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Velez FJ, Kandula N, Blech-Hermoni Y, Jackson CR, Bosilevac JM, Singh P. Digital PCR assay for the specific detection and estimation of Salmonella contamination levels in poultry rinse. Curr Res Food Sci 2024; 9:100807. [PMID: 39076681 PMCID: PMC11284941 DOI: 10.1016/j.crfs.2024.100807] [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: 04/30/2024] [Revised: 07/06/2024] [Accepted: 07/08/2024] [Indexed: 07/31/2024] Open
Abstract
Strains of Salmonella are a frequent cause of foodborne illness and are known to contaminate poultry products. Most Salmonella testing methods can qualitatively detect Salmonella and cannot quantify or estimate the Salmonella load in samples. Therefore, the aim of this study was to standardize and validate a partitioned-based digital PCR (dPCR) assay for the detection and estimation of Salmonella contamination levels in poultry rinses. Pure culture Salmonella strains were cultured, enumerated, cold-stressed for 48 h, and used to inoculate whole carcass chicken rinse (WCCR) at 1-4 log CFU/30 mL and enriched at 37 °C for 5 h. Undiluted DNA samples with primer and probes targeting the Salmonella-specific invA gene were used for the dPCR assay. The dPCR assay was highly specific, with a limit of detection of 0.001 ng/μL and a limit of quantification of 0.01 ng/μL. The dPCR assay further showed no PCR reaction inhibition up to 5 μg of crude DNA extract. The assays accurately detected all cold-stressed Salmonella in inoculated WCCR samples following a 5-h enrichment. Most importantly, when converted to log, the dPCR copies/μL values accurately estimated the inoculated Salmonella levels. The dPCR assay standardized in this study is a robust method for the detection and estimation of Salmonella concentration in contaminated food samples. This approach can allow same-day decision-making for poultry processors attempting to maintain limits and controls on Salmonella contamination.
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Affiliation(s)
- Frank J. Velez
- Department of Health, Nutrition and Food Sciences, Florida State University, Tallahassee, FL, 32306, USA
| | - Nethraja Kandula
- Department of Health, Nutrition and Food Sciences, Florida State University, Tallahassee, FL, 32306, USA
| | | | - Charlene R. Jackson
- U.S. National Poultry Research Center, U.S. Department of Agriculture-Agricultural Research Service, 950 College Station Road, Athens, GA, 30605-2720, USA
| | - Joseph M. Bosilevac
- U.S. Department of Agriculture, Agricultural Research Service, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE, USA
| | - Prashant Singh
- Department of Health, Nutrition and Food Sciences, Florida State University, Tallahassee, FL, 32306, USA
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2
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Majumdar R, Taye B, Bjornberg C, Giljork M, Lynch D, Farah F, Abdullah I, Osiecki K, Yousaf I, Luckstein A, Turri W, Sampathkumar P, Moyer AM, Kipp BR, Cattaneo R, Sussman CR, Navaratnarajah CK. From pandemic to endemic: Divergence of COVID-19 positive-tests and hospitalization numbers from SARS-CoV-2 RNA levels in wastewater of Rochester, Minnesota. Heliyon 2024; 10:e27974. [PMID: 38515669 PMCID: PMC10955309 DOI: 10.1016/j.heliyon.2024.e27974] [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: 08/11/2023] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
Traditionally, public health surveillance relied on individual-level data but recently wastewater-based epidemiology (WBE) for the detection of infectious diseases including COVID-19 became a valuable tool in the public health arsenal. Here, we use WBE to follow the course of the COVID-19 pandemic in Rochester, Minnesota (population 121,395 at the 2020 census), from February 2021 to December 2022. We monitored the impact of SARS-CoV-2 infections on public health by comparing three sets of data: quantitative measurements of viral RNA in wastewater as an unbiased reporter of virus level in the community, positive results of viral RNA or antigen tests from nasal swabs reflecting community reporting, and hospitalization data. From February 2021 to August 2022 viral RNA levels in wastewater were closely correlated with the oscillating course of COVID-19 case and hospitalization numbers. However, from September 2022 cases remained low and hospitalization numbers dropped, whereas viral RNA levels in wastewater continued to oscillate. The low reported cases may reflect virulence reduction combined with abated inclination to report, and the divergence of virus levels in wastewater from reported cases may reflect COVID-19 shifting from pandemic to endemic. WBE, which also detects asymptomatic infections, can provide an early warning of impending cases, and offers crucial insights during pandemic waves and in the transition to the endemic phase.
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Affiliation(s)
| | - Biruhalem Taye
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | | | | | | | | | | | - Iris Yousaf
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | | | - Priya Sampathkumar
- Division of Infectious Diseases, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ann M. Moyer
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Benjamin R. Kipp
- Advanced Diagnostics Laboratory, Mayo Clinic, Rochester, MN, USA
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Roberto Cattaneo
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Caroline R. Sussman
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
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3
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Russo S, Cortimiglia C, Filippi A, Palladini G, Garbarino C, Massella E, Ricchi M. Validation of digital PCR assay for the quantification of Mycobacterium avium subsp. paratuberculosis in bovine faeces according to the ISO 20395:2019. J Microbiol Methods 2023; 213:106825. [PMID: 37739126 DOI: 10.1016/j.mimet.2023.106825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/18/2023] [Accepted: 09/19/2023] [Indexed: 09/24/2023]
Abstract
Paratuberculosis is an enteric disease caused by Mycobacterium avium subs. Paratuberculosis (MAP). Quantifying the load of MAP in faeces samples offers the advantage of determining the stage of infection and planning control measures. Currently, detection of MAP in faecal specimens relies on cultural assays and quantitative PCR (qPCR), but both methods have limitations such as prolonged isolation times for cultural assay and the absence of nucleic acid standards for qPCR. Digital PCR (dPCR) represents an advancement over qPCR as it allows direct quantification of nucleic acid in a sample without the need for a standard curve. The present paper reports about the validation process, following ISO 20395:2019 guidelines, of a F57 digital PCR assay for quantifying MAP cells in faecal samples. Based on our validation, the Limit Of Detection (LOD) corresponds to 7.85 104 MAP cells/g, and the Limit Of Quantification (LOQ) to 7.85 105 MAP cells, with an efficiency of recovery at LOQ estimated about 4.5%. To assess precision, we evaluated the same faecal sample extracted by two different operators at different times. The standard deviation under repeatability conditions (S Repeatability) and intersession variability conditions (S Intermediate) were calculated, resulting in values of 0.43 and 0.26, respectively. Trueness was determined at LOQ and a value ten times higher, yielding percentages of 3.35% and 5.16%, respectively. Linearity showed a R2 value of 0.998, indicating strong linear correlation. Measurement uncertainty was 26% in absolute value and 3% on a logarithmic base 10 scale. Overall, the assay exhibits good specificity and robustness. Our validation underlines the good performance of the quantification method and allow the laboratory to provide quantitative results of MAP/cells on faecal samples.
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Affiliation(s)
- Simone Russo
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Piacenza, Italy..
| | - Claudia Cortimiglia
- Dipartimento di Scienze e Tecnologie Alimentari per una Filiera Agro-Alimentare Sostenibile (DISTAS), Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Anita Filippi
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Piacenza, Italy
| | - Giorgia Palladini
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Piacenza, Italy..
| | - Chiara Garbarino
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Piacenza, Italy..
| | - Elisa Massella
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Piacenza, Italy..
| | - Matteo Ricchi
- National Reference Centre and WOAH Reference Laboratory for Paratuberculosis, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "Bruno Ubertini", Piacenza, Italy..
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4
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Rodgers BD, Herring SK, Carias DR, Chen J, Rocha AG. Development and validation of a model gene therapy biodistribution assay for AVGN7 using digital droplet polymerase chain reaction. Mol Ther Methods Clin Dev 2023; 29:494-503. [PMID: 37273901 PMCID: PMC10236005 DOI: 10.1016/j.omtm.2023.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 05/08/2023] [Indexed: 06/06/2023]
Abstract
Biodistribution assays are integral to gene therapy commercialization and have traditionally used real-time qPCR. Droplet digital PCR (ddPCR), however, has distinct advantages including higher sensitivity and absolute quantification but is underused because of lacking regulatory guidance and meaningful examples in the literature. We report a fit-for-purpose model process to validate a good laboratory practice (GLP)-compliant ddPCR assay for AVGN7, a Smad7 gene therapeutic for muscle wasting. Duplexed primer/probe sets for Smad7 and mouse TATA-box binding protein were optimized using gBlock DNA over a dynamic range of 10-80,000 copies/reaction in 250 ng mouse gDNA. Linearized plasmid and mouse gDNA were used for validation, which determined precision, accuracy, ruggedness/robustness, selectivity, recovery, specificity, dilution linearity, and stability. Inter-run precision and accuracy met previously established criteria with bias between -5% and 15%, coefficient of variation (CV) less than 19%, and total error within 8%-35%. The limit of detection was 2.5 copies/reaction, linearity was confirmed at 40-80,000 copies/reaction, specificity was demonstrated by single droplet populations and assay stability was demonstrated for benchtop, refrigerated storage, and repeated freeze-thaw cycles. The procedural road map provided exceeds recently established standards. It is also relevant to many IND-enabling processes, as validated ddPCR assays can be used in biodistribution studies and with vector titering and manufacturing quality control.
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Affiliation(s)
| | | | - Dereck R Carias
- Smithers Pharmaceutical Development Services, Ewing, NJ 08628, USA
| | - Joyce Chen
- Smithers Pharmaceutical Development Services, Ewing, NJ 08628, USA
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5
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Chen L, Zhang C, Yadav V, Wong A, Senapati S, Chang HC. A home-made pipette droplet microfluidics rapid prototyping and training kit for digital PCR, microorganism/cell encapsulation and controlled microgel synthesis. Sci Rep 2023; 13:184. [PMID: 36604528 PMCID: PMC9813469 DOI: 10.1038/s41598-023-27470-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 01/02/2023] [Indexed: 01/06/2023] Open
Abstract
Droplet microfluidics offers a platform from which new digital molecular assay, disease screening, wound healing and material synthesis technologies have been proposed. However, the current commercial droplet generation, assembly and imaging technologies are too expensive and rigid to permit rapid and broad-range tuning of droplet features/cargoes. This rapid prototyping bottleneck has limited further expansion of its application. Herein, an inexpensive home-made pipette droplet microfluidics kit is introduced. This kit includes elliptical pipette tips that can be fabricated with a simple DIY (Do-It-Yourself) tool, a unique tape-based or 3D printed shallow-center imaging chip that allows rapid monolayer droplet assembly/immobilization and imaging with a smart-phone camera or miniature microscope. The droplets are generated by manual or automatic pipetting without expensive and lab-bound microfluidic pumps. The droplet size and fluid viscosity/surface tension can be varied significantly because of our particular droplet generation, assembly and imaging designs. The versatility of this rapid prototyping kit is demonstrated with three representative applications that can benefit from a droplet microfluidic platform: (1) Droplets as microreactors for PCR reaction with reverse transcription to detect and quantify target RNAs. (2) Droplets as microcompartments for spirulina culturing and the optical color/turbidity changes in droplets with spirulina confirm successful photosynthetic culturing. (3) Droplets as templates/molds for controlled synthesis of gold-capped polyacrylamide/gold composite Janus microgels. The easily fabricated and user-friendly portable kit is hence ideally suited for design, training and educational labs.
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Affiliation(s)
- Liao Chen
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Chenguang Zhang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Vivek Yadav
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Angela Wong
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Satyajyoti Senapati
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA
| | - Hsueh-Chia Chang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN, 46556, USA.
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6
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Lei MK, Gibbons FX, Gerrard M, Beach SRH, Dawes K, Philibert R. Digital methylation assessments of alcohol and cigarette consumption account for common variance in accelerated epigenetic ageing. Epigenetics 2022; 17:1991-2005. [PMID: 35866695 PMCID: PMC9665121 DOI: 10.1080/15592294.2022.2100684] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Smoking and Heavy Alcohol Consumption (HAC) are established risk factors for myriad complex disorders of ageing. Yet many prior studies of Epigenetic Ageing (EA) have shown only modest effects of smoking and drinking on accelerated ageing. One potential reason for this conundrum might be the reliance of some prior EA studies on self-reported substance use, which may be unreliable in many samples. To test whether novel, non-self-reported indices would show a stronger association of smoking and HAC to EA, we used methylation sensitive digital PCR (MSdPCR) and data from 437 African American subjects from Wave 7 of the Family and Community Health Study Offspring Cohort to examine the effects of subjective and objective measures of smoking and HAC on 7 indices of EA. Because of limited overall correlations between the various EA indices, we examined patterns of association separately for each index. Consistent with expectations, MSdPCR assessments of smoking and HAC, but not self-reported alcohol consumption, were strongly correlated with accelerated EA. MSdPCR assessments of smoking and HAC accounted for 57% of GrimAge acceleration and the shared variance in GrimAge and DunedinPOAM accelerated EA. We conclude that MSdPCR assessments of smoking and HAC are valuable tools for understanding EA, represent directly targetable conditions for the prevention of premature ageing, and substantially improve upon self-reported assessment of smoking and HAC.
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Affiliation(s)
- Man-Kit Lei
- Department of Sociology, University of Georgia, Athens, GA, USA.,Center for Family Research, University of Georgia, Athens, GA, USA
| | - Frederick X Gibbons
- Department of Psychological Sciences, University of Connecticut, Storrs, CT, USA
| | - Meg Gerrard
- Department of Psychological Sciences, University of Connecticut, Storrs, CT, USA
| | - Steven R H Beach
- Center for Family Research, University of Georgia, Athens, GA, USA.,Department of Psychology, University of Georgia, Athens, GA, USA
| | - Kelsey Dawes
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Robert Philibert
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA.,Behavioral Diagnostics LLC, Coralville, IA, USA
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7
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Majumdar R, Vrana JA, Koepplin JW, Milosevic D, Roden AC, Garcia JJ, Kipp BR, Moyer AM. SARS-CoV-2 RNA detection in Formalin-Fixed Paraffin-Embedded (FFPE) tissue by droplet digital PCR (ddPCR). Clin Chim Acta 2022; 532:181-187. [PMID: 35550815 PMCID: PMC9085371 DOI: 10.1016/j.cca.2022.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/22/2022] [Accepted: 05/05/2022] [Indexed: 02/08/2023]
Abstract
BACKGROUND SARS-CoV-2 is an RNA virus that primarily causes respiratory disease; however, infection of other tissue has been reported. Evaluation of SARS-CoV-2 in tissue specimens may increase understanding of SARS-CoV-2 pathobiology. MATERIALS AND METHODS A qualitative test for detection of SARS-CoV-2 in formalin-fixed paraffin-embedded (FFPE) tissues was developed and validated using droplet digital PCR (ddPCR), which has a lower limit of detection than reverse transcription (RT)-qPCR. After extraction of total RNA from unstained FFPE tissue, SARS-CoV-2 nucleocapsid (N1, N2) target sequences were amplified and quantified, along with human RPP30 as a control using the Bio-Rad SARS-CoV-2 ddPCR kit. RESULTS SARS-CoV-2 was detected in all 21 known positive samples and none of the 16 negative samples. As few as approximately 5 viral copies were reliably detected. Since January 2021, many tissue types have been clinically tested. Of the 195 clinical specimens, the positivity rate was 35% with placenta and fetal tissue showing the highest percentage of positive cases. CONCLUSION This sensitive FFPE-based assay has broad clinical utility with applications as diverse as pregnancy loss and evaluation of liver transplant rejection. This assay will aid in understanding atypical presentations of COVID-19 as well as long-term sequelae.
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Affiliation(s)
- Ramanath Majumdar
- Advanced Diagnostics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, United States
| | - Julie A. Vrana
- Division of Anatomic Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, United States
| | - Justin W. Koepplin
- Division of Anatomic Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, United States
| | - Dragana Milosevic
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55902, United States
| | - Anja C. Roden
- Division of Anatomic Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, United States
| | - Joaquin J. Garcia
- Division of Anatomic Pathology, Department of Laboratory Medicine and Pathology, Mayo Clinic, United States
| | - Benjamin R. Kipp
- Advanced Diagnostics Laboratory, Department of Laboratory Medicine and Pathology, Mayo Clinic, United States,Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55902, United States
| | - Ann M. Moyer
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First Street SW, Rochester, MN 55902, United States,Corresponding author at: Mayo Clinic, 200 First Street SW, Rochester, MN 55902, United States
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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.
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9
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Dawes K, Andersen A, Reimer R, Mills JA, Hoffman E, Long JD, Miller S, Philibert R. The relationship of smoking to cg05575921 methylation in blood and saliva DNA samples from several studies. Sci Rep 2021; 11:21627. [PMID: 34732805 PMCID: PMC8566492 DOI: 10.1038/s41598-021-01088-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 10/18/2021] [Indexed: 11/23/2022] Open
Abstract
Numerous studies have shown that cg05575921 methylation decreases in response to smoking. However, secondary to methodological issues, the magnitude and dose dependency of that response is as of yet unclear. This lack of certainty is a barrier to the use of DNA methylation clinically to assess and monitor smoking status. To better define this relationship, we conducted a joint analysis of methylation sensitive PCR digital (MSdPCR) assessments of cg05575921 methylation in whole blood and/or saliva DNA to smoking using samples from 421 smokers and 423 biochemically confirmed non-smokers from 4 previously published studies. We found that cg05575921 methylation manifested a curvilinear dose dependent decrease in response to increasing cigarette consumption. In whole blood DNA, the Receiver Operating Characteristic (ROC) Area Under the Curve (AUC) of cg05575921 methylation for predicting daily smoking status was 0.98. In saliva DNA, the gross AUC was 0.91 with correction for cellular heterogeneity improving the AUC to 0.94. Methylation status was significantly associated with the Fagerstrom Test for Nicotine Dependence score, but with significant sampling heterogeneity. We conclude that MSdPCR assessments of cg05575921 methylation are a potentially powerful, clinically implementable tool for the assessment and management of smoking.
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Affiliation(s)
- Kelsey Dawes
- Department of Psychiatry, University of Iowa, Iowa City, IA, 52242, USA
- Molecular Medicine Program, University of Iowa, Iowa City, IA, 52242, USA
| | - Allan Andersen
- Department of Psychiatry, University of Iowa, Iowa City, IA, 52242, USA
| | - Rachel Reimer
- Department of Public Health, Des Moines University, Des Moines, IA, 50312, USA
| | - James A Mills
- Department of Psychiatry, University of Iowa, Iowa City, IA, 52242, USA
| | - Eric Hoffman
- Department of Radiology, University of Iowa, Iowa City, IA, 52242, USA
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA, 52242, USA
| | - Jeffrey D Long
- Department of Psychiatry, University of Iowa, Iowa City, IA, 52242, USA
- Department of Biostatistics, University of Iowa, Iowa City, IA, 52242, USA
| | - Shelly Miller
- Behavioral Diagnostics LLC, Coralville, IA, 52241, USA
| | - Robert Philibert
- Department of Psychiatry, University of Iowa, Iowa City, IA, 52242, USA.
- Department of Biomedical Engineering, University of Iowa, Iowa City, IA, 52242, USA.
- Behavioral Diagnostics LLC, Coralville, IA, 52241, USA.
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10
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Bivins A, Lowry S, Wankhede S, Hajare R, Murphy HM, Borchardt M, Labhasetwar P, Brown J. Microbial water quality improvement associated with transitioning from intermittent to continuous water supply in Nagpur, India. WATER RESEARCH 2021; 201:117301. [PMID: 34139512 DOI: 10.1016/j.watres.2021.117301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 05/12/2021] [Accepted: 05/23/2021] [Indexed: 06/12/2023]
Abstract
Nearly half a billion people living in Indian cities receive their drinking water from an intermittent water supply (IWS), which can be associated with degraded water quality and risk of waterborne disease. The municipal water supply in Nagpur, India is transitioning from intermittent to continuous supply in phases. We conducted cross-sectional sampling to compare microbial water quality under IWS and continuous water supply (CWS) in Nagpur. In 2015 and 2017, we collected 146 grab samples and 90 large-volume dead-end ultrafiltration (DEUF) samples (total volume: 6,925 liters). In addition to measuring traditional water quality parameters, we also assayed DEUF samples by droplet digital PCR (ddPCR) for waterborne pathogen gene targets. At household taps served by IWS, we detected targets from enterotoxigenic E. coli, Shigella spp./enteroinvasive E. coli, norovirus GI and GII, adenovirus A-F, Cryptosporidium spp., and Giardia duodenalis. We observed a significant increase in the proportion of grab samples positive for culturable E. coli (p = 0.0007) and DEUF concentrates positive for waterborne pathogen gene targets (p = 0.0098) at household taps served by IWS compared to those served by CWS. IWS continues to be associated with fecal contamination, and, in this study, with increased prevalence of molecular evidence of waterborne pathogens. These findings add mounting evidence that, despite the presence of piped on premise infrastructure, IWS is less likely to meet the requirements for safely-managed drinking water as defined by the Sustainable Development Goals. Importantly, these findings demonstrate the transition from IWS to CWS in Nagpur is yielding meaningful improvements in microbial water quality.
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Affiliation(s)
- Aaron Bivins
- Environmental Change Initiative, University of Notre Dame, 721 Flanner Hall, Notre Dame, IN 46556, USA; Department of Civil & Environmental Engineering & Earth Sciences, University of Notre Dame, 156 Fitzpatrick Hall, Notre Dame, IN 46556, USA
| | - Sarah Lowry
- School of Civil & Environmental Engineering, Georgia Institute of Technology, 311 Ferst Drive, Atlanta, GA 30332, USA
| | - Sonal Wankhede
- Director's Research Cell, Council of Scientific and Industrial Research, National Environmental Engineering Research Institute (CSIR-NEERI), Nagpur, India
| | - Rajashree Hajare
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Heather M Murphy
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Mark Borchardt
- Agricultural Research Service, U.S. Dept of Agriculture, 2615 Yellowstone Drive, Marshfield, WI 54449, USA
| | - Pawan Labhasetwar
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Joe Brown
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, 135 Dauer Drive, Chapel Hill NC 27599-7431, USA..
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11
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Gaňová M, Zhang H, Zhu H, Korabečná M, Neužil P. Multiplexed digital polymerase chain reaction as a powerful diagnostic tool. Biosens Bioelectron 2021; 181:113155. [PMID: 33740540 DOI: 10.1016/j.bios.2021.113155] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 02/13/2021] [Accepted: 03/06/2021] [Indexed: 01/30/2023]
Abstract
The digital polymerase chain reaction (dPCR) multiplexing method can simultaneously detect and quantify closely related deoxyribonucleic acid sequences in complex mixtures. The dPCR concept is continuously improved by the development of microfluidics and micro- and nanofabrication, and different complex techniques are introduced. In this review, we introduce dPCR techniques based on sample compartmentalization, droplet- and chip-based systems, and their combinations. We then discuss dPCR multiplexing methods in both laboratory research settings and advanced or routine clinical applications. We focus on their strengths and weaknesses with regard to the character of biological samples and to the required precision of such analysis, as well as showing recently published work based on those methods. Finally, we envisage possible future achievements in this field.
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Affiliation(s)
- Martina Gaňová
- Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic
| | - Haoqing Zhang
- School of Mechanical Engineering, Northwestern Polytechnical University, Xi'an, 710072, PR China
| | - Hanliang Zhu
- School of Mechanical Engineering, Northwestern Polytechnical University, Xi'an, 710072, PR China
| | - Marie Korabečná
- 1st Faculty of Medicine, Institute of Biology and Medical Genetics, Charles University and General University Hospital, 12800, Prague, Czech Republic
| | - Pavel Neužil
- Central European Institute of Technology, Brno University of Technology, 612 00, Brno, Czech Republic; School of Mechanical Engineering, Northwestern Polytechnical University, Xi'an, 710072, PR China; The Faculty of Electrical Engineering and Communication, Brno University of Technology, 616 00, Brno, Czech Republic.
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Sugimoto H, Chen S, Minembe JP, Chouitar J, He X, Wang H, Fang X, Qian MG. Insights on Droplet Digital PCR-Based Cellular Kinetics and Biodistribution Assay Support for CAR-T Cell Therapy. AAPS J 2021; 23:36. [PMID: 33655393 PMCID: PMC7925486 DOI: 10.1208/s12248-021-00560-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/13/2021] [Indexed: 01/03/2023] Open
Abstract
Characterizing in vivo cellular kinetics and biodistribution of chimeric antigen receptor T (CAR-T) cells is critical for toxicity assessment, nonclinical and clinical efficacy studies. To date, the standardized assay to characterize CAR-T cell distribution, expansion, contraction, and persistence profiles is not readily available. To overcome this limitation and increase comparability among studies, we have established a universal protocol for analysis. We established a duplexing ddPCR protocol for the CAR-T transgene and reference gene to normalize the genomic DNA input prepared from mouse blood and tissues. The high-throughput gDNA extraction method enabled highly reproducible gDNA extraction while eliminating labor-intensive steps. The investigational CAR-T cells were intravenously injected into immunodeficient mice bearing human colorectal cancer xenografts. The blood and tissue samples were collected to measure the cellular kinetics by ddPCR and flow cytometry. The standard curves were linear throughout the calibration range with acceptable intra- and inter-day precision and accuracy. The gDNA recovery study performed by spiking in the exo-gene plasmid DNA or CAR-T cells revealed that the recovery ranged from 60 to 100% in blood and tissue homogenates. The use of both units of copy/μg gDNA and copy/μL blood met the current regulatory requirement and allowed for a systematic understanding of CAR-T cell expansion and a direct comparison with the flow cytometry data. A standardized ddPCR assay, including automated gDNA extraction procedures, has been established for evaluating cellular kinetics and biodistribution in CAR-T cell therapies.
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Affiliation(s)
- Hiroshi Sugimoto
- Department of Drug Metabolism and Pharmacokinetics, Takeda Pharmaceuticals International Co, 125 Binney Street, Cambridge, Massachusetts, 02142, USA.
| | - Susan Chen
- Department of Drug Metabolism and Pharmacokinetics, Takeda Pharmaceuticals International Co, 35 Landsdowne Street, Cambridge, Massachusetts, 02139, USA
| | - Jean-Pierre Minembe
- Department of Drug Metabolism and Pharmacokinetics, Takeda Pharmaceuticals International Co, 35 Landsdowne Street, Cambridge, Massachusetts, 02139, USA
| | - Johara Chouitar
- Department of Immuno Oncology DDU, Takeda Pharmaceuticals International Co, 40 Landsdowne Street, Cambridge, Massachusetts, 02139, USA
| | - Xingyue He
- Department of Immuno Oncology DDU, Takeda Pharmaceuticals International Co, 40 Landsdowne Street, Cambridge, Massachusetts, 02139, USA
| | - Haiqing Wang
- Department of Drug Metabolism and Pharmacokinetics, Takeda Pharmaceuticals International Co, 35 Landsdowne Street, Cambridge, Massachusetts, 02139, USA
| | - Xiaodong Fang
- Department of Drug Metabolism and Pharmacokinetics, Takeda Pharmaceuticals International Co, 35 Landsdowne Street, Cambridge, Massachusetts, 02139, USA.
| | - Mark G Qian
- Department of Drug Metabolism and Pharmacokinetics, Takeda Pharmaceuticals International Co, 35 Landsdowne Street, Cambridge, Massachusetts, 02139, USA
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Syeda MM, Wiggins JM, Corless B, Spittle C, Karlin-Neumann G, Polsky D. Validation of Circulating Tumor DNA Assays for Detection of Metastatic Melanoma. Methods Mol Biol 2020; 2055:155-180. [PMID: 31502151 DOI: 10.1007/978-1-4939-9773-2_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The detection of cell-free, circulating tumor DNA (ctDNA) in the blood of patients with solid tumors is often referred to as "liquid biopsy." ctDNA is particularly attractive as a candidate biomarker in the blood. It is relatively stable after blood collection, can be easily purified, and can be quantitatively measured with high sensitivity and specificity using advanced technologies. Current liquid biopsy research has focused on detecting and quantifying ctDNA to (1) diagnose and characterize mutations in a patient's cancer to help select the appropriate treatment; (2) predict clinical outcomes associated with different treatments; and (3) monitor the response and/or progression of a patient's disease. The diagnostic use of liquid biopsies is probably greatest in tumors where the difficulty and/or risk of obtaining a tissue specimen for molecular diagnostics is high (e.g., lung, colon). In metastatic melanoma, however, obtaining a tissue sample for molecular diagnostics is not typically a major obstacle to patient care plans; rather predicting treatment outcomes and monitoring a patient's disease course during therapy are considered the current priorities for this cancer type. In this chapter we describe an approach to the validation of ctDNA detection assays for melanoma, focusing primarily on analytical validation, and provide methods to guide the use of droplet digital PCR assays for measuring ctDNA levels in plasma samples.
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Affiliation(s)
- Mahrukh M Syeda
- The Ronald O. Perelman Department of Dermatology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York University School of Medicine, New York, NY, USA
| | - Jennifer M Wiggins
- The Ronald O. Perelman Department of Dermatology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York University School of Medicine, New York, NY, USA
| | - Broderick Corless
- The Ronald O. Perelman Department of Dermatology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York University School of Medicine, New York, NY, USA
| | | | | | - David Polsky
- The Ronald O. Perelman Department of Dermatology, Laura and Isaac Perlmutter Cancer Center, NYU Langone Health, New York University School of Medicine, New York, NY, USA.
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Lin Y, Ye J, Luo M, Hu B, Wu D, Wen J, Yang C, Li Y, Ning Y. Group B Streptococcus DNA Copy Numbers Measured by Digital PCR Correlates with Perinatal Outcomes. Anal Chem 2019; 91:9466-9471. [PMID: 31269399 DOI: 10.1021/acs.analchem.8b05872] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Group B Streptococcus (GBS) is a one of the main causes of perinatal disease, yet the method for GBS detection, broth-enriched culture, is time-consuming and has low sensitivity and accuracy. We aimed to develop a GBS digital PCR (GBS-dPCR) assay for detecting GBS colonization. More rapid and accurate detection of GBS colonization could increase GBS diagnosis and treatment closer to delivery. A single-center, retrospective, case-controlled study was performed. A total of 182 rectovaginal swabs from pregnant women, who were undergoing prenatal screening by broth-enriched culture, were evaluated using GBS-dPCR targeting the cfb gene of GBS. Pregnant women with GBS colonization were followed up for correlation analysis between GBS DNA copy numbers and perinatal outcomes. The results of the GBS-dPCR assay were compared to those from the broth-enriched culture, which is the gold standard for GBS detection. The sensitivity and specificity of GBS-dPCR were 98% and 92.5%, respectively. By discrepant result analysis, the specificity of GBS-dPCR was raised to 97.4%. The incidence of premature rupture of membrane (PROM) and neonatal infection were statistically significantly positively correlated with GBS DNA copy numbers. GBS-dPCR has the advantage of directly detecting GBS colonization from swabs with high specificity and sensitivity, while reducing turnaround time (<4 h). Analysis of clinical samples with GBS-dPCR shows that GBS DNA copy numbers are positively correlated with the incidence of PROM and neonatal infection, suggesting that dPCR is a promising method for detection of GBS colonization during pregnancy.
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Affiliation(s)
- Yanqing Lin
- School of Laboratory Medicine and Biotechnology , Southern Medical University , Guangzhou 510515 , People's Republic of China.,Affiliated Shenzhen Maternity & Healthcare Hospital , Southern Medical University , Shenzhen 518028 , People's Republic of China
| | - Jianbin Ye
- School of Laboratory Medicine and Biotechnology , Southern Medical University , Guangzhou 510515 , People's Republic of China.,Zhuhai SMU Biomedicine Public Service Platform LLC , Zhuhai 519040 , People's Republic of China
| | - Meiqun Luo
- School of Laboratory Medicine and Biotechnology , Southern Medical University , Guangzhou 510515 , People's Republic of China
| | - Bingxin Hu
- School of Laboratory Medicine and Biotechnology , Southern Medical University , Guangzhou 510515 , People's Republic of China
| | - Danlin Wu
- School of Laboratory Medicine and Biotechnology , Southern Medical University , Guangzhou 510515 , People's Republic of China
| | - Junjie Wen
- School of Laboratory Medicine and Biotechnology , Southern Medical University , Guangzhou 510515 , People's Republic of China
| | - Chuanzhong Yang
- Affiliated Shenzhen Maternity & Healthcare Hospital , Southern Medical University , Shenzhen 518028 , People's Republic of China
| | - Yan Li
- School of Laboratory Medicine and Biotechnology , Southern Medical University , Guangzhou 510515 , People's Republic of China
| | - Yunshan Ning
- School of Laboratory Medicine and Biotechnology , Southern Medical University , Guangzhou 510515 , People's Republic of China
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