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Liang M, Liang L, Tayebi M, Zhong J, Ai Y. Lab-In-Fiber Optofluidic Device for Droplet Digital Polymerase Chain Reaction (DdPCR) with Real-Time Monitoring. ACS Sens 2024. [PMID: 39321112 DOI: 10.1021/acssensors.4c01467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
Droplet microfluidic systems have emerged as indispensable and advanced tools in contemporary biological science. A prominent example is the droplet digital polymerase chain reaction (ddPCR), which plays a pivotal role in next-generation sequencing and the detection of rare nucleic acids or mutations. However, existing optical detection configurations are bulky, intricate, and costly, and require meticulous optical alignment to optimize fluorescence sensing. Herein, we propose a lab-in-fiber optofluidic system (LiFO), which provides a stable and compact footprint, self-alignment, and enhanced optical coupling for high-accuracy ddPCR. Moreover, LiFO could expand its capabilities for multiangle-scattering light collection in which we collect focused forward-scattering light (fFSL) to enable real-time droplet counting and size monitoring. To accomplish these attributes, LiFO incorporates optical fibers, along with fabricated PDMS grooves, for a self-aligned optical setup to implement simultaneous fluorescence and scattering detection. Furthermore, LiFO harnesses the concept of flowing droplets functioning as microlenses, which allows us to collect and translate fFSL signals into droplet size information. We have demonstrated the effectiveness of LiFO in ddPCR applications, illustrating its capacity to enhance the accuracy and precision of DNA quantification. Notably, LiFO exhibits improved linearity in the measurement of serial DNA dilutions, reflected by an increase in R2 from 0.956 to 0.997. These results demonstrate the potential of LiFO to serve as a valuable tool across a wide spectrum of droplet microfluidic platforms, offering opportunities for advancement in practical applications.
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Affiliation(s)
- Minhui Liang
- Pillar of Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore 487372, Singapore
- School of Mechanical Engineering, Guangxi University, Nanning 530004, China
| | - Li Liang
- School of Physics and Electronic Technology, Anhui Normal University, Wuhu 241000, China
| | - Mahnoush Tayebi
- Pillar of Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore 487372, Singapore
| | - Jianwei Zhong
- Pillar of Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore 487372, Singapore
| | - Ye Ai
- Pillar of Engineering Product Development, Singapore University of Technology and Design, 8 Somapah Road, Singapore 487372, Singapore
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2
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Soares AB, de Albuquerque MC, Rosa LM, Klein MI, Pavarina AC, Barbugli PA, Dovigo LN, Mima EGDO. Quantification methods of Candida albicans are independent irrespective of fungal morphology. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:265-277. [PMID: 39081907 PMCID: PMC11287054 DOI: 10.15698/mic2024.07.831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 06/09/2024] [Accepted: 06/17/2024] [Indexed: 08/02/2024]
Abstract
The ability of Candida albicans to switch its morphology from yeast to filaments, known as polymorphism, may bias the methods used in microbial quantification. Here, we compared the quantification methods [cell/mL, colony forming units (CFU)/mL, and the number of nuclei estimated by viability polymerase chain reaction (vPCR)] of three strains of C. albicans (one reference strain and two clinical isolates) grown as yeast, filaments, and biofilms. Metabolic activity (XTT assay) was also used for biofilms. Comparisons between the methods were evaluated by agreement analyses [Intraclass and Concordance Correlation Coefficients (ICC and CCC, respectively) and Bland-Altman Plot] and Pearson Correlation (α = 0.05). Principal Component Analysis (PCA) was employed to visualize the similarities and differences between the methods. Results demonstrated a lack of agreement between all methods irrespective of fungal morphology/growth, even when a strong correlation was observed. Bland-Altman plot also demonstrated proportional bias between all methods for all morphologies/growth, except between CFU/mL X vPCR for yeasts and biofilms. For all morphologies, the correlation between the methods were strong, but without linear relationship between them, except for yeast where vPCR showed weak correlation with cells/mL and CFU/mL. XTT moderately correlated with CFU/mL and vPCR and weakly correlated with cells/mL. For all morphologies/growth, PCA showed that CFU/mL was similar to cells/mL and vPCR was distinct from them, but for biofilms vPCR became more similar to CFU/mL and cells/mL while XTT was the most distinct method. As conclusions, our investigation demonstrated that CFU/mL underestimated cells/mL, while vPCR overestimated both cells/mL and CFU/mL, and that the methods had poor agreement and lack of linear relationship, irrespective of C. albicans morphology/growth.1.
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Affiliation(s)
- Amanda B Soares
- Laboratory of Applied Microbiology, Department of Dental Materials and Prosthodontics, School of Dentistry, São Paulo State University (UNESP)Araraquara, Araraquara, São PauloBrazil
| | - Maria C de Albuquerque
- Laboratory of Applied Microbiology, Department of Dental Materials and Prosthodontics, School of Dentistry, São Paulo State University (UNESP)Araraquara, Araraquara, São PauloBrazil
| | - Leticia M Rosa
- Laboratory of Applied Microbiology, Department of Dental Materials and Prosthodontics, School of Dentistry, São Paulo State University (UNESP)Araraquara, Araraquara, São PauloBrazil
| | - Marlise I Klein
- Department of Oral Diagnosis, Piracicaba Dental School, State University of Campinas (UNICAMP)Piracicaba, São PauloBrazil
| | - Ana C Pavarina
- Laboratory of Applied Microbiology, Department of Dental Materials and Prosthodontics, School of Dentistry, São Paulo State University (UNESP)Araraquara, Araraquara, São PauloBrazil
| | - Paula A Barbugli
- Laboratory of Applied Microbiology, Department of Dental Materials and Prosthodontics, School of Dentistry, São Paulo State University (UNESP)Araraquara, Araraquara, São PauloBrazil
| | - Livia N Dovigo
- Department of Social Dentistry, School of Dentistry, São Paulo State University (UNESP)Araraquara, Araraquara, São PauloBrazil
| | - Ewerton G de O Mima
- Laboratory of Applied Microbiology, Department of Dental Materials and Prosthodontics, School of Dentistry, São Paulo State University (UNESP)Araraquara, Araraquara, São PauloBrazil
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Bücher C, Burtscher J, Zitz U, Domig KJ. One-Year Monitoring of Prevalence and Diversity of Dairy Propionic Acid Bacteria in Raw Milk by Means of Culture-Dependent and Culture-Independent Methods. Foods 2024; 13:1921. [PMID: 38928862 PMCID: PMC11203294 DOI: 10.3390/foods13121921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Even low levels of dairy propionic acid bacteria (dPAB) can cause cheese defects, resulting in severe economic losses for the producers of selected raw milk cheeses. Therefore, routine quality control of raw cheese milk for dPAB contamination is essential if propionic acid fermentation is undesired. Although knowledge of dPAB contamination of raw milk is important to understand cheese spoilage, long-term dPAB screening data are outdated, and studies taking into account different farm management parameters and their potential influence on dPAB levels are scarce. This study aims to provide insight into the dPAB levels of raw milk over time, to identify farm management factors that potentially influence dPAB levels, and to compare a cultural yeast extract lactate agar (YELA) and lithium glycerol agar (LGA) and a culture-independent method (qPCR) for dPAB quantification with respect to their applicability in routine quality control for the dairy industry. For this purpose, bulk tank milk from 25 dairy farms was screened for dPAB contamination over a one-year period. We were able to identify significant differences in the dPAB contamination levels in raw milk depending on selected farm-specific factors and observed relationships between the different types of milking systems and dPAB contamination levels in raw milk. When dPAB were quantified by cultivation on YELA, strong overgrowth of commensal microbiota impeded counting. Therefore, we conclude that quantification on LGA or by qPCR is preferable. Both methods, colony counting on LGA as well as quantification of dPAB using qPCR, have advantages for the application in (routine) quality control of raw milk, one being low-tech and inexpensive, the other being fast and highly specific, but the detection of (low level) dPAB contamination in raw milk remains a challenge.
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Affiliation(s)
- Carola Bücher
- Austrian Competence Centre for Feed and Food Quality, Safety and Innovation (FFoQSI), Technopark 1D, 3430 Tulln, Austria;
| | - Johanna Burtscher
- Institute of Food Science, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria; (U.Z.); (K.J.D.)
| | - Ulrike Zitz
- Institute of Food Science, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria; (U.Z.); (K.J.D.)
| | - Konrad J. Domig
- Institute of Food Science, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190 Vienna, Austria; (U.Z.); (K.J.D.)
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Saleem F, Li E, Tran KL, Rudra B, Edge TA, Schellhorn HE, Gupta RS. Utilizing novel Escherichia coli-specific conserved signature proteins for enhanced monitoring of recreational water quality. Microbiologyopen 2024; 13:e1410. [PMID: 38682792 PMCID: PMC11057252 DOI: 10.1002/mbo3.1410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/19/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
Escherichia coli serves as a proxy indicator of fecal contamination in aquatic ecosystems. However, its identification using traditional culturing methods can take up to 24 h. The application of DNA markers, such as conserved signature proteins (CSPs) genes (unique to all species/strains of a specific taxon), can form the foundation for novel polymerase chain reaction (PCR) tests that unambiguously identify and detect targeted bacterial taxa of interest. This paper reports the identification of three new highly-conserved CSPs (genes), namely YahL, YdjO, and YjfZ, which are exclusive to E. coli/Shigella. Using PCR primers based on highly conserved regions within these CSPs, we have developed quantitative PCR (qPCR) assays for the evaluation of E. coli/Shigella species in water ecosystems. Both in-silico and experimental PCR testing confirmed the absence of sequence match when tested against other bacteria, thereby confirming 100% specificity of the tested CSPs for E. coli/Shigella. The qPCR assays for each of the three CSPs provided reliable quantification for all tested enterohaemorrhagic and environmental E. coli strains, a requirement for water testing. For recreational water samples, CSP-based quantification showed a high correlation (r > 7, p < 0.01) with conventional viable E. coli enumeration. This indicates that novel CSP-based qPCR assays for E. coli can serve as robust tools for monitoring water ecosystems and other critical areas, including food monitoring.
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Affiliation(s)
- Faizan Saleem
- Department of BiologyMcMaster UniversityHamiltonOntarioCanada
| | - Enze Li
- Department of BiologyMcMaster UniversityHamiltonOntarioCanada
| | - Kevin L. Tran
- Department of BiologyMcMaster UniversityHamiltonOntarioCanada
| | - Bashudev Rudra
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityHamiltonOntarioCanada
| | - Thomas A. Edge
- Department of BiologyMcMaster UniversityHamiltonOntarioCanada
| | | | - Radhey S. Gupta
- Department of Biochemistry and Biomedical SciencesMcMaster UniversityHamiltonOntarioCanada
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Barbara B, Michela T, Lucia M, Roberto B, Veronica C, Alessandra S, Sonia S, Raffaella B, Pavoni E, Marina Nadia L, Simone P. Mammalian and avian species quantification in homogenized foods: real time PCR and digital PCR as tools for label compliance controls. Sci Rep 2024; 14:10668. [PMID: 38724593 PMCID: PMC11082228 DOI: 10.1038/s41598-024-61009-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 04/30/2024] [Indexed: 05/12/2024] Open
Abstract
Currently food fraud and authenticity of products composition are topics of great concern; ingredients quantification could allow to identify small amounts of contaminats or voluntary addition of improper components. Many molecular methods are available for species identification in foodstuffs but, for a better application, they should not be affected by the interference of other ingredients. The main purpose of this work was to verify the Real Time PCR and the Digital PCR (dPCR) quantification performances on baby food samples, specifically selected for their high miscibility to limit variability; chicken was selected as target to verify the performance of quantification of methods after having spiked the same quantity in different baby foods. The other aims were: (1) to verify a constant genome copies ratio existence between mammalian and avian species (2) to verify the dPCR performance, set up on housekeeping, to quantify mammalian and avian species in commercial products. Digital PCR showed fewer differences respect to Real Time PCR, at the same 15% w/w chicken spiking level. Despite the constant difference between mammalian and avian genome copies, in samples with the same spiking weight, the confidence intervals increasing towards the extreme values, made impossible to use genome copies ratio as a sort of correction factor between species. Finally, the dPCR system using the myostatin housekeeping gene to determine the chicken content seemed reliable to verify the labelling compliance in meat-based commercial products.
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Affiliation(s)
- Bertasi Barbara
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, Via A. Bianchi 9, 15124, Brescia, Italy.
| | - Tilola Michela
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, Via A. Bianchi 9, 15124, Brescia, Italy
| | - Mangeri Lucia
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, Via A. Bianchi 9, 15124, Brescia, Italy
| | - Benevenia Roberto
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, Via A. Bianchi 9, 15124, Brescia, Italy
| | - Cappa Veronica
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, Via A. Bianchi 9, 15124, Brescia, Italy
| | - Scaburri Alessandra
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, Via A. Bianchi 9, 15124, Brescia, Italy
| | - Scaramagli Sonia
- COOP ITALIA, Via del Lavoro 6/8, 40033, Casalecchio di Reno, Bologna, Italy
| | - Bergami Raffaella
- COOP ITALIA, Via del Lavoro 6/8, 40033, Casalecchio di Reno, Bologna, Italy
| | - Enrico Pavoni
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, Via A. Bianchi 9, 15124, Brescia, Italy
| | - Losio Marina Nadia
- Istituto Zooprofilattico Sperimentale della Lombardia ed Emilia Romagna, Via A. Bianchi 9, 15124, Brescia, Italy
| | - Peletto Simone
- Istituto Zooprofilattico Sperimentale del Piemonte, Liguria e Valle D'Aosta, Via Bologna 148, 10154, Turin, Italy
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Lee SS, Kim AL, Park JH, Lee DH, Bae YK. Optimization of duplex digital PCR for the measurement of SARS-CoV-2 RNA. J Virol Methods 2024; 326:114911. [PMID: 38447644 DOI: 10.1016/j.jviromet.2024.114911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/19/2024] [Accepted: 03/02/2024] [Indexed: 03/08/2024]
Abstract
Quantitative PCR (qPCR) is the gold standard for detecting nucleic acid sequences specific to the target pathogen. For COVID-19 diagnosis, several molecular assays have been developed. In this study, we present an optimization strategy for the measurement of SARS-CoV-2 RNA via multiplex qPCR and digital PCR (dPCR). Compared to qPCR, both droplet and chip-based dPCR, which are known to be more sensitive and accurate, showed a better resilience to suboptimal assay compositions and cycling conditions following the proposed optimizations. In particular, the formation of heterodimers among assays greatly interfered with qPCR results, but only minimally with dPCR results. In dPCR, existing heterodimers lowered the PCR efficiency, producing a dampened fluorescent signal in positive partitions. This can be corrected by adjusting the PCR cycling conditions, after which dPCR shows the capability of measuring the expected copy number. In addition, we present a process to improve the existing RdRp assay by correcting the primer sequences and matching the melting temperature, ultimately producing highly sensitive and robust assays. The results of this study can reduce the cost and time of SARS-CoV-2 diagnosis while increasing accuracy. Furthermore, our results suggest that dPCR is a reliable method for the accurate measurement of nucleic acid targets.
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Affiliation(s)
- Sang-Soo Lee
- Biometrology Group, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Ah Leum Kim
- Biometrology Group, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea
| | - Jae-Hyung Park
- Biometrology Group, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Da-Hye Lee
- Biometrology Group, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea.
| | - Young-Kyung Bae
- Biometrology Group, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea; Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Republic of Korea.
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Martins WF, Severo DDS, Longhi DA, de Aragão GMF. Comparison of SYBR® Green qPCR assay and plate count method to describe growth of Weissella viridescens and Leuconostoc mesenteroides in pure and mixed cultivation. Food Microbiol 2024; 119:104452. [PMID: 38225053 DOI: 10.1016/j.fm.2023.104452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/28/2023] [Accepted: 12/18/2023] [Indexed: 01/17/2024]
Abstract
The current study was conducted to statistically compare the SYBR® Green quantitative polymerase chain reaction (qPCR) assay and the conventional plate counting (PC) method to construct growth curves of a cocktail of Weissella viridescens in pure culture under different isothermal storage conditions (4, 8, 14, and 30 °C) and in mixed culture with Leuconostoc mesenteroides at 8 °C. The efficiency and specificity of the qPCR standard curves were confirmed, and both methods were adequate to quantify the growth kinetics of W. viridescens at all isothermal temperatures, demonstrating a good correlation and agreement. The efficiencies of the standard curves varied between 98% and 102%. The SYBR® Green qPCR assay was also able to differentiate the growth curves of W. viridescens and L. mesenteroides in the mixed culture at 8 °C. Additionally, the SYBR® Green qPCR method was considered a faster and more sensitive alternative to construct growth curves under different isothermal conditions and differentiate morphologically similar lactic acid bacteria. Overall, the results suggest that the SYBR® Green qPCR method is a reliable and efficient tool to study microbial growth kinetics in pure and mixed cultures.
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Affiliation(s)
- Wiaslan Figueiredo Martins
- Department of Food Technology, Goiano Federal Institute of Education, Science, and Technology, IF Goiano/Morrinhos Campus, Zip Code 75650-000, Morrinhos, GO, Brazil; Chemical and Food Engineering Department, Federal University of Santa Catarina, EQA/UFSC, Zip Code 88040-900, Florianopolis, SC, Brazil.
| | - Danielle de Sousa Severo
- Chemical and Food Engineering Department, Federal University of Santa Catarina, EQA/UFSC, Zip Code 88040-900, Florianopolis, SC, Brazil
| | - Daniel Angelo Longhi
- LaBeM - Laboratory of Bioactives and Microbiology, School of Food Engineering, Federal University of Paraná, UFPR/Jandaia do Sul Campus, Zip Code 86900-000, Jandaia do Sul, PR, Brazil
| | - Gláucia Maria Falcão de Aragão
- Chemical and Food Engineering Department, Federal University of Santa Catarina, EQA/UFSC, Zip Code 88040-900, Florianopolis, SC, Brazil
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Lee SH, Glover T, Lavey N, Fu X, Donohue M, Karunasena E. Modified in-vitro AATCC-100 procedure to measure viable bacteria from wound dressings. PLoS One 2024; 19:e0298829. [PMID: 38512908 PMCID: PMC10956864 DOI: 10.1371/journal.pone.0298829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 01/30/2024] [Indexed: 03/23/2024] Open
Abstract
Chronic wounds are reoccurring healthcare problems in the United States and cost up to $50 billion annually. Improper wound care results in complications such as wound debridement, surgical amputation, and increased morbidity/ mortality due to opportunistic infections. To eliminate wound infections, many antimicrobial dressings are developed and submitted to FDA for evaluation. AATCC-100 is a standard method widely used to evaluate cloth wound dressings. This method, requires enrichment, followed by culturing to measure the concentration of culturable organisms; a caveat to this method could result in neglected viable but nonculturable (VBNC) bacteria and overestimate the antimicrobial properties of wound dressings. Therefore, the objectives of this study were to assess this accepted protocol with quantitative real-time polymerase chain reaction (qRT-PCR), to measure time dependent antimicrobial efficacy of wound dressing, and to examine for potential viable bacteria but non-culturable as compared with traditional plating methods. The test organisms included opportunistic pathogens: Pseudomonas aeruginosa (ATCC 15692) and Staphylococcus aureus (ATCC 43300). To mimic a wound dressing environment, samples of commercially available wound dressings (McKesson Inc.) with silver ion (positive control) and dressings without silver ion (positive control) were assessed under sterile conditions. All samples were examined by the original protocol (the extended AATCC-100 method) and qRT-PCR. The expression of specific housekeeping genes was measured (proC for P. aeruginosa and 16s rRNA for S. aureus). Based on these tests, log reduction of experimental conditions was compared to identify time dependent and precise antimicrobial properties from wound dressing samples. These results showed antimicrobial properties of wound dressings diminished as incubation days are increased for both methods from day 1 PCR result of 4.31 ± 0.54 and day 1 plating result of 6.31 ± 3.04 to day 3 PCR result of 1.22 ± 0.97 and day 3 plating result of 5.89 ± 2.41. These results show that data from qRT-PCR generally produced lower standard deviation than that of culture methods, hence shown to be more precise. Complementary parallel analysis of samples using both methods better characterized antimicrobial properties of the tested samples.
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Affiliation(s)
- Sang Hyuk Lee
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, United States of America
- Division of Biology, Chemistry, and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, US Food and Drug Administration (FDA), Silver Spring, MD, United States of America
- US Department of Energy, Oak Ridge Institute for Science and Education, Office of Science, Oak Ridge, TN, United States of America
| | - Thomas Glover
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, United States of America
- Division of Biology, Chemistry, and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, US Food and Drug Administration (FDA), Silver Spring, MD, United States of America
- US Department of Energy, Oak Ridge Institute for Science and Education, Office of Science, Oak Ridge, TN, United States of America
| | - Nathan Lavey
- Division of Biology, Chemistry, and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, US Food and Drug Administration (FDA), Silver Spring, MD, United States of America
- US Department of Energy, Oak Ridge Institute for Science and Education, Office of Science, Oak Ridge, TN, United States of America
| | - Xiao Fu
- Division of Biology, Chemistry, and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, US Food and Drug Administration (FDA), Silver Spring, MD, United States of America
- US Department of Energy, Oak Ridge Institute for Science and Education, Office of Science, Oak Ridge, TN, United States of America
| | - Marc Donohue
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, United States of America
| | - Enusha Karunasena
- Division of Biology, Chemistry, and Materials Science, Office of Science and Engineering Laboratories, Center for Devices and Radiological Health, US Food and Drug Administration (FDA), Silver Spring, MD, United States of America
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Lima Â, Muzny CA, Cerca N. An Indirect Fluorescence Microscopy Method to Assess Vaginal Lactobacillus Concentrations. Microorganisms 2024; 12:114. [PMID: 38257941 PMCID: PMC10820742 DOI: 10.3390/microorganisms12010114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/24/2024] Open
Abstract
Lactobacillus species are the main colonizers of the vaginal microbiota in healthy women. Their absolute quantification by culture-based methods is limited due to their fastidious growth. Flow cytometry can quantify the bacterial concentration of these bacteria but requires the acquisition of expensive equipment. More affordable non-culturable methods, such as fluorescence microscopy, are hampered by the small size of the bacteria. Herein, we developed an indirect fluorescence microscopy method to determine vaginal lactobacilli concentration by determining the correlation between surface area bacterial measurement and initial concentration of an easily cultivable bacterium (Escherichia coli) and applying it to lactobacilli fluorescence microscopy counts. In addition, vaginal lactobacilli were quantified by colony-forming units and flow cytometry in order to compare these results with the indirect method results. The colony-forming-unit values were lower than the results obtained from the other two techniques, while flow cytometry and fluorescence microscopy results agreed. Thus, our developed method was able to accurately quantify vaginal lactobacilli.
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Affiliation(s)
- Ângela Lima
- Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal;
| | - Christina A. Muzny
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL 35233, USA;
| | - Nuno Cerca
- Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), Centre of Biological Engineering (CEB), University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal;
- LABBELS—Associate Laboratory, 4710-057 Braga, Portugal
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10
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Da Silva CGN, Monteiro EDC, Diniz PP, Terra LA, Schwab S, Reis VM, Simoes-Araujo JL, Urquiaga S. Designing and validation of specific primers for the quantitative detection of bacteria in sugarcane inoculant. Braz J Microbiol 2023; 54:2627-2640. [PMID: 37843794 PMCID: PMC10689644 DOI: 10.1007/s42770-023-01144-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 10/02/2023] [Indexed: 10/17/2023] Open
Abstract
Endophytic diazotrophic plant growth-promoting bacteria Herbaspirillum rubrisubalbicans (HCC103), Herbaspirillum seropedicae (HRC54), Paraburkholderia tropica (Ppe8T), Gluconacetobacter diazotrophicus (Pal5T), and Nitrospirillum amazonense (CBAmC) have been used as inoculants for sugarcane. The genome sequences of these strains were used to design a set of specific primers for the real-time PCR (qPCR) assay. Primer specificity was confirmed by conventional PCR using the genomic DNAs of 25 related bacterial species and the five target strains. The qPCR assays were conducted using root and shoot samples from two sugarcane varieties (RB867515 and RB92579). These samples were collected both with and without inoculation, using the target strains specified in this study. The sugarcane plants were grown in a greenhouse, utilizing a substrate composed of sterile sand and vermiculite in a 2:1 ratio, for a duration of 55 days. The primers designed for this study successfully amplified target DNA fragments from each of the bacterial species, enabling their differentiation at the species level. The total bacterial population present in the sugarcane quantified using qPCR was on average 105.2 cells g-1 of fresh tissue. Across both evaluated varieties, it was observed that the population of inoculated bacteria tended to decrease over time and became more concentrated in the sugarcane roots compared to the aerial parts. The qPCR results suggest that both the host and the microbes influence the endophytic population and the bacterial number decreases with plant age.
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Affiliation(s)
- Cleudison Gabriel Nascimento Da Silva
- Instituto de Agronomia, Programa de Pós Graduação em Fitotecnia, Universidade Federal Rural Do Rio de Janeiro (UFRRJ), Km 07, BR 465, 23890-000, Seropédica, Rio de Janeiro, Brazil.
| | - Edevaldo de Castro Monteiro
- Instituto de Agronomia, Programa de Pós Graduação em Agronomia - Ciência Do Solo, UFRRJ, Km 07, BR 465, 23890-000, Seropédica, Rio de Janeiro, Brazil
| | - Priscila Pereira Diniz
- Instituto de Agronomia, Programa de Pós Graduação em Agronomia - Ciência Do Solo, UFRRJ, Km 07, BR 465, 23890-000, Seropédica, Rio de Janeiro, Brazil
| | - Leonardo Araujo Terra
- Instituto de Agronomia, Programa de Pós Graduação em Ciência, Tecnologia e Inovação Agropecuária, UFRRJ, Km 07, BR 465, 23890-000, Seropédica, Rio de Janeiro, Brazil
| | - Stefan Schwab
- Embrapa Agrobiologia, Km 07, BR 465, 23891-000, Seropédica, Rio de Janeiro, Brazil
| | | | | | - Segundo Urquiaga
- Embrapa Agrobiologia, Km 07, BR 465, 23891-000, Seropédica, Rio de Janeiro, Brazil
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11
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Tschritter CM, V. C. de Groot P, Branigan M, Dyck M, Sun Z, Lougheed SC. A new multiplexed magnetic capture-Droplet digital PCR tool for monitoring wildlife population health and pathogen surveillance. Ecol Evol 2023; 13:e10655. [PMID: 37915804 PMCID: PMC10616740 DOI: 10.1002/ece3.10655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 10/09/2023] [Indexed: 11/03/2023] Open
Abstract
Anthropogenic stressors are exacerbating the emergence and spread of pathogens worldwide. In regions like the Arctic, where ecosystems are particularly susceptible, marked changes are predicted in regional diversity, intensity, and patterns of infectious diseases. To understand such rapidly changing host-pathogen dynamics and mitigate the impacts of novel pathogens, we need sensitive disease surveillance tools. We developed and validated a novel multiplexed, magnetic capture, and ddPCR tool for the surveillance of multiple pathogens in polar bears, a sentinel species that is considered susceptible to climate change and other stressors with a pan-Arctic distribution. Through sequence-specific magnetic capture, we concentrated five target template sequences from three zoonotic bacteria (Erysipelothrix rhusiopathiae, Francisella tularensis, and Mycobacterium tuberculosis complex) and two parasitic (Toxoplasma gondii and Trichinella spp.) pathogens from large quantities (<100 g) of host tissue. We then designed and validated two multiplexed probe-based ddPCR assays for the amplification and detection of the low-concentration target DNA. Validations used 48 polar bear tissues (muscle and liver). We detected 14, 1, 3, 4, and 22 tissue positives for E. rhusiopathiae, F. tularensis, M. tuberculosis complex, T. gondii, and Trichinella spp., respectively. These multiplexed assays offer a rapid, specific tool for quantifying and monitoring the changing geographical and host distributions of pathogens relevant to human and animal health.
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Affiliation(s)
| | | | - Marsha Branigan
- Department of Environment and Natural ResourcesGovernment of the Northwest TerritoriesInuvikNorthwest TerritoriesCanada
| | - Markus Dyck
- Department of EnvironmentGovernment of NunavutIgloolikNunavutCanada
| | - Zhengxin Sun
- Department of BiologyQueen's UniversityKingstonOntarioCanada
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12
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Russo S, Cortimiglia C, Filippi A, Palladini G, Garbarino C, Massella E, Ricchi M. Validation of digital PCR assay for the quantification of Mycobacterium avium subsp. paratuberculosis in bovine faeces according to the ISO 20395:2019. J Microbiol Methods 2023; 213:106825. [PMID: 37739126 DOI: 10.1016/j.mimet.2023.106825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
Paratuberculosis is an enteric disease caused by Mycobacterium avium subs. Paratuberculosis (MAP). Quantifying the load of MAP in faeces samples offers the advantage of determining the stage of infection and planning control measures. Currently, detection of MAP in faecal specimens relies on cultural assays and quantitative PCR (qPCR), but both methods have limitations such as prolonged isolation times for cultural assay and the absence of nucleic acid standards for qPCR. Digital PCR (dPCR) represents an advancement over qPCR as it allows direct quantification of nucleic acid in a sample without the need for a standard curve. The present paper reports about the validation process, following ISO 20395:2019 guidelines, of a F57 digital PCR assay for quantifying MAP cells in faecal samples. Based on our validation, the Limit Of Detection (LOD) corresponds to 7.85 104 MAP cells/g, and the Limit Of Quantification (LOQ) to 7.85 105 MAP cells, with an efficiency of recovery at LOQ estimated about 4.5%. To assess precision, we evaluated the same faecal sample extracted by two different operators at different times. The standard deviation under repeatability conditions (S Repeatability) and intersession variability conditions (S Intermediate) were calculated, resulting in values of 0.43 and 0.26, respectively. Trueness was determined at LOQ and a value ten times higher, yielding percentages of 3.35% and 5.16%, respectively. Linearity showed a R2 value of 0.998, indicating strong linear correlation. Measurement uncertainty was 26% in absolute value and 3% on a logarithmic base 10 scale. Overall, the assay exhibits good specificity and robustness. Our validation underlines the good performance of the quantification method and allow the laboratory to provide quantitative results of MAP/cells on faecal samples.
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Affiliation(s)
- Simone Russo
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Piacenza, Italy..
| | - Claudia Cortimiglia
- Dipartimento di Scienze e Tecnologie Alimentari per una Filiera Agro-Alimentare Sostenibile (DISTAS), Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Anita Filippi
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Piacenza, Italy
| | - Giorgia Palladini
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Piacenza, Italy..
| | - Chiara Garbarino
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Piacenza, Italy..
| | - Elisa Massella
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Piacenza, Italy..
| | - Matteo Ricchi
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Piacenza, Italy..
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13
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Kim E, Yang SM, Choi CH, Shin MK, Kim HY. Droplet digital PCR method for the absolute quantitative detection and monitoring of Lacticaseibacillus casei. Food Microbiol 2023; 113:104265. [PMID: 37098421 DOI: 10.1016/j.fm.2023.104265] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/09/2023] [Accepted: 03/09/2023] [Indexed: 03/12/2023]
Abstract
Droplet digital polymerase chain reaction (ddPCR) is an emerging molecular detection assay that provides an absolute quantification of targets. Despite its emerging applications in the detection of food microorganisms, there are limited reports of its use for the monitoring of microorganisms utilized as starters in the dairy industry. This study investigated the applicability of ddPCR as a detection platform for Lacticaseibacillus casei, a probiotic found in fermented foods and exerts beneficial effects on human health. In addition, this study compared the performance of ddPCR with that of real-time PCR. The ddPCR targeting the haloacid dehalogenase-like hydrolase (LBCZ_1793) exhibited high specificity against 102 nontarget bacteria, including Lacticaseibacillus species that is very closely related to L. casei. The ddPCR exhibited high linearity and efficiency within the quantitation range (105-100 CFU/ml), with the limit of detection being 100 CFU/ml. The ddPCR also demonstrated a higher sensitivity than real-time PCR in detecting low bacterial concentration in spiked milk samples. Furthermore, it provided an accurate absolute quantification of the concentration of L. casei, without the need for standard calibration curves. This study demonstrated that ddPCR is a useful method for monitoring starter cultures in dairy fermentations and detecting L. casei in foods.
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14
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Nuraeni U, Malau J, Astuti RT, Dewantoro A, Apriori D, Lusiana ED, Prasetya B. Droplet digital PCR versus real-time PCR for in-house validation of porcine detection and quantification protocol: An artificial recombinant plasmid approach. PLoS One 2023; 18:e0287712. [PMID: 37450440 PMCID: PMC10348585 DOI: 10.1371/journal.pone.0287712] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 06/09/2023] [Indexed: 07/18/2023] Open
Abstract
Authenticity and traceability are essential for modern food and medicine inspection, and reliable techniques are important for the trade of halal foods, which reach more than 20 percent of the world market. A sensitive and accurate porcine detection method is required to develop a conformity assessment system that includes laboratory testing for porcine-free certification. This study proposes a procedure that could be incorporated into the development of a standardized control and protocol for real-time PCR (qPCR) methods and their traceability using droplet digital PCR (ddPCR). The design used a recombinant pUC57 plasmid as an amplification target to carry the 97 bp fragment of the porcine ATCB gene. The absolute quantification and linearity assessment showed high precision with R2 values of 0.9971 and 0.9998 for qPCR and ddPCR, respectively. In general, both methods showed comparable results in terms of linearity and detection limit. However, both limit of detection assessments showed high sensitivity, although ddPCR showed a slightly higher sensitivity than that of qPCR, especially at low DNA concentrations. Multiple-sample and inter-participatory testing evaluations revealed a high sensitivity, broad applicability, and robustness of the qPCR method. Therefore, we conclude that based on a recombinant plasmid analysis with a low quantity (less than five copy number), the digital PCR method produced more reliable results. These results could provide scientific information for regulatory authorities, especially those in Indonesia, to consider the development and formulation of a well-established qPCR protocol for porcine detection using expected DNA concentrations.
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Affiliation(s)
- Umi Nuraeni
- Laboratory of National Measurement Standards of Biology, The National Standard Agency of Indonesia (BSN), South Tangerang, Banten, Indonesia
| | - Jekmal Malau
- Department of Pharmacy, Faculty of Health Science, Universitas Singaperbangsa Karawang, West Java, Indonesia
| | - Retno Tri Astuti
- Department of Fisheries Product Technology, Faculty of Fisheries and Marine Science, Universitas Brawijaya, East Java, Indonesia
| | - Auraga Dewantoro
- Research Center for Genetic Engineering, The National Research and Innovation Agency of Indonesia (BRIN), Bogor, Indonesia
| | - Dini Apriori
- Laboratory of National Measurement Standards of Biology, The National Standard Agency of Indonesia (BSN), South Tangerang, Banten, Indonesia
| | - Evellin Dewi Lusiana
- Department of Aquatic Resource Management, Faculty of Fisheries and Marine Science, Universitas Brawijaya, East Java, Indonesia
| | - Bambang Prasetya
- Research Center for Testing Technology and Standards, The National Research and Innovation Agency of Indonesia (BRIN), South Tangerang, Indonesia
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15
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Elnaggar JH, Ardizzone CM, Cerca N, Toh E, Łaniewski P, Lillis RA, Herbst-Kralovetz MM, Quayle AJ, Muzny CA, Taylor CM. A novel Gardnerella, Prevotella, and Lactobacillus standard that improves accuracy in quantifying bacterial burden in vaginal microbial communities. Front Cell Infect Microbiol 2023; 13:1198113. [PMID: 37404722 PMCID: PMC10315654 DOI: 10.3389/fcimb.2023.1198113] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 06/05/2023] [Indexed: 07/06/2023] Open
Abstract
Bacterial vaginosis (BV) is the most common vaginal dysbiosis. In this condition, a polymicrobial biofilm develops on vaginal epithelial cells. Accurately quantifying the bacterial burden of the BV biofilm is necessary to further our understanding of BV pathogenesis. Historically, the standard for calculating total bacterial burden of the BV biofilm has been based on quantifying Escherichia coli 16S rRNA gene copy number. However, E. coli is improper for measuring the bacterial burden of this unique micro-environment. Here, we propose a novel qPCR standard to quantify bacterial burden in vaginal microbial communities, from an optimal state to a mature BV biofilm. These standards consist of different combinations of vaginal bacteria including three common BV-associated bacteria (BVAB) Gardnerella spp. (G), Prevotella spp. (P), and Fannyhessea spp. (F) and commensal Lactobacillus spp. (L) using the 16S rRNA gene (G:P:F:L, G:P:F, G:P:L and 1G:9L). We compared these standards to the traditional E. coli (E) reference standard using known quantities of mock vaginal communities and 16 vaginal samples from women. The E standard significantly underestimated the copy numbers of the mock communities, and this underestimation was significantly greater at lower copy numbers of these communities. The G:P:L standard was the most accurate across all mock communities and when compared to other mixed vaginal standards. Mixed vaginal standards were further validated with vaginal samples. This new G:P:L standard can be used in BV pathogenesis research to enhance reproducibility and reliability in quantitative measurements of BVAB, spanning from the optimal to non-optimal (including BV) vaginal microbiota.
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Affiliation(s)
- Jacob H. Elnaggar
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Caleb M. Ardizzone
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Nuno Cerca
- Laboratory of Research in Biofilms Rosário Oliveira (LIBRO), Centre of Biological Engineering (CEB), University of Minho, Braga, Portugal
| | - Evelyn Toh
- Department of Microbiology & Immunology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Paweł Łaniewski
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, United States
| | - Rebecca A. Lillis
- Division of Infectious Diseases, Department of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Melissa M. Herbst-Kralovetz
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ, United States
| | - Alison J. Quayle
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
| | - Christina A. Muzny
- Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Christopher M. Taylor
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, LA, United States
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16
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Sun A, Mirzayans PM, Piggott AM, Stanton JAL, Sunna A. Adapted method for rapid detection and quantification of pathogen Campylobacter jejuni from environmental water samples. FEMS Microbiol Ecol 2023; 99:fiad058. [PMID: 37245057 DOI: 10.1093/femsec/fiad058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 04/23/2023] [Accepted: 05/26/2023] [Indexed: 05/29/2023] Open
Abstract
Building on a previously developed workflow for rapid and sensitive pathogen detection by qPCR, this work has established a sample treatment strategy that produces consistent quantification efficiencies (QEs) for Campylobacter jejuni against a complex and highly variable sample matrix from a suburban river. The individual treatments most effective at minimizing the inhibitory effects of the sample matrix were pH buffering with HEPES (50 mM, pH 5.7) and addition of the surfactant Tween 20 (2% v/v). Unexpectedly, sample acidification (pH 4-5) resulting from the use of aged Tween 20 that had undergone partial hydrolysis, appeared to play a key role in enhancing QE. This effect could be replicated by direct pH adjustment with dilute hydrochloric acid and may be linked to the solubilization and removal of inhibitory particles at an acidic pH. While the effectiveness of each individual treatment method varied, a combined treatment of either HEPES buffer + Tween 20, or direct pH adjustment + Tween 20, consistently produced QEs of 60%-70% and up to 100%, respectively, over a sampling period of one year. The consistency and scalability of this workflow make it a suitable alternative to culture-based ISO methods for detecting Campylobacter spp.
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Affiliation(s)
- Angela Sun
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Paul M Mirzayans
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Andrew M Piggott
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW 2109, Australia
| | - Jo-Ann L Stanton
- Department of Anatomy, School of Biomedical Sciences, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Anwar Sunna
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW 2109, Australia
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17
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Nikolaou M, Tam VH. Rapid In Vitro Assessment of Antimicrobial Drug Effect Bridging Clinically Relevant Pharmacokinetics: A Comprehensive Methodology. Pharmaceutics 2023; 15:1671. [PMID: 37376120 DOI: 10.3390/pharmaceutics15061671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 06/29/2023] Open
Abstract
Rapid in vitro assessment of antimicrobial drug efficacy under clinically relevant pharmacokinetic conditions is an essential element of both drug development and clinical use. Here, we present a comprehensive overview of a recently developed novel integrated methodology for rapid assessment of such efficacy, particularly against the emergence of resistant bacterial strains, as jointly researched by the authors in recent years. This methodology enables rapid in vitro assessment of the antimicrobial efficacy of single or multiple drugs in combination, following clinically relevant pharmacokinetics. The proposed methodology entails (a) the automated collection of longitudinal time-kill data in an optical-density instrument; (b) the processing of collected time-kill data with the aid of a mathematical model to determine optimal dosing regimens under clinically relevant pharmacokinetics for single or multiple drugs; and (c) in vitro validation of promising dosing regimens in a hollow fiber system. Proof-of-concept of this methodology through a number of in vitro studies is discussed. Future directions for the refinement of optimal data collection and processing are discussed.
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Affiliation(s)
- Michael Nikolaou
- Chemical & Biomolecular Engineering Department, University of Houston, Houston, TX 77204, USA
| | - Vincent H Tam
- Chemical & Biomolecular Engineering Department, University of Houston, Houston, TX 77204, USA
- Department of Pharmacy Practice & Translational Research, University of Houston, Houston, TX 77204, USA
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18
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Venbrux M, Crauwels S, Rediers H. Current and emerging trends in techniques for plant pathogen detection. FRONTIERS IN PLANT SCIENCE 2023; 14:1120968. [PMID: 37223788 PMCID: PMC10200959 DOI: 10.3389/fpls.2023.1120968] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 03/21/2023] [Indexed: 05/25/2023]
Abstract
Plant pathogenic microorganisms cause substantial yield losses in several economically important crops, resulting in economic and social adversity. The spread of such plant pathogens and the emergence of new diseases is facilitated by human practices such as monoculture farming and global trade. Therefore, the early detection and identification of pathogens is of utmost importance to reduce the associated agricultural losses. In this review, techniques that are currently available to detect plant pathogens are discussed, including culture-based, PCR-based, sequencing-based, and immunology-based techniques. Their working principles are explained, followed by an overview of the main advantages and disadvantages, and examples of their use in plant pathogen detection. In addition to the more conventional and commonly used techniques, we also point to some recent evolutions in the field of plant pathogen detection. The potential use of point-of-care devices, including biosensors, have gained in popularity. These devices can provide fast analysis, are easy to use, and most importantly can be used for on-site diagnosis, allowing the farmers to take rapid disease management decisions.
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Affiliation(s)
- Marc Venbrux
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
| | - Sam Crauwels
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
| | - Hans Rediers
- Centre of Microbial and Plant Genetics, Laboratory for Process Microbial Ecology and Bioinspirational Management (PME&BIM), Department of Microbial and Molecular Systems (M2S), KU Leuven, Leuven, Belgium
- Leuven Plant Institute (LPI), KU Leuven, Leuven, Belgium
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19
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Shehata HR, Hassane B, Newmaster SG. Real-time polymerase chain reaction methods for strain specific identification and enumeration of strain Lacticaseibacillus paracasei 8700:2. Front Microbiol 2023; 13:1076631. [PMID: 36741903 PMCID: PMC9889646 DOI: 10.3389/fmicb.2022.1076631] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/21/2022] [Indexed: 01/19/2023] Open
Abstract
Introduction Reliable and accurate methods for probiotic identification and enumeration, at the strain level plays a major role in confirming product efficacy since probiotic health benefits are strain-specific and dose-dependent. In this study, real-time PCR methods were developed for strain specific identification and enumeration of L. paracasei 8700:2, a probiotic strain that plays a role in fighting the common cold. Methods The assay was designed to target a unique region in L. paracasei 8700:2 genome sequence to achieve strain level specificity. The identification assay was evaluated for specificity and sensitivity. The enumeration viability real-time PCR (v-qPCR) method was first optimized for the viability treatment, then the method was evaluated for efficiency, limit of quantification, precision, and its performance was compared to plate count (PC) and viability droplet digital PCR (v-ddPCR) methods. Results The identification method proved to be strain specific and highly sensitive with a limit of detection of 0.5 pg of DNA. The optimal viability dye (PMAxx) concentration was 50 μM. The method was efficient (> 90% with R 2 values > 0.99), with a linear dynamic range between 6*102 and 6*105 copies. The method was highly precise with a relative standard deviation below 5%. The Pearson correlation coefficient (r) was 0.707 for PC and v-qPCR methods, and 0.922 for v-qPCR and v-ddPCR. Bland-Altman method comparison showed that v-qPCR always gave higher values compared to PC method (relative difference ranging from 119% to 184%) and showed no consistent trend (relative difference ranging from -20% to 22%) when comparing v-qPCR and v-ddPCR methods. Discussion The difference between PC and v-PCR methods can potentially be attributed to the proportion of cells that exist in a viable but non culturable (VBNC) state, which can be count by v-PCR but not with PC. The developed v-qPCR method was confirmed to be strain specific, sensitive, efficient, with low variance, able to count VBNC cells, and has shorter time to results compared to plate count methods. Thus, the identification and enumeration methods developed for L. paracasei 8700:2 will be of great importance to achieve high quality and efficacious probiotic products.
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Affiliation(s)
- Hanan R. Shehata
- Natural Health Product Research Alliance, Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada
- Department of Microbiology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
- Purity-IQ Inc., Guelph, ON, Canada
| | | | - Steven G. Newmaster
- Natural Health Product Research Alliance, Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada
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20
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Chiang HM, Lyu JL, Lu ME, Lin YH, Chan ST, Lin YK, Chiang CF. Wasabi leaf supplementation had antioxidant, anti-glycation, and improved skin melanin, spot and moisture. J Funct Foods 2023. [DOI: 10.1016/j.jff.2022.105398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
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21
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Rapid identification and absolute quantitation of zero tolerance-Salmonella enterica subsp. enterica serovar Thompson using droplet digital polymerase chain reaction. Lebensm Wiss Technol 2023. [DOI: 10.1016/j.lwt.2022.114333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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22
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Loskyll M, Podbiel D, Guber A, Hoffmann J. Partitioning and subsampling statistics in compartment-based quantification methods. PLoS One 2023; 18:e0285784. [PMID: 37186607 PMCID: PMC10184943 DOI: 10.1371/journal.pone.0285784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 05/01/2023] [Indexed: 05/17/2023] Open
Abstract
The precision of compartment-based quantification methods is subject to multiple effects, of which partitioning and subsampling play a major role. Partitioning is the process of aliquoting the sample liquid and consequently the contained target molecules, whereas subsampling denotes the fact that usually only a portion of a sample is analyzed. In this work, we present a detailed statistical description comprising the effects of partitioning and subsampling on the relative uncertainty of the test result. We show that the state-of-the-art binomial model does not provide accurate results for the level of subsampling present when analyzing the nucleic acid content of single specific cells. Hence, in this work we address partitioning and subsampling effects separately and subsequently combine them to derive the relative uncertainty of a test system and compare it for single cell content analysis and body fluid analysis. In point-of-care test systems the area for partitioning and detection is usually limited, which means that a trade-off between the number of partitions (related to a partitioning uncertainty) and the amount of analyzed volume (related to a subsampling uncertainty) might be inevitable. In case of low target concentration, the subsampling uncertainty is dominant whereas for high target concentration, the partitioning uncertainty increases, and a larger number of partitions is beneficial to minimize the combined uncertainty. We show, that by minimizing the subsampling uncertainty in the test system, the quantification uncertainty of low target concentrations in single cell content analysis is much smaller than in body fluid analysis. In summary, the work provides the methodological basis for a profound statistical evaluation of partitioning and subsampling effects in compartment-based quantification methods and paves the way towards an improved design of future digital quantification devices for highly accurate molecular diagnostic analysis at the point-of-care.
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Affiliation(s)
- Manuel Loskyll
- Advanced Technologies and Microsystems, Corporate Sector Research and Advance Engineering, Robert Bosch GmbH, Renningen, Baden-Württemberg, Germany
| | - Daniel Podbiel
- Advanced Technologies and Microsystems, Corporate Sector Research and Advance Engineering, Robert Bosch GmbH, Renningen, Baden-Württemberg, Germany
| | - Andreas Guber
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Baden-Württemberg, Germany
- BioMEMS Consulting, Karlsruhe, Baden-Württemberg, Germany
| | - Jochen Hoffmann
- Advanced Technologies and Microsystems, Corporate Sector Research and Advance Engineering, Robert Bosch GmbH, Renningen, Baden-Württemberg, Germany
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23
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Barsi F, Dalzini E, Russo S, Cosciani-Cunico E, Monastero P, Arrigoni N, Garbarino CA, Cortimiglia C, Losio MN, Ricchi M. Isothermal inactivation of Mycobacterium avium subsp. paratuberculosis in curd simulating the stretching phase in pasta-filata cheese process. Front Microbiol 2022; 13:1052222. [PMID: 36532449 PMCID: PMC9751633 DOI: 10.3389/fmicb.2022.1052222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 11/08/2022] [Indexed: 09/11/2024] Open
Abstract
Raw milk and dairy products are usually considered the major sources of Mycobacterium avium subsp. paratuberculosis (MAP) exposure for humans. During the production process of mozzarella cheese, as well as of other pasta-filata cheeses made with pasteurized or raw milk, curd is heated and stretched by addition of hot or boiling water. This step is the critical point for the inactivation of MAP during the production process, but, to our knowledge, no studies have been published about the thermal death time values of MAP in curd. The aim of this study was to determine the inactivation kinetics of MAP in curd used to produce pasta-filata cheese in six independent experiments. The milk was inoculated with a mix of MAP strains (field and registered strains) and, with the aim to simulate the thermal treatment of the curd during the stretching step, samples of 10 g of contaminated curd were vacuum packed and treated separately at six different temperatures from 60°C to 75°C in a water bath. MAP survival was then evaluated by plate count method and inactivation parameters were estimated for determining the thermal resistance of the pathogen directly in the curd. D-values increased from 0.15 min (D75-value) to 4.22 min (D60-value) and the calculated z-value was 10.2°C. These data aid: (i) to design food thermal process treatments defining acceptance limits of critical control points to ensure safety against MAP; (ii) to predict the time/temperature combinations needed to obtain a certain MAP log reduction during the curd stretching step; (iii) to optimize or validate pasta-filata cheese process.
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Affiliation(s)
- Filippo Barsi
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, Piacenza, Italy
| | - Elena Dalzini
- National Reference Centre for Emerging Risks in Food Safety, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, Milan, Italy
- Food Control Division, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, Brescia, Italy
| | - Simone Russo
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, Piacenza, Italy
| | - Elena Cosciani-Cunico
- National Reference Centre for Emerging Risks in Food Safety, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, Milan, Italy
- Food Control Division, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, Brescia, Italy
| | - Paola Monastero
- National Reference Centre for Emerging Risks in Food Safety, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, Milan, Italy
| | - Norma Arrigoni
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, Piacenza, Italy
| | - Chiara Anna Garbarino
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, Piacenza, Italy
| | - Claudia Cortimiglia
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, Piacenza, Italy
| | - Marina Nadia Losio
- National Reference Centre for Emerging Risks in Food Safety, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, Milan, Italy
- Food Control Division, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, Brescia, Italy
| | - Matteo Ricchi
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna “Bruno Ubertini”, Piacenza, Italy
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Bolzon V, Pesando M, Bulfoni M, Nencioni A, Nencioni E. An Integrated Analytical Approach for the Characterization of Probiotic Strains in Food Supplements. Nutrients 2022; 14:nu14235085. [PMID: 36501115 PMCID: PMC9736879 DOI: 10.3390/nu14235085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/23/2022] [Accepted: 11/26/2022] [Indexed: 12/03/2022] Open
Abstract
Research surrounding health benefits from probiotics is becoming popular because of the increasing demand for safer products with protective and therapeutic effects. Proven benefits are species- or genus-specific; however, no certified assays are available for their characterization and quantification at the strain level in the food supplement industry. The objective of this study was to develop a strain-specific Real-time quantitative polymerase chain reaction (RT-qPCR)-based method to be implemented in routine tests for the identification and quantification of Bifidobacterium longum, Bifidobacterium animalis spp. lactis, Lactobacillus paracasei, Lactobacillus rhamnosus, Lactobacillus casei, Bifidobacterium breve, Lactobacillus acidophilus, Lactobacillus plantarum, and Lactobacillus helveticus, starting from a powder mixture of food supplements. The method optimization was carried out in combination with flow cytometry to compare results between the two strategies and implement the analytical workflow with the information also regarding cell viability. These assays were validated in accordance with the International Council for Harmonization of Technical Requirements for Pharmaceuticals for Human Use (ICH) criteria using the plate count enumeration as the gold standard reference. Briefly, probiotic DNAs were extracted from two powder food supplements. Strain-specific primers targeting unique sequence regions of 16S RNA were identified and amplified by RT-qPCR. Primers were tested for specificity, sensitivity, and efficiency. Both RT-qPCR and flow-cytometry methods described in our work for the quantification and identification of Lactobacillus and Bifidobacterium strains were specific, sensitive, and precise, showing better performances with respect to the morphological colony identification. This work demonstrated that RT-qPCR can be implemented in the quality control workflow of commercial probiotic products giving more standardized and effective results regarding species discrimination.
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Affiliation(s)
| | | | - Michela Bulfoni
- Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Alessandro Nencioni
- IBSA Institut Biochimique SA, Via del Piano 29, CH-6915 Pambio Noranco, Switzerland
| | - Emanuele Nencioni
- Biofarma Group Srl., Via Castelliere 2, 33036 Udine, Italy
- Correspondence:
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Badia-Bringué G, Canive M, Casais R, Blanco-Vázquez C, Amado J, Iglesias N, González A, Bascones M, Juste RA, Alonso-Hearn M. Evaluation of a droplet digital PCR assay for quantification of Mycobacterium avium subsp. paratuberculosis DNA in whole-blood and fecal samples from MAP-infected Holstein cattle. Front Vet Sci 2022; 9:944189. [PMID: 36246323 PMCID: PMC9563315 DOI: 10.3389/fvets.2022.944189] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/02/2022] [Indexed: 01/17/2023] Open
Abstract
Bovine paratuberculosis (PTB) is an infectious disease that affects ruminants worldwide and is a burden on the dairy industry. PTB control measures include culling of Mycobacterium avium subsp. paratuberculosis (MAP)-infected animals from the herd and the enhancement of farm-biosecurity measures. Diagnostics tools for the direct detection of MAP are fecal real-time qPCR and bacteriological culture, the last one being considered the gold standard. However, both show limitations for detecting subclinical MAP-infected cattle with low bacterial load in feces and gut tissues. Droplet digital polymerase chain reaction (ddPCR) is a third-generation PCR method that shows high reproducibility for the quantification of low DNA copy numbers. The objective of this study was to design a ddPCR assay to detect and quantify a fragment of the F57 MAP-specific sequence in samples of naturally MAP-infected Holstein cattle. DNA was isolated from whole-blood and fecal samples from control cows with a negative ELISA and qPCR result (N = 75) and from cows with PTB-associated focal (N = 32), multifocal (N = 21), and diffuse lesions (N = 17) in gut tissues. After ddPCR, the DNA extracted from fecal samples of cows with diffuse lesions showed higher mean copies per microliter (13,791.2 copies/μl) than samples from cows with multifocal lesions (78.8 copies/μl), focal lesions (177.1 copies/μl) or control cows (4.8 copies/μl) (P ≤ 0.05). Significant differences in mean DNA copies/μl were also observed in the blood samples from cows with focal lesions (47.7 copies/μl) when compared with cows with multifocal and diffuse lesions; 18.1 and 12.4 copies/μl, respectively. Using a principal component analysis, the results of the fecal ddPCR clustered together with the results of a commercial ELISA for the specific detection of MAP antibodies, fecal and tissue qPCR, and bacteriological culture results. In contrast, blood ddPCR results clustered together with the results of an ELISA for the detection of a biomarker of subclinical PTB, the ABCA13 transporter. Blood ddPCR was the most sensitive tool (sensitivity 71%, specificity 100%) of all the quantitative methods used in the study for the detection of subclinical cows with focal lesions.
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Affiliation(s)
- Gerard Badia-Bringué
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance, Derio, Spain
- Doctoral Program in Molecular Biology and Biomedicine, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Leioa, Spain
| | - Maria Canive
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance, Derio, Spain
| | - Rosa Casais
- Center for Animal Biotechnology, Servicio Regional de Investigación y Desarrollo Agroalimentario, Deva, Spain
| | - Cristina Blanco-Vázquez
- Center for Animal Biotechnology, Servicio Regional de Investigación y Desarrollo Agroalimentario, Deva, Spain
| | - Javier Amado
- Department of Microbiology, Laboratorio Regional de Sanidad Animal del Principado de Asturias, Gijón, Spain
| | - Natalia Iglesias
- Center for Animal Biotechnology, Servicio Regional de Investigación y Desarrollo Agroalimentario, Deva, Spain
| | - Aitor González
- Department of Conservation of Natural Resources, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance, Derio, Spain
| | - Mertxe Bascones
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance, Derio, Spain
| | - Ramon A. Juste
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance, Derio, Spain
| | - Marta Alonso-Hearn
- Department of Animal Health, NEIKER- Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance, Derio, Spain
- *Correspondence: Marta Alonso-Hearn
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26
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Tiwari A, Ahmed W, Oikarinen S, Sherchan SP, Heikinheimo A, Jiang G, Simpson SL, Greaves J, Bivins A. Application of digital PCR for public health-related water quality monitoring. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 837:155663. [PMID: 35523326 DOI: 10.1016/j.scitotenv.2022.155663] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 05/25/2023]
Abstract
Digital polymerase chain reaction (dPCR) is emerging as a reliable platform for quantifying microorganisms in the field of water microbiology. This paper reviews the fundamental principles of dPCR and its application for health-related water microbiology. The relevant literature indicates increasing adoption of dPCR for measuring fecal indicator bacteria, microbial source tracking marker genes, and pathogens in various aquatic environments. The adoption of dPCR has accelerated recently due to increasing use for wastewater surveillance of Severe Acute Respiratory Coronavirus 2 (SARS-CoV-2) - the virus that causes Coronavirus Disease 2019 (COVID-19). The collective experience in the scientific literature indicates that well-optimized dPCR assays can quantify genetic material from microorganisms without the need for a calibration curve and often with superior analytical performance (i.e., greater sensitivity, precision, and reproducibility) than quantitative polymerase chain reaction (qPCR). Nonetheless, dPCR should not be viewed as a panacea for the fundamental uncertainties and limitations associated with measuring microorganisms in water microbiology. With dPCR platforms, the sample analysis cost and processing time are typically greater than qPCR. However, if improved analytical performance (i.e., sensitivity and accuracy) is critical, dPCR can be an alternative option for quantifying microorganisms, including pathogens, in aquatic environments.
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Affiliation(s)
- Ananda Tiwari
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland
| | - Warish Ahmed
- CSIRO Land and Water, Ecosciences Precinct, Queensland, Australia
| | - Sami Oikarinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA, USA; Department of Biology, Morgan State University, Baltimore, MD 21251, USA; BioEnvironmental Science Program, Department of Biology, Morgan State University, Baltimore, MD 21251, USA
| | - Annamari Heikinheimo
- Department of Food Hygiene and Environmental Health, Faculty of Veterinary Medicine, University of Helsinki, Finland; Finnish Food Authority, Seinäjoki, Finland
| | - Guangming Jiang
- School of Civil, Mining and Environmental Engineering, University of Wollongong, Australia; Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, Australia
| | | | - Justin Greaves
- School of Environmental Sustainability, Loyola University Chicago, 6364 N. Sheridan Rd, Chicago, IL 60660, USA
| | - Aaron Bivins
- Department of Civil & Environmental Engineering, Louisiana State University, LA, USA.
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Russo S, Giorgio G, Leo S, Arrigoni N, Garbarino C, Ricchi M. Validation of IS900- qPCR assay to assess the presence of Mycobacterium avium subs. paratuberculosis in faecal samples according to the OIE procedure. Prev Vet Med 2022; 208:105732. [DOI: 10.1016/j.prevetmed.2022.105732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 07/19/2022] [Accepted: 07/31/2022] [Indexed: 11/24/2022]
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Du Y, Yan Z, Song K, Jin J, Xiao L, Sun Z, Tan Y, Zhang P, Du Z, Yang R, Zhao Y, Song Y. Development and evaluation of a multiplex droplet digital polymerase chain reaction method for simultaneous detection of five biothreat pathogens. Front Microbiol 2022; 13:970973. [PMID: 35966705 PMCID: PMC9366144 DOI: 10.3389/fmicb.2022.970973] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 07/11/2022] [Indexed: 11/20/2022] Open
Abstract
Biothreat agents pose a huge threat to human and public health, necessitating the development of rapid and highly sensitive detection approaches. This study establishes a multiplex droplet digital polymerase chain reaction (ddPCR) method for simultaneously detecting five high-risk bacterial biothreats: Yersinia pestis, Bacillus anthracis, Brucella spp., Burkholderia pseudomallei, and Francisella tularensis. Unlike conventional multiplex real-time PCR (qPCR) methods, the multiplex ddPCR assay was developed using two types of probe fluorophores, allowing the assay to perform with a common two-color ddPCR system. After optimization, the assay performance was evaluated, showing a lower limit of detection (LOD) (0.1–1.0 pg/μL) and good selectivity for the five bacteria targets. The multiplex assay’s ability to simultaneously detect two or more kinds of targets in a sample was also demonstrated. The assay showed strong sample tolerance when testing simulated soil samples; the LOD for bacteria in soil was 2 × 102–2 × 103 colony-forming unit (CFU)/100 mg soil (around 5–50 CFU/reaction), which was 10-fold lower than that of the single-target qPCR method. When testing simulated soil samples at bacterial concentrations of 2 × 103–2 × 104 CFU/100 mg soil, the assay presented a higher sensitivity (100%, 35/35) than that of the qPCR method (65.71%, 23/35) and a good specificity (100%, 15/15). These results suggest that the developed 5-plex ddPCR method is more sensitive than conventional qPCR methods and is potentially suitable for rapidly detecting or screening the five selected bacterial biothreats in suspicious samples.
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Affiliation(s)
- Yipu Du
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- The First Department, General Hospital of Northern Theater Command, Shenyang, China
| | - Ziheng Yan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Kai Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Junyan Jin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Liting Xiao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Zhulin Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Yafang Tan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Pingping Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Zongmin Du
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Ruifu Yang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
| | - Yong Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- *Correspondence: Yong Zhao,
| | - Yajun Song
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, China
- Yajun Song,
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29
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Choi CH, Kim E, Yang SM, Kim DS, Suh SM, Lee GY, Kim HY. Comparison of Real-Time PCR and Droplet Digital PCR for the Quantitative Detection of Lactiplantibacillus plantarum subsp. plantarum. Foods 2022; 11:foods11091331. [PMID: 35564054 PMCID: PMC9105557 DOI: 10.3390/foods11091331] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/26/2022] [Accepted: 04/30/2022] [Indexed: 12/04/2022] Open
Abstract
Droplet digital polymerase chain reaction (ddPCR) is one of the newest and most promising tools providing absolute quantification of target DNA molecules. Despite its emerging applications in microorganisms, few studies reported its use for detecting lactic acid bacteria. This study evaluated the applicability of a ddPCR assay targeting molecular genes obtained from in silico analysis for detecting Lactiplantibacillus plantarum subsp. plantarum, a bacterium mainly used as a starter or responsible for fermentation in food. The performance characteristics of a ddPCR were compared to those of a quantitative real-time PCR (qPCR). To compare the linearity and sensitivity of a qPCR and ddPCR, the calibration curve for a qPCR and the regression curve for a ddPCR were obtained using genomic DNA [102−108 colony-forming units (CFU)/mL] extracted from a pure culture and spiked food sample. Both the qPCR and ddPCR assays exhibited good linearity with a high coefficient of determination in the pure culture and spiked food sample (R2 ≥ 0.996). The ddPCR showed a 10-fold lower limit of detection, suggesting that a ddPCR is more sensitive than a qPCR. However, a ddPCR has limitations in the absolute quantitation of high bacterial concentrations (>106 CFU/mL). In conclusion, a ddPCR can be a reliable method for detecting and quantifying lactic acid bacteria in food.
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Affiliation(s)
| | | | | | | | | | | | - Hae-Yeong Kim
- Correspondence: ; Tel.: +82-31-201-2600; Fax: +82-31-204-8116
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30
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Kline A, Dean K, Kossik AL, Harrison JC, Januch JD, Beck NK, Zhou NA, Shirai JH, Boyle DS, Mitchell J, Meschke JS. Persistence of poliovirus types 2 and 3 in waste-impacted water and sediment. PLoS One 2022; 17:e0262761. [PMID: 35081146 PMCID: PMC8791527 DOI: 10.1371/journal.pone.0262761] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 01/04/2022] [Indexed: 11/19/2022] Open
Abstract
Eradication of poliovirus (PV) is a global public health priority, and as clinical cases decrease, the role of environmental surveillance becomes more important. Persistence of PV and the environmental factors that influence it (such as temperature and sample type) are an important part of understanding and interpreting positive environmental surveillance samples. The objective of this study was to evaluate the persistence of poliovirus type 2 (PV2) and type 3 (PV3) in wastewater and sediment. Microcosms containing either 1) influent wastewater or 2) influent wastewater with a sediment matrix were seeded with either PV2 or PV3, and stored for up to 126 days at three temperatures (4°C, room temperature [RT], and 30°C). Active PV in the liquid of (1), and the sediment and liquid portions of (2) were sampled and quantified at up to 10 time points via plaque assay and RT-qPCR. A suite of 17 models were tested for best fit to characterize decay of PV2 and PV3 over time and determine the time points at which >90% (T90) and >99% (T99) reduction was reached. Linear models assessed the influence of experimental factors (matrix, temperature, virus type and method of detection) on the predicted T90 and T99 values. Results showed that when T90 was the dependent variable, virus type, matrix, and temperature significantly affected decay, and there was a clear interaction between the sediment matrix and temperature. When T99 was the dependent variable, only temperature and matrix type significantly influenced the decay metric. This study characterizes the persistence of both active and molecular PV2 and PV3 in relevant environmental conditions, and demonstrates that temperature and sediment both play important roles in PV viability. As eradication nears and clinical cases decrease, environmental surveillance and knowledge of PV persistence will play a key role in understanding the silent circulation in endemic countries.
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Affiliation(s)
- Allison Kline
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Kara Dean
- Biosystems & Agricultural Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - Alexandra L. Kossik
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Joanna Ciol Harrison
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | - James D. Januch
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Nicola K. Beck
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Nicolette A. Zhou
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Jeffry H. Shirai
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
| | | | - Jade Mitchell
- Biosystems & Agricultural Engineering, Michigan State University, East Lansing, Michigan, United States of America
| | - John Scott Meschke
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, WA, United States of America
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31
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Horn KJ, Jaberi Vivar AC, Arenas V, Andani S, Janoff EN, Clark SE. Corynebacterium Species Inhibit Streptococcus pneumoniae Colonization and Infection of the Mouse Airway. Front Microbiol 2022; 12:804935. [PMID: 35082772 PMCID: PMC8784410 DOI: 10.3389/fmicb.2021.804935] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 12/03/2021] [Indexed: 12/21/2022] Open
Abstract
The stability and composition of the airway microbiome is an important determinant of respiratory health. Some airway bacteria are considered to be beneficial due to their potential to impede the acquisition and persistence of opportunistic bacterial pathogens such as Streptococcus pneumoniae. Among such organisms, the presence of Corynebacterium species correlates with reduced S. pneumoniae in both adults and children, in whom Corynebacterium abundance is predictive of S. pneumoniae infection risk. Previously, Corynebacterium accolens was shown to express a lipase which cleaves host lipids, resulting in the production of fatty acids that inhibit growth of S. pneumoniae in vitro. However, it was unclear whether this mechanism contributes to Corynebacterium-S. pneumoniae interactions in vivo. To address this question, we developed a mouse model for Corynebacterium colonization in which colonization with either C. accolens or another species, Corynebacterium amycolatum, significantly reduced S. pneumoniae acquisition in the upper airway and infection in the lung. Moreover, the lungs of co-infected mice had reduced pro-inflammatory cytokines and inflammatory myeloid cells, indicating resolution of infection-associated inflammation. The inhibitory effect of C. accolens on S. pneumoniae in vivo was mediated by lipase-dependent and independent effects, indicating that both this and other bacterial factors contribute to Corynebacterium-mediated protection in the airway. We also identified a previously uncharacterized bacterial lipase in C. amycolatum that is required for inhibition of S. pneumoniae growth in vitro. Together, these findings demonstrate the protective potential of airway Corynebacterium species and establish a new model for investigating the impact of commensal microbiota, such as Corynebacterium, on maintaining respiratory health.
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Affiliation(s)
- Kadi J. Horn
- Department of Otolaryngology Head and Neck Surgery, University of Colorado School of Medicine, Aurora, CO, United States
| | - Alexander C. Jaberi Vivar
- Department of Otolaryngology Head and Neck Surgery, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - Vera Arenas
- Department of Otolaryngology Head and Neck Surgery, University of Colorado School of Medicine, Aurora, CO, United States
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Sameer Andani
- Department of Otolaryngology Head and Neck Surgery, University of Colorado School of Medicine, Aurora, CO, United States
| | - Edward N. Janoff
- Division of Infectious Diseases, University of Colorado School of Medicine, Aurora, CO, United States
- Denver Veterans Affairs Medical Center, Aurora, CO, United States
| | - Sarah E. Clark
- Department of Otolaryngology Head and Neck Surgery, University of Colorado School of Medicine, Aurora, CO, United States
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32
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Jałowiecki Ł, Hubeny J, Harnisz M, Płaza G. Seasonal and Technological Shifts of the WHO Priority Multi-Resistant Pathogens in Municipal Wastewater Treatment Plant and Its Receiving Surface Water: A Case Study. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2021; 19:336. [PMID: 35010596 PMCID: PMC8751097 DOI: 10.3390/ijerph19010336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/17/2021] [Accepted: 12/20/2021] [Indexed: 06/14/2023]
Abstract
The present study was focused on the identification of multi-resistant bacteria from the WHO priority pathogens list in the samples taken from different stages of the full-scale municipal wastewater treatment plant and receiving water. Additionally, the seasonal variations of the selected multi-resistant pathogens were analyzed in the samples. In order to the aim of the study, the metagenomic DNA from the collected samples was isolated and sequenced. The samples were collected in three campaigns (spring, summer, autumn). Metagenomic DNA was isolated by the commercial kits, according to the manufacturer's instruction. Illumina sequencing system was employed, and the R program was used to metagenomic analysis. It was found that the wastewater samples and receiving water contained the multi-resistant bacteria from the WHO priority pathogens list. The seasonal and technological variations affected the distribution of the pathogens in the wastewater. No effect of the effluent on the pathogens in the receiving water was observed. The results indicated that antibiotic-resistant "priority pathogens" from the WHO list are there in the waste- and receiving water. Technological process and seasons effected their distribution in the environment. Metagenomic analysis can be used as sufficient tool in microbiological and human health risk assessment.
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Affiliation(s)
- Łukasz Jałowiecki
- Environmental Microbiology Unit, Institute for Ecology of Industrial Areas, 40-844 Katowice, Poland;
| | - Jakub Hubeny
- Department of Engineering of Water Protection and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury, 10-719 Olsztyn, Poland; (J.H.); (M.H.)
| | - Monika Harnisz
- Department of Engineering of Water Protection and Environmental Microbiology, Faculty of Geoengineering, University of Warmia and Mazury, 10-719 Olsztyn, Poland; (J.H.); (M.H.)
| | - Grażyna Płaza
- Environmental Microbiology Unit, Institute for Ecology of Industrial Areas, 40-844 Katowice, Poland;
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Jacky L, Yurk D, Alvarado J, Leatham B, Schwartz J, Annaloro J, MacDonald C, Rajagopal A. Virtual-Partition Digital PCR for High-Precision Chromosomal Counting Applications. Anal Chem 2021; 93:17020-17029. [PMID: 34905685 DOI: 10.1021/acs.analchem.1c03527] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Digital PCR (dPCR) is the gold-standard analytical platform for rapid high-precision quantification of genomic fragments. However, current dPCR assays are generally limited to monitoring 1-2 analytes per sample, thereby limiting the platform's ability to address some clinical applications that require the simultaneous monitoring of 20-50 analytes per sample. Here, we present virtual-partition dPCR (VPdPCR), a novel analysis methodology enabling the detection of 10 or more target regions per color channel using conventional dPCR hardware and workflow. Furthermore, VPdPCR enables dPCR instruments to overcome upper quantitation limits caused by partitioning error. While traditional dPCR analysis establishes a single threshold to separate negative and positive partitions, VPdPCR establishes multiple thresholds to identify the number of unique targets present in each positive droplet based on fluorescence intensity. Each physical partition is then divided into a series of virtual partitions, and the resulting increase in partition count substantially decreases partitioning error. We present both a theoretical analysis of the advantages of VPdPCR and an experimental demonstration in the form of a 20-plex assay for noninvasive fetal aneuploidy testing. This demonstration assay─tested on 432 samples contrived from sheared cell-line DNA at multiple input concentrations and simulated fractions of euploid or trisomy-21 "fetal" DNA─is analyzed using both traditional dPCR thresholding and VPdPCR. VPdPCR analysis significantly lowers the variance of the chromosomal ratio across replicates and increases the accuracy of trisomy identification when compared to traditional dPCR, yielding > 98% single-well sensitivity and specificity. VPdPCR has substantial promise for increasing the utility of dPCR in applications requiring ultrahigh-precision quantitation.
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Affiliation(s)
- Lucien Jacky
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States
| | - Dominic Yurk
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States.,Department of Electrical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - John Alvarado
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States
| | - Bryan Leatham
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States
| | - Jerrod Schwartz
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States
| | - John Annaloro
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States
| | - Chris MacDonald
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States
| | - Aditya Rajagopal
- ChromaCode Inc., 2330 Faraday Ave Suite 100, Carlsbad, California 92008, United States.,Department of Electrical Engineering, California Institute of Technology, Pasadena, California 91125, United States.,Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089, United States
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Ghosh S, Straus DL, Good C, Phuntumart V. Development and comparison of loop-mediated isothermal amplification with quantitative PCR for the specific detection of Saprolegnia spp. PLoS One 2021; 16:e0250808. [PMID: 34898622 PMCID: PMC8668100 DOI: 10.1371/journal.pone.0250808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 11/07/2021] [Indexed: 11/26/2022] Open
Abstract
Saprolegniasis is an important disease in freshwater aquaculture, and is associated with oomycete pathogens in the genus Saprolegnia. Early detection of significant levels of Saprolegnia spp. pathogens would allow informed decisions for treatment which could significantly reduce losses. This study is the first to report the development of loop-mediated isothermal amplification (LAMP) for the detection of Saprolegnia spp. and compares it with quantitative PCR (qPCR). The developed protocols targeted the internal transcribed spacer (ITS) region of ribosomal DNA and the cytochrome C oxidase subunit 1 (CoxI) gene and was shown to be specific only to Saprolegnia genus. This LAMP method can detect as low as 10 fg of S. salmonis DNA while the qPCR method has a detection limit of 2 pg of S. salmonis DNA, indicating the superior sensitivity of LAMP compared to qPCR. When applied to detect the pathogen in water samples, both methods could detect the pathogen when only one zoospore of Saprolegnia was present. We propose LAMP as a quick (about 20–60 minutes) and sensitive molecular diagnostic tool for the detection of Saprolegnia spp. suitable for on-site applications.
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Affiliation(s)
- Satyaki Ghosh
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
| | - David L. Straus
- United States Department of Agriculture, Agricultural Research Service, Harry K. Dupree-Stuttgart National Aquaculture Research Center, Stuttgart, Arkansas, United States of America
| | - Christopher Good
- The Conservation Fund’s Freshwater Institute, Shepherdstown, West Virginia, United States of America
| | - Vipaporn Phuntumart
- Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America
- * E-mail:
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Shin J, Shin S, Jung SH, Park C, Cho SY, Lee DG, Chung YJ. Duplex dPCR System for Rapid Identification of Gram-Negative Pathogens in the Blood of Patients with Bloodstream Infection: A Culture-Independent Approach. J Microbiol Biotechnol 2021; 31:1481-1489. [PMID: 34528911 PMCID: PMC9705831 DOI: 10.4014/jmb.2103.03044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/17/2021] [Accepted: 09/09/2021] [Indexed: 12/15/2022]
Abstract
Early and accurate detection of pathogens is important to improve clinical outcomes of bloodstream infections (BSI), especially in the case of drug-resistant pathogens. In this study, we aimed to develop a culture-independent digital PCR (dPCR) system for multiplex detection of major sepsiscausing gram-negative pathogens and antimicrobial resistance genes using plasma DNA from BSI patients. Our duplex dPCR system successfully detected nine targets (five bacteria-specific targets and four antimicrobial resistance genes) through five reactions within 3 hours. The minimum detection limit was 50 ag of bacterial DNA, suggesting that 1 CFU/ml of bacteria in the blood can be detected. To validate the clinical applicability, cell-free DNA samples from febrile patients were tested with our system and confirmed high consistency with conventional blood culture. This system can support early identification of some drug-resistant gram-negative pathogens, which can help improving treatment outcomes of BSI.
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Affiliation(s)
- Juyoun Shin
- Department of Microbiology, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea
| | - Sun Shin
- Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea
| | - Seung-Hyun Jung
- Department of Biochemistry, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea
| | - Chulmin Park
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea
| | - Sung-Yeon Cho
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea,Department of Internal Medicine, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea
| | - Dong-Gun Lee
- Vaccine Bio Research Institute, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea,Department of Internal Medicine, The Catholic University of Korea, College of Medicine, Seoul St. Mary’s Hospital, Seoul 06591, Republic of Korea
| | - Yeun-Jun Chung
- Department of Microbiology, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea,Precision Medicine Research Center, Integrated Research Center for Genome Polymorphism, The Catholic University of Korea, College of Medicine, Seoul 06591, Republic of Korea,Corresponding author Phone: +82-2-2258-7343 Fax: +82-2-537-0572 E-mail:
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Sun A, Stanton JAL, Bergquist PL, Sunna A. Universal Enzyme-Based Field Workflow for Rapid and Sensitive Quantification of Water Pathogens. Microorganisms 2021; 9:2367. [PMID: 34835492 PMCID: PMC8618791 DOI: 10.3390/microorganisms9112367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 11/17/2022] Open
Abstract
A universal filtration and enzyme-based workflow has been established to allow for the rapid and sensitive quantification of leading pathogens Cryptosporidium parvum, Giardia gamblia, Campylobacter jejuni, and Escherichia coli from tap water samples with volumes up to 100 mL, and the potential to scale up to larger volumes. qPCR limits of quantification as low as four oocysts for Cryptosporidium, twelve cysts for Giardia, two cells for C. jejuni, and nineteen cells for E. coli per reaction were achieved. A polycarbonate filter-based sampling method coupled with the prepGEM enzyme-based DNA extraction system created a single-step transfer workflow that required as little as 20 min of incubation time and a 100 µL reaction mix. The quantification via qPCR was performed directly on the prepGEM extract, bypassing time-consuming, labour-intensive conventional culture-based methods. The tap water samples were shown to contain insoluble particles that inhibited detection by reducing the quantification efficiency of a representative pathogen (C. jejuni) to 30-60%. This sample inhibition was effectively removed by an on-filter treatment of 20% (v/v) phosphoric acid wash. Overall, the established workflow was able to achieve quantification efficiencies of 92% and higher for all four leading water pathogens, forming the basis of a rapid, portable, and low-cost solution to water monitoring.
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Affiliation(s)
- Angela Sun
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; (A.S.); (P.L.B.); (A.S.)
| | - Jo-Ann L. Stanton
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Peter L. Bergquist
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; (A.S.); (P.L.B.); (A.S.)
- Department of Molecular Medicine & Pathology, University of Auckland, Auckland 1142, New Zealand
| | - Anwar Sunna
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia; (A.S.); (P.L.B.); (A.S.)
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW 2109, Australia
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Lee SS, Park JH, Bae YK. Comparison of two digital PCR methods for EGFR DNA and SARS-CoV-2 RNA quantification. Clin Chim Acta 2021; 521:9-18. [PMID: 34144041 PMCID: PMC8206622 DOI: 10.1016/j.cca.2021.06.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/09/2021] [Indexed: 12/16/2022]
Abstract
BACKGROUND The COVID-19 pandemic caused by the severe acute SARS-CoV-2 virus has undeniably highlighted the importance of reliable nucleic acid quantification. Digital PCR (dPCR) is capable of the absolute quantification of nucleic acids. METHOD By using the droplet dPCR (QX200) and the digital real-time PCR (LOAA), the copy numbers were compared via multiple assays for three distinct targerts; EGFR DNA, SARS-CoV-2 and HIV-1 RNA. RESULTS The droplet dPCR and digital real-time PCR showed similar copy numbers for both DNA and RNA quantification. When the limit of detection (LOD) and limit of quantitation (LOQ) of each method were estimated for DNA and RNA targets, the digital real-time PCR showed a higher sensitivity and precision especially with low copy number targets. CONCLUSION The breath of nucleic acid testing in diagnostic applications continues to expand. In this study we applied common diagnostic targets to a novel digital real-time PCR methodology. It performed comparably to the established dPCR method with distinctive advantages and disadvantages for implementing in laboratories. These rapidly developing dPCR systems can be applied to benefit the accurate and sensitive nucleic acid testing for various clinical areas.
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Affiliation(s)
- Sang-Soo Lee
- Biomolecular Measurement Team, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea
| | - Jae-Hyeong Park
- Biomolecular Measurement Team, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea; Department of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Young-Kyung Bae
- Biomolecular Measurement Team, Korea Research Institute of Standards and Science, Daejeon, Republic of Korea.
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Pagliasso G, Di Blasio A, Vitale N, Romano A, Decastelli L, Quasso A, Ricchi M, Dondo A, Pastorino P, Gennero MS, Bergagna S. Goat Paratuberculosis: Experimental Model for the Evaluation of Mycobacterium Persistence in Raw Milk Cheese. Microorganisms 2021; 9:microorganisms9102032. [PMID: 34683352 PMCID: PMC8538418 DOI: 10.3390/microorganisms9102032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/20/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022] Open
Abstract
Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of chronic proliferative enteritis found in ruminants, known as paratuberculosis (PTB). The spread of PTB is increasing in countries with advanced animal husbandry practices, leading to significant economic losses. Moreover, a supposed zoonotic role of MAP in Crohn's disease (CD) in humans has been discussed by the scientific community; however, although the association between MAP and CD has generally been accepted, it is still up for debate if MAP is the main cause of CD, a contributing factor, or merely a commensal organism for the development of CD. The aim of this study was to assess the survival of MAP during the entire production process of a traditional Italian goat's raw milk fresh cheese, the "Robiola di Roccaverano", assessing the survival rate and persistence of MAP in the final product. A mix of MAP field isolates from goats of the Roccaverano area and a reference ATCC strain were used to carry out milk in experimental inoculation. Samples of milk, curd and cheese were taken in two consecutive batches of production. Microbiological challenge tests, evaluated by f57-qPCR, showed a significant decrease in MAP charge during the cheesemaking process for both batches, suggesting the productive process has an impact on MAP survival.
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Affiliation(s)
- Giulia Pagliasso
- The Veterinary Medical Research Institute for Piemonte, Liguria and Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (G.P.); (A.D.B.); (N.V.); (A.R.); (L.D.); (A.D.); (M.S.G.); (S.B.)
| | - Alessia Di Blasio
- The Veterinary Medical Research Institute for Piemonte, Liguria and Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (G.P.); (A.D.B.); (N.V.); (A.R.); (L.D.); (A.D.); (M.S.G.); (S.B.)
- Azienda Sanitaria Locale TO3, S.C. Sanità Animale, 10064 Torino, Italy
| | - Nicoletta Vitale
- The Veterinary Medical Research Institute for Piemonte, Liguria and Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (G.P.); (A.D.B.); (N.V.); (A.R.); (L.D.); (A.D.); (M.S.G.); (S.B.)
| | - Angelo Romano
- The Veterinary Medical Research Institute for Piemonte, Liguria and Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (G.P.); (A.D.B.); (N.V.); (A.R.); (L.D.); (A.D.); (M.S.G.); (S.B.)
| | - Lucia Decastelli
- The Veterinary Medical Research Institute for Piemonte, Liguria and Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (G.P.); (A.D.B.); (N.V.); (A.R.); (L.D.); (A.D.); (M.S.G.); (S.B.)
| | - Antonio Quasso
- Azienda Sanitaria Locale AT, S.C. Sanità Animale, 14100 Asti, Italy;
| | - Matteo Ricchi
- National Reference Centre for Paratuberculosis, Istituto Zooprofilattico Sperimentale dell’Emilia Romagna e della Lombardia, Sezione di Piacenza-Gariga, Strada della Faggiola 1, 29027 Gariga di Podenzano, Italy;
| | - Alessandro Dondo
- The Veterinary Medical Research Institute for Piemonte, Liguria and Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (G.P.); (A.D.B.); (N.V.); (A.R.); (L.D.); (A.D.); (M.S.G.); (S.B.)
| | - Paolo Pastorino
- The Veterinary Medical Research Institute for Piemonte, Liguria and Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (G.P.); (A.D.B.); (N.V.); (A.R.); (L.D.); (A.D.); (M.S.G.); (S.B.)
- Correspondence: ; Tel.: +39-011-268-6251
| | - Maria Silvia Gennero
- The Veterinary Medical Research Institute for Piemonte, Liguria and Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (G.P.); (A.D.B.); (N.V.); (A.R.); (L.D.); (A.D.); (M.S.G.); (S.B.)
| | - Stefania Bergagna
- The Veterinary Medical Research Institute for Piemonte, Liguria and Valle d’Aosta, Via Bologna 148, 10154 Torino, Italy; (G.P.); (A.D.B.); (N.V.); (A.R.); (L.D.); (A.D.); (M.S.G.); (S.B.)
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Manzari C, Oranger A, Fosso B, Piancone E, Pesole G, D'Erchia AM. Accurate quantification of bacterial abundance in metagenomic DNAs accounting for variable DNA integrity levels. Microb Genom 2021; 6. [PMID: 32749951 PMCID: PMC7660251 DOI: 10.1099/mgen.0.000417] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The quantification of the total microbial content in metagenomic samples is critical for investigating the interplay between the microbiome and its host, as well as for assessing the accuracy and precision of the relative microbial composition which can be strongly biased in low microbial biomass samples. In the present study, we demonstrate that digital droplet PCR (ddPCR) can provide accurate quantification of the total copy number of the 16S rRNA gene, the gene usually exploited for assessing total bacterial abundance in metagenomic DNA samples. Notably, using DNA templates with different integrity levels, as measured by the DNA integrity number (DIN), we demonstrated that 16S rRNA copy number quantification is strongly affected by DNA quality and determined a precise correlation between quantification underestimation and DNA degradation levels. Therefore, we propose an input DNA mass correction, according to the observed DIN value, which could prevent inaccurate quantification of 16S copy number in degraded metagenomic DNAs. Our results highlight that a preliminary evaluation of the metagenomic DNA integrity should be considered before performing metagenomic analyses of different samples, both for the assessment of the reliability of observed differential abundances in different conditions and to obtain significant functional insights.
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Affiliation(s)
- Caterina Manzari
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola 122/D-O, 70126 Bari, Italy
| | - Annarita Oranger
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola 122/D-O, 70126 Bari, Italy
| | - Bruno Fosso
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola 122/D-O, 70126 Bari, Italy
| | - Elisabetta Piancone
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola 122/D-O, 70126 Bari, Italy
| | - Graziano Pesole
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola 122/D-O, 70126 Bari, Italy.,Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Via Orabona 4, 70126 Bari, Italy
| | - Anna Maria D'Erchia
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, Via Amendola 122/D-O, 70126 Bari, Italy.,Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Via Orabona 4, 70126 Bari, Italy
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Pourmahdi Borujeni M, Haji Hajikolaei MR, Ghorbanpoor M, Elhaei Sahar H, Bagheri S, Roveyshedzadeh S. Comparison of Mycobacterium avium subsp. paratuberculosis infection in cattle, sheep and goats in the Khuzestan Province of Iran: Results of a preliminary survey. Vet Med Sci 2021; 7:1970-1979. [PMID: 34228398 PMCID: PMC8464266 DOI: 10.1002/vms3.559] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background Paratuberculosis or Johne's disease, the chronic infectious granulomatous enteritis of ruminants, is a worldwide infection, which is caused by Mycobacterium avium subsp. paratuberculosis (MAP). The most common symptoms of this disease in cattle are loss of milk production, weight loss and diarrhoea, whereas in sheep and goats, the symptoms are emaciation, anorexia and severe disability. Objectives The aim of this study was to compare the seroprevalence of MAP in cattle, sheep and goats in the southwest of Iran. Methods Blood samples were randomly collected from 530 cattle, 568 sheep and 368 goats in southwest of Iran. Sera were tested by a commercial ELISA kit (ID vet; ID Screen® Paratuberculosis Indirect) for detection of antibodies of MAP. Results Overall apparent and true seroprevalence rate of MAP was 6.00% (95% CI: 4.90%–7.30%) and 13.25% (95% CI: 11.55%– 14.95%). Apparent and true seroprevalence of MAP, respectively, was 4.34% (95% CI: 3.88%–6.46%) and 9.19% (95% CI: 6.98%–11.98%) in cattle, 6.87% (95% CI: 5.05%–9.27%) and 15.37% (95% CI: 12.60%–16.60%) in sheep and 7.07% (95% CI: 4.82%–10.18%) and 15.86% (95% CI: 12.41%–20.01%) in goats, respectively. As a result, there was no significant relationship between animal species and MAP infection. Moreover, multivariate logistic regression showed that the infection rate is not associated with age, gender and geographical location in cattle, sheep and goats (P > 0.05). Conclusion This study confirms that the seroprevalence of MAP is relatively considerable in the cattle, sheep and goats in the southwest of Iran, although in cattle, it is less than goats and sheep. Therefore, preventive and control measures should be considered by animal health authorities and meat and dairy processing units.
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Affiliation(s)
- Mahdi Pourmahdi Borujeni
- Department of Food Hygiene, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | | | - Masoud Ghorbanpoor
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Hamzeh Elhaei Sahar
- Department of Food Hygiene, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Saeed Bagheri
- Department of Food Hygiene, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Sanaz Roveyshedzadeh
- Department of Clinical Sciences, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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Willemse D, Kaushal D. Using genomic DNA copies to enumerate Mycobacterium tuberculosis load in macaque tissue samples. Tuberculosis (Edinb) 2021; 129:102102. [PMID: 34139570 DOI: 10.1016/j.tube.2021.102102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 05/30/2021] [Accepted: 06/06/2021] [Indexed: 11/29/2022]
Abstract
It is important to accurately quantify Mycobacterium tuberculosis (Mtb) load in laboratory-based tuberculosis (TB) research. This study aims to determine if real-time quantitative PCR (qPCR) and digital PCR (dPCR) can be used instead of colony forming unit (CFU) enumeration, to quantify Mtb load in rhesus and cynomolgus macaque tissue samples. Tissue samples of actively infected high Mtb-burden rhesus and cynomolgus macaques were selected from historic sample collections. CFUs were enumerated by plating, and Chelex-extracted genomic DNA used to quantify bacterial load by qPCR and dPCR. Three genes, sigA, 16S and CFP10, were assessed for their ability to quantify Mtb. All genes showed comparable quantification of Mtb between 2 and 20 000 copies/μl in the qPCR and 5-4000 copies/μl in the dPCR assay. The highest bacterial load was observed with dPCR, followed by qPCR, and CFU enumeration. Although the CFU count was consistently lower than the genomic copy numbers predicted by qPCR and dPCR, a significant correlation was observed. Quantification of Mtb by PCR was, however, only possible in higher-Mtb-load samples, suggesting that qPCR and dPCR quantification assays can predict bacterial load in actively infected and higher-Mtb-burden macaque tissue samples.
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Affiliation(s)
- Danicke Willemse
- Southwest National Primate Research Center, Texas Biomedical Research Institute, 8715 West Military Drive, San Antonio, TX, 78227, Texas, USA
| | - Deepak Kaushal
- Southwest National Primate Research Center, Texas Biomedical Research Institute, 8715 West Military Drive, San Antonio, TX, 78227, Texas, USA.
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Jia R, Zhang G, Liu H, Chen Y, Zhou J, Liu Y, Ding P, Wang Y, Zang W, Wang A. Novel Application of Nanofluidic Chip Digital PCR for Detection of African Swine Fever Virus. Front Vet Sci 2021; 7:621840. [PMID: 33614757 PMCID: PMC7894257 DOI: 10.3389/fvets.2020.621840] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/11/2020] [Indexed: 01/06/2023] Open
Abstract
African swine fever virus (ASFV) gives rise to a grievous transboundary and infectious disease, African swine fever (ASF), which has caused a great economic loss in the swine industry. To prevent and control ASF, once suspicious symptoms have presented, the movement of animal and pork products should be stopped, and then, laboratory testing should be adopted to diagnose ASF. A method for ASFV DNA quantification is presented in this research, which utilizes the next-generation PCR platform, nanofluidic chip digital PCR (cdPCR). The cdPCR detection showed good linearity and repeatability. The limit of detection for cdPCR is 30.1995 copies per reaction, whereas no non-specific amplification curve was found with other swine viruses. In the detection of 69 clinical samples, the cdPCR showed significant consistency [91.30% (63/69)] to the Office International des Epizooties-approved quantitative PCR. Compared with the commercial quantitative PCR kit, the sensitivity of the cdPCR assay was 86.27% (44/50), and the specificity was 94.44% (17/18). The positive coincidence rate of the cdPCR assay was 88% (44/50). The total coincidence rate of the cdPCR and kit was 89.86% (62/69), and the kappa value reached 0.800 (P < 0.0001). This is the first time that cdPCR has been applied to detecting ASFV successfully.
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Affiliation(s)
- Rui Jia
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Gaiping Zhang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Hongliang Liu
- Henan Zhongze Biological Engineering Co. LTD, Zhengzhou, China
| | - Yumei Chen
- School of Life Sciences, Zhengzhou University, Zhengzhou, China.,Henan Zhongze Biological Engineering Co. LTD, Zhengzhou, China
| | - Jingming Zhou
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yankai Liu
- Henan Zhongze Biological Engineering Co. LTD, Zhengzhou, China
| | - Peiyang Ding
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
| | - Yanwei Wang
- Henan Zhongze Biological Engineering Co. LTD, Zhengzhou, China
| | - Weimin Zang
- Henan Zhongze Biological Engineering Co. LTD, Zhengzhou, China
| | - Aiping Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, China
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Prasannakumar MK, Parivallal PB, Pramesh D, Mahesh HB, Raj E. LAMP-based foldable microdevice platform for the rapid detection of Magnaporthe oryzae and Sarocladium oryzae in rice seed. Sci Rep 2021; 11:178. [PMID: 33420312 PMCID: PMC7794292 DOI: 10.1038/s41598-020-80644-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 12/24/2020] [Indexed: 11/11/2022] Open
Abstract
Rice blast (caused by Magnaporthe oryzae) and sheath rot diseases (caused by Sarocladium oryzae) are the most predominant seed-borne pathogens of rice. The detection of both pathogens in rice seed is essential to avoid production losses. In the present study, a microdevice platform was designed, which works on the principles of loop-mediated isothermal amplification (LAMP) to detect M. oryzae and S. oryzae in rice seeds. Initially, a LAMP, polymerase chain reaction (PCR), quantitative PCR (qPCR), and helicase dependent amplification (HDA) assays were developed with primers, specifically targeting M. oryzae and S. oryzae genome. The LAMP assay was highly efficient and could detect the presence of M. oryzae and S. oryzae genome at a concentration down to 100 fg within 20 min at 60 °C. Further, the sensitivity of the LAMP, HDA, PCR, and qPCR assays were compared wherein; the LAMP assay was highly sensitive up to 100 fg of template DNA. Using the optimized LAMP assay conditions, a portable foldable microdevice platform was developed to detect M. oryzae and S. oryzae in rice seeds. The foldable microdevice assay was similar to that of conventional LAMP assay with respect to its sensitivity (up to 100 fg), rapidity (30 min), and specificity. This platform could serve as a prototype for developing on-field diagnostic kits to be used at the point of care centers for the rapid diagnosis of M. oryzae and S. oryzae in rice seeds. This is the first study to report a LAMP-based foldable microdevice platform to detect any plant pathogens.
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Affiliation(s)
- M K Prasannakumar
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India.
| | - P Buela Parivallal
- Department of Plant Pathology, University of Agricultural Sciences, Bangalore, India
| | - Devanna Pramesh
- Rice Pathology Laboratory, All India Coordinated Rice Improvement Programme, University of Agricultural Sciences, Raichur, India.
| | - H B Mahesh
- Department of Genetics and Plant Breeding, College of Agriculture, V.C. Farm, Mandya, India
| | - Edwin Raj
- Plant Pathology Division, ICAR - National Research Center for Banana, Thayanur, India
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Campos Muzquiz LG, Martínez Gómez D, Reyes Cruz T, Méndez Olvera ET. Evaluation of intracellular survival of Campylobacter fetus subsp. fetus in bovine endometrial cells by qPCR. IRANIAN JOURNAL OF VETERINARY RESEARCH 2021; 22:94-99. [PMID: 34306105 PMCID: PMC8294819 DOI: 10.22099/ijvr.2021.38693.5632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/02/2021] [Accepted: 02/28/2021] [Indexed: 09/30/2022]
Abstract
BACKGROUND Campylobacter fetus subsp. fetus is the causal agent of sporadic abortion and infertility in bovines that produces economic losses in livestock. AIMS This study evaluates the capability of C. fetus subsp. fetus to invade and survive in bovine endometrial epithelial cells and attempts to describe a pathogenic mechanism of this microorganism. METHODS Primary culture of bovine endometrial epithelial cells was challenged with C. fetus subsp. fetus. Intracellular bacteria, represented by the number of genomic copies (g.c.) were quantified at 0, 2, 4, 10, and 24 hours post-infection (h.p.i.), by quantitative polymerase chain reaction (qPCR). The presence of intracellular bacteria was evaluated by immunofluorescence and immunohistochemistry. RESULTS The results showed that only viable C. fetus subsp. fetus could invade endometrial cells. The g.c. number in assays with viable C. fetus subsp. fetus reached an average value of 656 g.c., remained constant until 4 h.p.i., then decreased to 100 g.c, at 24 h.p.i. In assays with non-viable microorganisms, the average value of g.c. was less than 1 g.c. and never changed. The intracellular presence of this bacteria was confirmed at 2 h.p.i. by immunofluorescence and immunohistochemistry. CONCLUSION The results suggest that only C. fetus subsp. fetus viable can invade bovine endometrial epithelial cells but will not replicate in them, indicating that the endometrial cells do not represent a replication niche for this pathogen. Nonetheless, this invasion capability suggests that this type of cell could be employed by the pathogen to spread to other tissues.
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Affiliation(s)
- L. G. Campos Muzquiz
- Department of Genetics and Virology, Faculty of Chemical Sciences, Autonomous University of Coahuila, Saltillo, Mexico
| | - D. Martínez Gómez
- Laboratory of Agricultural Microbiology, Department of Agricultural and Animal Production, Metropolitan Autonomous University-Xochimilco, Mexico City, Mexico
| | - T. Reyes Cruz
- Biological and Health Sciences Division, Department of Agricultural and Animal Production, Metropolitan Autonomous University-Xochimilco, Mexico City, Mexico
| | - E. T. Méndez Olvera
- Laboratory of Molecular Biology, Department of Agricultural and Animal Production, Metropolitan Autonomous University-Xochimilco, Mexico City, Mexico
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Noviyanti F, Hosotani Y, Inatsu Y, Kawasaki S. A comparison of Listeria monocytogenes growth monitoring in ground pork samples by real-time polymerase chain reaction to conventional agar and most probable number methods. FOOD SCIENCE AND TECHNOLOGY RESEARCH 2021. [DOI: 10.3136/fstr.27.647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Fia Noviyanti
- National Food Research Institute, Food Hygiene Laboratory
| | - Yukie Hosotani
- National Food Research Institute, Food Hygiene Laboratory
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Tao Y, Yun J, Wang J, Xu P, Li C, Liu H, Lan Y, Pan J, Du W. High-performance detection of Mycobacterium bovis in milk using digital LAMP. Food Chem 2020; 327:126945. [DOI: 10.1016/j.foodchem.2020.126945] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 04/21/2020] [Accepted: 04/28/2020] [Indexed: 11/24/2022]
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Hodgkin M, Purseglove SM, Chan LLY, Perry J, Bolton J. A novel image cytometry-based Lactobacillus bacterial enumeration method for the production of kettle sour beer. J Microbiol Methods 2020; 177:106031. [PMID: 32805365 DOI: 10.1016/j.mimet.2020.106031] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/19/2020] [Accepted: 07/23/2020] [Indexed: 11/29/2022]
Abstract
The demands for a variety of craft beer flavors have been increasing in the United States. To meet this rising demand, breweries have been experimenting with kettle sour beer that utilizes lactic acid-producing bacteria for fermentation. The current standard bacterial quantification method is insufficient for rigorous quality control, thus there is a need for a better method to monitor lactobacilli concentration in a kettle sour environment. In this work, an automated Lactobacillus counting method was developed using fluorescence-based image cytometry. Three commonly used species were cultured, the concentrations were measured using image cytometry and evaluated against the standard spread-plating method. This procedure was undertaken in vitro at different dilutions and the method was repeated with two species in a kettle sour environment at different time points. Both the in vitro and fermentation experiments were repeated three times. Results demonstrated that the new method was not significantly different when compared to the standard plating method in either controlled settings or within the kettle sour fermentation. The proposed method provides a rapid tool to monitor and control lactobacilli growth in kettle sour beer production, and allows for standardization of the products due to the availability of near instantaneous information for quality control.
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Affiliation(s)
- Matthew Hodgkin
- Food Science and Human Nutrition, School of Food and Agriculture, University of Maine, Orono, ME 04469, United States of America
| | - Suzanne M Purseglove
- Department of Technology R&D, Nexcelom Bioscience LLC, 360 Merrimack St. Building 9, Lawrence, MA 01843, United States of America
| | - Leo Li-Ying Chan
- Department of Technology R&D, Nexcelom Bioscience LLC, 360 Merrimack St. Building 9, Lawrence, MA 01843, United States of America.
| | - Jennifer Perry
- Food Science and Human Nutrition, School of Food and Agriculture, University of Maine, Orono, ME 04469, United States of America
| | - Jason Bolton
- Cooperative Extension, University of Maine, Orono, ME 04469, United States of America; Innovation Engineering, University of Maine, Orono, ME 04469, United States of America
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Haas CN. Quantitative Microbial Risk Assessment and Molecular Biology: Paths to Integration. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:8539-8546. [PMID: 32539352 DOI: 10.1021/acs.est.0c00664] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Quantitative microbial risk assessment (QMRA) has now been in use for over 35 years and has formed the basis for developing criteria for ensuring public health related to water, food, and remediation, to name a few areas. The initial data for QMRA (both in exposure assessment and in dose response assessment) came from measurements using assays for viability, such as plate counts, plaque assays, or animal infectivity. With the increasing use of molecular methods for the measurement of microorganisms in the environment, it has become important to assess how to use such data to estimate infectious disease risks. The limitations to the use of such data and needs to resolve the limitations will be addressed.
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Affiliation(s)
- Charles N Haas
- Department of Civil, Architectural & Environmental Engineering, Drexel University, Philadelphia, Pennsylvania 19104, United States
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Preliminary Evidence of a Molecular Detection Method to Analyze Bacterial DNA as a Quality Indicator in Cosmetics. COSMETICS 2020. [DOI: 10.3390/cosmetics7030054] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Cosmetics are a category of widely consumed and distributed products, and their manufacture is always subject to specific guidelines. Quality Control (QC) tests provide information supporting the absence of injurious organisms and regarding the microbiological stability of cosmetics. The microbiological risk analysis is typically performed using the plate count method, which is a time-consuming and operator-dependent approach. Molecular technologies allow a deeper and more sensitive testing than traditional cultures. The demand for rapid and sensitive methods is recently increasing. The aim of our study was to compare different DNA extraction methods in order to detect and quantify bacterial load in cosmetics using a qPCR system. Known numbers of microorganisms were spiked into six different cosmetics to simulate contaminated samples. DNA was extracted with seven extraction kits and then quantified by real-time qPCR. Results revealed differences in terms of cell recovery, DNA yield, and quality. The bead-beating approaches were the most suitable in our molecular workflow and lead to good quality DNA for analysis by qPCR within four hours. Combined with mechanical extraction, qPCR may represent an efficient and easy method for microorganism identification in cosmetics, and can be automated. This approach also is also applicable for the detection of probiotics used as beneficial biological components in cosmetic products. The results of our molecular method provided preliminary evidences for the rapid identification of cells (10–100) and nucleic acids in complex preparations employed for human health, in compliance with regulatory limits. The suggested methodology is easy, fast, and sensitive. Its scalability allows serial microbiological evaluation at every manufacturing step.
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50
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Amalfitano S, Levantesi C, Copetti D, Stefani F, Locantore I, Guarnieri V, Lobascio C, Bersani F, Giacosa D, Detsis E, Rossetti S. Water and microbial monitoring technologies towards the near future space exploration. WATER RESEARCH 2020; 177:115787. [PMID: 32315899 DOI: 10.1016/j.watres.2020.115787] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 06/11/2023]
Abstract
Space exploration is demanding longer lasting human missions and water resupply from Earth will become increasingly unrealistic. In a near future, the spacecraft water monitoring systems will require technological advances to promptly identify and counteract contingent events of waterborne microbial contamination, posing health risks to astronauts with lowered immune responsiveness. The search for bio-analytical approaches, alternative to those applied on Earth by cultivation-dependent methods, is pushed by the compelling need to limit waste disposal and avoid microbial regrowth from analytical carryovers. Prospective technologies will be selected only if first validated in a flight-like environment, by following basic principles, advantages, and limitations beyond their current applications on Earth. Starting from the water monitoring activities applied on the International Space Station, we provide a critical overview of the nucleic acid amplification-based approaches (i.e., loop-mediated isothermal amplification, quantitative PCR, and high-throughput sequencing) and early-warning methods for total microbial load assessments (i.e., ATP-metry, flow cytometry), already used at a high readiness level aboard crewed space vehicles. Our findings suggest that the forthcoming space applications of mature technologies will be necessarily bounded by a compromise between analytical performances (e.g., speed to results, identification depth, reproducibility, multiparametricity) and detrimental technical requirements (e.g., reagent usage, waste production, operator skills, crew time). As space exploration progresses toward extended missions to Moon and Mars, miniaturized systems that also minimize crew involvement in their end-to-end operation are likely applicable on the long-term and suitable for the in-flight water and microbiological research.
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Affiliation(s)
- Stefano Amalfitano
- Water Research Institute - National Research Council of Italy (IRSA-CNR), Via Salaria Km 29,300, 00015, Monterotondo, Roma, Italy.
| | - Caterina Levantesi
- Water Research Institute - National Research Council of Italy (IRSA-CNR), Via Salaria Km 29,300, 00015, Monterotondo, Roma, Italy
| | - Diego Copetti
- Water Research Institute - National Research Council of Italy (IRSA-CNR), Via del Mulino 19, 20861, Brugherio, Monza-Brianza, Italy
| | - Fabrizio Stefani
- Water Research Institute - National Research Council of Italy (IRSA-CNR), Via del Mulino 19, 20861, Brugherio, Monza-Brianza, Italy
| | - Ilaria Locantore
- Thales Alenia Space Italia SpA, Strada Antica di Collegno, 253 - 10146, Turin, Italy
| | - Vincenzo Guarnieri
- Thales Alenia Space Italia SpA, Strada Antica di Collegno, 253 - 10146, Turin, Italy
| | - Cesare Lobascio
- Thales Alenia Space Italia SpA, Strada Antica di Collegno, 253 - 10146, Turin, Italy
| | - Francesca Bersani
- Centro Ricerche SMAT, Società Metropolitana Acque Torino S.p.A., C.so Unità d'Italia 235/3, 10127, Torino, Italy
| | - Donatella Giacosa
- Centro Ricerche SMAT, Società Metropolitana Acque Torino S.p.A., C.so Unità d'Italia 235/3, 10127, Torino, Italy
| | - Emmanouil Detsis
- European Science Foundation, 1 quai Lezay Marnésia, BP 90015, 67080, Strasbourg Cedex, France
| | - Simona Rossetti
- Water Research Institute - National Research Council of Italy (IRSA-CNR), Via Salaria Km 29,300, 00015, Monterotondo, Roma, Italy
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