time, we applied automated ribosomal intergenic spacer analysis (ARISA) approach to diagnose the presence of C. tyrobutyricum in raw milk before cheesemaking. A species-specific primer set was designed and used for this original application of the ARISA. Sensitivity of detection, reproducibility of the fluorescent PCR assay, and repeatability of the capillary electrophoretic analysis of amplicons were evaluated using DNA extracted from milk added with known amounts of C. tyrobutyricum genome copies, ranging from 3 × 10(6) to 3. Results indicated that the sensitivity of the technique permits to detect the bacterium in all the samples. The reproducibility, evaluated by analyzing 3 sets of serial dilutions, resulted satisfactory, with little deviation within PCR reactions amplifying the same starting amount of template (standard deviations ≤ 0.1, coefficients of variation ≤ 3%). The peaks' fluorescence displayed an evident correspondence with the number of genome copies contained in each dilution. The capillary electrophoretic analysis, tested by running a single PCR product per dilution point in 10 repeats, resulted efficient and highly repeatable, with excellent coefficients of variation ≤ 2% and standard deviations ≤ 0.1 in all the sample sets. This application of ARISA gives good estimates of the total C. tyrobutyricum DNA content allowing a specific, fine-scale resolution of this pollutant species in a complex system as milk. A further advantage linked to the automatization of the process.
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Affiliation(s)
- Simona Panelli
- Laboratorio Qualità dei Prodotti, Ist. Sperimentale Italiano "Lazzaro Spallanzani," Località La Quercia, Rivolta d'Adda, (Cremona), 26027, Italy
| | - Eva Brambati
- Laboratorio Qualità dei Prodotti, Ist. Sperimentale Italiano "Lazzaro Spallanzani," Località La Quercia, Rivolta d'Adda, (Cremona), 26027, Italy
| | - Cesare Bonacina
- Laboratorio Qualità dei Prodotti, Ist. Sperimentale Italiano "Lazzaro Spallanzani," Località La Quercia, Rivolta d'Adda, (Cremona), 26027, Italy
| | - Maria Feligini
- Laboratorio Qualità dei Prodotti, Ist. Sperimentale Italiano "Lazzaro Spallanzani," Località La Quercia, Rivolta d'Adda, (Cremona), 26027, Italy
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9
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Spoilage microbiota associated to the storage of raw meat in different conditions. Int J Food Microbiol 2012; 157:130-41. [DOI: 10.1016/j.ijfoodmicro.2012.05.020] [Citation(s) in RCA: 365] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Revised: 05/21/2012] [Accepted: 05/22/2012] [Indexed: 02/03/2023]
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Silva AR, Tahara ACC, Chaves RD, Sant'Ana AS, Faria JDAF, Massaguer PR. Influence of different shrinking temperatures and vacuum conditions on the ability of psychrotrophic Clostridium to cause 'blown pack' spoilage in chilled vacuum-packaged beef. Meat Sci 2012; 92:498-505. [PMID: 22721639 DOI: 10.1016/j.meatsci.2012.05.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 05/07/2012] [Accepted: 05/18/2012] [Indexed: 10/28/2022]
Abstract
This study determined the ability of psychrotrophic Clostridium strains isolated from vacuum-packaged beefs and abattoir environments to cause 'blown-pack' spoilage of vacuum-packaged beef stored at 2 and 15 °C. The influence of shrinking temperatures (83, 84 and 87 °C) and vacuum pressure (6 and 9 mbar) on the occurrence of such spoilage as well as the effects of simulated transportation (500 km) on the integrity of packages was determined. At 15 °C and 2 °C, twelve and six strains caused 'blown-pack' spoilage, respectively. The combination of vacuum pressure (9 mbar) combined with shrinking temperature (87 °C) retarded the occurrence of spoilage. The simulated transportation under the experimental conditions did not affect the integrity of packages. More studies that assess the factors that may contribute for the occurrence of 'blown-pack' spoilage should be performed to avoid the occurrence of such spoilage during its shelf-life.
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Affiliation(s)
- Alessandra R Silva
- Department of Food Science, Faculty of Food Engineering, University of Campinas, Campinas, SP, Brazil.
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Detection of cold-tolerant clostridia other than Clostridium estertheticum in raw vacuum-packed chill-stored meat. Food Microbiol 2011; 28:957-63. [DOI: 10.1016/j.fm.2011.01.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 01/15/2011] [Accepted: 01/17/2011] [Indexed: 11/22/2022]
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12
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Moschonas G, Bolton DJ, McDowell DA, Sheridan JJ. Diversity of culturable psychrophilic and psychrotrophic anaerobic bacteria isolated from beef abattoirs and their environments. Appl Environ Microbiol 2011; 77:4280-4. [PMID: 21498765 PMCID: PMC3127721 DOI: 10.1128/aem.01778-10] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2010] [Accepted: 04/01/2011] [Indexed: 11/20/2022] Open
Abstract
This study identified 431 psychrophilic or psychrotrophic isolates from commercial Irish beef abattoir environments and "blown packs" of vacuum-packed beef, using PCR and 16S rRNA sequencing, and estimated their intraspecies genetic diversity using restriction fragment length polymorphism (RFLP) analysis and spacer region PCR (SR-PCR). Twenty-five species were identified in the 431 isolates, with the most frequently recovered species being Clostridium gasigenes (n=315), Clostridium estertheticum (n=17), and a potentially novel species designated strain TC1 (n=52). These species were previously found to be associated with a particular type of spoilage known as blown-pack spoilage (BPS), which occurs in chilled-stored (i.e., -1.5°C to 4°C) vacuum-packaged meat within 2 to 4 weeks and involves the production of large volumes of gas. Overall, the study demonstrates the considerable and not previously reported diversity of the anaerobic microflora in abattoirs and the presence of a wide range of organisms capable of causing BPS at chilled temperatures.
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MESH Headings
- Abattoirs
- Animals
- Bacteria, Anaerobic/classification
- Bacteria, Anaerobic/growth & development
- Bacteria, Anaerobic/isolation & purification
- Bacteria, Anaerobic/metabolism
- Cattle
- Cluster Analysis
- Cold Temperature
- DNA, Bacterial/chemistry
- DNA, Bacterial/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Electrophoresis, Polyacrylamide Gel
- Environmental Microbiology
- Ireland
- Meat/microbiology
- Molecular Typing
- Phylogeny
- Polymerase Chain Reaction
- RNA, Ribosomal, 16S/genetics
- Sequence Analysis, DNA
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Affiliation(s)
- G Moschonas
- Teagasc, Ashtown Food Research Centre, Ashtown, Dublin 15, Ireland
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Hernández-Macedo ML, Barancelli GV, Contreras-Castillo CJ. Microbial deterioration of vacuum-packaged chilled beef cuts and techniques for microbiota detection and characterization: a review. Braz J Microbiol 2011; 42:1-11. [PMID: 24031598 PMCID: PMC3768908 DOI: 10.1590/s1517-83822011000100001] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Revised: 04/04/2010] [Accepted: 07/04/2010] [Indexed: 11/28/2022] Open
Abstract
Gas production from microbial deterioration in vacuum-packs of chilled meat leads to pack distension, which is commonly referred as blown pack. This phenomenon is attributed to some psychrophilic and psychrotrophic Clostridium species, as well as Enterobacteria. The ability of these microorganisms to grow at refrigeration temperatures makes the control by the meat industry a challenge. This type of deterioration has been reported in many countries including some plants in the Midwestern and Southeastern regions of Brazil. In addition to causing economic losses, spoilage negatively impacts the commercial product brand, thereby impairing the meat industry. In the case of strict anaerobes species they are difficult to grow and isolate using culture methods in conventional microbiology laboratories. Furthermore, conventional culture methods are sometimes not capable of distinguishing species or genera. DNA-based molecular methods are alternative strategies for detecting viable and non-cultivable microorganisms and strict anaerobic microorganisms that are difficult to cultivate. Here, we review the microorganisms and mechanisms involved in the deterioration of vacuum-packaged chilled meat and address the use of molecular methods for detecting specific strict anaerobic microorganisms and microbial communities in meat samples.
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Affiliation(s)
- Maria Lucila Hernández-Macedo
- Escola Superior de Agricultura Luiz de Queiroz, Departamento de Agroindústria, Alimentos e Nutrição, Universidade de São Paulo, Piracicaba, SP, Brasil
| | | | - Carmen Josefina Contreras-Castillo
- Escola Superior de Agricultura Luiz de Queiroz, Departamento de Agroindústria, Alimentos e Nutrição, Universidade de São Paulo, Piracicaba, SP, Brasil
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BYRNE B, MONAGHAN A, LYNG J, SHERIDAN J, BOLTON D. A CASE OF “BLOWN PACK” MEAT LINKED TOCLOSTRIDIUM ESTERTHETICUMIN IRELAND. J Food Saf 2009. [DOI: 10.1111/j.1745-4565.2009.00182.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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15
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Moschonas G, Bolton D, Sheridan J, McDowell D. Isolation and sources of ‘blown pack’ spoilage clostridia in beef abattoirs. J Appl Microbiol 2009; 107:616-24. [DOI: 10.1111/j.1365-2672.2009.04229.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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16
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Substrate utilization by Clostridium estertheticum cultivated in meat juice medium. Int J Food Microbiol 2009; 128:501-5. [DOI: 10.1016/j.ijfoodmicro.2008.10.024] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2008] [Revised: 10/08/2008] [Accepted: 10/23/2008] [Indexed: 11/21/2022]
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17
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Opinion of the Scientific Panel on biological hazards (BIOHAZ) related to Clostridium spp in foodstuffs. EFSA J 2005. [DOI: 10.2903/j.efsa.2005.199] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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