1
|
Zhang Z, Xu D, Huang T, Zhang Q, Li Y, Zhou J, Zou R, Li X, Chen J. High levels of cadmium altered soil archaeal activity, assembly, and co-occurrence network in volcanic areas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 924:171529. [PMID: 38453065 DOI: 10.1016/j.scitotenv.2024.171529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 02/23/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
Soil microbial communities are essential to biogeochemical cycles. However, the responses of microorganisms in volcanic soil with high heavy metal levels remain poorly understood. Here, two areas with high levels of cadmium (Cd) from the same volcano were investigated to determine their archaeal composition and assembly. In this study, the Cd concentrations (0.32-0.38 mg/ kg) in the volcanic soils exceeded the standard risk screening values (GB15618-2018) and correlated with archaeal communities strongly (P < 0.05). Moreover, the area with elevated levels of Cd (periphery) exhibited a greater diversity of archaeal species, albeit with reduced archaeal activity, compared to the area with lower levels of Cd (center). Besides, stochastic processes mainly governed the archaeal communities. Furthermore, the co-occurrence network was simplest in the periphery. The proportion of positive links between taxa increased positively with Cd concentration. Moreover, four keystone taxa (all from the family Nitrososphaeraceae) were identified from the archaeal networks. In its entirety, this study has expanded our comprehension of the variations of soil archaeal communities in volcanic areas with elevated cadmium levels and serves as a point of reference for the agricultural development of volcanic soils in China.
Collapse
Affiliation(s)
- Zihua Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; Key Laboratory of Crop Stress Resistance and High Quality Biology of Anhui Province, Anhui Agricultural University, Hefei 230036, China
| | - Daolong Xu
- Inner Mongolia Academy of Science and Technology, Hohhot 010010, Inner Mongolia, China
| | - Tao Huang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; Key Laboratory of Crop Stress Resistance and High Quality Biology of Anhui Province, Anhui Agricultural University, Hefei 230036, China
| | - Qing Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; Key Laboratory of Crop Stress Resistance and High Quality Biology of Anhui Province, Anhui Agricultural University, Hefei 230036, China
| | - Yingyue Li
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; Key Laboratory of Crop Stress Resistance and High Quality Biology of Anhui Province, Anhui Agricultural University, Hefei 230036, China
| | - Jing Zhou
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; Key Laboratory of Crop Stress Resistance and High Quality Biology of Anhui Province, Anhui Agricultural University, Hefei 230036, China
| | - Ruifan Zou
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; Key Laboratory of Crop Stress Resistance and High Quality Biology of Anhui Province, Anhui Agricultural University, Hefei 230036, China
| | - Xiaoyu Li
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; Key Laboratory of Crop Stress Resistance and High Quality Biology of Anhui Province, Anhui Agricultural University, Hefei 230036, China.
| | - Jin Chen
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China; Key Laboratory of Crop Stress Resistance and High Quality Biology of Anhui Province, Anhui Agricultural University, Hefei 230036, China.
| |
Collapse
|
2
|
Tadielo LE, Dos Santos EAR, Possebon FS, Schmiedt JA, Juliano LCB, Cerqueira-Cézar CK, de Oliveira JP, Sampaio ANDCE, Melo PRL, Caron EFF, Pinto JPDAN, Bersot LDS, Pereira JG. Characterization of microbial ecology, Listeria monocytogenes, and Salmonella sp. on equipment and utensil surfaces in Brazilian poultry, pork, and dairy industries. Food Res Int 2023; 173:113422. [PMID: 37803760 DOI: 10.1016/j.foodres.2023.113422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/09/2023] [Accepted: 08/29/2023] [Indexed: 10/08/2023]
Abstract
This study aimed to evaluate the level of counting by indicator microorganisms, identify the microbial ecology, detect Listeria monocytogenes and Salmonella sp., and determine the presence of virulence genes and biofilm formation. A total of 480 samples were collected from the surfaces of the equipment and utensils using sterile swabs for the detection of L. monocytogenes and Salmonella sp. and counting mesophilic aerobes, Enterobacteriaceae, Escherichia coli, and Pseudomonas sp. The microbial ecology was evaluated by sequencing the 16S rRNA gene. Genes for virulence and biofilm formation were analyzed and adhesion capacity was evaluated for L. monocytogenes and Salmonella sp. The mesophilic aerobe count was the highest in the dairy processing facility, followed by the pork and poultry slaughterhouses. L. monocytogenes was detected in all facilities, with the highest detection in the pork slaughterhouse, followed by the poultry and dairy facilities. Salmonella sp. was only detected in the dairy. Isolates of L. monocytogenes and Salmonella sp. showed poor adhesion to polystyrene surfaces, virulence genes, and biofilm formation. The frequent contaminants in the slaughterhouses were Pseudomonas, Acinetobacter, and Aeromonas in poultry, Acinetobacter, Pseudomonas, and Brevundimonas in pork, and Pseudomonas, Kocuria, and Staphylococcus in dairy. Our results provide useful information to understand the microbiological risks associated with contamination.
Collapse
Affiliation(s)
- Leonardo Ereno Tadielo
- São Paulo State University (UNESP), Botucatu Campus, School of Veterinary Medicine and Animal Science, Distrito de Rubião Jr, SN, 18618-681 Botucatu, São Paulo, Brazil
| | - Emanoelli Aparecida Rodrigues Dos Santos
- São Paulo State University (UNESP), Botucatu Campus, School of Veterinary Medicine and Animal Science, Distrito de Rubião Jr, SN, 18618-681 Botucatu, São Paulo, Brazil
| | - Fábio Sossai Possebon
- São Paulo State University (UNESP), Botucatu Campus, School of Veterinary Medicine and Animal Science, Distrito de Rubião Jr, SN, 18618-681 Botucatu, São Paulo, Brazil
| | - Jhennifer Arruda Schmiedt
- Federal University of Paraná (UFPR), Palotina Campus, Department of Veterinary Sciences, Rua Pioneiro, 2153, Jardim Dallas, 85950-000 Palotina, PR, Brazil
| | - Lara Cristina Bastos Juliano
- São Paulo State University (UNESP), Botucatu Campus, School of Veterinary Medicine and Animal Science, Distrito de Rubião Jr, SN, 18618-681 Botucatu, São Paulo, Brazil
| | - Camila Koutsodontis Cerqueira-Cézar
- São Paulo State University (UNESP), Botucatu Campus, School of Veterinary Medicine and Animal Science, Distrito de Rubião Jr, SN, 18618-681 Botucatu, São Paulo, Brazil
| | - Janaina Prieto de Oliveira
- São Paulo State University (UNESP), Botucatu Campus, School of Veterinary Medicine and Animal Science, Distrito de Rubião Jr, SN, 18618-681 Botucatu, São Paulo, Brazil
| | - Aryele Nunes da Cruz Encide Sampaio
- São Paulo State University (UNESP), Botucatu Campus, School of Veterinary Medicine and Animal Science, Distrito de Rubião Jr, SN, 18618-681 Botucatu, São Paulo, Brazil
| | - Patrícia Regina Lopes Melo
- São Paulo State University (UNESP), Botucatu Campus, School of Veterinary Medicine and Animal Science, Distrito de Rubião Jr, SN, 18618-681 Botucatu, São Paulo, Brazil
| | - Evelyn Fernanda Flores Caron
- São Paulo State University (UNESP), Botucatu Campus, School of Veterinary Medicine and Animal Science, Distrito de Rubião Jr, SN, 18618-681 Botucatu, São Paulo, Brazil
| | - José Paes de Almeida Nogueira Pinto
- São Paulo State University (UNESP), Botucatu Campus, School of Veterinary Medicine and Animal Science, Distrito de Rubião Jr, SN, 18618-681 Botucatu, São Paulo, Brazil
| | - Luciano Dos Santos Bersot
- Federal University of Paraná (UFPR), Palotina Campus, Department of Veterinary Sciences, Rua Pioneiro, 2153, Jardim Dallas, 85950-000 Palotina, PR, Brazil.
| | - Juliano Gonçalves Pereira
- São Paulo State University (UNESP), Botucatu Campus, School of Veterinary Medicine and Animal Science, Distrito de Rubião Jr, SN, 18618-681 Botucatu, São Paulo, Brazil.
| |
Collapse
|
3
|
Xu ZS, Ju T, Yang X, Gänzle M. A Meta-Analysis of Bacterial Communities in Food Processing Facilities: Driving Forces for Assembly of Core and Accessory Microbiomes across Different Food Commodities. Microorganisms 2023; 11:1575. [PMID: 37375077 DOI: 10.3390/microorganisms11061575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 05/31/2023] [Accepted: 06/04/2023] [Indexed: 06/29/2023] Open
Abstract
Microbial spoilage is a major cause of food waste. Microbial spoilage is dependent on the contamination of food from the raw materials or from microbial communities residing in food processing facilities, often as bacterial biofilms. However, limited research has been conducted on the persistence of non-pathogenic spoilage communities in food processing facilities, or whether the bacterial communities differ among food commodities and vary with nutrient availability. To address these gaps, this review re-analyzed data from 39 studies from various food facilities processing cheese (n = 8), fresh meat (n = 16), seafood (n = 7), fresh produce (n = 5) and ready-to-eat products (RTE; n = 3). A core surface-associated microbiome was identified across all food commodities, including Pseudomonas, Acinetobacter, Staphylococcus, Psychrobacter, Stenotrophomonas, Serratia and Microbacterium. Commodity-specific communities were additionally present in all food commodities except RTE foods. The nutrient level on food environment surfaces overall tended to impact the composition of the bacterial community, especially when comparing high-nutrient food contact surfaces to floors with an unknown nutrient level. In addition, the compositions of bacterial communities in biofilms residing in high-nutrient surfaces were significantly different from those of low-nutrient surfaces. Collectively, these findings contribute to a better understanding of the microbial ecology of food processing environments, the development of targeted antimicrobial interventions and ultimately the reduction of food waste and food insecurity and the promotion of food sustainability.
Collapse
Affiliation(s)
- Zhaohui S Xu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Tingting Ju
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Xianqin Yang
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB T4L 1W1, Canada
| | - Michael Gänzle
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| |
Collapse
|
4
|
Rolon ML, Tan X, Chung T, Gonzalez-Escalona N, Chen Y, Macarisin D, LaBorde LF, Kovac J. The composition of environmental microbiota in three tree fruit packing facilities changed over seasons and contained taxa indicative of L. monocytogenes contamination. MICROBIOME 2023; 11:128. [PMID: 37271802 DOI: 10.1186/s40168-023-01544-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 04/06/2023] [Indexed: 06/06/2023]
Abstract
BACKGROUND Listeria monocytogenes can survive in cold and wet environments, such as tree fruit packing facilities and it has been implicated in outbreaks and recalls of tree fruit products. However, little is known about microbiota that co-occurs with L. monocytogenes and its stability over seasons in tree fruit packing environments. In this 2-year longitudinal study, we aimed to characterize spatial and seasonal changes in microbiota composition and identify taxa indicative of L. monocytogenes contamination in wet processing areas of three tree fruit packing facilities (F1, F2, F3). METHODS A total of 189 samples were collected during two apple packing seasons from floors under the washing, drying, and waxing areas. The presence of L. monocytogenes was determined using a standard culturing method, and environmental microbiota was characterized using amplicon sequencing. PERMANOVA was used to compare microbiota composition among facilities over two seasons, and abundance-occupancy analysis was used to identify shared and temporal core microbiota. Differential abundance analysis and random forest were applied to detect taxa indicative of L. monocytogenes contamination. Lastly, three L. monocytogenes-positive samples were sequenced using shotgun metagenomics with Nanopore MinION, as a proof-of-concept for direct detection of L. monocytogenes' DNA in environmental samples. RESULTS The occurrence of L. monocytogenes significantly increased from 28% in year 1 to 46% in year 2 in F1, and from 41% in year 1 to 92% in year 2 in F3, while all samples collected from F2 were L. monocytogenes-positive in both years. Samples collected from three facilities had a significantly different microbiota composition in both years, but the composition of each facility changed over years. A subset of bacterial taxa including Pseudomonas, Stenotrophomonas, and Microbacterium, and fungal taxa, including Yarrowia, Kurtzmaniella, Cystobasidium, Paraphoma, and Cutaneotrichosporon, were identified as potential indicators of L. monocytogenes within the monitored environments. Lastly, the DNA of L. monocytogenes was detected through direct Nanopore sequencing of metagenomic DNA extracted from environmental samples. CONCLUSIONS This study demonstrated that a cross-sectional sampling strategy may not accurately reflect the representative microbiota of food processing facilities. Our findings also suggest that specific microorganisms are indicative of L. monocytogenes, warranting further investigation of their role in the survival and persistence of L. monocytogenes. Video Abstract.
Collapse
Affiliation(s)
- M Laura Rolon
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Microbiome Center, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Xiaoqing Tan
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Microbiome Center, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Taejung Chung
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Microbiome Center, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Narjol Gonzalez-Escalona
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, 20740, USA
| | - Yi Chen
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, 20740, USA
| | - Dumitru Macarisin
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, 20740, USA
| | - Luke F LaBorde
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA.
- Microbiome Center, The Pennsylvania State University, University Park, PA, 16802, USA.
| |
Collapse
|
5
|
Elnemr I, Mushtaha M, Sundararaju S, Hasan MR, Tsui KM, Goktepe I. Monitoring the effect of environmental conditions on safety of fresh produce sold in Qatar's wholesale market. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2022; 32:1986-2004. [PMID: 34085573 DOI: 10.1080/09603123.2021.1931050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 05/12/2021] [Indexed: 06/12/2023]
Abstract
Fresh produce imported by Qatar are mostly sold at the wholesale produce market (WPM) located in open-air and near major animal markets and slaughterhouses. This study was the first in Qatar to monitor the effect of environmental conditions on the microbial quality and safety of fresh produce sold at the WPM over 1 year. The monitoring involved the collection of 540 produce samples along with samples of air, soil, and surface swabs. Samples were analyzed for total aerobic bacteria (TAB); generic Listeria spp., Staphylococcus spp., Salmonella spp.; total coliforms and total fungi. Bacterial and fungal isolates were identified using 16S rRNA/ITS rRNA markers. Environmental/sanitary factors significantly impacted the prevalence of microorganisms in all samples tested. Produce quality was rated 'poor' during the months of November-February or May-August, with TAB and coliform counts exceeding 6 and 4 log10 CFU/g, respectively. Bacillus subtilus, Enterobacter cloacae, E. faecium, P. expansium, P. aurantiocandidum, and A. niger were the most abundant species with prevalence rate of 11-30%. The high microbial load of environmental samples indicates that the location of the WPM near livestock markets is likely impacting the microbial quality of fresh produce. Therefore, effective control measures need to be implemented at WPM to improve produce safety yearlong.
Collapse
Affiliation(s)
- I Elnemr
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - M Mushtaha
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | | | - Mohammad Rubayet Hasan
- Department of Pathology, Sidra Medicine, Doha, Qatar
- Department of Clinical Pathology and Laboratory Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Kin-Ming Tsui
- Department of Pathology, Sidra Medicine, Doha, Qatar
- Department of Clinical Pathology and Laboratory Medicine, Weill Cornell Medical College in Qatar, Doha, Qatar
| | - I Goktepe
- Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| |
Collapse
|
6
|
Investigation on the Microbial Diversity of Fresh-Cut Lettuce during Processing and Storage Using High Throughput Sequencing and Their Relationship with Quality. Foods 2022; 11:foods11121683. [PMID: 35741879 PMCID: PMC9222426 DOI: 10.3390/foods11121683] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/04/2022] [Accepted: 06/06/2022] [Indexed: 02/04/2023] Open
Abstract
Microbial community distribution in vegetables can affect their quality. This study analyzed the distribution of the microbial community at various stages during processing and storage with the microbial diversity analysis, and evaluated the correlation between the dominant bacteria and sensory quality of lettuce using correspondence analysis with multiple regression analysis. Results showed that the process of washing, cutting, then disinfection and dewatering could change the community distribution and dominant bacteria in lettuce, and maintain better texture, morphology, aroma, color qualities of lettuce. The total number of colonies and relative abundance of Xanthomonas in fresh-cut lettuce decreased, while Afipia and Ralstonia increased during processing and pre-storage (storage for 6 h, 12 h and 1 d). After storage for 3 d, the total number of colonies in lettuce increased (more than 5 log CFU/g), especially the relative abundance of Pseudomonas, which led to the obvious deterioration of the sensory quality of lettuce. Throughout the process, the number of Bacillus cereus, Staphylococcus aureus, and E. coli was less than 100 CFU/g and 3 MPN/g. The number of typical pathogenic bacteria, Salmonella, Listeria monocytogenes and E. coli O157:H7, was below the detection limit. Overall, the prevention and control of psychrotrophic Pseudomonas in lettuce was still necessary. These results will provide useful information for the fresh-cut lettuce industry.
Collapse
|
7
|
Dong M, Feng H. Microbial Community Analysis and Food Safety Practice Survey-Based Hazard Identification and Risk Assessment for Controlled Environment Hydroponic/Aquaponic Farming Systems. Front Microbiol 2022; 13:879260. [PMID: 35663856 PMCID: PMC9161294 DOI: 10.3389/fmicb.2022.879260] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 04/21/2022] [Indexed: 11/26/2022] Open
Abstract
Hydroponic and aquaponic farming is becoming increasingly popular as a solution to address global food security. Plants in hydroponic systems are grown hydroponically under controlled environments and are considered to have fewer food safety concerns than traditional field farming. However, hydroponics and aquaponics might have very different sources of microbial food safety risks that remain under-examined. In this study, we investigated the microbiomes, microbial hazards, and potential bacterial transmission routes inside two commercial hydroponic and aquaponic farming systems using 16S-ITS-23S rRNA sequencing and a hydroponic food safety practice survey. The hydroponic farming system microbiome was analyzed from the fresh produce, nutrient solution, tools, and farmworkers. Proteobacteria, Actinobacteria, Cyanobacteria, Bacteroidetes, and Firmicutes were the main components of hydroponic/aquaponic farming systems, with Pseudomonas being the most abundant genus in fresh produce samples. We further identified the presence of multiple spoilage bacteria and potential human, plant, and fish pathogens at the subspecies level. Spoilage Pseudomonas spp. and spoilage Clostridium spp. were abundant in the hydroponic microgreen farm and aquaponic lettuce farm, respectively. Moreover, we demonstrated the mapping of Escherichia coli 16s-ITS-23s rRNA sequence reads (∼2,500 bp) to small or large subunit rRNA databases and whole-genome databases to confirm pathogenicity and showed the potential of using 16s-ITS-23s rRNA sequencing for pathogen identification. With the SourceTracker and overlapping amplicon sequence variants, we predicted the bidirectional transmission route between plants and the surrounding environment and constructed the bacteria transmission map, which can be implemented in future food safety risk control plans.
Collapse
Affiliation(s)
| | - Hao Feng
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| |
Collapse
|
8
|
Xu JG, Huang XN, Meng J, Chen JY, Han BZ. Characterization and comparison of the bacterial community on environmental surfaces through a fresh-cut vegetables processing line in China. Food Res Int 2022; 155:111075. [DOI: 10.1016/j.foodres.2022.111075] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 02/23/2022] [Accepted: 02/25/2022] [Indexed: 12/20/2022]
|
9
|
Cobo-Díaz JF, Alvarez-Molina A, Alexa EA, Walsh CJ, Mencía-Ares O, Puente-Gómez P, Likotrafiti E, Fernández-Gómez P, Prieto B, Crispie F, Ruiz L, González-Raurich M, López M, Prieto M, Cotter P, Alvarez-Ordóñez A. Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity. MICROBIOME 2021; 9:204. [PMID: 34645520 PMCID: PMC8515711 DOI: 10.1186/s40168-021-01131-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/17/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The microorganisms that inhabit food processing environments (FPE) can strongly influence the associated food quality and safety. In particular, the possibility that FPE may act as a reservoir of antibiotic-resistant microorganisms, and a hotspot for the transmission of antibiotic resistance genes (ARGs) is a concern in meat processing plants. Here, we monitor microbial succession and resistome dynamics relating to FPE through a detailed analysis of a newly opened pork cutting plant over 1.5 years of activity. RESULTS We identified a relatively restricted principal microbiota dominated by Pseudomonas during the first 2 months, while a higher taxonomic diversity, an increased representation of other taxa (e.g., Acinetobacter, Psychrobacter), and a certain degree of microbiome specialization on different surfaces was recorded later on. An increase in total abundance, alpha diversity, and β-dispersion of ARGs, which were predominantly assigned to Acinetobacter and associated with resistance to certain antimicrobials frequently used on pig farms of the region, was detected over time. Moreover, a sharp increase in the occurrence of extended-spectrum β-lactamase-producing Enterobacteriaceae and vancomycin-resistant Enterococcaceae was observed when cutting activities started. ARGs associated with resistance to β-lactams, tetracyclines, aminoglycosides, and sulphonamides frequently co-occurred, and mobile genetic elements (i.e., plasmids, integrons) and lateral gene transfer events were mainly detected at the later sampling times in drains. CONCLUSIONS The observations made suggest that pig carcasses were a source of resistant bacteria that then colonized FPE and that drains, together with some food-contact surfaces, such as equipment and table surfaces, represented a reservoir for the spread of ARGs in the meat processing facility. Video Abstract.
Collapse
Affiliation(s)
- José F. Cobo-Díaz
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | | | - Elena A. Alexa
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
- Present address: Microbiology Department, National University of Ireland, Galway, Ireland
| | - Calum J. Walsh
- Teagasc Food Research Centre, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Paula Puente-Gómez
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
| | - Eleni Likotrafiti
- Department of Food Science & Technology, International Hellenic University, Thessaloniki, Greece
| | | | - Bernardo Prieto
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Fiona Crispie
- Teagasc Food Research Centre, Fermoy, Co. Cork, Ireland
| | - Lorena Ruiz
- Dairy Research Institute, Spanish National Research Council, Instituto de Productos Lácteos de Asturias-CSIC, Villaviciosa, Spain
- MicroHealth Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Asturias Spain
| | - Montserrat González-Raurich
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Mercedes López
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Miguel Prieto
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| | - Paul Cotter
- Teagasc Food Research Centre, Fermoy, Co. Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology, Universidad de León, León, Spain
- Institute of Food Science and Technology, Universidad de León, León, Spain
| |
Collapse
|
10
|
Donaghy JA, Danyluk MD, Ross T, Krishna B, Farber J. Big Data Impacting Dynamic Food Safety Risk Management in the Food Chain. Front Microbiol 2021; 12:668196. [PMID: 34093486 PMCID: PMC8177817 DOI: 10.3389/fmicb.2021.668196] [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: 02/15/2021] [Accepted: 04/01/2021] [Indexed: 01/11/2023] Open
Abstract
Foodborne pathogens are a major contributor to foodborne illness worldwide. The adaptation of a more quantitative risk-based approach, with metrics such as Food safety Objectives (FSO) and Performance Objectives (PO) necessitates quantitative inputs from all stages of the food value chain. The potential exists for utilization of big data, generated through digital transformational technologies, as inputs to a dynamic risk management concept for food safety microbiology. The industrial revolution in Internet of Things (IoT) will leverage data inputs from precision agriculture, connected factories/logistics, precision healthcare, and precision food safety, to improve the dynamism of microbial risk management. Furthermore, interconnectivity of public health databases, social media, and e-commerce tools as well as technologies such as blockchain will enhance traceability for retrospective and real-time management of foodborne cases. Despite the enormous potential of data volume and velocity, some challenges remain, including data ownership, interoperability, and accessibility. This paper gives insight to the prospective use of big data for dynamic risk management from a microbiological safety perspective in the context of the International Commission on Microbiological Specifications for Foods (ICMSF) conceptual equation, and describes examples of how a dynamic risk management system (DRMS) could be used in real-time to identify hazards and control Shiga toxin-producing Escherichia coli risks related to leafy greens.
Collapse
Affiliation(s)
- John A Donaghy
- Corporate Operations - Quality Management (Food Safety) Société des Produits Nestlé S.A., Vevey, Switzerland
| | - Michelle D Danyluk
- IFAS Food Science and Human Nutrition, University of Florida, Gainesville, FL, United States
| | - Tom Ross
- Centre for Food Safety and Innovation, University of Tasmania, Hobart, TSA, Australia
| | - Bobby Krishna
- Department of Food Safety, Dubai Municipality, Dubai, United Arab Emirates
| | - Jeff Farber
- Department of Food Science, University of Guelph, Guelph, ON, Canada
| |
Collapse
|
11
|
Fagerlund A, Wubshet SG, Møretrø T, Schmidt G, Borge GI, Langsrud S. Anti-listerial properties of chemical constituents of Eruca sativa (rocket salad): From industrial observation to in vitro activity. PLoS One 2021; 16:e0250648. [PMID: 33905441 PMCID: PMC8078797 DOI: 10.1371/journal.pone.0250648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 04/12/2021] [Indexed: 12/16/2022] Open
Abstract
The frequency of foodborne outbreaks epidemiologically associated with Listeria monocytogenes in fresh produce has increased in recent years. Although L. monocytogenes may be transferred from the environment to vegetables during farming, contamination of food products most commonly occurs in food processing facilities, where L. monocytogenes has the ability to establish and persist on processing equipment. The current study was undertaken to collect data on the occurrence of L. monocytogenes and the identity of the endogenous microbiota in a fresh produce processing facility, for which information has remained scarce. L. monocytogenes was not detected in the facility. Experiments simulating conditions in the processing environment were performed, including examination of bacterial growth in nutrients based on vegetables (salad juice) compared to in other types of nutrients (fish, meat). Results showed that the endogenous microbiota (dominated by Pseudomonas) grew well in iceberg lettuce and rocket salad juice at low temperatures, while growth inhibition of L. monocytogenes was observed, particularly in rocket salad juice. The anti-listerial activity in rocket salad juice was retained in a polar chromatographic fraction containing several metabolites. Characterization of this active fraction, using LC-MS/MS, led to identification of 19 compounds including nucleosides and amino acids. Further work is necessary to determine the molecular mechanism responsible for the inhibitory activity of rocket salad constituents. The study nevertheless suggests that the available nutrients, as well as a low temperature (3 °C) and the in-house bacterial flora, may influence the prevalence of L. monocytogenes in fresh produce processing facilities.
Collapse
Affiliation(s)
- Annette Fagerlund
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
- * E-mail:
| | | | - Trond Møretrø
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Gesine Schmidt
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Grethe Iren Borge
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| | - Solveig Langsrud
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Ås, Norway
| |
Collapse
|
12
|
Xu JG, Meng J, Bao WJ, Kang JM, Chen JY, Han BZ. Occurrence of disinfectant-resistant bacteria in a fresh-cut vegetables processing facility and their role in protecting Salmonella enteritidis. RSC Adv 2021; 11:10291-10299. [PMID: 35423506 PMCID: PMC8695711 DOI: 10.1039/d0ra09325d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/25/2021] [Indexed: 12/14/2022] Open
Abstract
Chemical disinfectants are widely used to control foodborne pathogen contamination in fresh-cut vegetables (FVs) processing facilities. In this study, we investigated the disinfectant-resistant bacteria in a FVs processing facility and evaluate the effects of these bacteria on Salmonella enteritidis biofilm formation and disinfectant resistance. The disinfectant-resistance profiles were determined using 0.02% sodium hypochlorite (NaClO), 0.2% benzalkonium bromide (BAB) and 2% hydrogen peroxide (H2O2) solutions. The results showed the high occurrence of disinfectant resistant bacteria in the FVs processing environment, especially in the clean area. All isolates showed planktonic susceptibility to H2O2 and BAB, while the Gram-positive isolates were specifically resistant to NaClO. Isolates with biofilm-forming ability showed resistance to tested disinfectants. Disinfectant resistance of S. enteritidis was not significantly enhanced in most of the mixed-species biofilms, except for Bacillus paramycoides B5 which not only increased the biomass but also enhanced the survival ability of the Salmonella under NaClO treatment. Increased biomass and compact biofilm structures were observed in mixed-species biofilms by scanning electron microscopy (SEM). This study provides new insights into the disinfectant-resistant bacteria from food processing facilities and highlights their relevance for foodborne pathogen contamination. The occurrence of disinfectant-resistant bacteria in a fresh-cut vegetables processing facility was observed, and Bacillus paramycoides B5 enhanced S. enteritidis survival under NaClO treatment.![]()
Collapse
Affiliation(s)
- Jing-Guo Xu
- Beijing Laboratory for Food Quality and Safety, College of Food Science & Nutritional Engineering, China Agricultural University Beijing 100083 China
| | - Jiao Meng
- Beijing Laboratory for Food Quality and Safety, College of Food Science & Nutritional Engineering, China Agricultural University Beijing 100083 China
| | - Wen-Jing Bao
- Beijing Laboratory for Food Quality and Safety, College of Food Science & Nutritional Engineering, China Agricultural University Beijing 100083 China
| | - Jia-Mu Kang
- Beijing Laboratory for Food Quality and Safety, College of Food Science & Nutritional Engineering, China Agricultural University Beijing 100083 China
| | - Jing-Yu Chen
- Beijing Laboratory for Food Quality and Safety, College of Food Science & Nutritional Engineering, China Agricultural University Beijing 100083 China
| | - Bei-Zhong Han
- Beijing Laboratory for Food Quality and Safety, College of Food Science & Nutritional Engineering, China Agricultural University Beijing 100083 China
| |
Collapse
|
13
|
Fagerlund A, Langsrud S, Møretrø T. Microbial diversity and ecology of biofilms in food industry environments associated with Listeria monocytogenes persistence. Curr Opin Food Sci 2021. [DOI: 10.1016/j.cofs.2020.10.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
14
|
Agüeria DA, Libonatti C, Civit D. Cleaning and disinfection programmes in food establishments: a literature review on verification procedures. J Appl Microbiol 2020; 131:23-35. [PMID: 33300256 DOI: 10.1111/jam.14962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/27/2020] [Accepted: 12/03/2020] [Indexed: 01/01/2023]
Abstract
In food establishments, cleaning and disinfection programmes contribute to provide the environmental conditions that are necessary for the production of safe and healthy food. Compliance with validated programmes is evaluated through verification activities, in order to establish, through objective evidence, if they are implemented as they were written and if they are effective, achieving continuous improvement of the sanitation programmes. In accordance with the specific guidelines of each country, food companies set up their technical specifications and develop their own cleaning and disinfection programmes. Depending on the analytical method used, one of the main challenges was to establish a reasonable limit of acceptability according to the impact that each surface has on the safety and hygiene of the food that is prepared. This review was focused on the procedures implemented to verify the cleaning and disinfection programmes in food establishments. In particular, this study examines the methodologies used (audits and analytical methods), sites for the collection of samples, acceptance criteria and main findings. The results of the analysed studies constitute a scientific basis for designing or improving sanitation procedures and their verification in food companies, and also provide relevant information for food safety authorities.
Collapse
Affiliation(s)
- D A Agüeria
- Facultad de Ciencias Veterinarias, Universidad Nacional del Centro de la Provincia de Buenos Aires, Tandil, Buenos Aires, Argentina
| | - C Libonatti
- Facultad de Ciencias Veterinarias, Universidad Nacional del Centro de la Provincia de Buenos Aires, Tandil, Buenos Aires, Argentina
| | - D Civit
- Facultad de Ciencias Veterinarias, Universidad Nacional del Centro de la Provincia de Buenos Aires, Tandil, Buenos Aires, Argentina
| |
Collapse
|
15
|
The Microbial Diversity of Non-Korean Kimchi as Revealed by Viable Counting and Metataxonomic Sequencing. Foods 2020; 9:foods9111568. [PMID: 33137924 PMCID: PMC7693646 DOI: 10.3390/foods9111568] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 10/21/2020] [Accepted: 10/26/2020] [Indexed: 11/22/2022] Open
Abstract
Kimchi is recognized worldwide as the flagship food of Korea. To date, most of the currently available microbiological studies on kimchi deal with Korean manufactures. Moreover, there is a lack of knowledge on the occurrence of eumycetes in kimchi. Given these premises, the present study was aimed at investigating the bacterial and fungal dynamics occurring during the natural fermentation of an artisan non-Korean kimchi manufacture. Lactic acid bacteria were dominant, while Enterobacteriaceae, Pseudomonadaceae, and yeasts progressively decreased during fermentation. Erwinia spp., Pseudomonasveronii, Pseudomonasviridiflava, Rahnellaaquatilis, and Sphingomonas spp. were detected during the first 15 days of fermentation, whereas the last fermentation phase was dominated by Leuconostoc kimchi, together with Weissellasoli. For the mycobiota at the beginning of the fermentation process, Rhizoplaca and Pichia orientalis were the dominant Operational Taxonomic Units (OTUs) in batch 1, whereas in batch 2 Protomyces inundatus prevailed. In the last stage of fermentation, Saccharomyces cerevisiae, Candida sake,Penicillium, and Malassezia were the most abundant taxa in both analyzed batches. The knowledge gained in the present study represents a step forward in the description of the microbial dynamics of kimchi produced outside the region of origin using local ingredients. It will also serve as a starting point for further isolation of kimchi-adapted microorganisms to be assayed as potential starters for the manufacturing of novel vegetable preserves with high quality and functional traits.
Collapse
|
16
|
Risk Assessment and Monitoring of Green Logistics for Fresh Produce Based on a Support Vector Machine. SUSTAINABILITY 2020. [DOI: 10.3390/su12187569] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The sustainability and profitability of fresh produce supply chains are contingent upon several risk factors. This work, therefore, examines several risk indicators that affect the quality and safety of fresh produce in transit, including technological, biological, sustainability, environmental, and emergency risks. Then, we developed a risk assessment and monitoring model that employs a machine learning algorithm, a support vector machine, based on historical monitoring data. The proposed methodology was then applied to simulation and numerical analysis to assess the risks incurred in the strawberry cold chain. After training, the algorithm predicted the risks incurred during transportation with an average accuracy of 90.4%. Therefore, the developed methodology can effectively and accurately perform a risk assessment. Furthermore, the risk assessment model can be applied to other fresh produce due to comprehensive risk indicators. Decision-makers in fresh produce logistics companies can use the developed methodology to identify and mitigate risks incurred, thus improving food safety, reducing product loss, maximizing profits, and realizing sustainable development.
Collapse
|
17
|
Genome Sequences of Brevundimonas naejangsanensis Strain FS1091 and Bacillus amyloliquefaciens Strain FS1092, Isolated from a Fresh-Cut-Produce-Processing Plant. Microbiol Resour Announc 2020; 9:9/4/e01448-19. [PMID: 31974158 PMCID: PMC6979307 DOI: 10.1128/mra.01448-19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The complete genome sequences of Brevundimonas naejangsanensis strain FS1091 and Bacillus amyloliquefaciens strain FS1092, which were isolated from a commercial fresh-cut-produce-processing facility, were determined. Both FS1091 and FS1092 have one circular chromosome of approximately 3.15 and 4.24 Mb, respectively. The complete genome sequences of Brevundimonas naejangsanensis strain FS1091 and Bacillus amyloliquefaciens strain FS1092, which were isolated from a commercial fresh-cut-produce-processing facility, were determined. Both FS1091 and FS1092 have one circular chromosome of approximately 3.15 and 4.24 Mb, respectively.
Collapse
|
18
|
Tan X, Chung T, Chen Y, Macarisin D, LaBorde L, Kovac J. The occurrence of Listeria monocytogenes is associated with built environment microbiota in three tree fruit processing facilities. MICROBIOME 2019; 7:115. [PMID: 31431193 PMCID: PMC6702733 DOI: 10.1186/s40168-019-0726-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 07/29/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Multistate foodborne disease outbreaks and recalls of apples and apple products contaminated with Listeria monocytogenes demonstrate the need for improved pathogen control in the apple supply chain. Apple processing facilities have been identified in the past as potential sources of persisting L. monocytogenes contamination. In this study, we sought to understand the composition of microbiota in built apple and other tree fruit processing environments and its association with the occurrence of the foodborne pathogen L. monocytogenes. RESULTS Analysis of 117 samples collected from three apple and other tree fruit packing facilities (F1, F2, and F3) showed that facility F2 had a significantly higher L. monocytogenes occurrence compared to F1 and F3 (p < 0.01). The microbiota in facility F2 was distinct compared to facilities F1 and F3 as supported by the mean Shannon index for bacterial and fungal alpha diversities that was significantly lower in F2, compared to F1 and F3 (p < 0.01). Microbiota in F2 was uniquely predominated by bacterial family Pseudomonadaceae and fungal family Dipodascaceae. CONCLUSIONS The composition and diversity of microbiota and mycobiota present in the investigated built food processing environments may be indicative of persistent contamination with L. monocytogenes. These findings support the need for further investigation of the role of the microbial communities in the persistence of L. monocytogenes to support the optimization of L. monocytogenes control strategies in the apple supply chain.
Collapse
Affiliation(s)
- Xiaoqing Tan
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Taejung Chung
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
- Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Yi Chen
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, 20740, USA
| | - Dumitru Macarisin
- Center for Food Safety and Applied Nutrition, Food and Drug Administration, College Park, MD, 20740, USA
| | - Luke LaBorde
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Jasna Kovac
- Department of Food Science, The Pennsylvania State University, University Park, PA, 16802, USA.
- Microbiome Center, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, 16802, USA.
| |
Collapse
|
19
|
Abstract
The implementation of whole-genome sequencing in food safety has revolutionized foodborne pathogen tracking and outbreak investigations. The vast amounts of genomic data that are being produced through ongoing surveillance efforts continue advancing our understanding of pathogen diversity and genome biology. Produced genomic data are also supporting the use of metagenomics and metatranscriptomics for detection and functional characterization of microbiological hazards in foods and food processing environments. In addition to that, many studies have shown that metabolic and pathogenic potential, antimicrobial resistance, and other phenotypes relevant to food safety can be predicted from whole-genome sequences, omitting the need for multiple laboratory tests. Nevertheless, further work in the area of functional inference is necessary to enable accurate interpretation of functional information inferred from genomic and metagenomic data, as well as real-time detection and tracking of high-risk pathogen subtypes and microbiomes.
Collapse
|