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Zhang Y, Yu P, Tao F. Dynamic Interplay between Microbiota Shifts and Differential Metabolites during Dairy Processing and Storage. Molecules 2024; 29:2745. [PMID: 38930811 PMCID: PMC11206652 DOI: 10.3390/molecules29122745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Revised: 05/25/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Due to the intricate complexity of the original microbiota, residual heat-resistant enzymes, and chemical components, identifying the essential factors that affect dairy quality using traditional methods is challenging. In this study, raw milk, pasteurized milk, and ultra-heat-treated (UHT) milk samples were collectively analyzed using metagenomic next-generation sequencing (mNGS), high-throughput liquid chromatography-mass spectrometry (LC-MS), and gas chromatography-mass spectrometry (GC-MS). The results revealed that raw milk and its corresponding heated dairy products exhibited different trends in terms of microbiota shifts and metabolite changes during storage. Via the analysis of differences in microbiota and correlation analysis of the microorganisms present in differential metabolites in refrigerated pasteurized milk, the top three differential microorganisms with increased abundance, Microbacterium (p < 0.01), unclassified Actinomycetia class (p < 0.05), and Micrococcus (p < 0.01), were detected; these were highly correlated with certain metabolites in pasteurized milk (r > 0.8). This indicated that these genera were the main proliferating microorganisms and were the primary genera involved in the metabolism of pasteurized milk during refrigeration-based storage. Microorganisms with decreased abundance were classified into two categories based on correlation analysis with certain metabolites. It was speculated that the heat-resistant enzyme system of a group of microorganisms with high correlation (r > 0.8), such as Pseudomonas and Acinetobacter, was the main factor causing milk spoilage and that the group with lower correlation (r < 0.3) had a lower impact on the storage process of pasteurized dairy products. By comparing the metabolic pathway results based on metagenomic and metabolite annotation, it was proposed that protein degradation may be associated with microbial growth, whereas lipid degradation may be linked to raw milk's initial heat-resistant enzymes. By leveraging the synergy of metagenomics and metabolomics, the interacting factors determining the quality evolution of dairy products were systematically investigated, providing a novel perspective for controlling dairy processing and storage effectively.
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Affiliation(s)
- Yinan Zhang
- Key Laboratory of Milk and Dairy Products Detection and Monitoring Technology for State Market Regulation, Shanghai Institute of Quality Inspection and Technical Research, Shanghai 200233, China
| | - Peng Yu
- State Key Laboratory of Dairy Biotechnology, Shanghai Engineering Research Center of Dairy Biotechnology, Dairy Research Institute, Bright Dairy & Food Co., Ltd., Shanghai 200436, China;
| | - Fei Tao
- State Key Laboratory of Microbial Metabolism, and School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Kerek Á, Németh V, Szabó Á, Papp M, Bányai K, Kardos G, Kaszab E, Bali K, Nagy Z, Süth M, Jerzsele Á. Monitoring Changes in the Antimicrobial-Resistance Gene Set (ARG) of Raw Milk and Dairy Products in a Cattle Farm, from Production to Consumption. Vet Sci 2024; 11:265. [PMID: 38922012 PMCID: PMC11209563 DOI: 10.3390/vetsci11060265] [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: 04/27/2024] [Revised: 05/20/2024] [Accepted: 06/06/2024] [Indexed: 06/27/2024] Open
Abstract
Raw milk and dairy products can serve as potential vectors for transmissible bacterial, viral and protozoal diseases, alongside harboring antimicrobial-resistance genes. This study monitors the changes in the antimicrobial-resistance gene pool in raw milk and cheese, from farm to consumer, utilizing next-generation sequencing. Five parallel sampling runs were conducted to assess the resistance gene pool, as well as phage or plasmid carriage and potential mobility. In terms of taxonomic composition, in raw milk the Firmicutes phylum made up 41%, while the Proteobacteria phylum accounted for 58%. In fresh cheese, this ratio shifted to 93% Firmicutes and 7% Proteobacteria. In matured cheese, the composition was 79% Firmicutes and 21% Proteobacteria. In total, 112 antimicrobial-resistance genes were identified. While a notable reduction in the resistance gene pool was observed in the freshly made raw cheese compared to the raw milk samples, a significant growth in the resistance gene pool occurred after one month of maturation, surpassing the initial gene frequency. Notably, the presence of extended-spectrum beta-lactamase (ESBL) genes, such as OXA-662 (100% coverage, 99.3% identity) and OXA-309 (97.1% coverage, 96.2% identity), raised concerns; these genes have a major public health relevance. In total, nineteen such genes belonging to nine gene families (ACT, CMY, EC, ORN, OXA, OXY, PLA, RAHN, TER) have been identified. The largest number of resistance genes were identified against fluoroquinolone drugs, which determined efflux pumps predominantly. Our findings underscore the importance of monitoring gene pool variations throughout the product pathway and the potential for horizontal gene transfer in raw products. We advocate the adoption of a new approach to food safety investigations, incorporating next-generation sequencing techniques.
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Affiliation(s)
- Ádám Kerek
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, István utca 2, H-1078 Budapest, Hungary; (V.N.); (Á.S.); (K.B.); (Á.J.)
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, István utca 2, H-1078 Budapest, Hungary; (M.P.); (G.K.); (E.K.); (K.B.); (M.S.)
| | - Virág Németh
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, István utca 2, H-1078 Budapest, Hungary; (V.N.); (Á.S.); (K.B.); (Á.J.)
| | - Ábel Szabó
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, István utca 2, H-1078 Budapest, Hungary; (V.N.); (Á.S.); (K.B.); (Á.J.)
| | - Márton Papp
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, István utca 2, H-1078 Budapest, Hungary; (M.P.); (G.K.); (E.K.); (K.B.); (M.S.)
- Centre for Bioinformatics, University of Veterinary Medicine, István utca 2, H-1078 Budapest, Hungary
| | - Krisztián Bányai
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, István utca 2, H-1078 Budapest, Hungary; (V.N.); (Á.S.); (K.B.); (Á.J.)
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, István utca 2, H-1078 Budapest, Hungary; (M.P.); (G.K.); (E.K.); (K.B.); (M.S.)
- Veterinary Medical Research Institute, HUN-REN, Hungária krt. 21, H-1143, Budapest, Hungary
| | - Gábor Kardos
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, István utca 2, H-1078 Budapest, Hungary; (M.P.); (G.K.); (E.K.); (K.B.); (M.S.)
- One Health Institute, University of Debrecen, Nagyerdei krt. 98, H-4032 Debrecen, Hungary
- National Public Health Center, Albert Flórián út 2-6, H-1097 Budapest, Hungary
- Department of Gerontology, Faculty of Health Sciences, University of Debrecen, Sóstói út 2-4, H-4400 Nyiregyhaza, Hungary
| | - Eszter Kaszab
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, István utca 2, H-1078 Budapest, Hungary; (M.P.); (G.K.); (E.K.); (K.B.); (M.S.)
- One Health Institute, University of Debrecen, Nagyerdei krt. 98, H-4032 Debrecen, Hungary
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, István utca 2, H-1078 Budapest, Hungary
| | - Krisztina Bali
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, István utca 2, H-1078 Budapest, Hungary; (M.P.); (G.K.); (E.K.); (K.B.); (M.S.)
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, István utca 2, H-1078 Budapest, Hungary
| | - Zoltán Nagy
- Biological Research and Development Department, CEVA-Phlyaxia Zrt., Szállás utca 5, H-1107 Budapest, Hungary;
| | - Miklós Süth
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, István utca 2, H-1078 Budapest, Hungary; (M.P.); (G.K.); (E.K.); (K.B.); (M.S.)
- Institute of Food Chain Science, University of Veterinary Medicine, István utca 2, H-1078 Budapest, Hungary
| | - Ákos Jerzsele
- Department of Pharmacology and Toxicology, University of Veterinary Medicine, István utca 2, H-1078 Budapest, Hungary; (V.N.); (Á.S.); (K.B.); (Á.J.)
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, István utca 2, H-1078 Budapest, Hungary; (M.P.); (G.K.); (E.K.); (K.B.); (M.S.)
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Yi S, Song H, Kim WH, Lee S, Guk JH, Woo J, Cho S. Dynamics of microbiota and antimicrobial resistance in on-farm dairy processing plants using metagenomic and culture-dependent approaches. Int J Food Microbiol 2024; 417:110704. [PMID: 38640816 DOI: 10.1016/j.ijfoodmicro.2024.110704] [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: 01/19/2024] [Revised: 03/22/2024] [Accepted: 04/12/2024] [Indexed: 04/21/2024]
Abstract
On-farm dairy processing plants, which are situated close to farms and larger dairy processing facilities, face unique challenges in maintaining environmental hygiene. This can impact various stages of dairy processing. These plants operate on smaller scales and use Low-Temperature-Long-Time (LTLT) pasteurization, making them more susceptible to microbial contamination through direct and indirect contact. Antimicrobial-resistant bacteria found on dairy farms pose risks to human health by potentially transferring resistance via dairy products. Our study aimed to investigate microbial distribution and antimicrobial resistance at four key stages: the farm, pre-pasteurization, post-pasteurization, and processing environments. We assessed microbial distribution by quantifying indicator bacteria and conducting metagenomic analysis. Antimicrobial resistance was examined by identifying resistance phenotypes and detecting resistance genes in bacterial isolates and metagenomes. Our results showed that the indicator bacteria were detected at all stages of on-farm dairy processing. We observed a significant reduction in aerobic microbes and coliforms post-pasteurization. However, contamination of the final dairy products increased, suggesting potential cross-contamination during post-pasteurization. Metagenomic analysis revealed that Pseudomonas, a representative psychrotrophic bacterium, was predominant in both the farm (24.1 %) and pre-pasteurization (65.9 %) stages, indicating microbial transfer from the farms to the processing plants. Post-pasteurization, Pseudomonas and other psychrotrophs like Acinetobacter and Enterobacteriaceae remained dominant. Core microbiota analysis identified 74 genera in total, including 13 psychrotrophic bacteria, across all stages. Of the 59 strains isolated from these plants, 49 were psychrotrophic. Antimicrobial resistance analysis showed that 74.6 % (44/59) of isolates were resistant to at least one antibiotic, with cefoxitin-, ampicillin-, amoxicillin-, and ticarcillin-resistant bacteria present at all stages. Identical antimicrobial resistance patterns were observed in isolates from serial stages of the same farm and season, suggesting bacterial transmission across stages. Additionally, 27.1 % (16/59) of isolates carried plasmid-mediated resistance genes, which were also detected in the metagenomes of non-isolated samples, indicating potential antimicrobial resistance gene transmission and their presence in uncultured bacteria. These findings reveal the persistence of antimicrobial-resistant psychrotrophic bacteria in on-farm dairy processing plants, which pose potential health risks via dairy consumption. Our study underscores the importance of both culture-dependent and culture-independent methods to fully understand their distribution and impact.
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Affiliation(s)
- Saehah Yi
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Hyokeun Song
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Woo-Hyun Kim
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Soomin Lee
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Jae-Ho Guk
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - JungHa Woo
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea
| | - Seongbeom Cho
- College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, South Korea.
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Yap M, O'Sullivan O, O'Toole PW, Sheehan JJ, Fenelon MA, Cotter PD. Seasonal and geographical impact on the Irish raw milk microbiota correlates with chemical composition and climatic variables. mSystems 2024; 9:e0129023. [PMID: 38445870 PMCID: PMC11019797 DOI: 10.1128/msystems.01290-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/14/2024] [Indexed: 03/07/2024] Open
Abstract
Season and location have previously been shown to be associated with differences in the microbiota of raw milk, especially in milk from pasture-based systems. Here, we further advance research in this area by examining differences in the raw milk microbiota from several locations across Ireland over 12 months, and by investigating microbiota associations with climatic variables and chemical composition. Shotgun metagenomic sequencing was used to investigate the microbiota of raw milk collected from nine locations (n = 241). Concurrent chemical analysis of the protein, fat, lactose, total solids, nonprotein nitrogen contents, and titratable acidity (TA) of the same raw milk were performed. Although the raw milk microbiota was highly diverse, a core microbiota was found, with Pseudomonas_E, Lactococcus, Acinetobacter, and Leuconostoc present in all samples. Microbiota diversity significantly differed by season and location, with differences in seasonality and geography corresponding to 11.8% and 10.5% of the variation in the microbiota. Functional and antibiotic resistance profiles also varied across season and location. The analysis of other metadata revealed additional interactions, such as an association between mean daily air and grass temperatures with the abundance of spoilage taxa like Pseudomonas species. Correlations were identified between pathogenic, mastitis-related species, fat content, and the number of sun hours, suggesting a seasonal effect. Ultimately, this study expands our understanding of the interconnected nature of the microbiota, environment/climate variables, and chemical composition of raw milk and provides evidence of a season- and location-specific microbiota. IMPORTANCE The microbiota of raw milk is influenced by many factors that encourage or prevent the introduction and growth of both beneficial and undesirable microorganisms. The seasonal and geographical impacts on the microbial communities of raw milk have been previously seen, but the relationships with environmental factors and the chemical composition has yet to be investigated. In this year-long study, we found that while raw milk is highly diverse, a core microbiota was detected for Irish raw milk, with strong evidence of seasonal and geographical influence. We also found associations between groups of microorganisms, environmental factors, and milk composition, which expand current knowledge on the relationships between microbial and chemical composition and the climate. These results provide evidence for the development of a tool to allow for the prediction of raw milk quality and safety.
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Affiliation(s)
- Min Yap
- Teagasc Food Research Centre, Cork, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Orla O'Sullivan
- Teagasc Food Research Centre, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
- VistaMilk SFI Research Centre, Cork, Ireland
| | - Paul W. O'Toole
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Jeremiah J. Sheehan
- Teagasc Food Research Centre, Cork, Ireland
- VistaMilk SFI Research Centre, Cork, Ireland
- Dairy Processing Technology Centre (DPTC), Limerick, Ireland
| | - Mark A. Fenelon
- Teagasc Food Research Centre, Cork, Ireland
- VistaMilk SFI Research Centre, Cork, Ireland
- Dairy Processing Technology Centre (DPTC), Limerick, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
- VistaMilk SFI Research Centre, Cork, Ireland
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Chai J, Zhuang Y, Cui K, Bi Y, Zhang N. Metagenomics reveals the temporal dynamics of the rumen resistome and microbiome in goat kids. MICROBIOME 2024; 12:14. [PMID: 38254181 PMCID: PMC10801991 DOI: 10.1186/s40168-023-01733-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 11/28/2023] [Indexed: 01/24/2024]
Abstract
BACKGROUND The gut microbiome of domestic animals carries antibiotic resistance genes (ARGs) which can be transmitted to the environment and humans, resulting in challenges of antibiotic resistance. Although it has been reported that the rumen microbiome of ruminants may be a reservoir of ARGs, the factors affecting the temporal dynamics of the rumen resistome are still unclear. Here, we collected rumen content samples of goats at 1, 7, 14, 28, 42, 56, 70, and 84 days of age, analyzed their microbiome and resistome profiles using metagenomics, and assessed the temporal dynamics of the rumen resistome in goats at the early stage of life under a conventional feeding system. RESULTS In our results, the rumen resistome of goat kids contained ARGs to 41 classes, and the richness of ARGs decreased with age. Four antibiotic compound types of ARGs, including drugs, biocides, metals, and multi-compounds, were found during milk feeding, while only drug types of ARGs were observed after supplementation with starter feed. The specific ARGs for each age and their temporal dynamics were characterized, and the network inference model revealed that the interactions among ARGs were related to age. A strong correlation between the profiles of rumen resistome and microbiome was found using Procrustes analysis. Ruminal Escherichia coli within Proteobacteria phylum was the main carrier of ARGs in goats consuming colostrum, while Prevotella ruminicola and Fibrobacter succinogenes associated with cellulose degradation were the carriers of ARGs after starter supplementation. Milk consumption was likely a source of rumen ARGs, and the changes in the rumen resistome with age were correlated with the microbiome modulation by starter supplementation. CONCLUSIONS Our data revealed that the temporal dynamics of the rumen resistome are associated with the microbiome, and the reservoir of ARGs in the rumen during early life is likely related to age and diet. It may be a feasible strategy to reduce the rumen and its downstream dissemination of ARGs in ruminants through early-life dietary intervention. Video Abstract.
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Affiliation(s)
- Jianmin Chai
- Institute of Feed Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan, 528225, China
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Yimin Zhuang
- Institute of Feed Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Kai Cui
- Institute of Feed Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China
| | - Yanliang Bi
- Institute of Feed Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China.
| | - Naifeng Zhang
- Institute of Feed Research of Chinese Academy of Agricultural Sciences, Key Laboratory of Feed Biotechnology of the Ministry of Agriculture and Rural Affairs, Beijing, 100081, China.
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Qin Y, Huang W, Yang J, Zhao Y, Zhao M, Xu H, Zhang M. The Antibiotic Resistome and Its Association with Bacterial Communities in Raw Camel Milk from Altay Xinjiang. Foods 2023; 12:3928. [PMID: 37959048 PMCID: PMC10647823 DOI: 10.3390/foods12213928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/21/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023] Open
Abstract
Raw camel milk is generally contaminated with varied microbiota, including antibiotic-resistant bacteria (ARB), that can act as a potential pathway for the spread of antibiotic resistance genes (ARGs). In this study, high-throughput quantitative PCR and 16S rRNA gene-based Illumine sequencing data were used to establish a comprehensive understanding of the antibiotic resistome and its relationship with the bacterial community in Bactrian camel milk from Xinjiang. A total of 136 ARGs and up to 1.33 × 108 total ARG copies per gram were identified, which predominantly encode resistance to β-lactamas and multidrugs. The ARGs' profiles were mainly explained by interactions between the bacteria community and physicochemical indicators (77.9%). Network analysis suggested that most ARGs exhibited co-occurrence with Corynebacterium, Leuconostoc and MGEs. Overall, raw camel milk serves as a reservoir for ARGs, which may aggravate the spread of ARGs through vertical and horizontal gene transfer in the food chain.
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Affiliation(s)
- Yanan Qin
- Correspondence: ; Tel.: +86-13999236502
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Jaudou S, Deneke C, Tran ML, Schuh E, Goehler A, Vorimore F, Malorny B, Fach P, Grützke J, Delannoy S. A step forward for Shiga toxin-producing Escherichia coli identification and characterization in raw milk using long-read metagenomics. Microb Genom 2022; 8:mgen000911. [PMID: 36748417 PMCID: PMC9836091 DOI: 10.1099/mgen.0.000911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) are a cause of severe human illness and are frequently associated with haemolytic uraemic syndrome (HUS) in children. It remains difficult to identify virulence factors for STEC that absolutely predict the potential to cause human disease. In addition to the Shiga-toxin (stx genes), many additional factors have been reported, such as intimin (eae gene), which is clearly an aggravating factor for developing HUS. Current STEC detection methods classically rely on real-time PCR (qPCR) to detect the presence of the key virulence markers (stx and eae). Although qPCR gives an insight into the presence of these virulence markers, it is not appropriate for confirming their presence in the same strain. Therefore, isolation steps are necessary to confirm STEC viability and characterize STEC genomes. While STEC isolation is laborious and time-consuming, metagenomics has the potential to accelerate the STEC characterization process in an isolation-free manner. Recently, short-read sequencing metagenomics have been applied for this purpose, but assembly quality and contiguity suffer from the high proportion of mobile genetic elements occurring in STEC strains. To circumvent this problem, we used long-read sequencing metagenomics for identifying eae-positive STEC strains using raw cow's milk as a causative matrix for STEC food-borne outbreaks. By comparing enrichment conditions, optimizing library preparation for MinION sequencing and generating an easy-to-use STEC characterization pipeline, the direct identification of an eae-positive STEC strain was successful after enrichment of artificially contaminated raw cow's milk samples at a contamination level as low as 5 c.f.u. ml-1. Our newly developed method combines optimized enrichment conditions of STEC in raw milk in combination with a complete STEC analysis pipeline from long-read sequencing metagenomics data. This study shows the potential of the innovative methodology for characterizing STEC strains from complex matrices. Further developments will nonetheless be necessary for this method to be applied in STEC surveillance.
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Affiliation(s)
- Sandra Jaudou
- COLiPATH Unit, Laboratory for Food Safety, ANSES, Maisons-Alfort, France,National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany,*Correspondence: Sandra Jaudou,
| | - Carlus Deneke
- National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Mai-Lan Tran
- COLiPATH Unit, Laboratory for Food Safety, ANSES, Maisons-Alfort, France,Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, Maisons-Alfort, France
| | - Elisabeth Schuh
- National Reference Laboratory for Escherichia coli including VTEC, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - André Goehler
- National Reference Laboratory for Escherichia coli including VTEC, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Fabien Vorimore
- Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, Maisons-Alfort, France
| | - Burkhard Malorny
- National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Patrick Fach
- COLiPATH Unit, Laboratory for Food Safety, ANSES, Maisons-Alfort, France,Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, Maisons-Alfort, France
| | - Josephine Grützke
- National Study Center for Sequencing, Department of Biological Safety, German Federal Institute for Risk Assessment, Berlin, Germany
| | - Sabine Delannoy
- COLiPATH Unit, Laboratory for Food Safety, ANSES, Maisons-Alfort, France,Genomics Platform IdentyPath, Laboratory for Food Safety, ANSES, Maisons-Alfort, France,*Correspondence: Sabine Delannoy,
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Shotgun metagenomic sequencing of bulk tank milk filters reveals the role of Moraxellaceae and Enterobacteriaceae as carriers of antimicrobial resistance genes. Food Res Int 2022; 158:111579. [DOI: 10.1016/j.foodres.2022.111579] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 01/06/2023]
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Billington C, Kingsbury JM, Rivas L. Metagenomics Approaches for Improving Food Safety: A Review. J Food Prot 2022; 85:448-464. [PMID: 34706052 DOI: 10.4315/jfp-21-301] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/21/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT Advancements in next-generation sequencing technology have dramatically reduced the cost and increased the ease of microbial whole genome sequencing. This approach is revolutionizing the identification and analysis of foodborne microbial pathogens, facilitating expedited detection and mitigation of foodborne outbreaks, improving public health outcomes, and limiting costly recalls. However, next-generation sequencing is still anchored in the traditional laboratory practice of the selection and culture of a single isolate. Metagenomic-based approaches, including metabarcoding and shotgun and long-read metagenomics, are part of the next disruptive revolution in food safety diagnostics and offer the potential to directly identify entire microbial communities in a single food, ingredient, or environmental sample. In this review, metagenomic-based approaches are introduced and placed within the context of conventional detection and diagnostic techniques, and essential considerations for undertaking metagenomic assays and data analysis are described. Recent applications of the use of metagenomics for food safety are discussed alongside current limitations and knowledge gaps and new opportunities arising from the use of this technology. HIGHLIGHTS
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Affiliation(s)
- Craig Billington
- Institute of Environmental Science and Research, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
| | - Joanne M Kingsbury
- Institute of Environmental Science and Research, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
| | - Lucia Rivas
- Institute of Environmental Science and Research, 27 Creyke Road, Ilam, Christchurch 8041, New Zealand
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