151
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Milanović V, Osimani A, Garofalo C, De Filippis F, Ercolini D, Cardinali F, Taccari M, Aquilanti L, Clementi F. Profiling white wine seed vinegar bacterial diversity through viable counting, metagenomic sequencing and PCR-DGGE. Int J Food Microbiol 2018; 286:66-74. [PMID: 30048915 DOI: 10.1016/j.ijfoodmicro.2018.07.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 07/05/2018] [Accepted: 07/18/2018] [Indexed: 12/19/2022]
Abstract
The production of traditional vinegar is usually carried out using the so-called "seed vinegar" or "mother of vinegar" that is composed of an undefined and complex pool of microorganisms deriving from a previous vinegar production. To date, there have been relatively few studies on the microbiota of seed vinegars. The present study was carried out to discover the bacterial biota of seed vinegar samples used in the homemade production of local vinegars obtained from the acetic fermentation of white wine. The seed vinegar samples were subjected to viable counting and advanced molecular analyses, namely, Illumina sequencing and PCR-DGGE. The adopted polyphasic approach allowed the bacterial diversity of the analyzed samples to be profiled, thus revealing the presence of acetic acid bacteria ascribed to the genera Acetobacter, Gluconacetobacter, Gluconobacter and Komagataeibacter. Moreover, other microbial genera as Pseudomonas, Bacillus and Clostridium were abundantly found in almost all the samples, together with other minority genera. The results of viable counting confirmed the well-acknowledged limitations inherent with acetic acid bacteria recovery on plate growth media. The overall results confirmed that seed vinegars have a complex and heterogeneous biodiversity, thus encouraging their exploitation for the isolation and future technological characterization of cultures to be selected for the manufacture of mixed starter cultures.
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Affiliation(s)
- Vesna Milanović
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Andrea Osimani
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
| | - Cristiana Garofalo
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Francesca De Filippis
- Department of Agricultural Sciences, Division of Microbiology, University of Naples "Federico II", Portici, Italy; Task Force on Microbiome Studies, University of Naples "Federico II", Naples, Italy
| | - Danilo Ercolini
- Department of Agricultural Sciences, Division of Microbiology, University of Naples "Federico II", Portici, Italy; Task Force on Microbiome Studies, University of Naples "Federico II", Naples, Italy
| | - Federica Cardinali
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Manuela Taccari
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Lucia Aquilanti
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Francesca Clementi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
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152
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Agustí G, Codony F. Commentary: Reducing Viability Bias in Analysis of Gut Microbiota in Preterm Infants at Risk of NEC and Sepsis. Front Cell Infect Microbiol 2018; 8:212. [PMID: 29974038 PMCID: PMC6020329 DOI: 10.3389/fcimb.2018.00212] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 06/05/2018] [Indexed: 12/12/2022] Open
Affiliation(s)
- Gemma Agustí
- Departament d'Òptica i Optometria, Universitat Politècnica de Catalunya-Barcelona Tech, Terrassa, Spain
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153
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Huang Z, Zheng J, Shi C, Chen Q. Flow cytometry-based method facilitates optimization of PMA treatment condition for PMA-qPCR method. Mol Cell Probes 2018; 40:37-39. [PMID: 29792916 DOI: 10.1016/j.mcp.2018.05.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/10/2018] [Accepted: 05/21/2018] [Indexed: 11/18/2022]
Abstract
Coupling propidium monoazide (PMA) with quantitative PCR (PMA-qPCR) has been successfully applied to specific detection and quantification of viable cells in various samples. The optimal PMA treatment condition is usually determined through qPCR. However, it is a tedious, time consuming and costly process including DNA extraction and qPCR. To overcome this problem, a flow cytometry-based (FCM-based) method was first proposed in this study to replace qPCR for screening of the optimal PMA treatment condition for Helicobacter pylori, since the pure culture treated with PMA was actually a single cell suspension with fluorescent dye. Results showed that the optimal PMA treatment condition (30 μM of PMA and 8 min of exposure time) determined by the novel method was the same as that determined by the qPCR-based method, which demonstrate the feasibility of this approach. In addition, with the comparison of the qPCR-based method, the FCM-based method allows screening of the optimal PMA treatment condition become much more simple, rapid and economical.
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Affiliation(s)
- Zhiqing Huang
- Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
| | - Jianwei Zheng
- Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
| | - Chunmei Shi
- Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
| | - Qiang Chen
- Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China; Fujian Medical University Stem Cell Research Institute, Fuzhou, Fujian Province 350004, China.
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154
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Fang J, Wu Y, Qu D, Ma B, Yu X, Zhang M, Han J. Propidium monoazide real-time loop-mediated isothermal amplification for specific visualization of viable Salmonella
in food. Lett Appl Microbiol 2018; 67:79-88. [DOI: 10.1111/lam.12992] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/25/2018] [Accepted: 04/06/2018] [Indexed: 01/07/2023]
Affiliation(s)
- J. Fang
- Food Safety Key Laboratory of Zhejiang Province; School of Food Science and Biotechnology; Zhejiang Gongshang University; Hangzhou China
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine; College of Life Science; China Jiliang University; Hangzhou China
| | - Y. Wu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine; College of Life Science; China Jiliang University; Hangzhou China
| | - D. Qu
- Food Safety Key Laboratory of Zhejiang Province; School of Food Science and Biotechnology; Zhejiang Gongshang University; Hangzhou China
| | - B. Ma
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine; College of Life Science; China Jiliang University; Hangzhou China
| | - X. Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine; College of Life Science; China Jiliang University; Hangzhou China
| | - M. Zhang
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine; College of Life Science; China Jiliang University; Hangzhou China
| | - J. Han
- Food Safety Key Laboratory of Zhejiang Province; School of Food Science and Biotechnology; Zhejiang Gongshang University; Hangzhou China
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155
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Monitoring Viable Cells of the Biological Control Agent Lactobacillus plantarum PM411 in Aerial Plant Surfaces by Means of a Strain-Specific Viability Quantitative PCR Method. Appl Environ Microbiol 2018. [PMID: 29523544 PMCID: PMC5930365 DOI: 10.1128/aem.00107-18] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A viability quantitative PCR (v-qPCR) assay was developed for the unambiguous detection and quantification of Lactobacillus plantarum PM411 viable cells in aerial plant surfaces. A 972-bp region of a PM411 predicted prophage with mosaic architecture enabled the identification of a PM411 strain-specific molecular marker. Three primer sets with different amplicon lengths (92, 188, and 317 bp) and one TaqMan probe were designed. All the qPCR assays showed good linearity over a 4-log range and good efficiencies but differed in sensitivity. The nucleic acid-binding dye PEMAX was used to selectively detect and enumerate viable bacteria by v-qPCR. The primer set amplifying a 188-bp DNA fragment was selected as the most suitable for v-qPCR. The performance of the method was assessed on apple blossoms, pear, strawberry, and kiwifruit leaves in potted plants under controlled environmental conditions, as well as pear and apple blossoms under field conditions, by comparing v-qPCR population estimations to those obtained by qPCR and specific plate counting on de Man-Rogosa-Sharpe (MRS)-rifampin. The population estimation did not differ significantly between methods when conditions were conducive to bacterial survival. However, under stressful conditions, differences between methods were observed due to cell death or viable-but-nonculturable state induction. While qPCR overestimated the population level, plate counting underestimated this value in comparison to v-qPCR. PM411 attained stable population levels of viable cells on the flower environment under high relative humidity. However, the unfavorable conditions on the leaf surface and the relatively dryness in the field caused an important decrease in the viable population. IMPORTANCE The v-qPCR method in combination with plate counting and qPCR is a powerful tool for studies of colonization and survival under field conditions, to improve formulations and delivery strategies of PM411, and to optimize the dose and timing of spray schedules. It is expected that PEMAX v-qPCR could also be developed for monitoring other strains on plant surfaces not only as biological control agents but also beneficial bacteria useful in the sustainable management of crop production.
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156
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Gobert G, Cotillard A, Fourmestraux C, Pruvost L, Miguet J, Boyer M. Droplet digital PCR improves absolute quantification of viable lactic acid bacteria in faecal samples. J Microbiol Methods 2018; 148:64-73. [DOI: 10.1016/j.mimet.2018.03.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 03/12/2018] [Accepted: 03/12/2018] [Indexed: 02/06/2023]
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157
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Lee S, Bae S. Evaluating the newly developed dye, DyeTox13 Green C-2 Azide, and comparing it with existing EMA and PMA for the differentiation of viable and nonviable bacteria. J Microbiol Methods 2018; 148:33-39. [DOI: 10.1016/j.mimet.2018.03.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/10/2018] [Accepted: 03/27/2018] [Indexed: 10/17/2022]
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158
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Hansen SJZ, Morovic W, DeMeules M, Stahl B, Sindelar CW. Absolute Enumeration of Probiotic Strains Lactobacillus acidophilus NCFM ® and Bifidobacterium animalis subsp. lactis Bl-04 ® via Chip-Based Digital PCR. Front Microbiol 2018; 9:704. [PMID: 29696008 PMCID: PMC5904286 DOI: 10.3389/fmicb.2018.00704] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 03/27/2018] [Indexed: 12/16/2022] Open
Abstract
The current standard for enumeration of probiotics to obtain colony forming units by plate counts has several drawbacks: long time to results, high variability and the inability to discern between bacterial strains. Accurate probiotic cell counts are important to confirm the delivery of a clinically documented dose for its associated health benefits. A method is described using chip-based digital PCR (cdPCR) to enumerate Bifidobacterium animalis subsp. lactis Bl-04 and Lactobacillus acidophilus NCFM both as single strains and in combination. Primers and probes were designed to differentiate the target strains against other strains of the same species using known single copy, genetic differences. The assay was optimized to include propidium monoazide pre-treatment to prevent amplification of DNA associated with dead probiotic cells as well as liberation of DNA from cells with intact membranes using bead beating. The resulting assay was able to successfully enumerate each strain whether alone or in multiplex. The cdPCR method had a 4 and 5% relative standard deviation (RSD) for Bl-04 and NCFM, respectively, making it more precise than plate counts with an industry accepted RSD of 15%. cdPCR has the potential to replace traditional plate counts because of its precision, strain specificity and the ability to obtain results in a matter of hours.
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Affiliation(s)
- Sarah J Z Hansen
- Probiotic Development, DuPont Nutrition & Health, Madison, WI, United States
| | - Wesley Morovic
- Genomics and Microbiome Sciences, DuPont Nutrition & Health, Madison, WI, United States
| | - Martha DeMeules
- Probiotic Development, DuPont Nutrition & Health, Madison, WI, United States
| | - Buffy Stahl
- Genomics and Microbiome Sciences, DuPont Nutrition & Health, Madison, WI, United States
| | - Connie W Sindelar
- Probiotic Development, DuPont Nutrition & Health, Madison, WI, United States
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159
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Dong L, Liu H, Meng L, Xing M, Wang J, Wang C, Chen H, Zheng N. Quantitative PCR coupled with sodium dodecyl sulfate and propidium monoazide for detection of viable Staphylococcus aureus in milk. J Dairy Sci 2018; 101:4936-4943. [PMID: 29605335 DOI: 10.3168/jds.2017-14087] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 01/04/2018] [Indexed: 11/19/2022]
Abstract
Conventional quantitative PCR (qPCR) are unable to differentiate DNA of viable Staphylococcus aureus cells from dead ones. The aim of this study was to use sodium dodecyl sulfate (SDS) and propidium monoazide (PMA) coupled with lysostaphin to detect viable Staph. aureus. The cell suspensions were treated with SDS and PMA before DNA extraction. The SDS is an anionic surfactant, which can increase the permeability of dead cells to PMA without compromising the viability of live cells. The lysostaphin was applied to improve the effectiveness of DNA extraction. The reliability and specificity of this method were further determined by the detection of Staph. aureus in spiked milk. The results showed that there were significant differences between the SDS-PMA-qPCR and qPCR when a final concentration of 200 μg/mL of lysostaphin was added in DNA extraction. The viable Staph. aureus could be effectively detected when SDS and PMA concentrations were 100 µg/mL and 40 μM, respectively. Compared with conventional qPCR, the SDS-PMA-qPCR assay coupled with lysostaphin was more specific and sensitive. Therefore, this method could accurately detect the number of viable Staph. aureus cells.
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Affiliation(s)
- Lei Dong
- Ministry of Agriculture Laboratory of Quality and Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China; Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, P. R. China; College of Food Science and Engineer, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Huimin Liu
- Ministry of Agriculture Laboratory of Quality and Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China; Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, P. R. China; Institute of Quality Standard and Testing Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, P. R. China
| | - Lu Meng
- Ministry of Agriculture Laboratory of Quality and Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China; Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, P. R. China
| | - Mengru Xing
- Ministry of Agriculture Laboratory of Quality and Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China; Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, P. R. China; College of Food Science and Engineer, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Jiaqi Wang
- Ministry of Agriculture Laboratory of Quality and Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China; Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, P. R. China
| | - Cheng Wang
- Institute of Quality Standard and Testing Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, P. R. China
| | - He Chen
- Institute of Quality Standard and Testing Technology, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, P. R. China
| | - Nan Zheng
- Ministry of Agriculture Laboratory of Quality and Safety Risk Assessment for Dairy Products (Beijing), Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China; Ministry of Agriculture-Milk and Dairy Product Inspection Center (Beijing), Beijing 100193, P. R. China.
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160
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Rousseau A, La Carbona S, Dumètre A, Robertson LJ, Gargala G, Escotte-Binet S, Favennec L, Villena I, Gérard C, Aubert D. Assessing viability and infectivity of foodborne and waterborne stages (cysts/oocysts) of Giardia duodenalis, Cryptosporidium spp., and Toxoplasma gondii: a review of methods. ACTA ACUST UNITED AC 2018; 25:14. [PMID: 29553366 PMCID: PMC5858526 DOI: 10.1051/parasite/2018009] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 02/09/2018] [Indexed: 11/14/2022]
Abstract
Giardia duodenalis, Cryptosporidium spp. and Toxoplasma gondii are protozoan parasites that have been highlighted as emerging foodborne pathogens by the Food and Agriculture Organization of the United Nations and the World Health Organization. According to the European Food Safety Authority, 4786 foodborne and waterborne outbreaks were reported in Europe in 2016, of which 0.4% were attributed to parasites including Cryptosporidium, Giardia and Trichinella. Until 2016, no standardized methods were available to detect Giardia, Cryptosporidium and Toxoplasma (oo)cysts in food. Therefore, no regulation exists regarding these biohazards. Nevertheless, considering their low infective dose, ingestion of foodstuffs contaminated by low quantities of these three parasites can lead to human infection. To evaluate the risk of protozoan parasites in food, efforts must be made towards exposure assessment to estimate the contamination along the food chain, from raw products to consumers. This requires determining: (i) the occurrence of infective protozoan (oo)cysts in foods, and (ii) the efficacy of control measures to eliminate this contamination. In order to conduct such assessments, methods for identification of viable (i.e. live) and infective parasites are required. This review describes the methods currently available to evaluate infectivity and viability of G. duodenalis cysts, Cryptosporidium spp. and T. gondii oocysts, and their potential for application in exposure assessment to determine the presence of the infective protozoa and/or to characterize the efficacy of control measures. Advantages and limits of each method are highlighted and an analytical strategy is proposed to assess exposure to these protozoa.
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Affiliation(s)
- Angélique Rousseau
- EA 3800, Protozooses transmises par l'alimentation, Laboratoire de Parasitologie Mycologie, Université de Reims Champagne Ardenne, Faculté de Médecine, SFR Cap Santé Fed 4231, 51 Rue Cognacq Jay, 51096 Reims, France - ACTALIA Food Safety Department, 310 Rue Popielujko, 50000 Saint-Lô, France - EA 3800, Protozooses transmises par l'alimentation, Laboratoire de Parasitologie Mycologie, Université de Rouen, 76183 Rouen Cedex, France
| | | | - Aurélien Dumètre
- Aix Marseille Univ, IRD (Dakar, Marseille, Papeete), AP-HM, IHU-Méditerranée Infection, UMR Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), Marseille, France
| | - Lucy J Robertson
- Department of Food Safety and Infection Biology, Faculty of Veterinary Medicine, Norwegian University of Life Sciences, PO Box 8146 Dep., 0033, Oslo, Norway
| | - Gilles Gargala
- EA 3800, Protozooses transmises par l'alimentation, Laboratoire de Parasitologie Mycologie, Université de Rouen, 76183 Rouen Cedex, France
| | - Sandie Escotte-Binet
- EA 3800, Protozooses transmises par l'alimentation, Laboratoire de Parasitologie Mycologie, Université de Reims Champagne Ardenne, Faculté de Médecine, SFR Cap Santé Fed 4231, 51 Rue Cognacq Jay, 51096 Reims, France
| | - Loïc Favennec
- EA 3800, Protozooses transmises par l'alimentation, Laboratoire de Parasitologie Mycologie, Université de Rouen, 76183 Rouen Cedex, France
| | - Isabelle Villena
- EA 3800, Protozooses transmises par l'alimentation, Laboratoire de Parasitologie Mycologie, Université de Reims Champagne Ardenne, Faculté de Médecine, SFR Cap Santé Fed 4231, 51 Rue Cognacq Jay, 51096 Reims, France
| | - Cédric Gérard
- Food Safety Microbiology, Nestlé Research Center, PO Box 44, CH-1000 Lausanne 26, Switzerland
| | - Dominique Aubert
- EA 3800, Protozooses transmises par l'alimentation, Laboratoire de Parasitologie Mycologie, Université de Reims Champagne Ardenne, Faculté de Médecine, SFR Cap Santé Fed 4231, 51 Rue Cognacq Jay, 51096 Reims, France
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161
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Fraisse A, Niveau F, Hennechart-Collette C, Coudray-Meunier C, Martin-Latil S, Perelle S. Discrimination of infectious and heat-treated norovirus by combining platinum compounds and real-time RT-PCR. Int J Food Microbiol 2018; 269:64-74. [DOI: 10.1016/j.ijfoodmicro.2018.01.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 01/12/2018] [Accepted: 01/15/2018] [Indexed: 01/16/2023]
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162
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Vondrakova L, Turonova H, Scholtz V, Pazlarova J, Demnerova K. Impact of various killing methods on EMA/PMA-qPCR efficacy. Food Control 2018. [DOI: 10.1016/j.foodcont.2017.09.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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163
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Marotz CA, Sanders JG, Zuniga C, Zaramela LS, Knight R, Zengler K. Improving saliva shotgun metagenomics by chemical host DNA depletion. MICROBIOME 2018; 6:42. [PMID: 29482639 PMCID: PMC5827986 DOI: 10.1186/s40168-018-0426-3] [Citation(s) in RCA: 175] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Accepted: 02/19/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND Shotgun sequencing of microbial communities provides in-depth knowledge of the microbiome by cataloging bacterial, fungal, and viral gene content within a sample, providing an advantage over amplicon sequencing approaches that assess taxonomy but not function and are taxonomically limited. However, mammalian DNA can dominate host-derived samples, obscuring changes in microbial populations because few DNA sequence reads are from the microbial component. We developed and optimized a novel method for enriching microbial DNA from human oral samples and compared its efficiency and potential taxonomic bias with commercially available kits. RESULTS Three commercially available host depletion kits were directly compared with size filtration and a novel method involving osmotic lysis and treatment with propidium monoazide (lyPMA) in human saliva samples. We evaluated the percentage of shotgun metagenomic sequencing reads aligning to the human genome, and taxonomic biases of those not aligning, compared to untreated samples. lyPMA was the most efficient method of removing host-derived sequencing reads compared to untreated sample (8.53 ± 0.10% versus 89.29 ± 0.03%). Furthermore, lyPMA-treated samples exhibit the lowest taxonomic bias compared to untreated samples. CONCLUSION Osmotic lysis followed by PMA treatment is a cost-effective, rapid, and robust method for enriching microbial sequence data in shotgun metagenomics from fresh and frozen saliva samples and may be extensible to other host-derived sample types.
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Affiliation(s)
- Clarisse A Marotz
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Jon G Sanders
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Cristal Zuniga
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Livia S Zaramela
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Karsten Zengler
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA, USA.
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164
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Agustí G, Fittipaldi M, Codony F. Optimization of a Viability PCR Method for the Detection of Listeria monocytogenes in Food Samples. Curr Microbiol 2018; 75:779-785. [DOI: 10.1007/s00284-018-1448-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 02/05/2018] [Indexed: 10/18/2022]
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165
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Kaplan HB, Miranda JA, Gogola GR, Gomez K, Ambrose CG. Persistence of bacterial DNA in orthopedic infections. Diagn Microbiol Infect Dis 2018; 91:136-140. [PMID: 29467085 DOI: 10.1016/j.diagmicrobio.2018.01.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 01/09/2018] [Accepted: 01/10/2018] [Indexed: 01/10/2023]
Abstract
Polymerase chain reaction (PCR) has been proposed as a method to identify bacteria in clinical samples because it is more sensitive than culture techniques and can produce results rapidly. However, PCR can detect DNA from dead cells and thus cannot distinguish between live and dead cells in a tissue sample. Killed Staphylococcus aureus cells were implanted into the femurs and knee joints of rats to determine the length of time that DNA from dead cells is detectable in a living animal under conditions similar to common orthopedic infections. In the joint infection model studied here, the DNA from the dead planktonic bacteria was detected using PCR immediately after injection or 24 h later, but was undetectable 48 and 72 h after injection. In the biofilm implanted-device model studied, the DNA from these dead biofilm cells was detected by PCR immediately after implantation and at 24 h, but not at 48 or 72 h. Thus, our results indicate that DNA from dead cells does not persist in these animal model systems for more than 2 days, which should reduce concerns about possible false positive results using molecular DNA-based techniques for the detection of pathogens.
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Affiliation(s)
- Heidi B Kaplan
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX
| | - Justin A Miranda
- Department of Orthopaedic Surgery, University of Texas Health Science Center at Houston, Houston, TX
| | | | - Karen Gomez
- Department of Microbiology and Molecular Genetics, University of Texas Health Science Center at Houston, Houston, TX
| | - Catherine G Ambrose
- Department of Orthopaedic Surgery, University of Texas Health Science Center at Houston, Houston, TX.
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166
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Microbial diversity of consumption milk during processing and storage. Int J Food Microbiol 2018; 266:21-30. [DOI: 10.1016/j.ijfoodmicro.2017.11.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Revised: 11/02/2017] [Accepted: 11/07/2017] [Indexed: 01/04/2023]
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167
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Scariot MC, Venturelli GL, Prudêncio ES, Arisi ACM. Quantification of Lactobacillus paracasei viable cells in probiotic yoghurt by propidium monoazide combined with quantitative PCR. Int J Food Microbiol 2018; 264:1-7. [DOI: 10.1016/j.ijfoodmicro.2017.10.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/16/2017] [Accepted: 10/17/2017] [Indexed: 12/21/2022]
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168
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Chang CW, Lin MH. Optimization of PMA-qPCR for Staphylococcus aureus and determination of viable bacteria in indoor air. INDOOR AIR 2018; 28:64-72. [PMID: 28683164 DOI: 10.1111/ina.12404] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 07/01/2017] [Indexed: 06/07/2023]
Abstract
Staphylococcus aureus may cause infections in humans from mild skin disorders to lethal pneumonia. Rapid and accurate monitoring of viable S. aureus is essential to characterize human exposure. This study evaluated quantitative PCR (qPCR) with propidium monoazide (PMA) to quantify S. aureus. The results showed comparable S. aureus counts between exclusively live cells and mixtures of live/dead cells by qPCR with 1.5 or 2.3 μg/mL PMA (P>.05), illustrating the ability of PMA-qPCR to detect DNA exclusively from viable cells. Moreover, qPCR with 1.5 or 2.3 μg/mL PMA performed optimally with linearity over 103 -108 CFU/mL (R2 ≥0.9), whereas qPCR with 10, 23 or 46 μg/mL PMA significantly underestimated viable counts. Staphylococcus aureus and total viable bacteria were further determined with PMA-qPCR (1.5 μg/mL) from 48 samples from a public library and two university dormitories and four from outside. Viable bacteria averaged 1.9×104 cells/m3 , and S. aureus were detected in 22 (42%) samples with a mean of 4.4×103 cells/m3 . The number of S. aureus and viable bacteria were positively correlated (r=.61, P<.005), and percentages of S. aureus relative to viable bacteria averaged 12-44%. The results of field samples suggest that PMA-qPCR can be used to quantify viable S. aureus cells.
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Affiliation(s)
- C-W Chang
- Institute of Environmental Health, College of Public Health, National Taiwan University, Taipei, Taiwan
- Center for Research on Environmental and Occupational Health, National Taiwan University, Taipei, Taiwan
- Research Center for Genes, Environmental and Human Health, National Taiwan University, Taipei, Taiwan
| | - M-H Lin
- Institute of Environmental Health, College of Public Health, National Taiwan University, Taipei, Taiwan
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169
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170
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Dinh Thanh M, Agustí G, Mader A, Appel B, Codony F. Improved sample treatment protocol for accurate detection of live Salmonella spp. in food samples by viability PCR. PLoS One 2017; 12:e0189302. [PMID: 29232387 PMCID: PMC5726647 DOI: 10.1371/journal.pone.0189302] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 11/23/2017] [Indexed: 11/19/2022] Open
Abstract
Culture-based detection is still considered as the standard way for detection of Salmonella in foods, although molecular methods, such as viability PCR (vPCR), have been introduced to overcome some disadvantages of traditional culture methods. Despite the success of the vPCR methodology, the problem of false-positive results is a major drawback, especially when applied to environmental samples, hindering the interpretation of the results. To improve the efficiency of vPCR, many approaches have been introduced by several authors during the last years. In the present work, the combination of PEMAX dye, double tube change, and double photo-activation step was established as a strategy to improve vPCR protocol. By combining these approaches, we developed an improved sample treatment protocol able to neutralize DNA signals of up to 5.0×107 dead cells/sample from both pure culture and artificially contaminated food samples. Our results indicate that vPCR can work reliable and has a potential for high throughput detection of live Salmonella cells in food samples, minimizing false-positive signals.
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Affiliation(s)
- Mai Dinh Thanh
- Freie Universität Berlin, Department of Biology, Chemistry and Pharmacy, Berlin, Germany
- German Federal Institute for Risk Assessment, Department Biological Safety, Berlin, Germany
| | | | - Anneluise Mader
- German Federal Institute for Risk Assessment, Department Biological Safety, Berlin, Germany
| | - Bernd Appel
- German Federal Institute for Risk Assessment, Department Biological Safety, Berlin, Germany
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171
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Lizana X, López A, Benito S, Agustí G, Ríos M, Piqué N, Marqués A, Codony F. Viability qPCR, a new tool for Legionella risk management. Int J Hyg Environ Health 2017; 220:1318-1324. [DOI: 10.1016/j.ijheh.2017.08.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Revised: 08/23/2017] [Accepted: 08/23/2017] [Indexed: 10/18/2022]
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172
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Wanted Alive: Finding Bacteria in Your Food. Cell Chem Biol 2017; 24:922-923. [PMID: 28820962 DOI: 10.1016/j.chembiol.2017.07.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
In this issue of Cell Chemical Biology, Pezacki and co-workers (Sherratt et al., 2017) report a simple method to metabolically label viable bacteria, which can be used to detect and capture foodborne pathogens. The method may also find many other applications because it can be used to recover live cells, pathogens and non-pathogens, from various biomedical and environmental samples.
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173
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Agrimonti C, Bottari B, Sardaro MLS, Marmiroli N. Application of real-time PCR (qPCR) for characterization of microbial populations and type of milk in dairy food products. Crit Rev Food Sci Nutr 2017; 59:423-442. [DOI: 10.1080/10408398.2017.1375893] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Caterina Agrimonti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Benedetta Bottari
- Department of Food and Drug Science, University of Parma, Parma, Italy
| | - Maria Luisa Savo Sardaro
- Department of Food and Drug Science, University of Parma, Parma, Italy; Department of Nutrition and Gastronomy, University San Raffaele Roma Srl, Rome, Italy
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
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174
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Yu S, Yan L, Wu X, Li F, Wang D, Xu H. Multiplex PCR coupled with propidium monoazide for the detection of viable Cronobacter sakazakii, Bacillus cereus, and Salmonella spp. in milk and milk products. J Dairy Sci 2017; 100:7874-7882. [DOI: 10.3168/jds.2017-13110] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 05/27/2017] [Indexed: 11/19/2022]
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175
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Casini B, Baggiani A, Totaro M, Mansi A, Costa AL, Aquino F, Miccoli M, Valentini P, Bruschi F, Lopalco PL, Privitera G. Detection of viable but non-culturable legionella in hospital water network following monochloramine disinfection. J Hosp Infect 2017; 98:46-52. [PMID: 28917570 DOI: 10.1016/j.jhin.2017.09.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/04/2017] [Accepted: 09/07/2017] [Indexed: 10/18/2022]
Abstract
BACKGROUND Prevention of legionellosis remains a critical issue in healthcare settings where monochloramine (MC) disinfection was recently introduced as an alternative to chlorine dioxide in controlling Legionella spp. contamination of the hospital water network. Continuous treatments with low MC doses in some instances have induced a viable but non-culturable state (VBNC) of Legionella spp. AIM To investigate the occurrence of such dormant cells during a long period of continuous MC treatment. METHODS Between November 2010 and April 2015, 162 water and biofilm samples were collected and Legionella spp. isolated in accordance with standard procedures. In sampling sites where MC was <1.5mg/L, VBNC cells were investigated by ethidium monoazide bromide (EMA)-real-time polymerase chain reaction (qPCR) and 'resuscitation' test into Acanthamoeba polyphaga CCAP 1501/18. According to the Health Protection Agency protocol, free-living protozoa were researched in 60 five-litre water samples. FINDINGS In all, 136 out of 156 (87.2%) of the samples taken from sites previously positive for L. pneumophila ST269 were negative by culture, but only 47 (34.5%) negative by qPCR. Although no positive results were obtained by EMA-qPCR, four out of 22 samples associated with MC concentration of 1.3 ± 0.5mg/L showed VBNC legionella resuscitation. The presence of the amoeba A. polyphaga in the hospital water network was demonstrated. CONCLUSION Our study is the first report evidencing the emergence of VNBC legionella during a long period of continuous MC treatment of a hospital water network, highlighting the importance of keeping an appropriate and uninterrupted MC dosage to ensure the control of legionella colonization in hospital water supplies.
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Affiliation(s)
- B Casini
- Department of Translational Research, N.T.M.S., University of Pisa, Pisa, Italy.
| | - A Baggiani
- Department of Translational Research, N.T.M.S., University of Pisa, Pisa, Italy
| | - M Totaro
- Department of Translational Research, N.T.M.S., University of Pisa, Pisa, Italy
| | - A Mansi
- INAIL, Department of Occupational and Environmental Medicine, Epidemiology and Hygiene, Monte Porzio Catone (Roma), Roma, Italy
| | - A L Costa
- Department of Translational Research, N.T.M.S., University of Pisa, Pisa, Italy
| | - F Aquino
- Department of Translational Research, N.T.M.S., University of Pisa, Pisa, Italy
| | - M Miccoli
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - P Valentini
- Department of Translational Research, N.T.M.S., University of Pisa, Pisa, Italy
| | - F Bruschi
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - P L Lopalco
- Department of Translational Research, N.T.M.S., University of Pisa, Pisa, Italy
| | - G Privitera
- Department of Translational Research, N.T.M.S., University of Pisa, Pisa, Italy
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176
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Comparison of EMA-, PMA- and DNase qPCR for the determination of microbial cell viability. Appl Microbiol Biotechnol 2017; 101:7371-7383. [PMID: 28875372 DOI: 10.1007/s00253-017-8471-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 07/21/2017] [Accepted: 08/03/2017] [Indexed: 01/13/2023]
Abstract
Ethidium monoazide (EMA) quantitative polymerase chain reaction (qPCR), propidium monoazide (PMA)-qPCR and DNase treatment in combination with qPCR were compared for the determination of microbial cell viability. Additionally, varying EMA and PMA concentrations were analysed to determine which dye and concentration allowed for the optimal identification of viable cells. Viable, heat treated (70 °C for 15 min) and autoclaved cultures of Legionella pneumophila, Pseudomonas aeruginosa, Salmonella typhimurium, Staphylococcus aureus and Enterococcus faecalis were utilised in the respective viability assays. Analysis of the viable and heat-treated samples indicated that variable log reductions were recorded for both EMA [log reductions ranging from 0.01 to 2.71 (viable) and 0.27 to 2.85 (heat treated)], PMA [log reductions ranging from 0.06 to 1.02 (viable) and 0.62 to 2.46 (heat treated)] and DNase treatment [log reductions ranging from 0.06 to 0.82 (viable) and 0.70 to 2.91 (heat treated)], in comparison to the no viability treatment controls. Based on the results obtained, 6 μM EMA and 50 μM PMA were identified as the optimal dye concentrations as low log reductions were recorded (viable and heat-treated samples) in comparison to the no viability treatment control. In addition, the results recorded for the 6 μM EMA concentration were comparable to the results obtained for both the 50 μM PMA and the DNase treatment. The use of EMA-qPCR (6 μM) may therefore allow for the rapid identification and quantification of multiple intact opportunistic pathogens in water sources, which would benefit routine water quality monitoring following disinfection treatment.
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177
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Li X, Huang R, Chen H. Evaluation of Assays to Quantify Infectious Human Norovirus for Heat and High-Pressure Inactivation Studies Using Tulane Virus. FOOD AND ENVIRONMENTAL VIROLOGY 2017; 9:314-325. [PMID: 28238030 DOI: 10.1007/s12560-017-9288-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 02/19/2017] [Indexed: 06/06/2023]
Abstract
We compared the heat and high hydrostatic pressure (HHP) inactivation results of Tulane virus (TV), a human norovirus (HuNoV) surrogate, obtained by plaque assay, direct quantitative reverse transcription PCR (RT-qPCR), porcine gastric mucin magnetic beads (PGM-MBs) binding assay followed by RT-qPCR (PGM/PCR), and propidium monoazide (PMA) assay followed by RT-qPCR (PMA/PCR). Heat and HHP inactivation of a HuNoV genotype I.1 (GI.1) strain and a genotype II.4 (GII.4) strain was also evaluated using those molecular assays. Viruses were heat treated at 50-90 °C for 2 min and HHP treated at 100-550 MPa at initial temperatures of 4 or 21 °C for 2 min. For heat treatment, the three molecular methods significantly underestimated the inactivation of TV. It could be logically concluded that the PGM/PCR assay was better than the PMA/PCR and direct RT-qPCR assays in estimating the inactivation of HuNoV GI.1. The three molecular methods were comparable in estimating the heat inactivation of GII.4. For HHP treatment, both PGM/PCR and PMA/PCR assays were able to estimate inactivation of TV at ≤~2-log reduction levels, but significantly underestimated its inactivation at >~2-log reduction levels. The direct RT-qPCR assay was the worst method for estimating HHP inactivation of TV. It could be logically concluded that the PGM/PCR and PMA/PCR assays were comparable in estimating the HHP inactivation of GI.1 and both were significantly better than the direct RT-qPCR assay. Among the three molecular methods, the PGM/PCR assay was the best in estimating the HHP inactivation of GII.4. These results demonstrated that the PGM/PCR assay was probably the method of choice in estimating the inactivation of HuNoV GI.1 and GII.4 for heat and HHP treatments, but this method would likely result in underestimation of HuNoV inactivation.
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Affiliation(s)
- Xinhui Li
- Department of Microbiology, University of Wisconsin-La Crosse, La Crosse, WI, 54601, USA
| | - Runze Huang
- Department of Animal & Food Sciences, University of Delaware, Newark, DE, 19716-2150, USA
| | - Haiqiang Chen
- Department of Animal & Food Sciences, University of Delaware, Newark, DE, 19716-2150, USA.
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178
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Seidel L, Strathmann M, Nocker A. The feasibility of improved live-dead distinction in qPCR-based microbial source tracking. J Microbiol Methods 2017. [DOI: 10.1016/j.mimet.2017.06.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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179
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Detection of Viable Vibrio cholerae Cells in Seafood Using a Real-Time Visual Loop-Mediated Isothermal Amplification Combined with Propidium Monoazide. FOOD ANAL METHOD 2017. [DOI: 10.1007/s12161-017-0981-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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180
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Emerson JB, Adams RI, Román CMB, Brooks B, Coil DA, Dahlhausen K, Ganz HH, Hartmann EM, Hsu T, Justice NB, Paulino-Lima IG, Luongo JC, Lymperopoulou DS, Gomez-Silvan C, Rothschild-Mancinelli B, Balk M, Huttenhower C, Nocker A, Vaishampayan P, Rothschild LJ. Schrödinger's microbes: Tools for distinguishing the living from the dead in microbial ecosystems. MICROBIOME 2017; 5:86. [PMID: 28810907 PMCID: PMC5558654 DOI: 10.1186/s40168-017-0285-3] [Citation(s) in RCA: 236] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 06/05/2017] [Indexed: 05/16/2023]
Abstract
While often obvious for macroscopic organisms, determining whether a microbe is dead or alive is fraught with complications. Fields such as microbial ecology, environmental health, and medical microbiology each determine how best to assess which members of the microbial community are alive, according to their respective scientific and/or regulatory needs. Many of these fields have gone from studying communities on a bulk level to the fine-scale resolution of microbial populations within consortia. For example, advances in nucleic acid sequencing technologies and downstream bioinformatic analyses have allowed for high-resolution insight into microbial community composition and metabolic potential, yet we know very little about whether such community DNA sequences represent viable microorganisms. In this review, we describe a number of techniques, from microscopy- to molecular-based, that have been used to test for viability (live/dead determination) and/or activity in various contexts, including newer techniques that are compatible with or complementary to downstream nucleic acid sequencing. We describe the compatibility of these viability assessments with high-throughput quantification techniques, including flow cytometry and quantitative PCR (qPCR). Although bacterial viability-linked community characterizations are now feasible in many environments and thus are the focus of this critical review, further methods development is needed for complex environmental samples and to more fully capture the diversity of microbes (e.g., eukaryotic microbes and viruses) and metabolic states (e.g., spores) of microbes in natural environments.
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Affiliation(s)
- Joanne B. Emerson
- Department of Microbiology, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210 USA
- Current Address: Department of Plant Pathology, University of California, Davis, CA USA
| | - Rachel I. Adams
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
| | - Clarisse M. Betancourt Román
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
| | - Brandon Brooks
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
- Department of Earth and Planetary Sciences, University of California, Berkeley, Berkeley, CA 94720 USA
| | - David A. Coil
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Katherine Dahlhausen
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Holly H. Ganz
- Genome Center, University of California Davis, 451 Health Sciences Drive, Davis, CA 95616 USA
| | - Erica M. Hartmann
- Biology and the Built Environment Center, Institute of Ecology and Evolution, University of Oregon, Eugene, OR 97403 USA
- Department of Civil and Environmental Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208 USA
| | - Tiffany Hsu
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Nicholas B. Justice
- Lawrence Berkeley National Lab, 1 Cyclotron Road, 955-512L, Berkeley, CA 94720 USA
| | - Ivan G. Paulino-Lima
- Universities Space Research Association, NASA Ames Research Center, Mail Stop 239-20, Building 239, room 377, Moffett Field, CA 94035-1000 USA
| | - Julia C. Luongo
- Department of Mechanical Engineering, University of Colorado at Boulder, 1111 Engineering Drive, 427 UCB, Boulder, CO 80309 USA
| | - Despoina S. Lymperopoulou
- Department of Plant & Microbial Biology, University of California, Berkeley, 111 Koshland Hall, Berkeley, CA 94720 USA
| | - Cinta Gomez-Silvan
- Lawrence Berkeley National Lab, 1 Cyclotron Road, 955-512L, Berkeley, CA 94720 USA
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94702 USA
| | | | - Melike Balk
- Department of Earth Sciences – Petrology, Faculty of Geosciences, Utrecht University, P.O. Box 80.021, 3508 TA Utrecht, The Netherlands
| | - Curtis Huttenhower
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 665 Huntington Avenue, Boston, MA 02115 USA
- The Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142 USA
| | - Andreas Nocker
- IWW Water Centre, Moritzstrasse 26, 45476 Mülheim an der Ruhr, Germany
| | - Parag Vaishampayan
- Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA USA
| | - Lynn J. Rothschild
- Planetary Sciences and Astrobiology, NASA Ames Research Center, Mail Stop 239-20, Building 239, room 361, Moffett Field, CA 94035-1000 USA
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181
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Li R, Tun HM, Jahan M, Zhang Z, Kumar A, Dilantha Fernando WG, Farenhorst A, Khafipour E. Comparison of DNA-, PMA-, and RNA-based 16S rRNA Illumina sequencing for detection of live bacteria in water. Sci Rep 2017; 7:5752. [PMID: 28720878 PMCID: PMC5515937 DOI: 10.1038/s41598-017-02516-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 03/30/2017] [Indexed: 12/22/2022] Open
Abstract
The limitation of 16S rRNA gene sequencing (DNA-based) for microbial community analyses in water is the inability to differentiate live (dormant cells as well as growing or non-growing metabolically active cells) and dead cells, which can lead to false positive results in the absence of live microbes. Propidium-monoazide (PMA) has been used to selectively remove DNA from dead cells during downstream sequencing process. In comparison, 16S rRNA sequencing (RNA-based) can target live microbial cells in water as both dormant and metabolically active cells produce rRNA. The objective of this study was to compare the efficiency and sensitivity of DNA-based, PMA-based and RNA-based 16S rRNA Illumina sequencing methodologies for live bacteria detection in water samples experimentally spiked with different combination of bacteria (2 gram-negative and 2 gram-positive/acid fast species either all live, all dead, or combinations of live and dead species) or obtained from different sources (First Nation community drinking water; city of Winnipeg tap water; water from Red River, Manitoba, Canada). The RNA-based method, while was superior for detection of live bacterial cells still identified a number of 16S rRNA targets in samples spiked with dead cells. In environmental water samples, the DNA- and PMA-based approaches perhaps overestimated the richness of microbial community compared to RNA-based method. Our results suggest that the RNA-based sequencing was superior to DNA- and PMA-based methods in detecting live bacterial cells in water.
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Affiliation(s)
- Ru Li
- Department of Soil Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.,Department of plant protection, Yunnan Agricultural University, Kunming, Yunnan province, 650201, China
| | - Hein Min Tun
- Department of Animal Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.,Department of Pediatrics, University of Alberta, AB, Canada
| | - Musarrat Jahan
- Department of Soil Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.,Department of Animal Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Zhengxiao Zhang
- Department of Animal Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.,Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | - Ayush Kumar
- Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.,Department of Microbiology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada
| | | | - Annemieke Farenhorst
- Department of Soil Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.
| | - Ehsan Khafipour
- Department of Animal Science, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada. .,Department of Medical Microbiology, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada.
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182
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Garcia-Benitez C, Melgarejo P, De Cal A. Detection of Latent Monilinia Infections in Nectarine Flowers and Fruit by qPCR. PLANT DISEASE 2017; 101:1002-1008. [PMID: 30682929 DOI: 10.1094/pdis-11-16-1682-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Most stone fruit with a latent brown rot infection caused by Monilinia do not develop visible signs of disease until the arrival of fruit at the markets or the consumer's homes. The overnight freezing-incubation technique (ONFIT) is a well-established method for detecting latent brown rot infections, but it takes between 7 to 9 days. In this report, we inform on the advantages of applying a qPCR-based method to (i) detect a latent brown rot infection in the blossoms and fruit of nectarine trees (Prunus persica var. nucipersica) and (ii) distinguish between the Monilinia spp. in them. For applying this qPCR-based method, artificial latent infections were established in nectarine flowers and fruit using 10 Monilinia fructicola isolates, 8 M. fructigena isolates, and 10 M. laxa isolates. We detected greater amounts of M. fructicola DNA than M. laxa and M. fructigena DNA in latently infected flowers using qPCR. However, greater DNA amounts of M. laxa than M. fructicola were detected in the mesocarp of latently infected nectarines. We found that the qPCR-based method is more sensitive, reliable, and quicker than ONFIT for detecting a latent brown rot infection, and could be very useful in those countries where Monilinia spp. are classified as quarantine pathogens.
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Affiliation(s)
- C Garcia-Benitez
- Department of Plant Protection, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain
| | - P Melgarejo
- Department of Plant Protection, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain
| | - A De Cal
- Department of Plant Protection, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), 28040 Madrid, Spain
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183
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Bonetta S, Pignata C, Bonetta S, Meucci L, Giacosa D, Marino E, Gilli G, Carraro E. Viability of Legionella pneumophila in Water Samples: A Comparison of Propidium Monoazide (PMA) Treatment on Membrane Filters and in Liquid. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2017; 14:ijerph14050467. [PMID: 28448459 PMCID: PMC5451918 DOI: 10.3390/ijerph14050467] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 04/18/2017] [Accepted: 04/20/2017] [Indexed: 11/16/2022]
Abstract
Legionella pneumophila is a ubiquitous microorganism widely distributed in aquatic environments and can cause Legionellosis in humans. A promising approach to detect viable cells in water samples involves the use of quantitative polymerase chain reaction (qPCR) in combination with photoactivatable DNA intercalator propidium monoazide (PMA). However, the PMA efficiency could be different depending on the experimental conditions used. The aim of this study was to compare two PMA exposure protocols: (A) directly on the membrane filter or (B) in liquid after filter washing. The overall PMA-induced qPCR means reductions in heat-killed L. pneumophila cells were 2.42 and 1.91 log units for exposure protocols A and B, respectively. A comparison between the results obtained reveals that filter exposure allows a higher PMA-qPCR signal reduction to be reached, mainly at low concentrations (p < 0.05). This confirms the potential use of this method to quantify L. pneumophila in water with low contamination.
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Affiliation(s)
- Sara Bonetta
- Department of Public Health and Pediatrics, University of Torino, P.zza Polonia 94, 10126 Torino, Italy.
| | - Cristina Pignata
- Department of Public Health and Pediatrics, University of Torino, P.zza Polonia 94, 10126 Torino, Italy.
| | - Silvia Bonetta
- Department of Public Health and Pediatrics, University of Torino, P.zza Polonia 94, 10126 Torino, Italy.
| | - Lorenza Meucci
- Società Metropolitana Acque Torino S.p.A., C.so XI Febbraio, 14, 10152 Torino, Italy.
| | - Donatella Giacosa
- Società Metropolitana Acque Torino S.p.A., C.so XI Febbraio, 14, 10152 Torino, Italy.
| | - Elena Marino
- Società Metropolitana Acque Torino S.p.A., C.so XI Febbraio, 14, 10152 Torino, Italy.
| | - Giorgio Gilli
- Department of Public Health and Pediatrics, University of Torino, P.zza Polonia 94, 10126 Torino, Italy.
| | - Elisabetta Carraro
- Department of Public Health and Pediatrics, University of Torino, P.zza Polonia 94, 10126 Torino, Italy.
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184
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Papić B, Pate M, Henigman U, Zajc U, Gruntar I, Biasizzo M, Ocepek M, Kušar D. New Approaches on Quantification of Campylobacter jejuni in Poultry Samples: The Use of Digital PCR and Real-time PCR against the ISO Standard Plate Count Method. Front Microbiol 2017; 8:331. [PMID: 28303130 PMCID: PMC5332403 DOI: 10.3389/fmicb.2017.00331] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/17/2017] [Indexed: 11/13/2022] Open
Abstract
Campylobacteriosis is the most frequently reported bacterial food-borne illness in the European Union and contaminated broiler meat is considered the most important source of infection in humans. The aim of the present study was to evaluate real-time PCR (qPCR) and digital PCR (dPCR) for quantification of Campylobacter jejuni in 75 broiler neck-skin samples collected from a poultry slaughterhouse, and to compare them with the ISO 10272-2 standard plate count method. For qPCR standard curve, C. jejuni-negative neck-skin samples were spiked with C. jejuni suspension with a known number of bacterial cells. The observed CFU/g values by qPCR correlated greatly with the expected values and qPCR showed good performance with the reliable limit of detection (rLOD) and limit of quantification (LOQ) of three and 31 target copies per reaction, respectively. However, both rLOD (1219 CFU/g) and LOQ (12,523 CFU/g) were beyond the EFSA-proposed critical limit of 500-1,000 CFU/g of neck skin. Although C. jejuni cell counts were ≤1,000 CFU/g in only 7/75 samples by plate counting, they were ≤LOQ in 60/75 and ≤rLOD in 26/75 (≤1,000 CFU/g in 24/75) samples by qPCR. A strong and statistically significant correlation was observed between qPCR and dPCR. Both PCR-based methods correlated significantly with the plate count method; however, the correlation was moderate. Using the Bland-Altman analysis, an average agreement was noted between all three methods, although with a large standard deviation. A significant bias toward overestimation in dPCR was observed, probably due to the relatively high number of false positive calls. The linear dynamic range was comparable in both PCR-based methods; however, qPCR proved to be more suitable for routine use. In the future, the establishment of a reliable molecular quantification of C. jejuni in poultry samples showing a wide range of contamination levels down to the proposed critical limit is needed to enable time- and cost-effective surveillance throughout all stages in the food production chain. As both rLOD and LOQ were beyond this limit, a modification of the procedure is suggested to include less sample dilution prior to DNA extraction to enable PCR-based quantification of C. jejuni at the proposed microbiological criteria.
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Affiliation(s)
- Bojan Papić
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of LjubljanaLjubljana, Slovenia
| | - Mateja Pate
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of LjubljanaLjubljana, Slovenia
| | - Urška Henigman
- Veterinary Faculty, Institute of Food Safety, Feed and Environment, University of LjubljanaLjubljana, Slovenia
| | - Urška Zajc
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of LjubljanaLjubljana, Slovenia
| | - Igor Gruntar
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of LjubljanaLjubljana, Slovenia
| | - Majda Biasizzo
- Veterinary Faculty, Institute of Food Safety, Feed and Environment, University of LjubljanaLjubljana, Slovenia
| | - Matjaž Ocepek
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of LjubljanaLjubljana, Slovenia
| | - Darja Kušar
- Veterinary Faculty, Institute of Microbiology and Parasitology, University of LjubljanaLjubljana, Slovenia
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185
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Sextuplex PCR combined with immunomagnetic separation and PMA treatment for rapid detection and specific identification of viable Salmonella spp., Salmonella enterica serovars Paratyphi B, Salmonella Typhimurium, and Salmonella Enteritidis in raw meat. Food Control 2017. [DOI: 10.1016/j.foodcont.2016.09.009] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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186
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Al-Daoud F, Gossen BD, Robson J, McDonald MR. Propidium Monoazide Improves Quantification of Resting Spores of Plasmodiophora brassicae with qPCR. PLANT DISEASE 2017; 101:442-447. [PMID: 30677347 DOI: 10.1094/pdis-05-16-0715-re] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Plasmodiophora brassicae, which causes clubroot of Brassica crops, persists in soil as long-lived resting spores. Quantitative polymerase chain reaction (qPCR) analysis is often used to quantify resting spores but does not distinguish between DNA of viable and nonviable spores. The impact of pretreating spores with propidium monoazide (PMA), which inhibits amplification of DNA from nonviable microorganisms, was assessed in several experiments. Spore suspensions from immature and mature clubs were heat treated; then, PMA-PCR analyses and bioassays were performed to assess spore viability. Prior to heat treatment, assessments comparing PMA-PCR to qPCR for mature spores were similar, indicating that most of these spores were viable. However, only a small proportion (<26%) of immature spores were amplified in PMA-PCR. Bioassays demonstrated that clubroot severity was much higher in plants inoculated with mature spores than with immature spores. Heat treatment produced little or no change in estimates of mature spores from qPCR but spore estimates from PMA-PCR and clubroot severity in bioassays were both substantially reduced. Estimates of spore concentration with PMA-PCR were less consistent for immature spores. To facilitate use of PMA-PCR on infested soil, a protocol for extracting spores from soil was developed that provided higher extraction efficiency than the standard methods.
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Affiliation(s)
- Fadi Al-Daoud
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Bruce D Gossen
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, SK, S7N 0X2, Canada
| | - Justin Robson
- Department of Plant Agriculture, University of Guelph
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187
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Orta de Velásquez MT, Yáñez Noguez I, Casasola Rodríguez B, Román Román PI. Effects of ozone and chlorine disinfection on VBNC Helicobacter pylori by molecular techniques and FESEM images. ENVIRONMENTAL TECHNOLOGY 2017; 38:744-753. [PMID: 27432258 DOI: 10.1080/09593330.2016.1210680] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Helicobacter pylori is a pathogen bacteria associated with chronic gastritis, peptic ulceration, and gastric carcinoma. H. pylori has a spiral morphology, which under certain conditions of stress becomes a coccoid form. This type of morphology has been linked to a viable but non-culturable (VBNC) state, which is thought to allow its persistence in the environment. Membrane damage in VBNC H. pylori in water as a mechanism for inactivation using ozone (O3) and chlorine disinfection has not been reported in the literature. In this paper, disinfection assays with ozone and chlorine were conducted to evaluate their effects on VBNC H. pylori cells. The use of fluorescent dyes such as propidium monoazide (PMA) coupled with quantitative real-time polymerase chain reactions produced results necessary to assess the viability of the microorganism and demonstrate the effect of each disinfectant on the bacterial count. Applying ozone showed a 5-log bacterial reduction using a disinfectant concentration and exposure time (CT) of 4 mg min/L. Chlorine disinfection for the same 5-log reduction required a higher CT value. Field emission scanning electron microscope images of ozone-treated VBNC H. pylori also showed severe cell damage. The use of PMA revealed that chlorine produced physical damage in the membrane in addition to the known inhibiting effect on cell enzymatic processes. These findings are important for the detection and control of VBNC H. pylori cells in drinking water systems.
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Affiliation(s)
- María Teresa Orta de Velásquez
- a Coordinación de Ingeniería Ambiental , Instituto de Ingeniería, Universidad Nacional Autónoma de México , Distrito Federal , Mexico
| | - Isaura Yáñez Noguez
- a Coordinación de Ingeniería Ambiental , Instituto de Ingeniería, Universidad Nacional Autónoma de México , Distrito Federal , Mexico
| | - Beatriz Casasola Rodríguez
- a Coordinación de Ingeniería Ambiental , Instituto de Ingeniería, Universidad Nacional Autónoma de México , Distrito Federal , Mexico
| | - Priscila Ivette Román Román
- a Coordinación de Ingeniería Ambiental , Instituto de Ingeniería, Universidad Nacional Autónoma de México , Distrito Federal , Mexico
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188
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Burnet JB, Faraj T, Cauchie HM, Joaquim-Justo C, Servais P, Prévost M, Dorner SM. How does the cladoceran Daphnia pulex affect the fate of Escherichia coli in water? PLoS One 2017; 12:e0171705. [PMID: 28178322 PMCID: PMC5298254 DOI: 10.1371/journal.pone.0171705] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 01/23/2017] [Indexed: 11/19/2022] Open
Abstract
The faecal indicator Escherichia coli plays a central role in water quality assessment and monitoring. It is therefore essential to understand its fate under various environmental constraints such as predation by bacterivorous zooplankton. Whereas most studies have examined how protozooplankton communities (heterotrophic nanoflagellates and ciliates) affect the fate of E. coli in water, the capacity of metazooplankton to control the faecal indicator remains poorly understood. In this study, we investigated how the common filter-feeding cladoceran, Daphnia pulex, affects the fate of E. coli under different experimental conditions. Daphnia ingested E. coli and increased its loss rates in water, but the latter rates decreased from 1.65 d-1 to 0.62 d-1 after a 1,000-fold reduction in E. coli initial concentrations, due to lower probability of encounter between Daphnia and E. coli. The combined use of culture and PMA qPCR (viability-qPCR) demonstrated that exposure to Daphnia did not result into the formation of viable but non-culturable E. coli cells. In lake water, a significant part of E. coli population loss was associated with matrix-related factors, most likely due to predation by other bacterivorous biota and/or bacterial competition. However, when exposing E. coli to a D. pulex gradient (from 0 to 65 ind.L-1), we observed an increasing impact of Daphnia on E. coli loss rates, which reached 0.47 d-1 in presence of 65 ind.L-1. Our results suggest that the filter-feeder can exert a non-negligible predation pressure on E. coli, especially during seasonal Daphnia population peaks. Similar trials using other Daphnia species as well as stressed E. coli cells will increase our knowledge on the capacity of this widespread zooplankter to control E. coli in freshwater resources. Based on our results, we strongly advocate the use of natural matrices to study these biotic interactions in order to avoid overestimation of Daphnia impact.
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Affiliation(s)
- Jean-Baptiste Burnet
- Canada Research Chair in Source Water Protection, Department of Civil, Geological and Mining Engineering, Polytechnique Montreal, Montreal, Quebec, Canada
- * E-mail:
| | - Tarek Faraj
- Canada Research Chair in Source Water Protection, Department of Civil, Geological and Mining Engineering, Polytechnique Montreal, Montreal, Quebec, Canada
| | - Henry-Michel Cauchie
- Environmental Research and Innovation, Luxembourg Institute of Science and Technology, Esch-sur-Alzette, Luxembourg
| | - Célia Joaquim-Justo
- Laboratoire d’Écologie Animale et d’Écotoxicologie, Institut de Chimie, Université de Liège, Liège, Belgium
| | - Pierre Servais
- Écologie des Systèmes Aquatiques, Université Libre de Bruxelles, Campus de la Plaine, CP 221, Boulevard du Triomphe, Bruxelles, Belgium
| | - Michèle Prévost
- NSERC Industrial Chair on Drinking Water, Department of Civil, Geological and Mining Engineering, Polytechnique Montreal, Montreal, Quebec, Canada
| | - Sarah M. Dorner
- Canada Research Chair in Source Water Protection, Department of Civil, Geological and Mining Engineering, Polytechnique Montreal, Montreal, Quebec, Canada
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189
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False-Positive Viability PCR Results: An Association with Microtubes. Curr Microbiol 2017; 74:377-380. [DOI: 10.1007/s00284-016-1189-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Accepted: 12/22/2016] [Indexed: 10/20/2022]
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190
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Takahashi H, Gao Y, Miya S, Kuda T, Kimura B. Discrimination of live and dead cells of Escherichia coli using propidium monoazide after sodium dodecyl sulfate treatment. Food Control 2017. [DOI: 10.1016/j.foodcont.2016.06.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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191
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Development of Reverse Transcription Quantitative Real-Time PCR (RT-qPCR) Assays for Monitoring Saccharomycopsis fibuligera, Rhizopus oryzae, and Monascus purpureus During the Traditional Brewing of Hong Qu Glutinous Rice Wine. FOOD ANAL METHOD 2017. [DOI: 10.1007/s12161-016-0565-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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192
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Nguyen LDN, Deschaght P, Merlin S, Loywick A, Audebert C, Van Daele S, Viscogliosi E, Vaneechoutte M, Delhaes L. Effects of Propidium Monoazide (PMA) Treatment on Mycobiome and Bacteriome Analysis of Cystic Fibrosis Airways during Exacerbation. PLoS One 2016; 11:e0168860. [PMID: 28030619 PMCID: PMC5193350 DOI: 10.1371/journal.pone.0168860] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 12/07/2016] [Indexed: 02/06/2023] Open
Abstract
Introduction and Purpose Propidium monoazide (PMA)-pretreatment has increasingly been applied to remove the bias from dead or damaged cell artefacts, which could impact the microbiota analysis by high-throughput sequencing. Our study aimed to determine whether a PMA-pretreatment coupled with high-throughput sequencing analysis provides a different picture of the airway mycobiome and bacteriome. Results and Discussion We compared deep-sequencing data of mycobiota and microbiota of 15 sputum samples from 5 cystic fibrosis (CF) patients with and without prior PMA-treatment of the DNA-extracts. PMA-pretreatment had no significant effect on the entire and abundant bacterial community (genera expressed as operational taxonomic units (OTUs) with a relative abundance greater than or equal to 1%), but caused a significant difference in the intermediate community (less than 1%) when analyzing the alpha biodiversity Simpson index (p = 0.03). Regarding PMA impact on the airway mycobiota evaluated for the first time here; no significant differences in alpha diversity indexes between PMA-treated and untreated samples were observed. Regarding beta diversity analysis, the intermediate communities also differed more dramatically than the total and abundant ones when studying both mycobiome and bacteriome. Our results showed that only the intermediate (or low abundance) population diversity is impacted by PMA-treatment, and therefore that abundant taxa are mostly viable during acute exacerbation in CF. Given such a cumbersome protocol (PMA-pretreatment coupled with high-throughput sequencing), we discuss its potential interest within the follow-up of CF patients. Further studies using PMA-pretreatment are warranted to improve our “omic” knowledge of the CF airways.
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Affiliation(s)
- Linh Do Ngoc Nguyen
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), INSERM U1019, CNRS UMR 8204, University of Lille, Lille, France
| | - Pieter Deschaght
- Laboratory for Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, Ghent, Belgium
| | - Sophie Merlin
- GenesDiffusion, Douai, France
- PEGASE, Biosciences, Institut Pasteur de Lille, Lille, France
| | - Alexandre Loywick
- GenesDiffusion, Douai, France
- PEGASE, Biosciences, Institut Pasteur de Lille, Lille, France
| | - Christophe Audebert
- GenesDiffusion, Douai, France
- PEGASE, Biosciences, Institut Pasteur de Lille, Lille, France
| | - Sabine Van Daele
- Department of Pediatrics and Genetics, Faculty of Medicine & Health Sciences, Ghent University, Ghent, Belgium
| | - Eric Viscogliosi
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), INSERM U1019, CNRS UMR 8204, University of Lille, Lille, France
| | - Mario Vaneechoutte
- Laboratory for Bacteriology Research, Faculty of Medicine & Health Sciences, Ghent University, Ghent, Belgium
| | - Laurence Delhaes
- Institut Pasteur de Lille, Center for Infection and Immunity of Lille (CIIL), INSERM U1019, CNRS UMR 8204, University of Lille, Lille, France
- Parasitology-Medical Mycology Department, Regional Hospital Center, Faculty of Medicine, Lille, France
- * E-mail:
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193
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Relic DNA is abundant in soil and obscures estimates of soil microbial diversity. Nat Microbiol 2016; 2:16242. [PMID: 27991881 DOI: 10.1038/nmicrobiol.2016.242] [Citation(s) in RCA: 403] [Impact Index Per Article: 50.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/20/2016] [Indexed: 12/27/2022]
Abstract
Extracellular DNA from dead microorganisms can persist in soil for weeks to years1-3. Although it is implicitly assumed that the microbial DNA recovered from soil predominantly represents intact cells, it is unclear how extracellular DNA affects molecular analyses of microbial diversity. We examined a wide range of soils using viability PCR based on the photoreactive DNA-intercalating dye propidium monoazide4. We found that, on average, 40% of both prokaryotic and fungal DNA was extracellular or from cells that were no longer intact. Extracellular DNA inflated the observed prokaryotic and fungal richness by up to 55% and caused significant misestimation of taxon relative abundances, including the relative abundances of taxa integral to key ecosystem processes. Extracellular DNA was not found in measurable amounts in all soils; it was more likely to be present in soils with low exchangeable base cation concentrations, and the effect of its removal on microbial community structure was more profound in high-pH soils. Together, these findings imply that this 'relic DNA' remaining in soil after cell death can obscure treatment effects, spatiotemporal patterns and relationships between microbial taxa and environmental conditions.
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194
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Quijada NM, Fongaro G, Barardi CRM, Hernández M, Rodríguez-Lázaro D. Propidium Monoazide Integrated with qPCR Enables the Detection and Enumeration of Infectious Enteric RNA and DNA Viruses in Clam and Fermented Sausages. Front Microbiol 2016; 7:2008. [PMID: 28018329 PMCID: PMC5156952 DOI: 10.3389/fmicb.2016.02008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 11/30/2016] [Indexed: 01/27/2023] Open
Abstract
The increase of foodborne viral outbreaks highlights the need for a rapid and sensitive method for the prediction of viral infectivity in food samples. This study assesses the use of propidium monoazide (PMA) coupled with real-time PCR methods (RT-qPCR or qPCR for RNA or DNA viruses, respectively) in the determination of viral infectivity in complex animal-related food matrices. Clam and Spanish fermented sausage (“chorizo”) samples were spiked with infectious and heat-inactivated human adenovirus-2 (HAdV-2) and mengovirus (vMC0). PMA-qPCR/RT-qPCR discriminated infective virus particles, with significant reductions (>2.7 log10 or 99.7%). Additionally, infectious HAdV-2 and vMC0 were quantified by plaque assay (in plaque forming units, PFU), and compared with those in virus genomes copies (GCs) quantified by PMA-qPCR/RT-qPCR. A consistent correlation (R2 > 0.92) was showed between PFU and GCs along serial 10-fold dilutions in both DNA and RNA virus and in both food matrices. This study shows the use of PMA coupled to qPCR/RT-qPCR as a promising alternative for prediction of viral infectivity in food samples in comparison to more expensive and time-consuming methods and for those viruses that are not able to grow under available cell culture techniques.
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Affiliation(s)
- Narciso M Quijada
- Laboratory of Molecular Biology and Microbiology, Instituto Tecnológico Agrario de Castilla y León Valladolid, Spain
| | - Gislaine Fongaro
- Laboratório de Virologia Aplicada, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina Florianópolis, Brazil
| | - Célia R M Barardi
- Laboratório de Virologia Aplicada, Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de Santa Catarina Florianópolis, Brazil
| | - Marta Hernández
- Laboratory of Molecular Biology and Microbiology, Instituto Tecnológico Agrario de Castilla y LeónValladolid, Spain; Departamento de Ingeniería Agrícola y Forestal, Tecnología de los Alimentos, Escuela Técnica Superior de Ingenierías Agrarias, Universidad de ValladolidPalencia, Spain
| | - David Rodríguez-Lázaro
- Division of Microbiology, Department of Biotechnology and Food Science, Universidad de Burgos Burgos, Spain
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195
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Strauss A, Dobrowsky PH, Ndlovu T, Reyneke B, Khan W. Comparative analysis of solar pasteurization versus solar disinfection for the treatment of harvested rainwater. BMC Microbiol 2016; 16:289. [PMID: 27938342 PMCID: PMC5148859 DOI: 10.1186/s12866-016-0909-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 12/06/2016] [Indexed: 12/20/2022] Open
Abstract
Background Numerous pathogens and opportunistic pathogens have been detected in harvested rainwater. Developing countries, in particular, require time- and cost-effective treatment strategies to improve the quality of this water source. The primary aim of the current study was thus to compare solar pasteurization (SOPAS; 70 to 79 °C; 80 to 89 °C; and ≥90 °C) to solar disinfection (SODIS; 6 and 8 hrs) for their efficiency in reducing the level of microbial contamination in harvested rainwater. The chemical quality (anions and cations) of the SOPAS and SODIS treated and untreated rainwater samples were also monitored. Results While the anion concentrations in all the samples were within drinking water guidelines, the concentrations of lead (Pb) and nickel (Ni) exceeded the guidelines in all the SOPAS samples. Additionally, the iron (Fe) concentrations in both the SODIS 6 and 8 hr samples were above the drinking water guidelines. A >99% reduction in Escherichia coli and heterotrophic bacteria counts was then obtained in the SOPAS and SODIS samples. Ethidium monoazide bromide quantitative polymerase chain reaction (EMA-qPCR) analysis revealed a 94.70% reduction in viable Legionella copy numbers in the SOPAS samples, while SODIS after 6 and 8 hrs yielded a 50.60% and 75.22% decrease, respectively. Similarly, a 99.61% reduction in viable Pseudomonas copy numbers was observed after SOPAS treatment, while SODIS after 6 and 8 hrs yielded a 47.27% and 58.31% decrease, respectively. Conclusion While both the SOPAS and SODIS systems reduced the indicator counts to below the detection limit, EMA-qPCR analysis indicated that SOPAS treatment yielded a 2- and 3-log reduction in viable Legionella and Pseudomonas copy numbers, respectively. Additionally, SODIS after 8 hrs yielded a 2-log and 1-log reduction in Legionella and Pseudomonas copy numbers, respectively and could be considered as an alternative, cost-effective treatment method for harvested rainwater.
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Affiliation(s)
- André Strauss
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Penelope Heather Dobrowsky
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Thando Ndlovu
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Brandon Reyneke
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa.
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196
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Shao Y, Wang Z, Bao Q, Zhang H. Application of propidium monoazide quantitative real-time PCR to quantify the viability of Lactobacillus delbrueckii ssp. bulgaricus. J Dairy Sci 2016; 99:9570-9580. [DOI: 10.3168/jds.2016-11597] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 07/17/2016] [Indexed: 11/19/2022]
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197
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Zhou B, Chen B, Wu X, Li F, Yu P, Aguilar ZP, Wei H, Xu H. A new application of a sodium deoxycholate-propidium monoazide-quantitative PCR assay for rapid and sensitive detection of viable Cronobacter sakazakii in powdered infant formula. J Dairy Sci 2016; 99:9550-9559. [DOI: 10.3168/jds.2016-11538] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 08/26/2016] [Indexed: 01/26/2023]
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198
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Designing primers and evaluation of the efficiency of propidium monoazide - Quantitative polymerase chain reaction for counting the viable cells of Lactobacillus gasseri and Lactobacillus salivarius. J Food Drug Anal 2016; 25:533-542. [PMID: 28911639 PMCID: PMC9328820 DOI: 10.1016/j.jfda.2016.10.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 10/21/2016] [Accepted: 10/30/2016] [Indexed: 01/12/2023] Open
Abstract
The purpose of this study is to evaluate the efficiency of using propidium monoazide (PMA) real-time quantitative polymerase chain reaction (qPCR) to count the viable cells of Lactobacillus gasseri and Lactobacillus salivarius in probiotic products. Based on the internal transcription spacer and 23S rRNA genes, two primer sets specific for these two Lactobacillus species were designed. For a probiotic product, the total deMan Rogosa Sharpe plate count was 8.65 ± 0.69 log CFU/g, while for qPCR, the cell counts of L. gasseri and L. salivarius were 8.39 ± 0.14 log CFU/g and 8.57 ± 0.24 log CFU/g, respectively. Under the same conditions, for its heat-killed product, qPCR counts for L. gasseri and L. salivarius were 6.70 ± 0.16 log cells/g and 7.67 ± 0.20 log cells/g, while PMA-qPCR counts were 5.33 ± 0.18 log cells/g and 5.05 ± 0.23 log cells/g, respectively. For cell dilutions with a viable cell count of 8.5 log CFU/mL for L. gasseri and L. salivarius, after heat killing, the PMA-qPCR count for both Lactobacillus species was near 5.5 log cells/mL. When the PMA-qPCR counts of these cell dilutions were compared before and after heat killing, although some DNA might be lost during the heat killing, significant qPCR signals from dead cells, i.e., about 4–5 log cells/mL, could not be reduced by PMA treatment. Increasing PMA concentrations from 100 μM to 200 μM or light exposure time from 5 minutes to 15 minutes had no or, if any, only minor effect on the reduction of qPCR signals from their dead cells. Thus, to differentiate viable lactic acid bacterial cells from dead cells using the PMA-qPCR method, the efficiency of PMA to reduce the qPCR signals from dead cells should be notable.
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Smith AD, Zhang Y, Barber RC, Minshall CT, Huebinger RM, Allen MS. Common Lung Microbiome Identified among Mechanically Ventilated Surgical Patients. PLoS One 2016; 11:e0166313. [PMID: 27898681 PMCID: PMC5127496 DOI: 10.1371/journal.pone.0166313] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 10/26/2016] [Indexed: 11/28/2022] Open
Abstract
The examination of the pulmonary microbiome in patients with non-chronic disease states has not been extensively examined. Traditional culture based screening methods are often unable to identify bacteria from bronchoalveolar lavage samples. The advancement of next-generation sequencing technologies allows for a culture-independent molecular based analysis to determine the microbial composition in the lung of this patient population. For this study, the Ion Torrent PGM system was used to assess the microbial complexity of culture negative bronchoalveolar lavage samples. A group of samples were identified that all displayed high diversity and similar relative abundance of bacteria. This group consisted of Hydrogenophaga, unclassified Bacteroidetes, Pedobacter, Thauera, and Acinetobacter. These bacteria may be representative of a common non-pathogenic pulmonary microbiome associated within this population of patients.
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Affiliation(s)
- Ashley D. Smith
- Department of Cell Biology and Immunology, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
- Center for Biosafety and Biosecurity, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Yan Zhang
- Center for Biosafety and Biosecurity, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
- Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Robert C. Barber
- Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
| | - Christian T. Minshall
- Department of Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
| | - Ryan M. Huebinger
- Department of Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail: (MA); (RH)
| | - Michael S. Allen
- Center for Biosafety and Biosecurity, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
- Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Texas, United States of America
- * E-mail: (MA); (RH)
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Azeredo J, Azevedo NF, Briandet R, Cerca N, Coenye T, Costa AR, Desvaux M, Di Bonaventura G, Hébraud M, Jaglic Z, Kačániová M, Knøchel S, Lourenço A, Mergulhão F, Meyer RL, Nychas G, Simões M, Tresse O, Sternberg C. Critical review on biofilm methods. Crit Rev Microbiol 2016; 43:313-351. [PMID: 27868469 DOI: 10.1080/1040841x.2016.1208146] [Citation(s) in RCA: 541] [Impact Index Per Article: 67.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Biofilms are widespread in nature and constitute an important strategy implemented by microorganisms to survive in sometimes harsh environmental conditions. They can be beneficial or have a negative impact particularly when formed in industrial settings or on medical devices. As such, research into the formation and elimination of biofilms is important for many disciplines. Several new methodologies have been recently developed for, or adapted to, biofilm studies that have contributed to deeper knowledge on biofilm physiology, structure and composition. In this review, traditional and cutting-edge methods to study biofilm biomass, viability, structure, composition and physiology are addressed. Moreover, as there is a lack of consensus among the diversity of techniques used to grow and study biofilms. This review intends to remedy this, by giving a critical perspective, highlighting the advantages and limitations of several methods. Accordingly, this review aims at helping scientists in finding the most appropriate and up-to-date methods to study their biofilms.
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Affiliation(s)
- Joana Azeredo
- a CEB ? Centre of Biological Engineering, LIBRO, Laboratórios de Biofilmes Rosário Oliveira, University of Minho Campus de Gualtar , Braga , Portugal
| | - Nuno F Azevedo
- b LEPABE, Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
| | - Romain Briandet
- c Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay , Jouy-en-Josas , France
| | - Nuno Cerca
- a CEB ? Centre of Biological Engineering, LIBRO, Laboratórios de Biofilmes Rosário Oliveira, University of Minho Campus de Gualtar , Braga , Portugal
| | - Tom Coenye
- d Laboratory of Pharmaceutical Microbiology , Ghent University , Ghent , Belgium
| | - Ana Rita Costa
- a CEB ? Centre of Biological Engineering, LIBRO, Laboratórios de Biofilmes Rosário Oliveira, University of Minho Campus de Gualtar , Braga , Portugal
| | - Mickaël Desvaux
- e INRA Centre Auvergne-Rhône-Alpes , UR454 Microbiologie , Saint-Genès Champanelle , France
| | - Giovanni Di Bonaventura
- f Department of Medical, Oral, and Biotechnological Sciences, and Center of Excellence on Aging and Translational Medicine (CeSI-MeT) , "G. d'Annunzio" University of Chieti-Pescara , Chieti , Italy
| | - Michel Hébraud
- e INRA Centre Auvergne-Rhône-Alpes , UR454 Microbiologie , Saint-Genès Champanelle , France
| | - Zoran Jaglic
- g Department of Food and Feed Safety, Laboratory of Food Bacteriology , Veterinary Research Institute , Brno , Czech Republic
| | - Miroslava Kačániová
- h Department of Microbiology, Faculty of Biotechnology and Food Sciences , Slovak University of Agriculture in Nitra , Nitra , Slovakia
| | - Susanne Knøchel
- i Department of Food Science (FOOD) , University of Copenhagen , Frederiksberg C , Denmark
| | - Anália Lourenço
- j Department of Computer Science , University of Vigo , Ourense , Spain
| | - Filipe Mergulhão
- b LEPABE, Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
| | - Rikke Louise Meyer
- k Aarhus University, Interdisciplinary Nanoscience Center (iNANO) , Aarhus , Denmark
| | - George Nychas
- l Agricultural University of Athens, Lab of Microbiology and Biotechnology of Foods , Athens , Greece
| | - Manuel Simões
- b LEPABE, Department of Chemical Engineering, Faculty of Engineering , University of Porto , Porto , Portugal
| | - Odile Tresse
- m LUNAM Université, Oniris, SECALIM UMR1024 INRA , Université de Nantes , Nantes , France
| | - Claus Sternberg
- n Department of Biotechnology and Biomedicine , Technical University of Denmark , Lyngby, Denmark
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