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Shedleur-Bourguignon F, Duchemin T, P. Thériault W, Longpré J, Thibodeau A, Hocine MN, Fravalo P. Distinct Microbiotas Are Associated with Different Production Lines in the Cutting Room of a Swine Slaughterhouse. Microorganisms 2023; 11:microorganisms11010133. [PMID: 36677425 PMCID: PMC9862343 DOI: 10.3390/microorganisms11010133] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/31/2022] [Accepted: 01/01/2023] [Indexed: 01/06/2023] Open
Abstract
The microorganisms found on fresh, raw meat cuts at a slaughterhouse can influence the meat's safety and spoilage patterns along further stages of processing. However, little is known about the general microbial ecology of the production environment of slaughterhouses. We used 16s rRNA sequencing and diversity analysis to characterize the microbiota heterogeneity on conveyor belt surfaces in the cutting room of a swine slaughterhouse from different production lines (each associated with a particular piece/cut of meat). Variation of the microbiota over a period of time (six visits) was also evaluated. Significant differences of alpha and beta diversity were found between the different visits and between the different production lines. Bacterial genera indicative of each visit and production line were also identified. We then created random forest models that, based on the microbiota of each sample, allowed us to predict with 94% accuracy to which visit a sample belonged and to predict with 88% accuracy from which production line it was taken. Our results suggest a possible influence of meat cut on processing surface microbiotas, which could lead to better prevention, surveillance, and control of microbial contamination of meat during processing.
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Affiliation(s)
- Fanie Shedleur-Bourguignon
- NSERC Industrial Research Chair in Meat Safety (CRSV), Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Tom Duchemin
- MESuRS Laboratory (Modelling, Epidemiology and Surveillance of Health Risks), Conservatoire National des Arts et Métiers (Cnam), 75003 Paris, France
| | - William P. Thériault
- NSERC Industrial Research Chair in Meat Safety (CRSV), Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Jessie Longpré
- F. Ménard, Division d’Olymel s.e.c., Ange-Gardien, QC J0E 1E0, Canada
| | - Alexandre Thibodeau
- NSERC Industrial Research Chair in Meat Safety (CRSV), Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada
- CRIPA Swine and Poultry Infectious Diseases Research Center, Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, QC J2S 2M2, Canada
| | - Mounia N. Hocine
- MESuRS Laboratory (Modelling, Epidemiology and Surveillance of Health Risks), Conservatoire National des Arts et Métiers (Cnam), 75003 Paris, France
| | - Philippe Fravalo
- Le Conservatoire National des Arts et Métiers (Cnam), 75003 Paris, France
- Correspondence:
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ÇETİN AS, DOĞAN M. Esnaf Lokantalarında Kullanılan Kesme/Doğrama Tahtalarının Gıda Güvenliği Açısından Değerlendirilmesi: İstanbul Örneği. İSTANBUL GELIŞIM ÜNIVERSITESI SAĞLIK BILIMLERI DERGISI 2022. [DOI: 10.38079/igusabder.1097532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Amaç: Çalışma, gastronomi kültürünün vazgeçilmez bir unsuru olan esnaf lokantalarında gerçekleşmesi olası kritik halk sağlığı ve gıda güvenliği risklerinin başında gelen kesme/doğrama tahtalarından kaynaklı mikrobiyal risklerin belirlenmesi amaçlanmıştır.Yöntem: Çalışma kapsamında İstanbul’un ilçeleri Büyükçekmece, Çatalca ve Silivri’de faaliyet gösteren esnaf lokantalarının mutfaklarında kullanılan kesme/doğrama tahtaların yüzeylerinden steril swap ile mikrobiyolojik numuneler alınmıştır. Numuneler uygun sıcaklık ve sürede inkübasyona bırakılarak, toplam mezofilik aerobik bakteri, Staphylococcus aureus, Escherichia coli ve küf-maya sayımı yapılmıştır.Bulgular: Kesme/doğrama tahtalarının yüzeylerinden alınan mikrobiyolojik numunelerde Staphylococcus aureus, Escherichia coli, toplam mezofil aerob bakteri sayısı ve küf - maya sayısının ortalamaları sırasıyla 0,74; 0,61; 1,53 ve 1,21 logkob/10 cm2 tespit edilmiştir. Numunelerde değişik sayılarda Staphylococcus aureus tespit edilmesi personel kaynaklı bir kontaminasyona ve yine değişik sayılarda Escherichia coli tespit edilmesi ise fekal kaynaklı bir kontaminasyona işaret etmektedir.Sonuç: Esnaf lokantalarının gıda güvenliği uygulamalarından biri olan iyi üretim uygulamalarına yeterince uyulmadığı tespit edilmiştir. Esnaf lokantalarında gıda güvenliğinin tamamen sağlanabilmesi için Hazard Analysis and Critical Control Point - Tehlike Analizleri ve Kritik Kontrol Noktaları (HACCP) gibi gıda güvenliği kontrol sistemlerinin de etkin şekilde uygulanması gerektiğini ifade etmek mümkündür.
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Affiliation(s)
- Ayşe Seray ÇETİN
- İSTANBUL GELİŞİM ÜNİVERSİTESİ, GÜZEL SANATLAR FAKÜLTESİ, GASTRONOMİ VE MUTFAK SANATLARI BÖLÜMÜ
| | - Murat DOĞAN
- İSTANBUL GELİŞİM ÜNİVERSİTESİ, GÜZEL SANATLAR FAKÜLTESİ, GASTRONOMİ VE MUTFAK SANATLARI BÖLÜMÜ
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3
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Nikolaev Y, Yushina Y, Mardanov A, Gruzdev E, Tikhonova E, El-Registan G, Beletskiy A, Semenova A, Zaiko E, Bataeva D, Polishchuk E. Microbial Biofilms at Meat-Processing Plant as Possible Places of Bacteria Survival. Microorganisms 2022; 10:microorganisms10081583. [PMID: 36014001 PMCID: PMC9415349 DOI: 10.3390/microorganisms10081583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022] Open
Abstract
Biofilm contamination in food production threatens food quality and safety, and causes bacterial infections. Study of food biofilms (BF) is of great importance. The taxonomic composition and structural organization of five foods BF taken in different workshops of a meat-processing plant (Moscow, RF) were studied. Samples were taken from the surface of technological equipment and premises. Metagenomic analysis showed both similarities in the presented microorganisms dominating in different samples, and unique families prevailing on certain objects were noted. The bacteria found belonged to 11 phyla (no archaea). The dominant ones were Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. The greatest diversity was in BFs taken from the cutting table of raw material. Biofilms’ bacteria may be the cause of meat, fish and dairy products spoilage possible representatives include Pseudomonas, Flavobacterium, Arcobacter, Vagococcus, Chryseobacterium, Carnobacterium, etc.). Opportunistic human and animal pathogens (possible representatives include Arcobacter, Corynebacterium, Kocuria, etc.) were also found. Electron-microscopic studies of BF thin sections revealed the following: (1) the diversity of cell morphotypes specific to multispecies BFs; (2) morphological similarity of cells in BFs from different samples, micro-colonial growth; (3) age heterogeneity of cells within the same microcolony (vegetative and autolyzed cells, resting forms); (4) heterogeneity of the polymer matrix chemical nature according to ruthenium red staining.
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Affiliation(s)
- Yury Nikolaev
- Federal Research Center “Fundamentals of Biotechnology” of RAS, Leninsky Prospect, 14, 119991 Moscow, Russia
- V.M. Gorbatov Federal Research Center for Food Systems of RAS, Talalikhina St., 26, 109316 Moscow, Russia
| | - Yulia Yushina
- Federal Research Center “Fundamentals of Biotechnology” of RAS, Leninsky Prospect, 14, 119991 Moscow, Russia
- Correspondence: ; Tel.: +7-(495)676-60-11
| | - Andrey Mardanov
- Federal Research Center “Fundamentals of Biotechnology” of RAS, Leninsky Prospect, 14, 119991 Moscow, Russia
- V.M. Gorbatov Federal Research Center for Food Systems of RAS, Talalikhina St., 26, 109316 Moscow, Russia
| | - Evgeniy Gruzdev
- Federal Research Center “Fundamentals of Biotechnology” of RAS, Leninsky Prospect, 14, 119991 Moscow, Russia
| | - Ekaterina Tikhonova
- Federal Research Center “Fundamentals of Biotechnology” of RAS, Leninsky Prospect, 14, 119991 Moscow, Russia
| | - Galina El-Registan
- Federal Research Center “Fundamentals of Biotechnology” of RAS, Leninsky Prospect, 14, 119991 Moscow, Russia
| | - Aleksey Beletskiy
- Federal Research Center “Fundamentals of Biotechnology” of RAS, Leninsky Prospect, 14, 119991 Moscow, Russia
| | - Anastasia Semenova
- V.M. Gorbatov Federal Research Center for Food Systems of RAS, Talalikhina St., 26, 109316 Moscow, Russia
| | - Elena Zaiko
- V.M. Gorbatov Federal Research Center for Food Systems of RAS, Talalikhina St., 26, 109316 Moscow, Russia
| | - Dagmara Bataeva
- V.M. Gorbatov Federal Research Center for Food Systems of RAS, Talalikhina St., 26, 109316 Moscow, Russia
| | - Ekaterina Polishchuk
- V.M. Gorbatov Federal Research Center for Food Systems of RAS, Talalikhina St., 26, 109316 Moscow, Russia
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4
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Lim ES, Kim JJ, Sul WJ, Kim JS, Kim B, Kim H, Koo OK. Metagenomic Analysis of Microbial Composition Revealed Cross-Contamination Pathway of Bacteria at a Foodservice Facility. Front Microbiol 2021; 12:636329. [PMID: 33912146 PMCID: PMC8071874 DOI: 10.3389/fmicb.2021.636329] [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: 12/01/2020] [Accepted: 03/18/2021] [Indexed: 11/24/2022] Open
Abstract
Bacterial contamination of food-contact surfaces can be a potential risk factor for food quality and safety. To evaluate the spatial and temporal variations of the potential cross-contamination routes, we conducted a biogeographical assessment of bacteria in a foodservice facility based on the diversity of microflora on each surface. To this end, we performed high-throughput amplicon sequencing of 13 food-contact and non-food contact surfaces in a foodservice facility throughout a year. The results showed that Bacillus, Acinetobacter, Streptophyta, Enterobacter, Pseudomonas, Serratia, Enhydrobacter, Staphylococcus, Paracoccus, and Lysinibacillus were the dominant genera found on the kitchen surfaces of the foodservice facility. Depending on the season, changes in Firmicute/Proteobacteria ratios were observed, and the fan becomes the main source of outdoor air contamination. The microbial flow associated with spoilage was also observed throughout food preparation. Taken together, our results would be a powerful reference to hygiene managers for improvement of food processes.
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Affiliation(s)
- Eun Seob Lim
- Department of Food Biotechnology, Korea University of Science and Technology, Daejeon, South Korea.,Food Safety Research Team, Korea Food Research Institute, Wanju-gun, South Korea
| | - Jin Ju Kim
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea
| | - Woo Jun Sul
- Department of Systems Biotechnology, Chung-Ang University, Anseong, South Korea
| | - Joo-Sung Kim
- Department of Food Biotechnology, Korea University of Science and Technology, Daejeon, South Korea.,Food Safety Research Team, Korea Food Research Institute, Wanju-gun, South Korea
| | - Bomin Kim
- Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon, South Korea.,Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, South Korea
| | - Hun Kim
- Department of Medicinal Chemistry and Pharmacology, University of Science and Technology, Daejeon, South Korea.,Center for Eco-Friendly New Materials, Korea Research Institute of Chemical Technology, Daejeon, South Korea
| | - Ok Kyung Koo
- Department of Food and Nutrition, Gyeongsang National University, Jinju, South Korea.,Institute of Agriculture and Life Science, Gyeongsang National University, Jinju, South Korea
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5
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Botta C, Ferrocino I, Pessione A, Cocolin L, Rantsiou K. Spatiotemporal Distribution of the Environmental Microbiota in Food Processing Plants as Impacted by Cleaning and Sanitizing Procedures: the Case of Slaughterhouses and Gaseous Ozone. Appl Environ Microbiol 2020; 86:e01861-20. [PMID: 32978124 PMCID: PMC7657643 DOI: 10.1128/aem.01861-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 09/15/2020] [Indexed: 12/16/2022] Open
Abstract
Microbial complexity and contamination levels in food processing plants heavily impact the final product fate and are mainly controlled by proper environmental cleaning and sanitizing. Among the emerging disinfection technologies, ozonation is considered an effective strategy to improve the ordinary cleaning and sanitizing of slaughterhouses. However, its effects on contamination levels and environmental microbiota still need to be understood. For this purpose, we monitored the changes in microbiota composition in different slaughterhouse environments during the phases of cleaning/sanitizing and ozonation at 40, 20, or 4 ppm. Overall, the meat processing plant microbiota differed significantly between secondary processing rooms and deboning rooms, with a greater presence of psychrotrophic taxa in secondary processing rooms because of their lower temperatures. Cleaning/sanitizing procedures significantly reduced the contamination levels and in parallel increased the number of detectable operational taxonomic units (OTUs), by removing the masking effect of the most abundant human/animal-derived OTUs, which belonged to the phylum Firmicutes Subsequently, ozonation at 40 or 20 ppm effectively decreased the remaining viable bacterial populations. However, we could observe selective ozone-mediated inactivation of psychrotrophic bacteria only in the secondary processing rooms. There, the Brochothrix and Pseudomonas abundances and their viable counts were significantly affected by 40 or 20 ppm of ozone, while more ubiquitous genera like Staphylococcus showed a remarkable resistance to the same treatments. This study showed the effectiveness of highly concentrated gaseous ozone as an adjunct sanitizing method that can minimize cross-contamination and so extend the meat shelf life.IMPORTANCE Our in situ survey demonstrates that RNA-based sequencing of 16S rRNA amplicons is a reliable approach to qualitatively probe, at high taxonomic resolution, the changes triggered by new and existing cleaning/sanitizing strategies in the environmental microbiota in human-built environments. This approach could soon represent a fast tool to clearly define which routine sanitizing interventions are more suitable for a specific food processing environment, thus limiting the costs of special cleaning interventions and potential product loss.
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Affiliation(s)
- Cristian Botta
- Department of Agriculture, Forestry, and Food Sciences, University of Turin, Turin, Italy
| | - Ilario Ferrocino
- Department of Agriculture, Forestry, and Food Sciences, University of Turin, Turin, Italy
| | | | - Luca Cocolin
- Department of Agriculture, Forestry, and Food Sciences, University of Turin, Turin, Italy
| | - Kalliopi Rantsiou
- Department of Agriculture, Forestry, and Food Sciences, University of Turin, Turin, Italy
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6
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Carvalheira A, Silva J, Teixeira P. Acinetobacter spp. in food and drinking water - A review. Food Microbiol 2020; 95:103675. [PMID: 33397609 DOI: 10.1016/j.fm.2020.103675] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Revised: 11/02/2020] [Accepted: 11/03/2020] [Indexed: 01/01/2023]
Abstract
Acinetobacter spp. has emerged as a pathogen of major public health concern due to their increased resistance to antibiotics and their association with a wide range of nosocomial infections, community-acquired infections and war and natural disaster-related infections. It is recognized as a ubiquitous organism however, information about the prevalence of different pathogenic species of this genus in food sources and drinking water is scarce. Since the implementation of molecular techniques, the role of foods as a source of several species, including the Acinetobacter baumannii group, has been elucidated. Multidrug resistance was also detected among Acinetobacter spp. isolated from food products. This highlights the importance of foods as potential sources of dissemination of Acinetobacter spp. between the community and clinical environments and reinforces the need for further investigations on the potential health risks of Acinetobacter spp. as foodborne pathogens. The aim of this review was to summarize the published data on the occurrence of Acinetobacter spp. in different food sources and drinking water. This information should be taken into consideration by those responsible for infection control in hospitals and other healthcare facilities.
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Affiliation(s)
- Ana Carvalheira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Joana Silva
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Paula Teixeira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal.
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7
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Caraballo Guzmán A, González Hurtado MI, Cuesta-Astroz Y, Torres G. Metagenomic characterization of bacterial biofilm in four food processing plants in Colombia. Braz J Microbiol 2020; 51:1259-1267. [PMID: 32221908 PMCID: PMC7455661 DOI: 10.1007/s42770-020-00260-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 03/09/2020] [Indexed: 12/26/2022] Open
Abstract
Bacteria inside biofilms are more persistent and resistant to stress conditions found in the production environment of food processing plants, thus representing a constant risk for product safety and quality. Therefore, the aim of this study was to characterize, using 16S rRNA sequencing, the bacterial communities from biofilms found in four food processing plants (P1, P2, P3, and P4). In total, 50 samples from these four processing plants were taken after cleaning and disinfection processes. Four phyla: Proteobacteria, Firmicutes, Actinobacteria, and Bacteroides represented over 94% of the operational taxonomic units found across these four plants. A total of 102 families and 189 genera were identified. Two genera, Pseudomonas spp. and Acinetobacter spp., were the most frequently found (93.47%) across the four plants. In P1, Pseudomonas spp. and Lactobacillus spp. were the dominant genera, whereas Lactobacillus spp. and Streptococcus spp. were identified in P2. On the other hand, biofilms found in P3 and P4 mainly consisted of Pseudomonas spp. and Acinetobacter spp. Our results indicate that different bacterial genera of interest to the food industry due to their ability to form biofilm and affect food quality can coexist inside biofilms, and as such, persist in production environments, representing a constant risk for manufactured foods. In addition, the core microbiota identified across processing plants evaluated was probably influenced by type of food produced and cleaning and disinfection processes performed in each one of these.
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Affiliation(s)
- Arley Caraballo Guzmán
- Colombian Institute of Tropical Medicine, CES University, Carrera 43A # 52 Sur 99, Sabaneta, Colombia
| | | | - Yesid Cuesta-Astroz
- Colombian Institute of Tropical Medicine, CES University, Carrera 43A # 52 Sur 99, Sabaneta, Colombia
| | - Giovanny Torres
- Colombian Institute of Tropical Medicine, CES University, Carrera 43A # 52 Sur 99, Sabaneta, Colombia
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8
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Wang H, Zhang X, Wang G, Jia K, Xu X, Zhou G. Bacterial Community and Spoilage Profiles Shift in Response to Packaging in Yellow-Feather Broiler, a Highly Popular Meat in Asia. Front Microbiol 2017; 8:2588. [PMID: 29312261 PMCID: PMC5743932 DOI: 10.3389/fmicb.2017.02588] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 12/12/2017] [Indexed: 11/27/2022] Open
Abstract
The consumption of yellow-feathered broiler has been advocated for purchasing with chilled meat rather than live broilers in Asia due to the outbreaks of animal influenza. Here, the microbial community of chilled yellow-feathered broiler response to modified-air packaging (MAP, 80% CO2/20% N2) and penetrated-air packaging (PAP, air-filling) during storage was revealed by a combination of whole-metagenome shotgun sequencing and traditional isolation methods, and the volatile organic compounds and proteolytic activity of representative dominant isolates were also accessed. The results revealed that MAP prolonged shelf life from 4 to 8 days compared to PAP, when the numbers of total viable counts and lactic acid bacteria reached more than 7 log CFU/g. Aeromonas, Acinetobacter, Escherichia, and Streptococcus occupied the bacteria communities in initial broiler carcasses. MAP dramatically increased the bacteria diversity during storage compared to PAP. Clear shifts of the dominant bacteria species were obviously observed, with the top genera of Aeromonas, Lactococcus, Serratia, and Shewanella in MAP, whereas the microbial communities in PAP were largely dominated by Pseudomonas. The isolates of Pseudomonas from PAP carcasses and Aeromonas from MAP carcasses displayed strong proteolytic activities. Meanwhile, the principal component analysis based on the volatile organic compounds indicated that the metabolic profiles greatly varied between each treatment, and no link between the natural odor of spoilage meat in situ and the volatile odor of the dominant isolates incubated in standard culture was found. These data could lead to new insights into the bacteria communities of yellow-feathered broiler meat during storage and would benefit the development of novel preservative approaches.
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Affiliation(s)
- Huhu Wang
- National Center of Meat Quality and Safety Control, Nanjing Agricultural University, Nanjing, China
| | - Xinxiao Zhang
- Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, Nanjing Agricultural University, Nanjing, China
| | - Guangyu Wang
- Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, Nanjing Agricultural University, Nanjing, China
| | - Kun Jia
- National Center of Meat Quality and Safety Control, Nanjing Agricultural University, Nanjing, China
| | - Xinglian Xu
- National Center of Meat Quality and Safety Control, Nanjing Agricultural University, Nanjing, China
| | - Guanghong Zhou
- Jiangsu Collaborative Innovation Center of Meat Production and Processing, Quality and Safety Control, Nanjing Agricultural University, Nanjing, China
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9
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Parente E, Zotta T, Faust K, De Filippis F, Ercolini D. Structure of association networks in food bacterial communities. Food Microbiol 2017. [PMID: 29526226 DOI: 10.1016/j.fm.2017.12.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure of microbial association networks was investigated for seventeen studies on food bacterial communities using the CoNet app. The results were compared with those for host and environmental microbiomes. Microbial association networks of food bacterial communities shared several properties with those of host microbiomes, although they were less complex and lacked a scale-free, small world structure that is characteristic of environmental microbial communities. This may depend on both the initial contamination pattern, whose main source is the raw material microbiome, and on the copiotrophic nature of food environments, with lack of well defined, specific niches. The selective factors which are characteristic of fermentation and spoilage drastically simplified microbial association networks and showed the emergence of negative hubs. Co-presence and mutual exclusion networks had a radically different structure, with high clustering coefficient in the first and high heterogeneity in the latter. Node properties (degree, positive degree, betweenness centrality, abundance) can be combined in plots, which allow a rapid identification of hub species. The combined use of three network inference tools (CoNet, SparCC, and SPIEC-EASI) confirmed that microbial association network detection is method specific, but several coherent copresence or mutual exclusion relationships were detected by at least two different methods.
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Affiliation(s)
- Eugenio Parente
- Dipartimento di Scienze, Università degli Studi della Basilicata, 85100 Potenza, Italy.
| | - Teresa Zotta
- Istituto di Scienze dell'Alimentazione, CNR, 83100 Avellino, Italy
| | - Karoline Faust
- Department of Microbiology and Immunology, REGA Institute, KU Leuven, 3000, Belgium
| | - Francesca De Filippis
- Department of Agricultural Sciences, Division of Microbiology, University of Naples "Federico II", 80055 Portici, Italy; Task Force on Microbiome Studies, University of Naples "Federico II", Naples, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples "Federico II", 80055 Portici, Italy; Task Force on Microbiome Studies, University of Naples "Federico II", Naples, Italy
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Prevalence, Molecular Diversity, and Antimicrobial Resistance Patterns of Pathogenic Bacteria Isolated From Medical Foods, Food Staff, Cooking Instruments, and Clinical Samples in a Teaching Hospital in Tehran, Iran. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2017. [DOI: 10.5812/archcid.62421] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Effect of inoculum size, bacterial species, type of surfaces and contact time to the transfer of foodborne pathogens from inoculated to non-inoculated beef fillets via food processing surfaces. Food Microbiol 2017; 62:51-57. [DOI: 10.1016/j.fm.2016.09.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 08/25/2016] [Accepted: 09/23/2016] [Indexed: 11/20/2022]
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12
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Stellato G, Utter DR, Voorhis A, De Angelis M, Eren AM, Ercolini D. A Few Pseudomonas Oligotypes Dominate in the Meat and Dairy Processing Environment. Front Microbiol 2017; 8:264. [PMID: 28303120 PMCID: PMC5332365 DOI: 10.3389/fmicb.2017.00264] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 02/07/2017] [Indexed: 11/13/2022] Open
Abstract
The occurrence of bacteria in the food processing environments plays a key role in food contamination and development of spoilage. Species of the genus Pseudomonas are recognized as major food spoilers and the capability to actually determine spoilage can be species- as well as strain-dependent. In order to improve the taxonomic resolution of 16S rRNA gene amplicons, in this study we used oligotyping to investigate the diversity of Pseudomonas populations in meat and dairy processing environments. Sequences of the V1-V3 regions from previous studies were used, including environmental swabs and food samples from both meat and dairy processing plants. We showed that the most frequently found oligotypes belonged to Pseudomonas fragi and P. fluorescens, that the most abundant oligotypes co-occurred, and were shared between the meat and dairy datasets. All the oligotypes occurring in foods were also identified in the environmental samples of the corresponding plants, highlighting the important role of the environment as a source of strains for food contamination. Oligotypes of the same species showed different levels depending on food processing and type of sample, suggesting that different strains of the same species can have different adaptation efficiency, leading to resilient bacterial associations.
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Affiliation(s)
- Giuseppina Stellato
- Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico IIPortici, Italy
| | - Daniel R. Utter
- Department of Organismic and Evolutionary Biology, Harvard University, CambridgeMA, USA
| | - Andy Voorhis
- Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods HoleMA, USA
| | - Maria De Angelis
- Department of Soil, Plant and Food Science, University of Bari Aldo MoroBari, Italy
| | - A. Murat Eren
- Department of Medicine, University of Chicago, ChicagoIL, USA
| | - Danilo Ercolini
- Division of Microbiology, Department of Agricultural Sciences, University of Naples Federico IIPortici, Italy
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Overlap of Spoilage-Associated Microbiota between Meat and the Meat Processing Environment in Small-Scale and Large-Scale Retail Distributions. Appl Environ Microbiol 2016; 82:4045-54. [PMID: 27129965 DOI: 10.1128/aem.00793-16] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 04/21/2016] [Indexed: 01/30/2023] Open
Abstract
UNLABELLED Microbial contamination in food processing plants can play a fundamental role in food quality and safety. The aims of this study were to learn more about the possible influence of the meat processing environment on initial fresh meat contamination and to investigate the differences between small-scale retail distribution (SD) and large-scale retail distribution (LD) facilities. Samples were collected from butcheries (n = 20), including LD (n = 10) and SD (n = 10) facilities, over two sampling campaigns. Samples included fresh beef and pork cuts and swab samples from the knife, the chopping board, and the butcher's hand. The microbiota of both meat samples and environmental swabs were very complex, including more than 800 operational taxonomic units (OTUs) collapsed at the species level. The 16S rRNA sequencing analysis showed that core microbiota were shared by 80% of the samples and included Pseudomonas spp., Streptococcus spp., Brochothrix spp., Psychrobacter spp., and Acinetobacter spp. Hierarchical clustering of the samples based on the microbiota showed a certain separation between meat and environmental samples, with higher levels of Proteobacteria in meat. In particular, levels of Pseudomonas and several Enterobacteriaceae members were significantly higher in meat samples, while Brochothrix, Staphylococcus, lactic acid bacteria, and Psychrobacter prevailed in environmental swab samples. Consistent clustering was also observed when metabolic activities were considered by predictive metagenomic analysis of the samples. An increase in carbohydrate metabolism was predicted for the environmental swabs and was consistently linked to Firmicutes, while increases in pathways related to amino acid and lipid metabolism were predicted for the meat samples and were positively correlated with Proteobacteria Our results highlighted the importance of the processing environment in contributing to the initial microbial levels of meat and clearly showed that the type of retail facility (LD or SD) did not apparently affect the contamination. IMPORTANCE The study provides an in-depth description of the microbiota of meat and meat processing environments. It highlights the importance of the environment as a contamination source of spoilage bacteria, and it shows that the size of the retail facility does not affect the level and type of contamination.
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Moen B, Røssvoll E, Måge I, Møretrø T, Langsrud S. Microbiota formed on attached stainless steel coupons correlates with the natural biofilm of the sink surface in domestic kitchens. Can J Microbiol 2015; 62:148-60. [PMID: 26758935 DOI: 10.1139/cjm-2015-0562] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Stainless steel coupons are frequently used in biofilm studies in the laboratory, as this material is commonly used in the food industry. The coupons are attached to different surfaces to create a "natural" biofilm to be studied further in laboratory trials. However, little has been done to investigate how well the microbiota on such coupons represents the surrounding environment. The microbiota on sink wall surfaces and on new stainless steel coupons attached to the sink wall for 3 months in 8 domestic kitchen sinks was investigated by next-generation sequencing (MiSeq) of the 16S rRNA gene derived from DNA and RNA (cDNA), and by plating and identification of colonies. The mean number of colony-forming units was about 10-fold higher for coupons than sink surfaces, and more variation in bacterial counts between kitchens was seen on sink surfaces than coupons. The microbiota in the majority of biofilms was dominated by Moraxellaceae (genus Moraxella/Enhydrobacter) and Micrococcaceae (genus Kocuria). The results demonstrated that the variation in the microbiota was mainly due to differences between kitchens (38.2%), followed by the different nucleic acid template (DNA vs RNA) (10.8%), and that only 5.1% of the variation was a result of differences between coupons and sink surfaces. The microbiota variation between sink surfaces and coupons was smaller for samples based on their RNA than on their DNA. Overall, our results suggest that new stainless steel coupons are suited to model the dominating part of the natural microbiota of the surrounding environment and, furthermore, are suitable for different downstream studies.
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Affiliation(s)
- Birgitte Moen
- a Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, N-1430 Aas, Norway
| | - Elin Røssvoll
- a Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, N-1430 Aas, Norway.,b Animalia, Norwegian Meat and Poultry Research Center, P.O. Box 396, Økern, 0513 Oslo, Norway
| | - Ingrid Måge
- a Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, N-1430 Aas, Norway
| | - Trond Møretrø
- a Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, N-1430 Aas, Norway
| | - Solveig Langsrud
- a Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, N-1430 Aas, Norway
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Coexistence of Lactic Acid Bacteria and Potential Spoilage Microbiota in a Dairy Processing Environment. Appl Environ Microbiol 2015; 81:7893-904. [PMID: 26341209 DOI: 10.1128/aem.02294-15] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/01/2015] [Indexed: 11/20/2022] Open
Abstract
Microbial contamination in food processing plants can play a fundamental role in food quality and safety. In this study, the microbiota in a dairy plant was studied by both 16S rRNA- and 26S rRNA-based culture-independent high-throughput amplicon sequencing. Environmental samples from surfaces and tools were studied along with the different types of cheese produced in the same plant. The microbiota of environmental swabs was very complex, including more than 200 operational taxonomic units with extremely variable relative abundances (0.01 to 99%) depending on the species and sample. A core microbiota shared by 70% of the samples indicated a coexistence of lactic acid bacteria with a remarkable level of Streptococcus thermophilus and possible spoilage-associated bacteria, including Pseudomonas, Acinetobacter, and Psychrobacter, with a relative abundance above 50%. The most abundant yeasts were Kluyveromyces marxianus, Yamadazyma triangularis, Trichosporon faecale, and Debaryomyces hansenii. Beta-diversity analyses showed a clear separation of environmental and cheese samples based on both yeast and bacterial community structure. In addition, predicted metagenomes also indicated differential distribution of metabolic pathways between the two categories of samples. Cooccurrence and coexclusion pattern analyses indicated that the occurrence of potential spoilers was excluded by lactic acid bacteria. In addition, their persistence in the environment can be helpful to counter the development of potential spoilers that may contaminate the cheeses, with possible negative effects on their microbiological quality.
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Meat Processing Plant Microbiome and Contamination Patterns of Cold-Tolerant Bacteria Causing Food Safety and Spoilage Risks in the Manufacture of Vacuum-Packaged Cooked Sausages. Appl Environ Microbiol 2015; 81:7088-97. [PMID: 26231646 DOI: 10.1128/aem.02228-15] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 07/27/2015] [Indexed: 02/07/2023] Open
Abstract
Refrigerated food processing facilities are specific man-made niches likely to harbor cold-tolerant bacteria. To characterize this type of microbiota and study the link between processing plant and product microbiomes, we followed and compared microbiota associated with the raw materials and processing stages of a vacuum-packaged, cooked sausage product affected by a prolonged quality fluctuation with occasional spoilage manifestations during shelf life. A total of 195 samples were subjected to culturing and amplicon sequence analyses. Abundant mesophilic psychrotrophs were detected within the microbiomes throughout the different compartments of the production plant environment. However, each of the main genera of food safety and quality interest, e.g., Leuconostoc, Brochothrix, and Yersinia, had their own characteristic patterns of contamination. Bacteria from the genus Leuconostoc, commonly causing spoilage of cold-stored, modified-atmosphere-packaged foods, were detected in high abundance (up to >98%) in the sausages studied. The same operational taxonomic units (OTUs) were, however, detected in lower abundances in raw meat and emulsion (average relative abundance of 2%±5%), as well as on the processing plant surfaces (<4%). A completely different abundance profile was found for OTUs phylogenetically close to the species Yersinia pseudotuberculosis. These OTUs were detected in high abundance (up to 28%) on the processing plant surfaces but to a lesser extent (<1%) in raw meat, sausage emulsion, and sausages. The fact that Yersinia-like OTUs were found on the surfaces of a high-hygiene packaging compartment raises food safety concerns related to their resilient existence on surfaces.
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Pothakos V, Stellato G, Ercolini D, Devlieghere F. Processing Environment and Ingredients Are Both Sources of Leuconostoc gelidum, Which Emerges as a Major Spoiler in Ready-To-Eat Meals. Appl Environ Microbiol 2015; 81:3529-41. [PMID: 25769837 PMCID: PMC4407211 DOI: 10.1128/aem.03941-14] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 03/10/2015] [Indexed: 11/20/2022] Open
Abstract
Mesophilic and psychrotrophic organism viable counts, as well as high-throughput 16S rRNA gene-based pyrosequencing, were performed with the aim of elucidating the origin of psychrotrophic lactic acid bacteria (LAB) in a ready-to-eat (RTE) meal manufacturing plant. The microbial counts of the products at the end of the shelf life were greatly underestimated when mesophilic incubation was implemented due to overlooked, psychrotrophic members of the LAB. Pseudomonas spp., Enterobacteriaceae, Streptococcaceae, and Lactobacillus spp. constituted the most widespread operational taxonomic units (OTUs), whereas Leuconostoc gelidum was detected as a minor member of the indigenous microbiota of the food ingredients and microbial community of the processing environment, albeit it colonized samples at almost every sampling point on the premises. However, L. gelidum became the most predominant microbe at the end of the shelf life. The ability of L. gelidum to outgrow notorious, spoilage-related taxa like Pseudomonas, Brochothrix, and Lactobacillus underpins its high growth dynamics and severe spoilage character under refrigeration temperatures. The use of predicted metagenomes was useful for observation of putative gene repertoires in the samples analyzed in this study. The end products grouped in clusters characterized by gene profiles related to carbohydrate depletion presumably associated with a fast energy yield, a finding which is consistent with the fastidious nature of highly competitive LAB that dominated at the end of the shelf life. The present study showcases the detrimental impact of contamination with psychrotrophic LAB on the shelf life of packaged and cold-stored foodstuffs and the long-term quality implications for production batches once resident microbiota are established in the processing environment.
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Affiliation(s)
- Vasileios Pothakos
- Laboratory of Food Microbiology and Food Preservation, Department of Food Safety and Food Quality, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy
| | - Giuseppina Stellato
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples Federico II, Portici, Italy
| | - Frank Devlieghere
- Laboratory of Food Microbiology and Food Preservation, Department of Food Safety and Food Quality, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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