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Azinheiro S, Carvalho J, Fuciños P, Pastrana L, Prado M, Garrido-Maestu A. Short pre-enrichment and modified matrix lysis. A comparative study towards same-day detection of Listeria monocytogenes. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Azinheiro S, Roumani F, Carvalho J, Prado M, Garrido-Maestu A. Suitability of the MinION long read sequencer for semi-targeted detection of foodborne pathogens. Anal Chim Acta 2021; 1184:339051. [PMID: 34625270 DOI: 10.1016/j.aca.2021.339051] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 09/07/2021] [Indexed: 12/20/2022]
Abstract
Foodborne pathogens are still a significant source of morbidity and mortality worldwide. In addition to this the current methodologies to track these microorganisms cannot cope with the current intensive production systems, thus novel methods are of outmost importance. DNA-based methods have already demonstrated suitable to address this issue, but most of them are targeted methods such as real-time PCR (qPCR), meaning that one will only find what is looking for, thus taking the risk of missing relevant pathogens in a given sample. To overcome this limitation we have developed an easy-to-implement methodology which enables the detection of several pathogens simultaneously by using long-read Next Generation Sequencing (NGS) with MinION. The method was named "semi-targeted" due to the combination of a non-targeted detection method, NGS, with the usage of selective media in order to partially eliminate non-pathogenic interfering bacteria. To this end, we included an enrichment step for the recovery of different pathogens, namely Salmonella Enteritidis and Typhimurium, Listeria monocytogenes and Escherichia coli O157:H7, after DNA extraction and library preparation, the samples were analyzed with MinION implementing the low-cost Flongle Flow Cells. The methodology was successfully evaluated in spiked milk samples with an excellent agreement with the results obtained by qPCR and culture-based methods. The method can provide accurate results after only 2 h of sequencing. Sample multiplexing, along with the lower cost of the Flongle Flow Cells and the reduced price of the MinION platform, make the assay cost-effective that is of importance for the food industry. Starting the method with a classical microbiological approach, the enrichment, the method is easy to implement in testing laboratories, it provides flexibility in terms of potential pathogens to be detected, and the positive results can be easily confirmed following culture-based, or other type, of confirmation procedures.
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Affiliation(s)
- Sarah Azinheiro
- Food Quality and Safety Research Group. International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga S/n, 4715-330 Braga, Portugal; College of Pharmacy/School of Veterinary Sciences. Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Spain
| | - Foteini Roumani
- Food Quality and Safety Research Group. International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga S/n, 4715-330 Braga, Portugal; College of Pharmacy/School of Veterinary Sciences. Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Spain
| | - Joana Carvalho
- Food Quality and Safety Research Group. International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga S/n, 4715-330 Braga, Portugal; College of Pharmacy/School of Veterinary Sciences. Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Spain
| | - Marta Prado
- Food Quality and Safety Research Group. International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga S/n, 4715-330 Braga, Portugal
| | - Alejandro Garrido-Maestu
- Food Quality and Safety Research Group. International Iberian Nanotechnology Laboratory, Av. Mestre José Veiga S/n, 4715-330 Braga, Portugal.
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Abstract
Quantitative PCR, if performed properly, is a highly sensitive and robust tool. Nevertheless, its application to the particular case of pathogen detection from foodstuffs necessitates special requirements for reliable results. Firstly, a robust analytical chain, involving sample preparation and DNA isolation with purification, is necessary to ensure optimal performance. Secondly, for reliable quantification of Listeria monocytogenes from food, reproducible controls for all steps of the analytical chain are needed, which can give quantitative information about the performance of each individual step of the detection chain. Ideally, each individual sample should include a so-called internal sample process control (ISPC) which passes through all steps of the analytical chain and is phenotypically similar to the target organism (in this case L. monocytogenes).This chapter describes the modular and rapid (3 h) sample preparation method "matrix lysis" for the quantification of L. monocytogenes from food and gives detailed information regarding the application of an ISPC based on the example of the L. monocytogenes Δ-prfA/+IAC strain.
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Affiliation(s)
- Patrick Mester
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria.
| | | | - Peter Rossmanith
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
- Unit of Food Microbiology, Institute of Food Safety, Food Technology and Veterinary Public Health, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine Vienna, Vienna, Austria
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Garrido-Maestu A, Azinheiro S, Roumani F, Carvalho J, Prado M. Application of Short Pre-enrichment, and Double Chemistry Real-Time PCR, Combining Fluorescent Probes and an Intercalating Dye, for Same-Day Detection and Confirmation of Salmonella spp. and Escherichia coli O157 in Ground Beef and Chicken Samples. Front Microbiol 2020; 11:591041. [PMID: 33162968 PMCID: PMC7581864 DOI: 10.3389/fmicb.2020.591041] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 09/22/2020] [Indexed: 11/13/2022] Open
Abstract
Molecular methods, particularly those based on real-time PCR (qPCR), have become a popular approach to detect pathogens in food samples. This technique may take advantage of hydrolysis fluorescent probes for increased specificity. Even though suitable, this approach loses the capacity of performing result confirmation by melt curve analysis. In the current study, we developed an alternative approach, combining fluorescent probes along with an intercalating dye (SYBR Green) in order to simultaneously detect, and confirm the result, of two foodborne pathogens (Salmonella spp. and Escherichia coli O157). This new approach named double chemistry qPCR was combined with a short pre-enrichment in order to obtain a multiplex “same-day” detection method for the selected pathogens. The evaluation of the novel method in spiked food samples (ground beef and chicken breast) obtained values of relative sensitivity, specificity, and accuracy higher than 95%, and Cohen’s kappa of 0.92, with a Limit of Detection95 below 5 cfu/25 g, demonstrating its reliability. In addition to this, the method was challenged by inoculating heat-stressed bacteria as well as dead ones. It was observed that it was also possible to detect stressed bacteria with an initial inoculation level below 10 cfu/25 g. Also, it was noticed that high initial concentration of either pathogen (higher than 104 cfu/25 g) was needed in order to generate false positive results due to the presence of dead bacteria, thus the method presents potential for its application in the specific detection of live microorganisms.
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Affiliation(s)
- Alejandro Garrido-Maestu
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
| | - Sarah Azinheiro
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal.,Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Foteini Roumani
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal.,Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Joana Carvalho
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal.,Department of Analytical Chemistry, Nutrition and Food Science, School of Veterinary Sciences, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Marta Prado
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory, Braga, Portugal
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Optimized sample treatment, combined with real-time PCR, for same-day detection of E. coli O157 in ground beef and leafy greens. Food Control 2020. [DOI: 10.1016/j.foodcont.2019.106790] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Zwirzitz B, Pinior B, Metzler-Zebeli B, Handler M, Gense K, Knecht C, Ladinig A, Dzieciol M, Wetzels SU, Wagner M, Schmitz-Esser S, Mann E. Microbiota of the Gut-Lymph Node Axis: Depletion of Mucosa-Associated Segmented Filamentous Bacteria and Enrichment of Methanobrevibacter by Colistin Sulfate and Linco-Spectin in Pigs. Front Microbiol 2019; 10:599. [PMID: 31031713 PMCID: PMC6470194 DOI: 10.3389/fmicb.2019.00599] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 03/08/2019] [Indexed: 12/11/2022] Open
Abstract
Microorganisms are translocated from the gut to lymphatic tissues via immune cells, thereby challenging and training the mammalian immune system. Antibiotics alter the gut microbiome and consecutively might also affect the corresponding translocation processes, resulting in an imbalanced state between the intestinal microbiota and the host. Hence, understanding the variant effects of antibiotics on the microbiome of gut-associated tissues is of vital importance for maintaining metabolic homeostasis and animal health. In the present study, we analyzed the microbiome of (i) pig feces, ileum, and ileocecal lymph nodes under the influence of antibiotics (Linco-Spectin and Colistin sulfate) using 16S rRNA gene sequencing for high-resolution community profiling and (ii) ileocecal lymph nodes in more detail with two additional methodological approaches, i.e., cultivation of ileocecal lymph node samples and (iii) metatranscriptome sequencing of a single lymph node sample. Supplementation of medicated feed showed a local effect on feces and ileal mucosa-associated microbiomes. Pigs that received antibiotics harbored significantly reduced amounts of segmented filamentous bacteria (SFB) along the ileal mucosa (p = 0.048; 199.17-fold change) and increased amounts of Methanobrevibacter, a methanogenic Euryarchaeote in fecal samples (p = 0.005; 20.17-fold change) compared to the control group. Analysis of the porcine ileocecal lymph node microbiome exposed large differences between the viable and the dead fraction of microorganisms and the microbiome was altered to a lesser extent by antibiotics compared with feces and ileum. The core microbiome of lymph nodes was constituted mainly of Proteobacteria. RNA-sequencing of a single lymph node sample unveiled transcripts responsible for amino acid and carbohydrate metabolism as well as protein turnover, DNA replication and signal transduction. The study presented here is the first comparative study of microbial communities in feces, ileum, and its associated ileocecal lymph nodes. In each analyzed site, we identified specific phylotypes susceptible to antibiotic treatment that can have profound impacts on the host physiological and immunological state, or even on global biogeochemical cycles. Our results indicate that pathogenic bacteria, e.g., enteropathogenic Escherichia coli, could escape antibiotic treatment by translocating to lymph nodes. In general ileocecal lymph nodes harbor a more diverse and active community of microorganisms than previously assumed.
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Affiliation(s)
- Benjamin Zwirzitz
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
| | - Beate Pinior
- Institute for Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
| | - Barbara Metzler-Zebeli
- University Clinic for Swine, University of Veterinary Medicine, Vienna, Austria.,Institute of Animal Nutrition and Functional Plant Compounds, University of Veterinary Medicine, Vienna, Austria
| | - Monika Handler
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria
| | - Kristina Gense
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria
| | - Christian Knecht
- University Clinic for Swine, University of Veterinary Medicine, Vienna, Austria
| | - Andrea Ladinig
- University Clinic for Swine, University of Veterinary Medicine, Vienna, Austria
| | - Monika Dzieciol
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria
| | - Stefanie U Wetzels
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
| | - Martin Wagner
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
| | | | - Evelyne Mann
- Institute of Milk Hygiene, University of Veterinary Medicine, Vienna, Austria.,Austrian Competence Centre for Feed and Food Quality, Safety and Innovation, FFoQSI GmbH, Tulln an der Donau, Austria
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Zhang C, Thakkar PV, Powell SE, Sharma P, Vennelaganti S, Betel D, Shah MA. A Comparison of Homogenization vs. Enzymatic Lysis for Microbiome Profiling in Clinical Endoscopic Biopsy Tissue Samples. Front Microbiol 2019; 9:3246. [PMID: 30671046 PMCID: PMC6331478 DOI: 10.3389/fmicb.2018.03246] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 12/14/2018] [Indexed: 12/14/2022] Open
Abstract
Identification of the human microbiome has proven to be of utmost importance with the emerging role of bacteria in various physiological and pathological processes. High throughput sequencing strategies have evolved to assess the composition of the microbiome. To identify possible bias that may exist in the processing of tissue for whole genome sequencing (WGS), it is important to evaluate the extraction method on the overall microbial content and composition. Here we compare two different methods of extraction, homogenization vs. enzymatic lysis, on gastric, esophageal and colorectal biopsies and survey the microbial content and composition using WGS and quantitative PCR (qPCR). We examined total bacterial content using universal 16S rDNA qPCR as well as the abundance of three phyla (Actinobacter, Firmicutes, Bacteroidetes) and one genus (Fusobacterium). We found minimal differences between the two extraction methods in the overall community structure. Furthermore, based on our qPCR analysis, neither method demonstrated preferential extraction of any particular clade of bacteria, nor significantly altered the detection of Gram-positive or Gram-negative organisms. However, although the overall microbial composition remained very similar and the most prevalent bacteria could be detected effectively using either method, the precise community structure and microbial abundances between the two methods were different, primarily due to variations in detection of low abundance genus. We also demonstrate that the homogenization extraction method provides higher microbial DNA content and higher read counts from human tissue biopsy samples of the gastrointestinal tract.
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Affiliation(s)
- Chao Zhang
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States.,Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Prashant V Thakkar
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Sarah Ellen Powell
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Prateek Sharma
- Veterans Affairs Medical Center and University of Kansas School of Medicine, Kansas City, MO, United States
| | - Sreekar Vennelaganti
- Veterans Affairs Medical Center and University of Kansas School of Medicine, Kansas City, MO, United States
| | - Doron Betel
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, United States.,Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
| | - Manish A Shah
- Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY, United States
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Leth C, Varadharajan A, Mester P, Fischaleck M, Rossmanith P, Schmoll F, Fink M. Matrixlysis, an improved sample preparation method for recovery of Mycobacteria from animal tissue material. PLoS One 2017; 12:e0181157. [PMID: 28723969 PMCID: PMC5517009 DOI: 10.1371/journal.pone.0181157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/27/2017] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium caprae, a member of the Mycobacterium tuberculosis complex, is the main causative agent of bovine tuberculosis in alpine regions. Bacterial culture is the gold standard in bovine tuberculosis diagnostic but takes up to twelve weeks. This increases the time and costs for stocks affected with bovine tuberculosis. Hence this study focused on the implementation of a fast and precise mycobacterial detection method and compared it with currently used methods. Matrix lysis is a chemical lysis using high concentrations of urea to solubilize bovine and red deer tissue and was used to detect even smallest amounts or non-visible lesions of mycobacteria. A total of 64 samples collected from 44 animals (37 red deer and 7 cattle) were tested by Matrix lysis. Forty-three of these samples were used for Mycobacterium tuberculosis complex detection by quantitative PCR and other 21 for subtyping the genetically different variants of M. caprae. Furthermore, three Matrix lysis samples were used for Next Generation Sequencing. Our results confirm that Matrix lysis is a fast and precise method for detecting Mycobacterium tuberculosis complex in native tissue samples. However, at the moment it reaches its limits when the samples were analyzed by Next Generation Sequencing and RD4 subtyping.
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Affiliation(s)
- Christoph Leth
- Austrian Agency for Health and Food Safety, Institute for Veterinary Disease Control, Moedling, Lower Austria, Austria
- University of Applied Sciences FH Campus Wien, Vienna, Austria
| | - Ashok Varadharajan
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Centre, LMU Munich, Munich, Germany
| | - Patrick Mester
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, University of Veterinary Medicine, Vienna, Austria
| | - Marlis Fischaleck
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Centre, LMU Munich, Munich, Germany
| | - Peter Rossmanith
- Christian Doppler Laboratory for Monitoring of Microbial Contaminants, University of Veterinary Medicine, Vienna, Austria
| | - Friedrich Schmoll
- Austrian Agency for Health and Food Safety, Institute for Veterinary Disease Control, Moedling, Lower Austria, Austria
| | - Maria Fink
- Austrian Agency for Health and Food Safety, Institute for Veterinary Disease Control, Moedling, Lower Austria, Austria
- * E-mail:
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Mann E, Wagner M, Schmoll F, Slaghuis J, Schönenbrücher H, Mester P. Rapid testing and quantification of Salmonella in ileocaecal lymph nodes of Austrian pigs slaughtered for consumption. Res Vet Sci 2014; 97:187-90. [DOI: 10.1016/j.rvsc.2014.06.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 05/20/2014] [Accepted: 06/28/2014] [Indexed: 12/01/2022]
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