1
|
Shehata HR, Hassane B, Newmaster SG. Real-time PCR methods for identification and stability monitoring of Bifidobacterium longum subsp. longum UABl-14 during shelf life. Front Microbiol 2024; 15:1360241. [PMID: 38706967 PMCID: PMC11066167 DOI: 10.3389/fmicb.2024.1360241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/03/2024] [Indexed: 05/07/2024] Open
Abstract
Bifidobacterium longum subsp. longum UABl-14™ is an important probiotic strain that was found to support digestive health. Here we present the development and validation of real-time PCR methods for strain-specific identification and enumeration of this important strain. The identification method was evaluated for specificity using 22 target samples and 30 non-target samples. All target samples successfully amplified, while no amplification was observed from any non-target samples including other B. longum strains. The identification method was evaluated for sensitivity using three DNA dilution series and the limit of detection was 2 pg. of DNA. Coupled with a viability dye, the method was further validated for quantitative use to enumerate viable cells of UABl-14. The viability dye treatment (PMAxx) was optimized, and a final concentration of 50 μM was found as an effective concentration to inactivate DNA in dead cells from reacting in PCR. The reaction efficiency, linear dynamic range, repeatability, and reproducibility were also evaluated. The reaction efficiency was determined to be 97.2, 95.2, and 95.0% with R2 values of 99%, in three replicates. The linear dynamic range was 1.3 × 102 to 1.3 × 105 genomes. The relative standard deviation (RSD%) for repeatability ranged from 0.03 to 2.80, and for reproducibility ranged from 0.04 to 2.18. The ability of the validated enumeration method to monitor cell counts during shelf life was evaluated by determining the viable counts and total counts of strain UABl-14 in 18 multi-strain finished products. The viable counts were lower than label claims in seven products tested post-expiration and were higher than label claims in products tested pre-expiration, with a slight decrease in viable counts below label claim in three samples that were tested 2-3 months pre-expiration. Interestingly, the total counts of strain UABl-14 were consistently higher than label claims in all 18 products. Thus, the method enables strain-specific stability monitoring in finished products during shelf life, which can be difficult or impossible to achieve using the standard plate count method. The validated methods allow for simultaneous and cost-effective identification and enumeration of strain UABl-14 and represent an advancement in the quality control and quality assurance of probiotics.
Collapse
Affiliation(s)
- Hanan R. Shehata
- Purity-IQ Inc., Guelph, ON, Canada
- Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada
- Department of Microbiology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | | | - Steven G. Newmaster
- Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada
| |
Collapse
|
2
|
Yang J, Wang J, Wu W, Su C, Wu Y, Li Q. Xylooligosaccharides ameliorate insulin resistance by increasing Akkermansia muciniphila and improving intestinal barrier dysfunction in gestational diabetes mellitus mice. Food Funct 2024; 15:3122-3129. [PMID: 38426554 DOI: 10.1039/d3fo04681h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Little is known regarding the effects of xylooligosaccharides (XOS) on insulin resistance (IR) in gestational diabetes mellitus (GDM). We aimed to investigate this issue and its mechanism. Sixty female mice were randomly allotted to 4 groups (n = 15): control, high fat diet (HFD), GDM, and GDM + XOS. The control mice were fed an AIN-93 diet, while the mice in the other groups were fed 45% HFD. After pregnancy, mice in GDM and GDM + XOS groups were intraperitoneally injected with 30 mg kg-1 streptozocin for 3 days from the first day of pregnancy. Mice in the GDM + XOS group were then fed an HFD containing 2% XOS. Fasting glucose and insulin levels were monitored. The fecal Akkermansia muciniphila (Akk. muciniphila) and Bifidobacterium were measured by qPCR. The Chiu scores were calculated from hematoxylin-eosin (HE)-stained ileal tissues. Phosphorylated Akt in the liver and occludin and ZO-1 in the intestinal tissues were determined by western blotting. XOS reduced (p < 0.05) fasting blood glucose and insulin and HOMA-IR, and increased (p < 0.05) Akt phosphorylation in the livers of GDM mice. Moreover, XOS decreased (p < 0.05) TNFα, IL-1β, IL-15 and LPS in the serum, increased (p < 0.05) fecal Akk. muciniphila abundance, lowered (p < 0.05) Chiu's scores, and enhanced (p < 0.05) occludin and ZO-1 expression. XOS ameliorate IR by increasing Akk. muciniphila and improving intestinal barrier dysfunction in GDM mice.
Collapse
Affiliation(s)
- Junyi Yang
- Department of Clinical Nutrition, Nanfang Hospital, Southern Medical University, China.
- Department of Nutrition and Food Hygiene, School of Public Health, Southern Medical University, China
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, China
- Guangdong Provincial Key Laboratory of Tropical Disease Research, China
| | - Jiexian Wang
- Department of Nutrition and Food Hygiene, School of Public Health, Southern Medical University, China
- Guangdong Provincial Key Laboratory of Tropical Disease Research, China
| | - Weiliang Wu
- Food Safety and Health Research Center, School of Public Health, Southern Medical University, China
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, China
- Guangdong-Hongkong-Macao Joint Laboratory for Contaminants Exposure and Health, China
- Guangdong Provincial Key Laboratory of Tropical Disease Research, China
| | - Chuhong Su
- Department of Nutrition and Food Hygiene, School of Public Health, Southern Medical University, China
- Guangdong Provincial Key Laboratory of Tropical Disease Research, China
| | - Yanhua Wu
- Department of Clinical Nutrition, Nanfang Hospital, Southern Medical University, China.
- Department of Nutrition and Food Hygiene, School of Public Health, Southern Medical University, China
- NMPA Key Laboratory for Safety Evaluation of Cosmetics, China
- Guangdong Provincial Key Laboratory of Tropical Disease Research, China
| | - Qing Li
- Department of Clinical Nutrition, Nanfang Hospital, Southern Medical University, China.
| |
Collapse
|
3
|
Rastmanesh A, Boruah JS, Lee MS, Park S. On-Site Bioaerosol Sampling and Airborne Microorganism Detection Technologies. BIOSENSORS 2024; 14:122. [PMID: 38534229 DOI: 10.3390/bios14030122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/09/2024] [Accepted: 02/21/2024] [Indexed: 03/28/2024]
Abstract
Bioaerosols are small airborne particles composed of microbiological fragments, including bacteria, viruses, fungi, pollens, and/or by-products of cells, which may be viable or non-viable wherever applicable. Exposure to these agents can cause a variety of health issues, such as allergic and infectious diseases, neurological disorders, and cancer. Therefore, detecting and identifying bioaerosols is crucial, and bioaerosol sampling is a key step in any bioaerosol investigation. This review provides an overview of the current bioaerosol sampling methods, both passive and active, as well as their applications and limitations for rapid on-site monitoring. The challenges and trends for detecting airborne microorganisms using molecular and immunological methods are also discussed, along with a summary and outlook for the development of prompt monitoring technologies.
Collapse
Affiliation(s)
- Afagh Rastmanesh
- Complex Fluids Laboratory, School of Mechanical Engineering, Korea University of Technology and Education, Cheonan 31253, Chungnam, Republic of Korea
| | - Jayanta S Boruah
- Complex Fluids Laboratory, School of Mechanical Engineering, Korea University of Technology and Education, Cheonan 31253, Chungnam, Republic of Korea
| | - Min-Seok Lee
- Complex Fluids Laboratory, School of Mechanical Engineering, Korea University of Technology and Education, Cheonan 31253, Chungnam, Republic of Korea
| | - Seungkyung Park
- Complex Fluids Laboratory, School of Mechanical Engineering, Korea University of Technology and Education, Cheonan 31253, Chungnam, Republic of Korea
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Huang X, Yan X, Gao L, Luo Y, Liao H, Long M, Duan L, Xia X. In-situ substitution and community dynamics modeling for enhanced safety in Chinese rice wine brewing. Food Res Int 2024; 176:113824. [PMID: 38163724 DOI: 10.1016/j.foodres.2023.113824] [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: 08/10/2023] [Revised: 11/28/2023] [Accepted: 12/02/2023] [Indexed: 01/03/2024]
Abstract
This research paper focuses on the application of the "Design-Build-Test-Learn" framework to design and evaluate a synthetic microbial community aimed at studying the impact of Lactic Acid Bacteria (LAB) interactions and fitness on the formation of biogenic amines (BAs) in Chinese rice wine (CRW). The study reveals a close correlation between the assembly model of LAB and the accumulation of BAs in CRW, and multiple interactions were observed between amine-producing and non-amine-producing LAB, including commensalism, amensalism, and competition. The commensalism among amine-producing LAB was found to promote BAs accumulation through metabolic cross-feeding of amino acids. Moreover, the higher-order interaction community was designed to regulate the BAs formation effectively. For instance, the interference of Lactiplantibacillus plantarum (ACBC271) resulted in the elimination of amine-producing LAB viability, resulting in a 22% decrease (not exceeding 43.54 mg/L) in the total amount of BAs. Simulation of community dynamics models further suggests that LAB with quantitative social interactions can effectively control LAB accumulation in CRW by forecasting fluctuation in BAs generation through fitness competition and metabolic interference. Overall, this study provides valuable insights into the complex interaction networks within microbial communities in traditional fermentation ecosystems. It also proposes a novel approach for quality control of nitrogen food safety factors in fermented foods.
Collapse
Affiliation(s)
- Xinlei Huang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, PR China
| | - Xinyuan Yan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, PR China
| | - Ling Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, PR China
| | - Yi Luo
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, PR China
| | - Hui Liao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, PR China
| | - Mengfei Long
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, PR China
| | - Liangjie Duan
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, PR China
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, PR China.
| |
Collapse
|
6
|
Boyte ME, Benkowski A, Pane M, Shehata HR. Probiotic and postbiotic analytical methods: a perspective of available enumeration techniques. Front Microbiol 2023; 14:1304621. [PMID: 38192285 PMCID: PMC10773886 DOI: 10.3389/fmicb.2023.1304621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/20/2023] [Indexed: 01/10/2024] Open
Abstract
Probiotics are the largest non-herbal/traditional dietary supplements category worldwide. To be effective, a probiotic strain must be delivered viable at an adequate dose proven to deliver a health benefit. The objective of this article is to provide an overview of the various technologies available for probiotic enumeration, including a general description of each technology, their advantages and limitations, and their potential for the future of the probiotics industry. The current "gold standard" for analytical quantification of probiotics in the probiotic industry is the Plate Count method (PC). PC measures the bacterial cell's ability to proliferate into detectable colonies, thus PC relies on cultivability as a measure of viability. Although viability has widely been measured by cultivability, there has been agreement that the definition of viability is not limited to cultivability. For example, bacterial cells may exist in a state known as viable but not culturable (VBNC) where the cells lose cultivability but can maintain some of the characteristics of viable cells as well as probiotic properties. This led to questioning the association between viability and cultivability and the accuracy of PC in enumerating all the viable cells in probiotic products. PC has always been an estimate of the number of viable cells and not a true cell count. Additionally, newer probiotic categories such as Next Generation Probiotics (NGPs) are difficult to culture in routine laboratories as NGPs are often strict anaerobes with extreme sensitivity to atmospheric oxygen. Thus, accurate quantification using culture-based techniques will be complicated. Another emerging category of biotics is postbiotics, which are inanimate microorganisms, also often referred to as tyndallized or heat-killed bacteria. Obviously, culture dependent methods are not suitable for these products, and alternative methods are needed for their quantification. Different methodologies provide a more complete picture of a heterogeneous bacterial population versus PC focusing exclusively on the eventual multiplication of the cells. Alternative culture-independent techniques including real-time PCR, digital PCR and flow cytometry are discussed. These methods can measure viability beyond cultivability (i.e., by measuring cellular enzymatic activity, membrane integrity or membrane potential), and depending on how they are designed they can achieve strain-specific enumeration.
Collapse
Affiliation(s)
- Marie-Eve Boyte
- NutraPharma Consulting Services Inc., Sainte-Anne-des-Plaines, QC, Canada
| | | | - Marco Pane
- Probiotical Research s.r.l., Novara, Italy
| | | |
Collapse
|
7
|
Chung CJ, Hermes BM, Gupta Y, Ibrahim S, Belheouane M, Baines JF. Genome-wide mapping of gene-microbe interactions in the murine lung microbiota based on quantitative microbial profiling. Anim Microbiome 2023; 5:31. [PMID: 37264412 DOI: 10.1186/s42523-023-00250-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/10/2023] [Indexed: 06/03/2023] Open
Abstract
BACKGROUND Mammalian lungs comprise a complex microbial ecosystem that interacts with host physiology. Previous research demonstrates that the environment significantly contributes to bacterial community structure in the upper and lower respiratory tract. However, the influence of host genetics on the makeup of lung microbiota remains ambiguous, largely due to technical difficulties related to sampling, as well as challenges inherent to investigating low biomass communities. Thus, innovative approaches are warranted to clarify host-microbe interactions in the mammalian lung. RESULTS Here, we aimed to characterize host genomic regions associated with lung bacterial traits in an advanced intercross mouse line (AIL). By performing quantitative microbial profiling (QMP) using the highly precise method of droplet digital PCR (ddPCR), we refined 16S rRNA gene amplicon-based traits to identify and map candidate lung-resident taxa using a QTL mapping approach. In addition, the two abundant core taxa Lactobacillus and Pelomonas were chosen for independent microbial phenotyping using genus-specific primers. In total, this revealed seven significant loci involving eight bacterial traits. The narrow confidence intervals afforded by the AIL population allowed us to identify several promising candidate genes related to immune and inflammatory responses, cell apoptosis, DNA repair, and lung functioning and disease susceptibility. Interestingly, one genomic region associated with Lactobacillus abundance contains the well-known anti-inflammatory cytokine Il10, which we confirmed through the analysis of Il10 knockout mice. CONCLUSIONS Our study provides the first evidence for a role of host genetic variation contributing to variation in the lung microbiota. This was in large part made possible through the careful curation of 16S rRNA gene amplicon data and the incorporation of a QMP-based methods. This approach to evaluating the low biomass lung environment opens new avenues for advancing lung microbiome research using animal models.
Collapse
Affiliation(s)
- C J Chung
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany
| | - B M Hermes
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany
| | - Y Gupta
- Division of Nephrology, Department of Medicine, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - S Ibrahim
- College of Medicine and Health Sciences, Khalifa University, Abu Dhabi, UAE
| | - Meriem Belheouane
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany.
- Research Center Borstel, Evolution of the Resistome, Leibniz Lung Center, Parkallee 1-40, 23845, Borstel, Germany.
| | - John F Baines
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany.
- Section of Evolutionary Medicine, Institute for Experimental Medicine, Kiel University, Arnold-Heller-Str. 3, 24105, Kiel, Germany.
| |
Collapse
|
8
|
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: 4] [Impact Index Per Article: 4.0] [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.
Collapse
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,*Correspondence: Hanan R. Shehata,
| | | | - Steven G. Newmaster
- Natural Health Product Research Alliance, Department of Integrative Biology, College of Biological Science, University of Guelph, Guelph, ON, Canada
| |
Collapse
|
9
|
Chen X, Niu X, Liu Y, Zheng R, Yang L, Lu J, Yin S, Wei Y, Pan J, Sayed A, Ma X, Liu M, Jing F, Liu M, Hu J, Wang L, Li D. Long-term correction of hemophilia B through CRISPR/Cas9 induced homology-independent targeted integration. J Genet Genomics 2022; 49:1114-1126. [PMID: 35691554 DOI: 10.1016/j.jgg.2022.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/29/2022] [Accepted: 06/01/2022] [Indexed: 01/14/2023]
Abstract
CRISPR/Cas9-mediated site-specific insertion of exogenous genes holds potential for clinical applications. However, it is still infeasible because homologous recombination (HR) is inefficient, especially for non-dividing cells. To overcome the challenge, we report that a homology-independent targeted integration (HITI) strategy is used for permanent integration of high-specificity-activity Factor IX variant (F9 Padua, R338L) at the albumin (Alb) locus in a novel hemophilia B (HB) rat model. The knock-in efficiency reaches 3.66%, as determined by droplet digital PCR (ddPCR). The clotting time is reduced to a normal level four weeks after treatment, and the circulating factor IX (FIX) level is gradually increased up to 52% of the normal level over nine months even after partial hepatectomy, demonstrating the amelioration of hemophilia. Through primer-extension-mediated sequencing (PEM-seq), no significant off-target effect is detected. This study not only provides a novel model for HB but also identifies a promising therapeutic approach for rare inherited diseases.
Collapse
Affiliation(s)
- Xi Chen
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Xuran Niu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yang Liu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Genome Editing Research Center, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Rui Zheng
- Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Lei Yang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jian Lu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Shuming Yin
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Yu Wei
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jiahao Pan
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Ahmed Sayed
- Biochemistry Laboratory, Chemistry Department, Faculty of Science, Assiut University, Assiut 71516, Egypt
| | - Xueyun Ma
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Meizhen Liu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | | | - Mingyao Liu
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Jiazhi Hu
- The MOE Key Laboratory of Cell Proliferation and Differentiation, Genome Editing Research Center, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
| | - Liren Wang
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.
| | - Dali Li
- Shanghai Frontiers Science Center of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China.
| |
Collapse
|
10
|
Kiefer A, Byrd PM, Tang P, Jones G, Galles K, Fallico V, Wong C. Viability droplet digital polymerase chain reaction accurately enumerates probiotics and provides insight into damage experienced during storage. Front Microbiol 2022; 13:966264. [PMID: 36386724 PMCID: PMC9648155 DOI: 10.3389/fmicb.2022.966264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 09/26/2022] [Indexed: 12/05/2022] Open
Abstract
Probiotics are typically enumerated by agar plate counting (PC) techniques. PC has several limitations including poor specificity, high variability, inability to enumerate dead cells, viable but non-culturable cells and cells in complex matrices. Viability droplet digital polymerase chain reaction (v-ddPCR) is an emerging enumeration technique with improved specificity, precision, and the ability to enumerate cells in varying states of culturability or in complex matrices. Good correlation and agreement between v-ddPCR and PC is well documented, but not much research has been published on the comparison when enumerating freeze-dried (FD) probiotics during storage. In this study, v-ddPCR utilizing PE51 (PE51-ddPCR), a combination of propidium monoazide (PMA) and ethidium monoazide (EMA), was evaluated as alternative enumeration technique to PC on blends of four FD probiotic strains over the course of a 3-month storage study with accelerated conditions. When PMA and EMA are combined (PE51), this study demonstrates agreement (bias = 7.63e+9, LOA = 4.38e+10 to 5.9e+10) and association (r = 0.762) between PC and v-ddPCR, at or above levels of an accepted alternative method. Additionally, v-ddPCR with individual dyes PMA and EMA provide insight into how they individually contribute to the viable counts obtained by PE51-ddPCR and provide a more specific physiological understanding of how probiotics cope with or experience damage during storage.
Collapse
|
11
|
Foliage of Tropical Trees and Shrubs and Their Secondary Metabolites Modify In Vitro Ruminal Fermentation, Methane and Gas Production without a Tight Correlation with the Microbiota. Animals (Basel) 2022; 12:ani12192628. [PMID: 36230369 PMCID: PMC9559637 DOI: 10.3390/ani12192628] [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: 08/07/2022] [Revised: 09/24/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Ruminants, mainly cattle, contribute to greenhouse gases (GHG) emissions as methane (CH4) is produced by ruminal fermentation. Hence, various anti-methanogenic feed strategies have been studied, including the use of plants with secondary metabolites. This study evaluated in vitro ruminal fermentation metrics, microbial composition by digital droplet PCR (ddPCR) and the CH4 production of the foliage of several tropical trees and shrubs: Leucaena leucocephala, Moringa oleifera, Albizia lebbeck, Enterolobium cyclocarpum, Piscidia piscipula, Brosimum alicastrum, Lysiloma latisiliquum, Guazuma ulmifolia, Cnidoscolus aconitifolius, Gliricidia sepium and Bursera simaruba, using Cynodon plectostachyus grass as control. The results showed a wide variation in the chemical composition of the foliage, as well as in the ruminal microbiota. The crude protein (CP) content ranged from 11 to 25%, whereas the content of condensed tannins (CT) and saponins (S) was from 0.02 to 7%, and 3.2 to 6.6%, respectively. The greatest dry matter degradability (DMD) after 72 h was 69% and the least 35%, the latter coinciding with the least gas production (GP). A negative correlation was found between the CT and CH4 production, also between protozoa and fungi with the SGMT group of archaea. We concluded that the foliage of some tropical trees and shrubs has a high nutritional value and the potential to decrease CH4 production due to its CT content.
Collapse
|
12
|
Skin microbiota analysis in patients with anorexia nervosa and healthy-weight controls reveals microbial indicators of healthy weight and associations with the antimicrobial peptide psoriasin. Sci Rep 2022; 12:15515. [PMID: 36109548 PMCID: PMC9477808 DOI: 10.1038/s41598-022-19676-6] [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: 05/20/2022] [Accepted: 09/01/2022] [Indexed: 12/29/2022] Open
Abstract
Anorexia nervosa (AN), a psychiatric condition defined by low body weight for age and height, is associated with numerous dermatological conditions. Yet, clinical observations report that patients with AN do not suffer from infectious skin diseases like those associated with primary malnutrition. Cell-mediated immunity appears to be amplified in AN; however, this proinflammatory state does not sufficiently explain the lower incidence of infections. Antimicrobial peptides (AMPs) are important components of the innate immune system protecting from pathogens and shaping the microbiota. In Drosophila melanogaster starvation precedes increased AMP gene expression. Here, we analyzed skin microbiota in patients with AN and age-matched, healthy-weight controls and investigated the influence of weight gain on microbial community structure. We then correlated features of the skin microbial community with psoriasin and RNase 7, two highly abundant AMPs in human skin, to clarify whether an association between AMPs and skin microbiota exists and whether such a relationship might contribute to the resistance to cutaneous infections observed in AN. We find significant statistical correlations between Shannon diversity and the highly abundant skin AMP psoriasin and bacterial load, respectively. Moreover, we reveal psoriasin significantly associates with Abiotrophia, an indicator for the healthy-weight control group. Additionally, we observe a significant correlation between an individual's body mass index and Lactobacillus, a microbial indicator of health. Future investigation may help clarify physiological mechanisms that link nutritional intake with skin physiology.
Collapse
|
13
|
Roy M, Sarkar D, Chatterjee M. Quantitative monitoring of experimental and human leishmaniasis employing amastigote-specific genes. Parasitology 2022; 149:1085-1093. [PMID: 35535469 PMCID: PMC11016204 DOI: 10.1017/s0031182022000610] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 11/07/2022]
Abstract
The gold standard for diagnosis of leishmaniasis is the microscopic detection of amastigotes/Leishman Donovan (LD) bodies, but its moderate sensitivity necessitates the development of molecular approaches. This study aimed to quantify in experimental animal models and human leishmaniasis the expression of amastigote-specific virulence genes, A2 and amastin by droplet digital polymerase chain reaction (ddPCR). Total RNA was isolated from L. donovani-infected hamsters or murine peritoneal macrophages and lesional biopsies from patients with post kala-azar dermal leishmaniasis (PKDL). Following cDNA conversion, EvaGreen-based ddPCR was performed using specific primers for A2 or amastin and parasite load expressed in copies per μL. Assay was optimized and the specificity of amastigote-specific A2 and amastin was confirmed. In hepatic and splenic tissues of L. donovani-infected hamsters and peritoneal macrophages, ddPCR demonstrated a greater abundance of A2 than amastin. Treatment of L. donovani-infected peritoneal macrophages with conventional anti-leishmanials, miltefosine and amphotericin B translated into a dose-dependent reduction in copies per μL of A2 and amastin, and the extrapolated IC50 was comparable with results obtained by counting LD bodies in Giemsa-stained macrophages. Similarly, in dermal biopsies of patients with PKDL, A2 and amastin were detected. Overall, monitoring of A2 by ddPCR can be an objective measure of parasite burden and potentially adaptable into a high throughput approach necessary for drug development and monitoring disease progression when the causative species is L. donovani.
Collapse
Affiliation(s)
- Madhurima Roy
- Department of Pharmacology, Institute of Postgraduate Medical Education and Research (IPGME&R), 244B, Acharya JC Bose Road, Kolkata 700020, India
| | - Deblina Sarkar
- Department of Pharmacology, Institute of Postgraduate Medical Education and Research (IPGME&R), 244B, Acharya JC Bose Road, Kolkata 700020, India
| | - Mitali Chatterjee
- Department of Pharmacology, Institute of Postgraduate Medical Education and Research (IPGME&R), 244B, Acharya JC Bose Road, Kolkata 700020, India
| |
Collapse
|
14
|
Absolute Quantification of Viable but Nonculturable Vibrio cholerae Using Droplet Digital PCR with Oil-Enveloped Bacterial Cells. Microbiol Spectr 2022; 10:e0070422. [PMID: 35762749 PMCID: PMC9430983 DOI: 10.1128/spectrum.00704-22] [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] [Indexed: 11/20/2022] Open
Abstract
When exposed to adverse conditions, many bacterial pathogens, including Vibrio cholerae, can adapt to the environment by entering the viable but nonculturable (VBNC) state. Cells in this state cannot grow on conventional media but still survive. The VBNC state is a significant threat to aquatic safety and public health due to the enhanced ability of the bacteria to remain in the environment and escape from monitoring. Detecting and quantifying VBNC cells and distinguishing them from nonviable cells is necessary for microbiological studies and pathogen monitoring. Cell staining and microscopy are used for the observation of VBNC cells, but it is difficult to quantify VBNC cells accurately. In this study, we developed droplet digital PCR (ddPCR) with a chromosomal single-copy gene as an internal reference combined with Propidium monoazide (PMA) treatment to enumerate VBNC cells of V. cholerae. In this method, bacterial cells, but not extracted chromosomal DNA, were used directly to form oil-enveloped droplets in the ddPCR procedure. One bacterial cell possesses one copy of the chromosome. Thus, enumeration of a single-copy gene on the chromosome can be used to count VBNC cells. ddPCR showed greater accuracy and sensitivity than qPCR. This study showed that the oil-enveloped bacterial method can reduce the number of steps needed and improve the accuracy of VBNC cells quantification and has the potential to be extended to quantify bacterial VBNC cells and assess pathogen survival in the environment. IMPORTANCE The viable but nonculturable (VBNC) state of bacteria represents an important life state for their survival in adverse environments. The VBNC cells of the pathogenic bacteria in the environment and food will be a potential threat to public health because these pathogens cannot be found by the detection of culture. We developed a sensitive molecular method to detect and enumerate the VBNC cells of V. cholerae, which can distinguish the VBNC and dead cells, and count the VBNC cells in the sample without the step of DNA extraction from cells. It can be used to improve the sensitivity of pathogen detection in the surveillance, risk assessment of environment and food contamination, and outbreak warning. The accurate identification and numeration of VBNC cells will also facilitate the microbiological and genetic studies on the development, adaptation, resuscitation, and elimination of the VBNC state.
Collapse
|
15
|
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.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Hae-Yeong Kim
- Correspondence: ; Tel.: +82-31-201-2600; Fax: +82-31-204-8116
| |
Collapse
|
16
|
Han Y, Wang J, Zhang S, Yang S, Wang X, Han Y, Shen Z, Xu X. Simultaneous quantification of hepatitis A virus and norovirus genogroup I and II by triplex droplet digital PCR. Food Microbiol 2022; 103:103933. [DOI: 10.1016/j.fm.2021.103933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/03/2021] [Accepted: 11/03/2021] [Indexed: 11/04/2022]
|
17
|
Daddy Gaoh S, Kweon O, Lee YJ, Hussong D, Marasa B, Ahn Y. A Propidium Monoazide (PMAxx)-Droplet Digital PCR (ddPCR) for the Detection of Viable Burkholderia cepacia Complex in Nuclease-Free Water and Antiseptics. Microorganisms 2022; 10:943. [PMID: 35630385 PMCID: PMC9147393 DOI: 10.3390/microorganisms10050943] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 12/26/2022] Open
Abstract
Pharmaceutical products contaminated with Burkholderia cepacia complex (BCC) strains constitute a serious health issue for susceptible individuals. New detection methods to distinguish DNA from viable cells are required to ensure pharmaceutical product quality and safety. In this study, we have assessed a droplet digital PCR (ddPCR) with a variant propidium monoazide (PMAxx) for selective detection of live/dead BCC cells in autoclaved nuclease-free water after 365 days, in 0.001% chlorhexidine gluconate (CHX), and in 0.005% benzalkonium chloride (BZK) solutions after 184 days. Using 10 μM PMAxx and 5 min light exposure, a proportion of dead BCC was quantified by ddPCR. The detection limit of culture-based method was 104 CFU/mL, equivalent to 9.7 pg/μL for B. cenocepacia J2315, while that of ddPCR was 9.7 fg/μL. The true positive rate from nuclease-free water and CHX using PMAxx-ddPCR assay was 60.0% and 38.3%, respectively, compared to 85.0% and 74.6% without PMAxx (p < 0.05), respectively. However, in BZK-treated cells, no difference in the detection rate was observed between the ddPCR assay on samples treated with PMAxx (67.1%) and without PMAxx (63.3%). This study shows that the PMAxx-ddPCR assay provides a better tool for selective detection of live BCC cells in non-sterile pharmaceutical products.
Collapse
Affiliation(s)
- Soumana Daddy Gaoh
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (S.D.G.); (O.K.)
| | - Ohgew Kweon
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (S.D.G.); (O.K.)
| | - Yong-Jin Lee
- Department of Natural Sciences, Albany State University, Albany, GA 31705, USA;
| | - David Hussong
- Office of Pharmaceutical Science, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Beltsville, MD 20993, USA;
| | - Bernard Marasa
- Office of Pharmaceutical Quality, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD 20993, USA;
| | - Youngbeom Ahn
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR 72079, USA; (S.D.G.); (O.K.)
| |
Collapse
|
18
|
Abstract
The ongoing coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has led to a global public health disaster. The current gold standard for the diagnosis of infected patients is real-time reverse transcription-quantitative PCR (RT-qPCR). As effective as this method may be, it is subject to false-negative and -positive results, affecting its precision, especially for the detection of low viral loads in samples. In contrast, digital PCR (dPCR), the third generation of PCR, has been shown to be more effective than the gold standard, RT-qPCR, in detecting low viral loads in samples. In this review article, we selected publications to show the broad-spectrum applications of dPCR, including the development of assays and reference standards, environmental monitoring, mutation detection, and clinical diagnosis of SARS-CoV-2, while comparing it analytically to the gold standard, RT-qPCR. In summary, it is evident that the specificity, sensitivity, reproducibility, and detection limits of RT-dPCR are generally unaffected by common factors that may affect RT-qPCR. As this is the first time that dPCR is being tested in an outbreak of such a magnitude, knowledge of its applications will help chart a course for future diagnosis and monitoring of infectious disease outbreaks.
Collapse
|
19
|
Lee AS, Lamanna OK, Ishida K, Hill E, Nguyen A, Hsieh MH. A Novel Propidium Monoazide-Based PCR Assay Can Measure Viable Uropathogenic E. coli In Vitro and In Vivo. Front Cell Infect Microbiol 2022; 12:794323. [PMID: 35178354 PMCID: PMC8844370 DOI: 10.3389/fcimb.2022.794323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/11/2022] [Indexed: 11/13/2022] Open
Abstract
Background Polymerase chain reaction (PCR) is an important means by which to study the urine microbiome and is emerging as possible alternative to urine cultures to identify pathogens that cause urinary tract infection (UTI). However, PCR is limited by its inability to differentiate DNA originating from viable, metabolically active versus non-viable, inactive bacteria. This drawback has led to concerns that urobiome studies and PCR-based diagnosis of UTI are confounded by the presence of relic DNA from non-viable bacteria in urine. Propidium monoazide (PMA) dye can penetrate cells with compromised cell membranes and covalently bind to DNA, rendering it inaccessible to amplification by PCR. Although PMA has been shown to differentiate between non-viable and viable bacteria in various settings, its effectiveness in urine has not been previously studied. We sought to investigate the ability of PMA to differentiate between viable and non-viable bacteria in urine. Methods Varying amounts of viable or non-viable uropathogenic E. coli (UTI89) or buffer control were titrated with mouse urine. The samples were centrifuged to collect urine sediment or not centrifuged. Urine samples were incubated with PMA and DNA cross-linked using blue LED light. DNA was isolated and uidA gene-specific PCR was performed. For in vivo studies, mice were inoculated with UTI89, followed by ciprofloxacin treatment or no treatment. After the completion of ciprofloxacin treatment, an aliquot of urine was plated on non-selective LB agar and another aliquot was treated with PMA and subjected to uidA-specific PCR. Results PMA’s efficiency in excluding DNA signal from non-viable bacteria was significantly higher in bacterial samples in phosphate-buffered saline (PBS, dCT=13.69) versus bacterial samples in unspun urine (dCT=1.58). This discrepancy was diminished by spinning down urine-based bacterial samples to collect sediment and resuspending it in PBS prior to PMA treatment. In 3 of 5 replicate groups of UTI89-infected mice, no bacteria grew in culture; however, there was PCR amplification of E. coli after PMA treatment in 2 of those 3 groups. Conclusion We have successfully developed PMA-based PCR methods for amplifying DNA from live bacteria in urine. Our results suggest that non-PMA bound DNA from live bacteria can be present in urine, even after antibiotic treatment. This indicates that viable but non-culturable E. coli can be present following treatment of UTI, and may explain why some patients have persistent symptoms but negative urine cultures following UTI treatment.
Collapse
Affiliation(s)
- Albert S. Lee
- Division of Pediatric Urology, Children’s National Hospital, Washington, DC, United States
| | - Olivia K. Lamanna
- Sheikh Zayed Institute, Children’s National Hospital, Washington, DC, United States
| | - Kenji Ishida
- Sheikh Zayed Institute, Children’s National Hospital, Washington, DC, United States
| | - Elaise Hill
- School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
- Center for Cancer and Immunology Research, Children’s National Hospital, Washington, DC, United States
| | - Andrew Nguyen
- School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
| | - Michael H. Hsieh
- Division of Pediatric Urology, Children’s National Hospital, Washington, DC, United States
- Sheikh Zayed Institute, Children’s National Hospital, Washington, DC, United States
- School of Medicine and Health Sciences, The George Washington University, Washington, DC, United States
- *Correspondence: Michael H. Hsieh,
| |
Collapse
|
20
|
Wendel U. Assessing Viability and Stress Tolerance of Probiotics—A Review. Front Microbiol 2022; 12:818468. [PMID: 35154042 PMCID: PMC8829321 DOI: 10.3389/fmicb.2021.818468] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 12/27/2021] [Indexed: 11/26/2022] Open
Abstract
The interest in probiotics has increased rapidly the latest years together with the global market for probiotic products. Consequently, establishing reliable microbiological methods for assuring the presence of a certain number of viable microorganisms in probiotic products has become increasingly important. To assure adequate numbers of viable cells, authorities are enquiring for information on viability rates within a certain shelf-life in colony forming units (CFU). This information is obtained from plate count enumeration, a method that enables detection of bacterial cells based on their ability to replicate. Although performing plate count enumeration is one manner of assessing viability, cells can still be viable without possessing the ability to replicate. Thus, to properly assess probiotic viability, further analysis of a broader group of characteristics using several types of methods is proposed. In addition to viability, it is crucial to identify how well the cells in a probiotic product can survive in the gastrointestinal tract (GIT) and thus be able to mediate the desired health benefit while passing through the human body. A broad spectrum of different assay designs for assessing probiotic gastric tolerance have been used in research and quality control. However, the absence of any consensus on how to assess these qualities makes it difficult to compare between laboratories and to translate the results into in vivo tolerance. This review presents and discusses the complexity of assuring that a probiotic is suitable for beneficial consumption. It summarizes the information that can be subtracted from the currently available methods for assessment of viability and stress tolerance of a probiotic, hereby altogether defined as “activity.” Strengths and limitations of the different methods are presented together with favorable method combinations. Finally, the importance of choosing a set of analyses that reveals the necessary aspects of probiotic activity for a certain product or application is emphasized.
Collapse
|
21
|
Mavridis K, Papapostolou KM, Riga M, Ilias A, Michaelidou K, Bass C, Van Leeuwen T, Tsagkarakou A, Vontas J. Multiple TaqMan qPCR and droplet digital PCR (ddPCR) diagnostics for pesticide resistance monitoring and management, in the major agricultural pest Tetranychus urticae. PEST MANAGEMENT SCIENCE 2022; 78:263-273. [PMID: 34480408 DOI: 10.1002/ps.6632] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/16/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Decisions on which pesticide to use in agriculture are expected to become more difficult, as the number of available chemicals is decreasing. For Tetranychus urticae (T. urticae), a major pest for which a number of candidate markers for pesticide resistance are in place, molecular diagnostics could support decision-making for the rational use of acaricides. RESULTS A suite of 12 TaqMan qPCR assays [G314D (GluCl1), G326E, I321T (GluCl3), G119S, F331W (Ace-1), H92R (PSST), L1024V, F1538I (VGSC), I1017F (CHS1), G126S, S141F, P262T (cytb)], were validated against Sanger-sequencing, and subsequently adapted for use with the ddPCR technology. The concordance correlation coefficient between the actual and ddPCR measured mutant allelic frequencies was 0.995 (95% CI = 0.991-0.998), and no systematic, proportional, or random differences were detected. The achieved Limit of Detection (LoD) was 0.1% (detection of one mutant in a background of 999 wild type mites). The ddPCR assay panel was then assessed in terms of agreement with phenotypic resistance, through a pilot application in field populations from Crete, with strong correlation and thus predictive and diagnostic value of the molecular assays in some cases (e.g., etoxazole and abamectin resistance). Molecular diagnostics were able to capture incipient resistance that was otherwise missed by phenotypic bioassays. The molecular and phenotypic resistance screening of T. urticae field populations from Crete, revealed both multi-resistant and susceptible populations. CONCLUSION The highly sensitive T. urticae molecular diagnostic platforms developed in this study could prove a valuable tool for pesticide resistance management. © 2021 Society of Chemical Industry.
Collapse
Affiliation(s)
- Konstantinos Mavridis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Kyriaki Maria Papapostolou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
| | - Maria Riga
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Aris Ilias
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
| | - Kleita Michaelidou
- Laboratory of Translational Oncology, School of Medicine, University of Crete, Heraklion, Greece
| | - Chris Bass
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Penryn, UK
| | - Thomas Van Leeuwen
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Anastasia Tsagkarakou
- Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization "DIMITRA", Heraklion, Greece
| | - John Vontas
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion, Greece
- Pesticide Science Laboratory, Department of Crop Science, Agricultural University of Athens, Athens, Greece
| |
Collapse
|
22
|
Abellan-Schneyder I, Schusser AJ, Neuhaus K. ddPCR allows 16S rRNA gene amplicon sequencing of very small DNA amounts from low-biomass samples. BMC Microbiol 2021; 21:349. [PMID: 34922460 PMCID: PMC8684222 DOI: 10.1186/s12866-021-02391-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 11/15/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND One limiting factor of short amplicon 16S rRNA gene sequencing approaches is the use of low DNA amounts in the amplicon generation step. Especially for low-biomass samples, insufficient or even commonly undetectable DNA amounts can limit or prohibit further analysis in standard protocols. RESULTS Using a newly established protocol, very low DNA input amounts were found sufficient for reliable detection of bacteria using 16S rRNA gene sequencing compared to standard protocols. The improved protocol includes an optimized amplification strategy by using a digital droplet PCR. We demonstrate how PCR products are generated even when using very low concentrated DNA, unable to be detected by using a Qubit. Importantly, the use of different 16S rRNA gene primers had a greater effect on the resulting taxonomical profiles compared to using high or very low initial DNA amounts. CONCLUSION Our improved protocol takes advantage of ddPCR and allows faithful amplification of very low amounts of template. With this, samples of low bacterial biomass become comparable to those with high amounts of bacteria, since the first and most biasing steps are the same. Besides, it is imperative to state DNA concentrations and volumes used and to include negative controls indicating possible shifts in taxonomical profiles. Despite this, results produced by using different primer pairs cannot be easily compared.
Collapse
Affiliation(s)
- Isabel Abellan-Schneyder
- Core Facility Microbiome, ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
| | - Andrea Janina Schusser
- Core Facility Microbiome, ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany
| | - Klaus Neuhaus
- Core Facility Microbiome, ZIEL - Institute for Food & Health, Technische Universität München, Freising, Germany.
| |
Collapse
|
23
|
Hu L, Xue Y, Cui L, Zhang D, Feng L, Zhang W, Wang S. Detection of viable Lacticaseibacillus paracasei in fermented milk using propidium monoazide combined with quantitative loop-mediated isothermal amplification. FEMS Microbiol Lett 2021; 368:6442182. [PMID: 34849766 DOI: 10.1093/femsle/fnab148] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/23/2021] [Indexed: 01/23/2023] Open
Abstract
To quantify viable probiotic Lacticaseibacillus paracasei (L. paracasei) in fermented milk accurately and quickly, propidium monoazide combined with quantitative loop-mediated isothermal amplification (PMA-qLAMP) was applied. The optimal PMA treatment conditions for treating a L. paracasei suspension were determined using an orthogonal test to eliminate the DNA amplification of 108 CFU/mL of dead L. paracasei. Primers were designed based on the species-specific gyrB gene of L. paracasei. A phylogenetic tree based on the gyrB gene showed that L. paracasei clustered on the same branch with 91% support. Compared with the 16 strains commonly found in fermented milk, three strains of L. paracasei showed positive PMA-qLAMP results, and the melting temperature was approximately 82.4°C. There was a linear relationship (R2 = 0.9983) between the Ct values and the logarithm of the concentration of viable bacteria. The PMA-qLAMP detection limit for the L. paracasei artificially added to fermented milk was 7.3 × 102 CFU/mL. There was no significant difference between the logarithm values of the concentration of viable L. paracasei of 50 fermented milk samples within shelf life using the PMA-qLAMP and plate count methods (P > 0.01). PMA-qLAMP is specific and accurate for obtaining reliable results faster than when using plate counts.
Collapse
Affiliation(s)
- Lianxia Hu
- College of Chemical Engineering, Shijiazhuang University, Shijiazhuang, Hebei 050035, China
| | - Yuling Xue
- Shijiazhuang Junlebao Dairy Co., Ltd., Shijiazhuang, Hebei 050221, China
| | - Liru Cui
- College of Food Science and Biology, Hebei University of Science and Technology, 26 Yuxiang Street, Shijiazhuang, Hebei 050018, China
| | - Dong Zhang
- Shijiazhuang Junlebao Dairy Co., Ltd., Shijiazhuang, Hebei 050221, China
| | - Lili Feng
- Shijiazhuang Junlebao Dairy Co., Ltd., Shijiazhuang, Hebei 050221, China
| | - Wei Zhang
- College of Life Sciences, Agricultural University of Hebei, Baoding, Hebei 071001, China
| | - Shijie Wang
- Shijiazhuang Junlebao Dairy Co., Ltd., Shijiazhuang, Hebei 050221, China.,College of Food Science and Biology, Hebei University of Science and Technology, 26 Yuxiang Street, Shijiazhuang, Hebei 050018, China
| |
Collapse
|
24
|
Ou Y, Cao S, Zhang J, Dong W, Yang Z, Yu Z. Droplet microfluidics on analysis of pathogenic microbes for wastewater-based epidemiology. Trends Analyt Chem 2021; 143:116333. [PMID: 34720276 PMCID: PMC8547957 DOI: 10.1016/j.trac.2021.116333] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Infectious diseases caused by pathogenic microbes have posed a major health issue for the public, such as the ongoing COVID-19 global pandemic. In recent years, wastewater-based epidemiology (WBE) is emerging as an effective and unbiased method for monitoring public health. Despite its increasing importance, the advancement of WBE requires more competent and streamlined analytical platforms. Herein we discuss the interactions between WBE and droplet microfluidics, focusing on the analysis of pathogens in droplets, which is hard to be tackled by traditional analytical tools. We highlight research works from three aspects, namely, quantitation of pathogen biomarkers in droplets, single-cell analysis in droplets, and living cell biosensors in droplets, as well as providing future perspectives on the synergy between WBE and droplet microfluidics.
Collapse
Affiliation(s)
- Yangteng Ou
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, PR China.,Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Shixiang Cao
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, PR China
| | - Jing Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, PR China
| | - Weiliang Dong
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, PR China
| | - Zhugen Yang
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK
| | - Ziyi Yu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Chemical Engineering, Nanjing Tech University, 30 Puzhu South Road, Nanjing, 211816, PR China
| |
Collapse
|
25
|
Zhao S, Zhang J, Li Z, Han Y, Kan B. Enumeration of Viable Non-Culturable Vibrio cholerae Using Droplet Digital PCR Combined With Propidium Monoazide Treatment. Front Cell Infect Microbiol 2021; 11:753078. [PMID: 34796126 PMCID: PMC8592976 DOI: 10.3389/fcimb.2021.753078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 10/12/2021] [Indexed: 11/24/2022] Open
Abstract
Many bacterial species, including Vibrio cholerae (the pathogen that causes cholera), enter a physiologically viable but non-culturable (VBNC) state at low temperature or in conditions of low nutrition; this is a survival strategy to resist environmental stress. Identification, detection, and differentiation of VBNC cells and nonviable cells are essential for both microbiological study and disease surveillance/control. Enumeration of VBNC cells requires an accurate method. Traditional counting methods do not allow quantification of VBNC cells because they are not culturable. Morphology-based counting cannot distinguish between live and dead cells. A bacterial cell possesses one copy of the chromosome. Hence, counting single-copy genes on the chromosome is a suitable approach to count bacterial cells. In this study, we developed quantitative PCR-based methods, including real-time quantitative PCR (qPCR) and droplet digital PCR (ddPCR), to enumerate VBNC V. cholerae cells by counting the numbers of single-copy genes in samples during VBNC-state development. Propidium monoazide (PMA) treatment was incorporated to distinguish dead cells from viable cells. Both PCR methods could be used to quantify the number of DNA copies/mL and determine the proportion of dead cells (when PMA was used). The methods produced comparable counts using three single-copy genes (VC1376, thyA, and recA). However, ddPCR showed greater accuracy and sensitivity than qPCR. ddPCR also allows direct counting without the need to establish a standard curve. Our study develops a PMA-ddPCR method as a new tool to quantify VBNC cells of V. cholerae. The method can be extended to other bacterial species.
Collapse
Affiliation(s)
| | | | | | | | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| |
Collapse
|
26
|
Rana A, Patton D, Turner NT, Dillon MM, Cooper VS, Sung W. Precise measurement of the fitness effects of spontaneous mutations by droplet digital PCR in Burkholderia cenocepacia. Genetics 2021; 219:6325026. [PMID: 34849876 DOI: 10.1093/genetics/iyab117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 11/12/2022] Open
Abstract
Understanding how mutations affect survivability is a key component to knowing how organisms and complex traits evolve. However, most mutations have a minor effect on fitness and these effects are difficult to resolve using traditional molecular techniques. Therefore, there is a dire need for more accurate and precise fitness measurements methods. Here, we measured the fitness effects in Burkholderia cenocepacia HI2424 mutation accumulation (MA) lines using droplet-digital polymerase chain reaction (ddPCR). Overall, the fitness measurements from ddPCR-MA are correlated positively with fitness measurements derived from traditional phenotypic marker assays (r = 0.297, P = 0.05), but showed some differences. First, ddPCR had significantly lower measurement variance in fitness (F = 3.78, P < 2.6 × 10-13) in control experiments. Second, the mean fitness from ddPCR-MA measurements were significantly lower than phenotypic marker assays (-0.0041 vs -0.0071, P = 0.006). Consistent with phenotypic marker assays, ddPCR-MA measurements observed multiple (27/43) lineages that significantly deviated from mean fitness, suggesting that a majority of the mutations are neutral or slightly deleterious and intermixed with a few mutations that have extremely large effects. Of these mutations, we found a significant excess of mutations within DNA excinuclease and Lys R transcriptional regulators that have extreme deleterious and beneficial effects, indicating that modifications to transcription and replication may have a strong effect on organismal fitness. This study demonstrates the power of ddPCR as a ubiquitous method for high-throughput fitness measurements in both DNA- and RNA-based organisms regardless of cell type or physiology.
Collapse
Affiliation(s)
- Anita Rana
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - David Patton
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Nathan T Turner
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Marcus M Dillon
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S3B2, Canada
| | - Vaughn S Cooper
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Way Sung
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| |
Collapse
|
27
|
Shehata HR, Newmaster SG. Enumeration of Probiotic Strain Lacticaseibacillus rhamnosus GG (ATCC 53103) Using Viability Real-time PCR. Probiotics Antimicrob Proteins 2021; 13:1611-1620. [PMID: 34591288 DOI: 10.1007/s12602-021-09849-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/21/2021] [Indexed: 12/18/2022]
Abstract
Probiotic health benefits are strain specific and are dose dependent. Hence, administering the correct strains, at the recommended doses is essential to achieve probiotic health benefits. Reliable methods are needed to facilitate probiotic strain identification and enumeration. Plate count methods are the most commonly used methods for probiotic enumeration. However, these methods are time-consuming, laborious, highly variable, and non-specific. Here, we developed a real-time PCR method for enumeration of a commonly used strain, Lacticaseibacillus rhamnosus GG. The method utilizes PMAxx as a viability dye to enumerate viable cells only. Optimization of viability treatment showed that PMAxx at a final concentration of 50 μM was effective in inactivating DNA from dead cells, and that bead beating for 5 min at 3000 rpm was effective in liberating DNA. The assay demonstrated high efficiency between 93 and 102%, with R2 values > 0.99. The assay showed high precision with relative standard deviation (RSD%) below 2.3%. Assay performance was compared to a plate count method in which there was a strong correlation between both methods (Pearson r = 0.8443). This method offers a 10 × shorter time for results and a higher precision compared to plate count methods. Furthermore, this method enables specific enumeration of L. rhamnosus GG in multi-strain products, which is not possible to achieve using plate count methods. This novel method facilitates faster and more accurate enumeration of L. rhamnosus GG as a raw ingredient as well as in finished products which enables better quality assurance and efficacy of probiotics for consumers.
Collapse
Affiliation(s)
- Hanan R Shehata
- College of Biological Science, NHP Research Alliance, University of Guelph, Guelph, ON, N1G 2W1, Canada.
- Department of Microbiology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt.
| | - Steven G Newmaster
- College of Biological Science, NHP Research Alliance, University of Guelph, Guelph, ON, N1G 2W1, Canada
| |
Collapse
|
28
|
Chen S, Gong P, Zhang J, Shan Y, Han X, Zhang L. Use of qPCR for the analysis of population heterogeneity and dynamics during Lactobacillus delbrueckii spp. bulgaricus batch fculture. ARTIFICIAL CELLS NANOMEDICINE AND BIOTECHNOLOGY 2021; 49:1-10. [PMID: 33356615 DOI: 10.1080/21691401.2020.1860074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Direct molecular methods such as real-time polymerase chain reaction (qPCR) and propidium monoazide (PMA)-qPCR have been successfully used for quantifying viable microorganisms in the food industry. This study attempted to use qPCR and PMA-qPCR for quantifying Lactobacillus delbrueckii spp. bulgaricus sp1.1 physiological states. The qPCR standards of the 16S rRNA gene were employed to calibrate the qPCR assay, which contributed to an amplification efficiency of 98.42%. The number of copies of the 16S rRNA gene was linearly related to cell density, and this linear relationship was used to construct a quantitative curve (R2 =0.9981) with a detection limit of 15.1 colony-forming units mL-1·reaction-1. qPCR in combination with an optimal PMA concentration (60 μM) helped in discriminating and quantifying the viable cells, without any interference by heat-killed cells. Compared with the conventional methods, the population heterogeneity of viable, culturable, dormant-like and membrane-permeabilized cells were well identified and quantified using qPCR during L. delbrueckii spp. bulgaricus sp1.1 batch culture. Despite the restriction in the enumeration of lysed cells, qPCR-based methods facilitated reliable identification and quantification of bacterial physiological states and provided additional knowledge on the dynamics of L. delbrueckii spp. bulgaricus sp1.1 physiological states.
Collapse
Affiliation(s)
- Shiwei Chen
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Pimin Gong
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Jianming Zhang
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Yujuan Shan
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Xue Han
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China
| | - Lanwei Zhang
- School of Chemistry and Chemical Engineering, Harbin Institute of Technology, Harbin, China.,College of Food Science and Engineering, Ocean University of China, Qingdao, China
| |
Collapse
|
29
|
Wang X, Howe S, Deng F, Zhao J. Current Applications of Absolute Bacterial Quantification in Microbiome Studies and Decision-Making Regarding Different Biological Questions. Microorganisms 2021; 9:1797. [PMID: 34576694 PMCID: PMC8467167 DOI: 10.3390/microorganisms9091797] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/16/2021] [Accepted: 08/21/2021] [Indexed: 11/17/2022] Open
Abstract
High throughput sequencing has emerged as one of the most important techniques for characterizing microbial dynamics and revealing bacteria and host interactions. However, data interpretation using this technique is mainly based on relative abundance and ignores total bacteria load. In certain cases, absolute abundance is more important than compositional relative data, and interpretation of microbiota data based solely on relative abundance can be misleading. The available approaches for absolute quantification are highly diverse and challenging, especially for quantification in differing biological situations, such as distinguishing between live and dead cells, quantification of specific taxa, enumeration of low biomass samples, large sample size feasibility, and the detection of various other cellular features. In this review, we first illustrate the importance of integrating absolute abundance into microbiome data interpretation. Second, we briefly discuss the most widely used cell-based and molecular-based bacterial load quantification methods, including fluorescence spectroscopy, flow cytometry, 16S qPCR, 16S qRT-PCR, ddPCR, and reference spike-in. Last, we present a specific decision-making scheme for absolute quantification methods based on different biological questions and some of the latest quantitative methods and procedure modifications.
Collapse
Affiliation(s)
- Xiaofan Wang
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Samantha Howe
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Feilong Deng
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
Rosenberg JN, Cady NC. Surveilling cellular vital signs: toward label-free biosensors and real-time viability assays for bioprocessing. Curr Opin Biotechnol 2021; 71:123-129. [PMID: 34358978 DOI: 10.1016/j.copbio.2021.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/20/2021] [Accepted: 07/08/2021] [Indexed: 10/20/2022]
Abstract
Cell viability is an essential facet of mammalian and microbial bioprocessing. While robust methods of monitoring cellular health remain critically important to biomanufacturing and biofabrication, the complexity of advanced cell culture platforms often poses challenges for conventional viability assays. This review surveys novel approaches to discern the metabolic, morphological, and mechanistic hallmarks of living systems - spanning subcellular and multicellular scales. While fluorescent probes coupled with 3D image analysis generate rapid results with spatiotemporal detail, molecular techniques like viability PCR can distinguish live cells with genetic specificity. Notably, label-free biosensors can detect nuanced attributes of cellular vital signs with single-cell resolution via optical, acoustic, and electrical signals. Ultimately, efforts to integrate these modalities with automation, machine learning, and high-throughput workflows will lead to exciting new vistas across the cell viability landscape.
Collapse
Affiliation(s)
- Julian N Rosenberg
- Stack Family Center for Biopharmaceutical Education and Training (CBET), Albany College of Pharmacy and Health Sciences, 257 Fuller Road, Albany, NY 12203, USA.
| | - Nathaniel C Cady
- Nanobioscience Constellation, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, 257 Fuller Road, Albany, NY 12203, USA
| |
Collapse
|
32
|
Lei S, Chen S, Zhong Q. Digital PCR for accurate quantification of pathogens: Principles, applications, challenges and future prospects. Int J Biol Macromol 2021; 184:750-759. [PMID: 34171259 DOI: 10.1016/j.ijbiomac.2021.06.132] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 12/25/2022]
Abstract
Pathogens pose a severe threat to food safety and human health. The traditional methods for pathogen detection can't meet the growing diagnosis and control need. Digital PCR (dPCR) attracts a considerable attention for its ability to absolutely quantify pathogens with features of high selectivity, simplicity, accuracy and rapidity. The dPCR technique that achieves absolute quantification based on end-point measurement without standard curve offers a guideline for further genetic analysis and molecular diagnosis. It could contribute to the quantification of low level of nucleic acid, early detection and timely prevention of pathogenic diseases. In this review, 1442 publications about dPCR were selected and the detections of various pathogens by dPCR were reviewed comprehensively, including viruses, bacteria, parasites and fungi. A number of examples are cited to illustrate that dPCR is a new powerful tool with desired accuracy, sensitivity, and reproducibility for quantification of different types of pathogens. Moreover, the benefits, challenges and future prospects of the dPCR were also highlighted in this review.
Collapse
Affiliation(s)
- Shuwen Lei
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Song Chen
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Qingping Zhong
- Guangdong Provincial Key Laboratory of Food Quality and Safety, College of Food Science, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory of Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China.
| |
Collapse
|
33
|
Rapid and absolute quantification of VBNC Cronobacter sakazakii by PMAxx combined with single intact cell droplet digital PCR in infant foods. Lebensm Wiss Technol 2021. [DOI: 10.1016/j.lwt.2021.111388] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
34
|
Salminen S, Collado MC, Endo A, Hill C, Lebeer S, Quigley EMM, Sanders ME, Shamir R, Swann JR, Szajewska H, Vinderola G. The International Scientific Association of Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of postbiotics. Nat Rev Gastroenterol Hepatol 2021; 18:649-667. [PMID: 33948025 PMCID: PMC8387231 DOI: 10.1038/s41575-021-00440-6] [Citation(s) in RCA: 595] [Impact Index Per Article: 198.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/09/2021] [Indexed: 02/03/2023]
Abstract
In 2019, the International Scientific Association for Probiotics and Prebiotics (ISAPP) convened a panel of experts specializing in nutrition, microbial physiology, gastroenterology, paediatrics, food science and microbiology to review the definition and scope of postbiotics. The term 'postbiotics' is increasingly found in the scientific literature and on commercial products, yet is inconsistently used and lacks a clear definition. The purpose of this panel was to consider the scientific, commercial and regulatory parameters encompassing this emerging term, propose a useful definition and thereby establish a foundation for future developments. The panel defined a postbiotic as a "preparation of inanimate microorganisms and/or their components that confers a health benefit on the host". Effective postbiotics must contain inactivated microbial cells or cell components, with or without metabolites, that contribute to observed health benefits. The panel also discussed existing evidence of health-promoting effects of postbiotics, potential mechanisms of action, levels of evidence required to meet the stated definition, safety and implications for stakeholders. The panel determined that a definition of postbiotics is useful so that scientists, clinical triallists, industry, regulators and consumers have common ground for future activity in this area. A generally accepted definition will hopefully lead to regulatory clarity and promote innovation and the development of new postbiotic products.
Collapse
Affiliation(s)
- Seppo Salminen
- grid.1374.10000 0001 2097 1371Functional Foods Forum, Faculty of Medicine, University of Turku, Turku, Finland
| | - Maria Carmen Collado
- grid.419051.80000 0001 1945 7738Institute of Agrochemistry and Food Technology-National Research Council (IATA-CSIC), Valencia, Spain
| | - Akihito Endo
- grid.410772.70000 0001 0807 3368Department of Food, Aroma and Cosmetic Chemistry, Faculty of Bioindustry, Tokyo University of Agriculture, Hokkaido, Japan
| | - Colin Hill
- grid.7872.a0000000123318773School of Microbiology, University College Cork, Cork, Ireland ,grid.7872.a0000000123318773APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Sarah Lebeer
- grid.5284.b0000 0001 0790 3681Department of Bioscience Engineering, University of Antwerp, Antwerp, Belgium
| | - Eamonn M. M. Quigley
- Division of Gastroenterology and Hepatology, Lynda K and David M Underwood Center for Digestive Disorders, Houston Methodist Hospital and Weill Cornell Medical College, Houston, TX USA
| | - Mary Ellen Sanders
- International Scientific Association for Probiotics and Prebiotics, Centennial, CO USA
| | - Raanan Shamir
- grid.414231.10000 0004 0575 3167Institute of Pediatric Gastroenterology, Nutrition and Liver Diseases, Schneider Children’s Medical Center, Petach Tikva, Israel ,grid.12136.370000 0004 1937 0546Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jonathan R. Swann
- grid.5491.90000 0004 1936 9297School of Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK ,grid.7445.20000 0001 2113 8111Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Hania Szajewska
- grid.13339.3b0000000113287408Department of Paediatrics, The Medical University of Warsaw, Warsaw, Poland
| | - Gabriel Vinderola
- grid.10798.370000 0001 2172 9456Instituto de Lactología Industrial (CONICET-UNL), Faculty of Chemical Engineering, National University of Litoral, Santa Fe, Argentina
| |
Collapse
|
35
|
Lv X, Wang L, Zhang J, Zeng H, Chen X, Shi L, Cui H, He X, Zhao L. Rapid and sensitive detection of VBNC Escherichia coli O157: H7 in beef by PMAxx and real-time LAMP. Food Control 2020. [DOI: 10.1016/j.foodcont.2020.107292] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
|
36
|
Rapid Detection of β-Lactamase-Producing Bacteria Using the Integrated Comprehensive Droplet Digital Detection (IC 3D) System. SENSORS 2020; 20:s20174667. [PMID: 32824984 PMCID: PMC7506896 DOI: 10.3390/s20174667] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 12/22/2022]
Abstract
Antibiotic-resistant bacteria have emerged as an imminent global threat. The lack of rapid and sensitive diagnostic techniques leaves health care providers with inadequate resources for guiding therapy and risks the lives of patients. The traditional plate culturing methods for identifying antibiotic-resistant bacteria is laborious and time-consuming. Bulk PCR (Polymerase Chain Reaction) and qPCR are limited by poor detection sensitivity, which is critical for the early-stage detection of bloodstream infections. In this study, we introduce a technique for detecting β-lactamase-producing bacteria at single-cell sensitivity based on a commercial β-lactamase sensor (Fluorocillin), droplet microfluidics, and a custom 3D particle counter. Bacteria-containing samples were encapsulated within picoliter-sized droplets at the single-cell level and cultured within water-in-oil droplets containing antibiotics and the Fluorocillin sensor. Then, fluorescent droplets were digitally quantified with the 3D particle counter, which is capable of analyzing milliliter-scale volumes of collected droplets within 10 min. The fluorescence signal from single-colony droplets was detectable in less than 5 h, and the 3D scanning was performed in less than 10 min, which was significantly faster than conventional culture-based methods. In this approach, the limit of detection achieved was about 10 bacterial cells per mL of sample, and the turnaround time from sample to result was less than 6 h. This study demonstrates a promising strategy for the detection of β-lactamase-producing bacteria using the recently developed IC 3D system.
Collapse
|
37
|
Peruzy MF, Proroga YTR, Capuano F, Corrado F, Santonicola S, De Medici D, Delibato E, Murru N. Detection and quantification of Campylobacter in foods: New analytic approaches to detect and quantify Campylobacter spp. in food samples. Ital J Food Saf 2020; 9:8591. [PMID: 32944567 PMCID: PMC7477723 DOI: 10.4081/ijfs.2020.8591] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/07/2020] [Indexed: 11/22/2022] Open
Abstract
The aim of the present study was to develop rapid qualitative and quantitative methods based on the use of Real-Time PCR and Droplet Digital PCR (ddPCR), in order to have reliable techniques to detect and quantify Campylobacter spp. in food samples. The gene 16S-rRNA was used as specific target for Campylobacter spp. Real- Time PCR evaluation assay and a not competitive internal control was ushered in it. To investigate the selectivity of the method, 26 Campylobacter strains and 40 non-Campylobacter strains were tested and in order to verify the application of Real- Time PCR method, 5 pork meat samples were experimentally inoculated with a Campylobacter jejuni strain. Subsequently, dilutions with a bacterial load of Campylobacter jejuni within 10-106 CFU/mL were chosen for the optimization of the ddPCR assay. Lastly, a total of 54 naturally contaminated foods samples were analyzed through molecular (Real-Time PCR and ddPCR) and traditional methods. The Real-Time PCR protocol demonstrated to amplify only the Campylobacter spp. strains and when Campylobacter jejuni was experimentally inoculated in meat samples the pathogen was always detected. The ddPCRs assay allowed to quantify a level of contamination of 10 CFU/mL, but it was unable to quantify levels of 105 - 106 CFU/mL. Lastly, Campylobacter spp. was never detected in the 54 samples tested. In conclusion, the novel analytic approach proposed, based on an initial screening of the samples with Real-Time PCR and then on quantification of Campylobacter spp. with a ddPCR on those positive, represents a quick monitoring tool and, if used correctly, it would allow the implementation of food safety.
Collapse
Affiliation(s)
- Maria Francesca Peruzy
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Napoli
| | | | - Federico Capuano
- Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici
| | - Federica Corrado
- Department of Food Microbiology, Istituto Zooprofilattico Sperimentale del Mezzogiorno, Portici
| | - Serena Santonicola
- Department of Medicine and Health Science Vincenzo Tiberio, University of Molise, Campobasso
| | - Dario De Medici
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Elisabetta Delibato
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, Rome, Italy
| | - Nicoletta Murru
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, Napoli
| |
Collapse
|
38
|
Galazzo G, van Best N, Benedikter BJ, Janssen K, Bervoets L, Driessen C, Oomen M, Lucchesi M, van Eijck PH, Becker HEF, Hornef MW, Savelkoul PH, Stassen FRM, Wolffs PF, Penders J. How to Count Our Microbes? The Effect of Different Quantitative Microbiome Profiling Approaches. Front Cell Infect Microbiol 2020; 10:403. [PMID: 32850498 PMCID: PMC7426659 DOI: 10.3389/fcimb.2020.00403] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/30/2020] [Indexed: 12/13/2022] Open
Abstract
Next-generation sequencing (NGS) has instigated the research on the role of the microbiome in health and disease. The compositional nature of such microbiome datasets makes it however challenging to identify those microbial taxa that are truly associated with an intervention or health outcome. Quantitative microbiome profiling overcomes the compositional structure of microbiome sequencing data by integrating absolute quantification of microbial abundances into the NGS data. Both cell-based methods (e.g., flow cytometry) and molecular methods (qPCR) have been used to determine the absolute microbial abundances, but to what extent different quantification methods generate similar quantitative microbiome profiles has so far not been explored. Here we compared relative microbiome profiling (without incorporation of microbial quantification) to three variations of quantitative microbiome profiling: (1) microbial cell counting using flow cytometry (QMP), (2) counting of microbial cells using flow cytometry combined with Propidium Monoazide pre-treatment of fecal samples before metagenomics DNA isolation in order to only profile the microbial composition of intact cells (QMP-PMA), and (3) molecular based quantification of the microbial load using qPCR targeting the 16S rRNA gene. Although qPCR and flow cytometry both resulted in accurate and strongly correlated results when quantifying the bacterial abundance of a mock community of bacterial cells, the two methods resulted in highly divergent quantitative microbial profiles when analyzing the microbial composition of fecal samples from 16 healthy volunteers. These differences could not be attributed to the presence of free extracellular prokaryotic DNA in the fecal samples as sample pre-treatment with Propidium Monoazide did not improve the concordance between qPCR-based and flow cytometry-based QMP. Also lack of precision of qPCR was ruled out as a major cause of the disconcordant findings, since quantification of the fecal microbial load by the highly sensitive digital droplet PCR correlated strongly with qPCR. In conclusion, quantitative microbiome profiling is an elegant approach to bypass the compositional nature of microbiome NGS data, however it is important to realize that technical sources of variability may introduce substantial additional bias depending on the quantification method being used.
Collapse
Affiliation(s)
- Gianluca Galazzo
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, Netherlands.,Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center+, Maastricht, Netherlands
| | - Niels van Best
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, Netherlands.,Institute of Medical Microbiology, RWTH University Hospital Aachen, Aachen, Germany
| | - Birke J Benedikter
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, Netherlands.,Member of the German Center for Lung Research (DZL), Universities of Giessen and Marburg Lung Centre, Institute for Lung Research, Philipps-University Marburg, Marburg, Germany.,Department of Respiratory Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, Netherlands
| | - Kevin Janssen
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center+, Maastricht, Netherlands
| | - Liene Bervoets
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, Netherlands
| | - Christel Driessen
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, Netherlands.,Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center+, Maastricht, Netherlands
| | - Melissa Oomen
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, Netherlands
| | - Mayk Lucchesi
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center+, Maastricht, Netherlands
| | - Pascalle H van Eijck
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, Netherlands
| | - Heike E F Becker
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, Netherlands.,Division of Gastroenterology-Hepatology, Department of Internal Medicine, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, Netherlands
| | - Mathias W Hornef
- Institute of Medical Microbiology, RWTH University Hospital Aachen, Aachen, Germany
| | - Paul H Savelkoul
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, Netherlands.,Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center+, Maastricht, Netherlands.,Department of Medical Microbiology and Infection Control, VU University Medical Center, Amsterdam, Netherlands
| | - Frank R M Stassen
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, Netherlands
| | - Petra F Wolffs
- Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center+, Maastricht, Netherlands
| | - John Penders
- Department of Medical Microbiology, School of Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University Medical Center+, Maastricht, Netherlands.,Department of Medical Microbiology, Care and Public Health Research Institute (CAPHRI), Maastricht University Medical Center+, Maastricht, Netherlands
| |
Collapse
|
39
|
Caillaud MA, Abeilhou M, Gonzalez I, Audonnet M, Gaucheron F, Cocaign-Bousquet M, Tormo H, Daveran-Mingot ML. Precise Populations’ Description in Dairy Ecosystems Using Digital Droplet PCR: The Case of L. lactis Group in Starters. Front Microbiol 2020; 11:1906. [PMID: 32849476 PMCID: PMC7423877 DOI: 10.3389/fmicb.2020.01906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/21/2020] [Indexed: 01/15/2023] Open
Affiliation(s)
- Marie-Aurore Caillaud
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- Université de Toulouse, Ecole d’Ingénieurs de Purpan, INPT, Toulouse, France
| | - Martine Abeilhou
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | - Ignacio Gonzalez
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
| | | | - Frédéric Gaucheron
- Centre National Interprofessionnel de l’Economie Laitière (CNIEL), Paris, France
| | - Muriel Cocaign-Bousquet
- TBI, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France
- *Correspondence: Muriel Cocaign-Bousquet,
| | - Hélène Tormo
- Université de Toulouse, Ecole d’Ingénieurs de Purpan, INPT, Toulouse, France
| | | |
Collapse
|
40
|
Lei S, Gu X, Zhong Q, Duan L, Zhou A. Absolute quantification of Vibrio parahaemolyticus by multiplex droplet digital PCR for simultaneous detection of tlh, tdh and ureR based on single intact cell. Food Control 2020. [DOI: 10.1016/j.foodcont.2020.107207] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
41
|
Exclusive use of digital PCR allows an absolute assay of heat-killed Lactobacilli in foods targeting multiple copies of 16S rDNA. Sci Rep 2020; 10:12691. [PMID: 32728064 PMCID: PMC7391674 DOI: 10.1038/s41598-020-69206-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 07/09/2020] [Indexed: 11/15/2022] Open
Abstract
The real-time PCR (qPCR) and digital PCR (dPCR) to amplify a single-copy of house-keeping genes (i.e., hsp60, pheS or tuf) are used for the assay of limited microbial species. In general, with a single-copy gene, there are obviously varied DNA sequences for even the same microbial species, which could cause difficulties with design of primers and probes for PCR when targeting various single copy genes. In general, for identification by dPCR (as a representative case: Lactobacillus paracasei), accumulated DNA sequence information of 16S rDNA, which is much more frequently used, should be targeted. In contrast, next-generation sequencing revealed that there are five copies of 16S rDNA in a live L. paracasei MCC1849. Therefore, we aimed to reveal, if heat-killed L. paracasei supplemented in nutritional foods that aid the host immune system have the relevant five copies per chromosomal DNA, and if the relevant copies remain unchanged on the same chromosomal DNA or remain to be different chromosomal DNA fragments. So, we revealed the actual distribution of the potential original five copies of 16S rDNA using our innovative dPCR, in which both 16S rDNA and hsp60 genes were simultaneously elongated. The molecular ratios of 16S rDNA/hsp60 dispersed in the dPCR chip were then estimated. The 16S rDNA/hsp60 molecular ratios of the heat-killed L. paracasei in foods, resultantly ranged from 5.0 to 7.2, being the same or higher than that of the five copies determined by next-generation sequencing. The 16S rDNA copy number/ratio indicated the chromosomal DNA molecular number and the associated cell number. As significance, different nutritional foods could potentially cause the loss of chromosomal DNA of supplemented beneficial microbes to a much greater degree. Our absolute dPCR does not require standard correlative samples for the estimation of final products. The estimation principle of the ratio of 16S rDNA/a house-keeping single-copy gene by our absolute dPCR could lead to a useful and accurate assay for various nutritional foods.
Collapse
|
42
|
Kiefer A, Tang P, Arndt S, Fallico V, Wong C. Optimization of Viability Treatment Essential for Accurate Droplet Digital PCR Enumeration of Probiotics. Front Microbiol 2020; 11:1811. [PMID: 32849418 PMCID: PMC7399075 DOI: 10.3389/fmicb.2020.01811] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 07/10/2020] [Indexed: 11/13/2022] Open
Abstract
Improvements offered by viability droplet digital PCR (v-ddPCR) include increased precision, specificity and decreased time to results making for an attractive alternative method to traditional plate count enumeration of probiotic products. A major hurdle faced in v-ddPCR, however, is distinguishing between live and dead cells. The objective of this study was to evaluate a combination of PMA and EMA (PE51) for viability treatment of freeze-dried probiotic powders. Lactobacillus acidophilus La-14 and Bifidobacterium animalis subsp. lactis Bi-07 were analyzed over a 2-log PE51 concentration gradient to investigate the efficiency across genus and assay targets. Results suggest a need to optimize viability dye concentration based on the genera of the organism, but also the assay target, even when analyzing the same organism. When optimized for PE51 concentration, strain specific v-ddPCR assays for both La-14 and Bi-07 were demonstrated to agree with plate count enumeration results. In conclusion, while these v-ddPCR assays require highly specific optimization, they are better suited for the future of the probiotic industry and are suggested to be implemented in probiotic product testing.
Collapse
Affiliation(s)
- Anthony Kiefer
- DuPont Nutrition & Biosciences, Madison, WI, United States
| | - Peipei Tang
- DuPont Nutrition & Biosciences, Madison, WI, United States
| | - Samuel Arndt
- DuPont Nutrition & Biosciences, Madison, WI, United States
| | | | - Connie Wong
- DuPont Nutrition & Biosciences, Madison, WI, United States
| |
Collapse
|
43
|
Kabir E, Azzouz A, Raza N, Bhardwaj SK, Kim KH, Tabatabaei M, Kukkar D. Recent Advances in Monitoring, Sampling, and Sensing Techniques for Bioaerosols in the Atmosphere. ACS Sens 2020; 5:1254-1267. [PMID: 32227840 DOI: 10.1021/acssensors.9b02585] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Bioaerosols in the form of microscopic airborne particles pose pervasive risks to humans and livestock. As either fully active components (e.g., viruses, bacteria, and fungi) or as whole or part of inactive fragments, they are among the least investigated pollutants in nature. Their identification and quantification are essential to addressing related dangers and to establishing proper exposure thresholds. However, difficulties in the development (and selection) of detection techniques and an associated lack of standardized procedures make the sensing of bioaerosols challenging. Through a comprehensive literature search, this review examines the mechanisms of conventional and advanced bioaerosol detection methods. It also provides a roadmap for future research and development in the selection of suitable methodologies for bioaerosol detection. The development of sample collection and sensing technology make it possible for continuous and automated operation. However, intensive efforts should be put to overcome the limitations of current technology as most of the currently available options tend to suffer from lengthy sample acquisition times and/or nonspecificity of probe material.
Collapse
Affiliation(s)
- Ehsanul Kabir
- Department of Farm Power and Machinery, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Abdelmonaim Azzouz
- Department of Chemistry, Faculty of Science, University of Abdelmalek Essaadi, B.P. 2121, M’Hannech II, 93002 Tétouan, Morocco
| | - Nadeem Raza
- Government Emerson College, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Sanjeev Kumar Bhardwaj
- Center of Innovative and Applied Bioprocessing, (CIAB) [DBT, Govt. of India], Knowledge
City, Sector 81, Mohali, Punjab 140306, India
| | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul 04763, Korea
| | - Meisam Tabatabaei
- Microbial Biotechnology Department, Agricultural Biotechnology Institute of Iran, Agricultural Research, Education, and Extension Organization (AREEO), 31535-1897 Karaj, Iran
| | - Deepak Kukkar
- Department of Civil and Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul 04763, Korea
| |
Collapse
|
44
|
Yang J, Zhang N, Lv J, Zhu P, Pan X, Hu J, Wu W, Li S, Li H. Comparing the performance of conventional PCR, RTQ-PCR, and droplet digital PCR assays in detection of Shigella. Mol Cell Probes 2020; 51:101531. [PMID: 32062018 DOI: 10.1016/j.mcp.2020.101531] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/19/2020] [Accepted: 02/06/2020] [Indexed: 12/15/2022]
Abstract
The incidence of foodborne infections caused by Shigella spp. is still very high in every year, which poses a great potential threat to public health. Conventional quantification methods based on culture techniques, biochemical, and serological identification are time-consuming and labor-intensive. To develop a more rapid and efficient detection method of Shigella spp., we compared the sensitivity and specificity of three different polymerase chain reaction (PCR) methods, including conventional PCR, quantitative real-time PCR (RTQ-PCR), and droplet digital PCR (ddPCR). Our results indicated that ddPCR method exhibited higher sensitivity, and the limit of detection was 10-5 ng/μl for genomic DNA templates, 10-1 cfu/ml for Shigella bacteria culture. In addition, we found that ddPCR was a time-saving method, which required a shorter pre-culturing time. Collectively, ddPCR assay was a reliable method for rapid and effective detection of Shigella spp.
Collapse
Affiliation(s)
- Jin Yang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, 400715, Chongqing, China.
| | - Nana Zhang
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, 400715, Chongqing, China.
| | - Jun Lv
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China.
| | - Ping Zhu
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China.
| | - Xing Pan
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China.
| | - Jiaqingzi Hu
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China.
| | - Wenfeng Wu
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, 400715, Chongqing, China.
| | - Shan Li
- Institute of Infection and Immunity, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, 442000, China.
| | - Hongtao Li
- Key Laboratory of Freshwater Fish Reproduction and Development, Ministry of Education, State Key Laboratory Breeding Base of Eco-Environment and Bio-Resource, Key Laboratory of Eco-environments in Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Beibei, 400715, Chongqing, China.
| |
Collapse
|
45
|
Baymiev AK, Baymiev AK, Kuluev BR, Shvets KY, Yamidanov RS, Matniyazov RT, Chemeris DA, Zubov VV, Alekseev YI, Mavzyutov AR, Ivanenkov YA, Chemeris AV. Modern Approaches to Differentiation of Live and Dead Bacteria Using Selective Amplification of Nucleic Acids. Microbiology (Reading) 2020. [DOI: 10.1134/s0026261720010038] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
|
46
|
Dong K, Pan H, Yang D, Rao L, Zhao L, Wang Y, Liao X. Induction, detection, formation, and resuscitation of viable but non‐culturable state microorganisms. Compr Rev Food Sci Food Saf 2019; 19:149-183. [DOI: 10.1111/1541-4337.12513] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 10/21/2019] [Accepted: 11/14/2019] [Indexed: 01/05/2023]
Affiliation(s)
- Kai Dong
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthCollege of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- College of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- Key Lab of Fruit and Vegetable ProcessingMinistry of Agriculture and Rural Affairs Beijing China
| | - Hanxu Pan
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthCollege of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- College of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- Key Lab of Fruit and Vegetable ProcessingMinistry of Agriculture and Rural Affairs Beijing China
| | - Dong Yang
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthCollege of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- College of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- Key Lab of Fruit and Vegetable ProcessingMinistry of Agriculture and Rural Affairs Beijing China
| | - Lei Rao
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthCollege of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- College of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- Key Lab of Fruit and Vegetable ProcessingMinistry of Agriculture and Rural Affairs Beijing China
| | - Liang Zhao
- College of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- Key Lab of Fruit and Vegetable ProcessingMinistry of Agriculture and Rural Affairs Beijing China
| | - Yongtao Wang
- College of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- Key Lab of Fruit and Vegetable ProcessingMinistry of Agriculture and Rural Affairs Beijing China
| | - Xiaojun Liao
- Beijing Advanced Innovation Center for Food Nutrition and Human HealthCollege of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- College of Food Science and Nutritional EngineeringChina Agricultural University Beijing China
- Key Lab of Fruit and Vegetable ProcessingMinistry of Agriculture and Rural Affairs Beijing China
| |
Collapse
|
47
|
Chen H, Shi M, Gilam A, Zheng Q, Zhang Y, Afrikanova I, Li J, Gluzman Z, Jiang R, Kong LJ, Chen-Tsai RY. Hemophilia A ameliorated in mice by CRISPR-based in vivo genome editing of human Factor VIII. Sci Rep 2019; 9:16838. [PMID: 31727959 PMCID: PMC6856096 DOI: 10.1038/s41598-019-53198-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 10/29/2019] [Indexed: 01/08/2023] Open
Abstract
Hemophilia A is a monogenic disease with a blood clotting factor VIII (FVIII) deficiency caused by mutation in the factor VIII (F8) gene. Current and emerging treatments such as FVIII protein injection and gene therapies via AAV-delivered F8 transgene in an episome are costly and nonpermanent. Here, we describe a CRISPR/Cas9-based in vivo genome editing method, combined with non-homologous end joining, enabling permanent chromosomal integration of a modified human B domain deleted-F8 (BDD-F8) at the albumin (Alb) locus in liver cells. To test the approach in mice, C57BL/6 mice received tail vein injections of two vectors, AAV8-SaCas9-gRNA, targeting Alb intron 13, and AAV8-BDD-F8. This resulted in BDD-F8 insertion at the Alb locus and FVIII protein expression in the liver of vector-, but not vehicle-, treated mice. Using this approach in hemophilic mice, BDD-F8 was expressed in liver cells as functional human FVIII, leading to increased plasma levels of FVIII and restoration of blood clotting properties in a dose-dependent manor for at least 7 months, with no detectable liver toxicity or meaningful off-target effects. Based on these findings, our BDD-F8 genome editing approach may offer an efficacious, long-term and safe treatment for patients with hemophilia A.
Collapse
Affiliation(s)
- Hainan Chen
- Applied Stemcell, Inc., 521 Cottonwood Drive, Milpitas, CA, 95035, USA
| | - Mi Shi
- Applied Stemcell, Inc., 521 Cottonwood Drive, Milpitas, CA, 95035, USA
| | - Avital Gilam
- Applied Stemcell, Inc., 521 Cottonwood Drive, Milpitas, CA, 95035, USA
| | - Qi Zheng
- Applied Stemcell, Inc., 521 Cottonwood Drive, Milpitas, CA, 95035, USA
| | - Yin Zhang
- Applied Stemcell, Inc., 521 Cottonwood Drive, Milpitas, CA, 95035, USA
| | - Ivka Afrikanova
- Applied Stemcell, Inc., 521 Cottonwood Drive, Milpitas, CA, 95035, USA
| | - Jinling Li
- Applied Stemcell, Inc., 521 Cottonwood Drive, Milpitas, CA, 95035, USA
| | - Zoya Gluzman
- Applied Stemcell, Inc., 521 Cottonwood Drive, Milpitas, CA, 95035, USA
| | - Ruhong Jiang
- Applied Stemcell, Inc., 521 Cottonwood Drive, Milpitas, CA, 95035, USA
| | - Ling-Jie Kong
- Applied Stemcell, Inc., 521 Cottonwood Drive, Milpitas, CA, 95035, USA.
| | | |
Collapse
|
48
|
Zhang Z, Zhang Y, Lin X, Chen Z, Wu S. Development of a novel reverse transcription droplet digital PCR assay for the sensitive detection of Senecavirus A. Transbound Emerg Dis 2018; 66:517-525. [PMID: 30375741 DOI: 10.1111/tbed.13056] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/08/2018] [Accepted: 10/24/2018] [Indexed: 12/27/2022]
Abstract
In pigs, Senecavirus A (SVA) causes a vesicular disease that is clinically indistinguishable from foot-and-mouth disease, vesicular stomatitis and swine vesicular disease. Sensitive and specific detection of SVA is critical for controlling this emerging disease. In this study, a novel reverse transcription droplet digital PCR (RT-ddPCR) assay, targeting the conserved viral polymerase 3D gene, was established for the detection of SVA. This assay exhibited good linearity, repeatability and reproducibility, and maintained linearity at extremely low concentrations of SVA nucleic acid templates. The detection limit of RT-ddPCR was 1.53 ± 0.22 copies of SVA RNA per reaction (n = 8), and the assay showed approximately 10-fold greater sensitivity than a reverse transcription real-time PCR (RT-rPCR) assay. Moreover, specificity analysis showed that the RT-ddPCR for SVA had no cross-reactivity with other important swine pathogens. In clinical diagnosis of 134 pig serum and tissue samples, 26 and 21 samples were identified as positive by RT-ddPCR and RT-rPCR, respectively. The overall agreement between the two assays was 96.27% (129/134). Further linear regression analysis showed a significant correlation between the RT-ddPCR and RT-rPCR assays with an R2 value of 0.9761. Our results indicate that the RT-ddPCR assay is a robust diagnostic tool for the sensitive detection of SVA, even in samples with a low viral load.
Collapse
Affiliation(s)
- Zhou Zhang
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Yongning Zhang
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Xiangmei Lin
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Zhenhai Chen
- College of Veterinary Medicine, Yangzhou University, Jiangsu, China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Jiangsu, China
| | - Shaoqiang Wu
- Institute of Animal Quarantine, Chinese Academy of Inspection and Quarantine, Beijing, China
| |
Collapse
|