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Li L, Bae S. Quantitative detection and survival analysis of VBNC Salmonella Typhimurium in flour using droplet digital PCR and DNA-intercalating dyes. Microbiol Spectr 2024; 12:e0024924. [PMID: 38975767 PMCID: PMC11302299 DOI: 10.1128/spectrum.00249-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 05/13/2024] [Indexed: 07/09/2024] Open
Abstract
The difficulty in detecting viable but non-culturable (VBNC) Salmonella by culture-dependent methods poses a risk to food safety. In our study, we applied a viability test to Salmonella following a lethal treatment and to flour samples inoculated with Salmonella to evaluate the effectiveness of viability polymerase chain reaction (PCR). Our findings revealed that the combination of both ddPCR and qPCR with those DNA-intercalating dyes could quantify viable cells at low concentrations when the plate counting method failed to detect them post-inactivation. Prolonged UV exposure did not induce cell membrane disruption, as confirmed with PMA-ddPCR, with insignificant differences in gene copies. However, samples exposed to DyeTox13 and DyeTox13 + EMA showed lower gene copy numbers, implying that enzymatic activity was decreased by UV exposure duration. In addition, temperature-dependent survival in flour revealed uniform decay rates and D values (time required for a 1 log reduction) of DNA in untreated samples across various temperatures. By contrast, different decay rates were observed with DNA-intercalating dyes (DyeTox13 and DyeTox13 + EMA), showing faster metabolic activity loss at higher temperatures in flour. The decay rates and D values, determined through plate counting and those DNA-intercalating dyes, indicated the potential presence of VBNC Salmonella. A strong correlation between DyeTox13 dyes and the plate counting method suggested DyeTox13 as a rapid alternative for detecting Salmonella in flour. The ddPCR with DNA-intercalating dyes could effectively evaluate Salmonella viability, facilitating more precise monitoring of VBNC in food. IMPORTANCE Salmonella, a major foodborne pathogen, poses significant risks, particularly to vulnerable groups like infants, older people, and the immunocompromised. Accurate detection is vital for public health and food safety, given its potential to cause severe and life-threatening symptoms. Our study demonstrated digital polymerase chain reaction (ddPCR) with DNA-intercalating dyes for identifying the different physiological statuses of Salmonella. Also, the application of ddPCR with DNA-intercalating dyes offers quantification of viable cells post-disinfection as an alternative method in food. Utilizing ddPCR and DNA-intercalating dyes, we enhanced the detection of VBNC Salmonella, a form often undetectable by conventional methods. This innovative approach could significantly improve the precision and efficiency of detection for viable Salmonella. By providing deeper insights into its transmission potential, our method is a critical tool in preventing outbreaks and ensuring the safety of food products. This research contributes substantially to global efforts in controlling foodborne illnesses and safeguarding public health.
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Affiliation(s)
- Liyan Li
- Department of Civil and Environmental Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Sungwoo Bae
- Department of Civil and Environmental Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
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2
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Arvia R, Tanturli M, Ugolini F, Vannucchi M, Massi D, Zakrzewska K. Molecular investigation of some DNA viruses in mucosal melanoma: Case-control study. J Med Virol 2023; 95:e29269. [PMID: 38009623 DOI: 10.1002/jmv.29269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 10/12/2023] [Accepted: 11/13/2023] [Indexed: 11/29/2023]
Abstract
The association between viral infections and both cutaneous and mucosal melanoma (MM) has not been fully investigated. Here, we assessed the prevalence of the DNA of a broad range of viruses in 31 MMs and 15 biopsies of healthy mucosa (HM) using molecular methods. The parvoviruses CuV and B19V, herpesviruses HSV1, HSV2, EBV, HHV6, and HHV8, polyomavirus MCPyV, and α-HPVs were not detected, or rarely found, in MMs, and in HM, of the digestive, respiratory, and female genital tract. The overall prevalence of β-HPV in MMs was not significantly higher compared to that in HM (70.9% and 53.3% respectively; p = 0.514). However, the number of MMs positive for β-HPV types belonging to Species 3 and 5 and for some viral types belonging to Species 1, 2, 3, and 5 were significantly higher compared with HM (p < 0.05). Moreover, compared to HM, the MM samples contained a significantly higher number of β-HPV types, mainly belonging to Species 1, 3, and 5 (p < 0.05). Our data, although suggesting a role for certain β-HPV types in MM oncogenesis, require additional investigation in larger populations to support this hypothesis.
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Affiliation(s)
- Rosaria Arvia
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Michele Tanturli
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio", University of Florence, Florence, Italy
| | - Filippo Ugolini
- Department of Health Sciences, University of Florence, Florence, Italy
| | - Margherita Vannucchi
- Department of Medical Biotechnology, Section of Pathology, University of Siena, Siena, Italy
| | - Daniela Massi
- Department of Health Sciences, University of Florence, Florence, Italy
| | - Krystyna Zakrzewska
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
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3
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Yasuura M, Tan ZL, Horiguchi Y, Ashiba H, Fukuda T. Improvement of Sensitivity and Speed of Virus Sensing Technologies Using nm- and μm-Scale Components. SENSORS (BASEL, SWITZERLAND) 2023; 23:6830. [PMID: 37571612 PMCID: PMC10422600 DOI: 10.3390/s23156830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 07/20/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023]
Abstract
Various viral diseases can be widespread and cause severe disruption to global society. Highly sensitive virus detection methods are needed to take effective measures to prevent the spread of viral infection. This required the development of rapid virus detection technology to detect viruses at low concentrations, even in the biological fluid of patients in the early stages of the disease or environmental samples. This review describes an overview of various virus detection technologies and then refers to typical technologies such as beads-based assay, digital assay, and pore-based sensing, which are the three modern approaches to improve the performance of viral sensing in terms of speed and sensitivity.
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Affiliation(s)
- Masato Yasuura
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Central 5, 1-1-1 Higashi, Tsukuba 305-8565, Ibaraki, Japan; (Z.L.T.); (Y.H.); (H.A.); (T.F.)
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4
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Zanella MC, Vu DL, Hosszu-Fellous K, Neofytos D, Van Delden C, Turin L, Poncet A, Simonetta F, Masouridi-Levrat S, Chalandon Y, Cordey S, Kaiser L. Longitudinal Detection of Twenty DNA and RNA Viruses in Allogeneic Hematopoietic Stem Cell Transplant Recipients Plasma. Viruses 2023; 15:v15040928. [PMID: 37112908 PMCID: PMC10142697 DOI: 10.3390/v15040928] [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: 02/12/2023] [Revised: 03/29/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Metagenomics revealed novel and routinely overlooked viruses, representing sources of unrecognized infections after allogeneic hematopoietic stem cell transplantation (allo-HSCT). We aim to describe DNA and RNA virus prevalence and kinetics in allo-HSCT recipients' plasma for one year post HSCT. We included 109 adult patients with first allo-HSCT from 1 March 2017 to 31 January 2019 in this observational cohort study. Seventeen DNA and three RNA viral species were screened with qualitative and/or quantitative r(RT)-PCR assays using plasma samples collected at 0, 1, 3, 6, and 12 months post HSCT. TTV infected 97% of patients, followed by HPgV-1 (prevalence: 26-36%). TTV (median 3.29 × 105 copies/mL) and HPgV-1 (median 1.18 × 106 copies/mL) viral loads peaked at month 3. At least one Polyomaviridae virus (BKPyV, JCPyV, MCPyV, HPyV6/7) was detected in >10% of patients. HPyV6 and HPyV7 prevalence reached 27% and 12% at month 3; CMV prevalence reached 27%. HSV, VZV, EBV, HHV-7, HAdV and B19V prevalence remained <5%. HPyV9, TSPyV, HBoV, EV and HPg-V2 were never detected. At month 3, 72% of patients had co-infections. TTV and HPgV-1 infections were highly prevalent. BKPyV, MCPyV and HPyV6/7 were frequently detected relative to classical culprits. Further investigation is needed into associations between these viral infections and immune reconstitution or clinical outcomes.
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Affiliation(s)
- Marie-Céline Zanella
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Diem-Lan Vu
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Krisztina Hosszu-Fellous
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, 1211 Geneva, Switzerland
| | - Dionysios Neofytos
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Chistian Van Delden
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Lara Turin
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Antoine Poncet
- Center for Clinical Research, Department of Health and Community Medicine, University of Geneva, 1206 Geneva, Switzerland
- Division of Clinical Epidemiology, Department of Health and Community Medicine, University Hospital of Geneva, 1211 Geneva, Switzerland
| | - Federico Simonetta
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Division of Hematology, Department of Oncology, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Stavroula Masouridi-Levrat
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Division of Hematology, Department of Oncology, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Yves Chalandon
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Division of Hematology, Department of Oncology, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Samuel Cordey
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
| | - Laurent Kaiser
- Division of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1211 Geneva, Switzerland
- Faculty of Medicine, University of Geneva Medical School, 1206 Geneva, Switzerland
- Geneva Centre for Emerging Viral Diseases, 1211 Geneva, Switzerland
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5
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Parra LM, Sartori BGC, Fernandes DR, Fachin LRV, Nogueira MRS, Belone AFF, Nunes AJF, Souza-Santana FC. HLA-G expression in Merkel cell carcinoma and the correlation with Merkel cell polyomavirus infection. Immunogenetics 2023; 75:81-89. [PMID: 36229691 DOI: 10.1007/s00251-022-01279-0] [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: 06/28/2022] [Accepted: 09/30/2022] [Indexed: 11/05/2022]
Abstract
Merkel cell carcinoma (MCC) is a rare aggressive neuroendocrine cutaneous carcinoma with a high mortality rate. The MCC etiology is not fully understood. Merkel cell-associated polyomavirus (MCPyV) was found in MCC patients, indicating a risk factor for the tumor. Caucasian, elderly, and immunocompromised individuals are more likely to develop this tumor. HLA-G consists of a non-classical class I (Ib) HLA molecule with an immunoregulatory function and was associated with tumor escape in different types of tumors, nonetheless, never been studied in MCC. The purpose of this study was to evaluate the HLA-G expression and also to detect the MCPyV in MCC patients and correlate it with the clinical course of the disease. Forty-five MCC patients were included in a retrospective study. Formalin-fixed paraffin-embedded cutaneous skin biopsies were used by immunohistochemistry and RT-PCR to verify the HLA-G expression and MCPyV infection. HLA-G expression was found in 7 (15.6%), while the presence of MCPyV was detected in 28 (62.2%) of the studied patients. No significant association was found between HLA-G expression and MCPyV infection (p = 0.250). The presence of MCPyV was associated with areas of low sunlight exposure (p = 0.042) and the HLA-G expression with progression to death (p = 0.038). HLA-G expression was detected in MCC patients, as well as the MCPyV presence was confirmed. These markers could represent factors with a possible impact on patient survival; however, further studies with a greater number of patients are needed, to better elucidate the possible role in disease progression.
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Affiliation(s)
- L M Parra
- Clinical Laboratory, Amaral Carvalho Hospital-Jaú, Dona Silvéria, 150 - Chácara Braz Miraglia, São Paulo, 17210-070, Brazil.
| | - B G C Sartori
- Molecular Biology Laboratory, Lauro de Souza Lima Institute, Bauru, São Paulo, Brazil
| | - D R Fernandes
- Pathological Anatomy Laboratory, Lauro de Souza Lima Institute, Bauru, São Paulo, Brazil
| | - L R V Fachin
- Molecular Biology Laboratory, Lauro de Souza Lima Institute, Bauru, São Paulo, Brazil
| | - M R S Nogueira
- Biology Laboratory, Lauro de Souza Lima Institute, Bauru, São Paulo, Brazil
| | - A F F Belone
- Pathological Anatomy Laboratory, Lauro de Souza Lima Institute, Bauru, São Paulo, Brazil
| | - A J F Nunes
- Pathological Anatomy Laboratory, Lauro de Souza Lima Institute, Bauru, São Paulo, Brazil
- Pathological Anatomy Department, Amaral Carvalho Hospital, Jaú, São Paulo, Brazil
| | - F C Souza-Santana
- Immunology Laboratory, Lauro de Souza Lima Institute, Bauru, São Paulo, Brazil
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6
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Morón-López S, Riveira-Muñoz E, Urrea V, Gutiérrez-Chamorro L, Ávila-Nieto C, Noguera-Julian M, Carrillo J, Mitjà O, Mateu L, Massanella M, Ballana E, Martinez-Picado J. Comparison of Reverse Transcription (RT)-Quantitative PCR and RT-Droplet Digital PCR for Detection of Genomic and Subgenomic SARS-CoV-2 RNA. Microbiol Spectr 2023; 11:e0415922. [PMID: 36943067 PMCID: PMC10100669 DOI: 10.1128/spectrum.04159-22] [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: 10/25/2022] [Accepted: 02/24/2023] [Indexed: 03/23/2023] Open
Abstract
Most individuals acutely infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exhibit mild symptoms. However, 10 to 20% of those infected develop long-term symptoms, referred to as post-coronavirus disease 2019 (COVID-19) condition (PCC). One hypothesis is that PCC might be exacerbated by viral persistence in tissue sanctuaries. Therefore, the accurate detection and quantification of SARS-CoV-2 are not only necessary for viral load monitoring but also crucial for detecting long-term viral persistence and determining whether viral replication is occurring in tissue reservoirs. In this study, the sensitivity and robustness of reverse transcription (RT)-droplet digital PCR (ddPCR) and RT-quantitative PCR (qPCR) techniques have been compared for the detection and quantification of SARS-CoV-2 genomic and subgenomic RNAs from oropharyngeal swabs taken from confirmed SARS-CoV-2-positive, SARS-CoV-2-exposed, and nonexposed individuals as well as from samples from mice infected with SARS-CoV-2. Our data demonstrated that both techniques presented equivalent results in the mid- and high-viral-load ranges. Additionally, RT-ddPCR was more sensitive than RT-qPCR in the low-viral-load range, allowing the accurate detection of positive results in individuals exposed to the virus. Overall, these data suggest that RT-ddPCR might be an alternative to RT-qPCR for detecting low viral loads in samples and for assessing viral persistence in samples from individuals with PCC. IMPORTANCE We developed one-step reverse transcription (RT)-droplet digital PCR (ddPCR) protocols to detect SARS-CoV-2 RNA and compared them to the gold-standard RT-quantitative PCR (RT-qPCR) method. RT-ddPCR was more sensitive than RT-qPCR in the low-viral-load range, while both techniques were equivalent in the mid- and high-viral-load ranges. Overall, these results suggest that RT-ddPCR might be a viable alternative to RT-qPCR when it comes to detecting low viral loads in samples, which is a highly relevant issue for determining viral persistence in as-yet-unknown tissue reservoirs in individuals suffering from post-COVID conditions or long COVID.
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Affiliation(s)
- Sara Morón-López
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- CIBER de Enfermedades Infecciosas, Madrid, Spain
| | | | - Victor Urrea
- IrsiCaixa AIDS Research Institute, Badalona, Spain
| | | | | | - Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- CIBER de Enfermedades Infecciosas, Madrid, Spain
| | - Jorge Carrillo
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- CIBER de Enfermedades Infecciosas, Madrid, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Oriol Mitjà
- Fight Infections Foundation, Badalona, Spain
- Hospital Universitari Germans Trias i Pujol, Badalona, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
- Lihir Medical Centre, International SOS, Londolovit, Lihir Island, Papua New Guinea
| | - Lourdes Mateu
- Fight Infections Foundation, Badalona, Spain
- Hospital Universitari Germans Trias i Pujol, Badalona, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
- Autonomous University of Barcelona (UAB), Barcelona, Spain
| | - Marta Massanella
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- CIBER de Enfermedades Infecciosas, Madrid, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
| | - Ester Ballana
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute, Badalona, Spain
- CIBER de Enfermedades Infecciosas, Madrid, Spain
- Germans Trias i Pujol Research Institute (IGTP), Badalona, Spain
- University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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7
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Barchitta M, Maugeri A, Campisi E, Magnano San Lio R, Favara G, Soto Parra HJ, Salvatorelli L, Magro G, Basile G, Agodi A. Comparison of Quantitative Real-Time PCR and Digital PCR to Detect the Polyomavirus in Merkel Cell Carcinoma. Viruses 2022; 14:v14102195. [PMID: 36298750 PMCID: PMC9610963 DOI: 10.3390/v14102195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 09/30/2022] [Accepted: 10/01/2022] [Indexed: 11/16/2022] Open
Abstract
Merkel cell polyomavirus (MCPyV) prevalence in Merkel cell carcinoma (MCC) cases is controversial. The detection and quantification of MCPyV DNA is mainly performed by PCR techniques using formalin-fixed, paraffin-embedded (FFPE) tissues. The aim of this study is to compare the performance of two different molecular techniques, specifically the quantitative Real-Time PCR (qPCR) and digital PCR (dPCR). Samples from 31 cases of MCC excisional surgical biopsies were analyzed. DNA extraction and purification from clinical samples were performed using the QIAcube Qiagen automated nucleic acid extractor. After the extraction, MCPyV was detected by qPCR and dPCR using specially designed primers and probes. Of the 31 MCC samples under study, the MCPyV genome was detected in 11 samples (35%) by qPCR compared with 20 samples (65%) detected by dPCR. Notably, 65% of primary tumors were positive for MCPyV (15/23). The viral genome was detected in 75% of tumors located at UV-exposed sites (6/8), 55% of tumors at partially UV-protected sites (5/9), and 67% of tumors at UV-protected sites (4/6). Our results showed a better sensitivity of dPCR in detecting the MCPyV genome in MCC samples compared with traditional qPCR techniques.
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Affiliation(s)
- Martina Barchitta
- Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia”, University of Catania, Via S. Sofia 87, 95123 Catania, Italy
| | - Andrea Maugeri
- Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia”, University of Catania, Via S. Sofia 87, 95123 Catania, Italy
| | - Elisabetta Campisi
- Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia”, University of Catania, Via S. Sofia 87, 95123 Catania, Italy
| | - Roberta Magnano San Lio
- Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia”, University of Catania, Via S. Sofia 87, 95123 Catania, Italy
| | - Giuliana Favara
- Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia”, University of Catania, Via S. Sofia 87, 95123 Catania, Italy
| | - Hector Jose Soto Parra
- Medical Oncology, Azienda Ospedaliero Universitaria Policlinico “G. Rodolico-S. Marco”, 95123 Catania, Italy
| | - Lucia Salvatorelli
- Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia”, University of Catania, Via S. Sofia 87, 95123 Catania, Italy
| | - Gaetano Magro
- Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia”, University of Catania, Via S. Sofia 87, 95123 Catania, Italy
| | - Guido Basile
- Department of General Surgery and Medical-Surgical Specialties, University of Catania, Via S. Sofia 78, 95123 Catania, Italy
| | - Antonella Agodi
- Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia”, University of Catania, Via S. Sofia 87, 95123 Catania, Italy
- Correspondence:
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8
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Long S. In pursuit of sensitivity: Lessons learned from viral nucleic acid detection and quantification on the Raindance ddPCR platform. Methods 2022; 201:82-95. [PMID: 33839286 PMCID: PMC8501152 DOI: 10.1016/j.ymeth.2021.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/27/2021] [Accepted: 04/06/2021] [Indexed: 12/11/2022] Open
Abstract
Sensitive PCR detection of viral nucleic acids plays a critical role in infectious disease research, diagnosis and monitoring. In the context of SARS-CoV-2 detection, recent reports indicate that digital PCR-based tests are significantly more sensitive than traditional qPCR tests. Numerous factors can influence digital PCR reaction sensitivity. In this review, using a model for human HIV infection and the Raindance ddPCR platform as an example, we describe technical aspects that contribute to sensitive viral signal detection in DNA and RNA from tissue samples, which often harbor viral reservoirs and serve as better predictors of disease outcome and indicators of treatment efficacy.
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Affiliation(s)
- Samuel Long
- AIDS and Cancer Virus Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, United States.
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9
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Pirozzi F, Berkseth M, Shear R, Gonzalez L, Timms AE, Sulc J, Pao E, Oyama N, Forzano F, Conti V, Guerrini R, Doherty ES, Saitta SC, Lockwood CM, Pritchard CC, Dobyns WB, Novotny E, Wright JNN, Saneto RP, Friedman S, Hauptman J, Ojemann J, Kapur RP, Mirzaa GM. Profiling PI3K-AKT-MTOR variants in focal brain malformations reveals new insights for diagnostic care. Brain 2022; 145:925-938. [PMID: 35355055 PMCID: PMC9630661 DOI: 10.1093/brain/awab376] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 09/04/2021] [Accepted: 09/09/2021] [Indexed: 12/28/2022] Open
Abstract
Focal malformations of cortical development including focal cortical dysplasia, hemimegalencephaly and megalencephaly, are a spectrum of neurodevelopmental disorders associated with brain overgrowth, cellular and architectural dysplasia, intractable epilepsy, autism and intellectual disability. Importantly, focal cortical dysplasia is the most common cause of focal intractable paediatric epilepsy. Gain and loss of function variants in the PI3K-AKT-MTOR pathway have been identified in this spectrum, with variable levels of mosaicism and tissue distribution. In this study, we performed deep molecular profiling of common PI3K-AKT-MTOR pathway variants in surgically resected tissues using droplet digital polymerase chain reaction (ddPCR), combined with analysis of key phenotype data. A total of 159 samples, including 124 brain tissue samples, were collected from 58 children with focal malformations of cortical development. We designed an ultra-sensitive and highly targeted molecular diagnostic panel using ddPCR for six mutational hotspots in three PI3K-AKT-MTOR pathway genes, namely PIK3CA (p.E542K, p.E545K, p.H1047R), AKT3 (p.E17K) and MTOR (p.S2215F, p.S2215Y). We quantified the level of mosaicism across all samples and correlated genotypes with key clinical, neuroimaging and histopathological data. Pathogenic variants were identified in 17 individuals, with an overall molecular solve rate of 29.31%. Variant allele fractions ranged from 0.14 to 22.67% across all mutation-positive samples. Our data show that pathogenic MTOR variants are mostly associated with focal cortical dysplasia, whereas pathogenic PIK3CA variants are more frequent in hemimegalencephaly. Further, the presence of one of these hotspot mutations correlated with earlier onset of epilepsy. However, levels of mosaicism did not correlate with the severity of the cortical malformation by neuroimaging or histopathology. Importantly, we could not identify these mutational hotspots in other types of surgically resected epileptic lesions (e.g. polymicrogyria or mesial temporal sclerosis) suggesting that PI3K-AKT-MTOR mutations are specifically causal in the focal cortical dysplasia-hemimegalencephaly spectrum. Finally, our data suggest that ultra-sensitive molecular profiling of the most common PI3K-AKT-MTOR mutations by targeted sequencing droplet digital polymerase chain reaction is an effective molecular approach for these disorders with a good diagnostic yield when paired with neuroimaging and histopathology.
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Affiliation(s)
- Filomena Pirozzi
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Matthew Berkseth
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Rylee Shear
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | | | - Andrew E Timms
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Josef Sulc
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Emily Pao
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Nora Oyama
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA
| | - Francesca Forzano
- Department of Clinical Genetics, Guy's and St Thomas NHS Foundation Trust and King's College London, London, UK
| | - Valerio Conti
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children's Hospital A. Meyer-University of Florence, Italy
| | - Renzo Guerrini
- Pediatric Neurology, Neurogenetics and Neurobiology Unit and Laboratories, Children's Hospital A. Meyer-University of Florence, Italy
| | - Emily S Doherty
- Section of Clinical Genetics, Carilion Clinic Children's Hospital, Roanoke, VA, USA
| | - Sulagna C Saitta
- Division of Medical Genetics, Department of Obstetrics and Gynecology, David Geffen School of Medicine at the University of California Los Angeles, Los Angeles, CA, USA
| | - Christina M Lockwood
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.,Brotman-Baty Institute for Precision Medicine, University of Minnesota, Seattle, WA, USA
| | - Colin C Pritchard
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.,Brotman-Baty Institute for Precision Medicine, University of Minnesota, Seattle, WA, USA
| | - William B Dobyns
- Division of Genetics and Metabolism, Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
| | - Edward Novotny
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.,Division of Pediatric Neurology, Department of Neurology, Seattle Children's Hospital, Seattle, WA, USA.,Department of Neurology, University of Washington, Seattle, WA, USA
| | - Jason N N Wright
- Department of Radiology, Seattle Children's Hospital, Seattle, WA, USA
| | - Russell P Saneto
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.,Division of Pediatric Neurology, Department of Neurology, Seattle Children's Hospital, Seattle, WA, USA
| | - Seth Friedman
- Center for Clinical and Translational Research, Seattle Children's Hospital, Seattle, WA, USA
| | - Jason Hauptman
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Jeffrey Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Raj P Kapur
- Department of Laboratories, Seattle Children's Hospital, Seattle, WA, USA
| | - Ghayda M Mirzaa
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA, USA.,Brotman-Baty Institute for Precision Medicine, University of Minnesota, Seattle, WA, USA.,Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA, USA.,Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA
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10
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Ursu RG, Damian C, Porumb-Andrese E, Ghetu N, Cobzaru RG, Lunca C, Ripa C, Costin D, Jelihovschi I, Petrariu FD, Iancu LS. Merkel Cell Polyoma Virus and Cutaneous Human Papillomavirus Types in Skin Cancers: Optimal Detection Assays, Pathogenic Mechanisms, and Therapeutic Vaccination. Pathogens 2022; 11:pathogens11040479. [PMID: 35456154 PMCID: PMC9032856 DOI: 10.3390/pathogens11040479] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Revised: 04/14/2022] [Accepted: 04/15/2022] [Indexed: 02/06/2023] Open
Abstract
Oncogenic viruses are recognized to be involved in some cancers, based on very well-established criteria of carcinogenicity. For cervical cancer and liver cancer, the responsible viruses are well-known (e.g., HPV, HBV); in the case of skin cancer, there are still many studies which are trying to identify the possible viral etiologic agents as principal co-factors in the oncogenic process. We analysed scientific literature published in the last 5 years regarding mechanisms of carcinogenicity, methods of detection, available targeted therapy, and vaccination for Merkel cell polyomavirus, and beta human papillomavirus types, in relation to skin cancer. This review is targeted at presenting the recent findings which support the involvement of these viruses in the development of some types of skin cancers. In order to optimize the management of skin cancer, a health condition of very high importance, it would be ideal that the screening of skin cancer for these two analysed viruses (MCPyV and beta HPV types) to be implemented in each region's/country's cancer centres' molecular detection diagnostic platforms, with multiplex viral capability, optimal sensitivity, and specificity; clinically validated, and if possible, at acceptable costs. For confirmatory diagnosis of skin cancer, another method should be used, with a different principle, such as immunohistochemistry, with specific antibodies for each virus.
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Affiliation(s)
- Ramona Gabriela Ursu
- Department of Preventive Medicine and Interdisciplinarity (IX)—Microbiology, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (R.G.U.); (C.D.); (R.G.C.); (C.L.); (C.R.); (D.C.); (I.J.); (F.D.P.); (L.S.I.)
| | - Costin Damian
- Department of Preventive Medicine and Interdisciplinarity (IX)—Microbiology, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (R.G.U.); (C.D.); (R.G.C.); (C.L.); (C.R.); (D.C.); (I.J.); (F.D.P.); (L.S.I.)
| | - Elena Porumb-Andrese
- Department of Medical Specialties (III)—Dermatology, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania;
| | - Nicolae Ghetu
- Department of Plastic Surgery, Regional Oncology Institute, 700483 Iasi, Romania
- Correspondence:
| | - Roxana Gabriela Cobzaru
- Department of Preventive Medicine and Interdisciplinarity (IX)—Microbiology, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (R.G.U.); (C.D.); (R.G.C.); (C.L.); (C.R.); (D.C.); (I.J.); (F.D.P.); (L.S.I.)
| | - Catalina Lunca
- Department of Preventive Medicine and Interdisciplinarity (IX)—Microbiology, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (R.G.U.); (C.D.); (R.G.C.); (C.L.); (C.R.); (D.C.); (I.J.); (F.D.P.); (L.S.I.)
| | - Carmen Ripa
- Department of Preventive Medicine and Interdisciplinarity (IX)—Microbiology, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (R.G.U.); (C.D.); (R.G.C.); (C.L.); (C.R.); (D.C.); (I.J.); (F.D.P.); (L.S.I.)
| | - Diana Costin
- Department of Preventive Medicine and Interdisciplinarity (IX)—Microbiology, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (R.G.U.); (C.D.); (R.G.C.); (C.L.); (C.R.); (D.C.); (I.J.); (F.D.P.); (L.S.I.)
| | - Igor Jelihovschi
- Department of Preventive Medicine and Interdisciplinarity (IX)—Microbiology, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (R.G.U.); (C.D.); (R.G.C.); (C.L.); (C.R.); (D.C.); (I.J.); (F.D.P.); (L.S.I.)
| | - Florin Dumitru Petrariu
- Department of Preventive Medicine and Interdisciplinarity (IX)—Microbiology, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (R.G.U.); (C.D.); (R.G.C.); (C.L.); (C.R.); (D.C.); (I.J.); (F.D.P.); (L.S.I.)
| | - Luminita Smaranda Iancu
- Department of Preventive Medicine and Interdisciplinarity (IX)—Microbiology, “Grigore T. Popa” University of Medicine and Pharmacy, 700115 Iasi, Romania; (R.G.U.); (C.D.); (R.G.C.); (C.L.); (C.R.); (D.C.); (I.J.); (F.D.P.); (L.S.I.)
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11
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Wijaya WA, Liu Y, Qing Y, Li Z. Prevalence of Merkel Cell Polyomavirus in Normal and Lesional Skin: A Systematic Review and Meta-Analysis. Front Oncol 2022; 12:868781. [PMID: 35392226 PMCID: PMC8980839 DOI: 10.3389/fonc.2022.868781] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 02/28/2022] [Indexed: 02/05/2023] Open
Abstract
The prevalence of Merkel cell polyomavirus(MCPyV) in Merkel cell carcinoma(MCC) and non-MCC skin lesions and its possible role in the etiology of other skin diseases remain controversial. To systematically assess the association between MCPyV infection and MCC, non-MCC skin lesions, and normal skin. For this systematic review and meta-analysis, a comprehensive search for eligible studies was conducted using Medline Ovid, Pubmed, Web of Science, and the Cochrane CENTRAL databases until August 2021; references were searched to identify additional studies. Observational studies that investigated the association between MCPyV infection and MCC, non-MCC skin lesions, and normal skin using polymerase chain reaction(PCR) as a detection method and provided sufficient data to calculate the prevalence of MCPyV positivity. A total of 50 articles were included in the study after exclusion criteria were applied. Two reviewers independently reviewed and assessed the eligibility of the studies, and all disagreements were resolved by consensus. To determine the association between MCPyV and MCC, overall odds ratio (OR) were calculated with 95% CI using a random-effects model. Single-arm meta-analyses were performed to examine the prevalence rate of MCPyV+ in MCC, non-MCC skin lesions, and normal skin. The primary analysis was the prevalence rate of MCPyV+ in MCC. Secondary outcomes included the prevalence rate of MCPyV+ in non-MCC skin lesions and normal skin. A total of 50 studies involving 5428 patients were reviewed based on our inclusion and exclusion criteria. Compared with the control group, MCPyV infection was significantly associated with MCC (OR = 3.51, 95% CI = 2.96 - 4.05). The global prevalence of MCPyV+ in MCC, melanoma, squamous cell carcinoma, basal cell carcinoma, Bowen's disease, actinic keratosis, keratoacanthoma, seborrheic keratosis, and normal skin was 80%, 4%, 15%, 15%, 21%, 6%, 20%, 10%, and 11%, respectively. The current results suggest that MCPyV infection is significantly associated with an increased risk of MCC. However, the low prevalence rate of MCPyV+ in non-MCC skin lesions does not exclude a pathogenic association of this virus with the development of non-MCC skin lesions.
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Affiliation(s)
- Wilson A Wijaya
- Department of Burn and Plastic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Liu
- Department of Burn and Plastic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Yong Qing
- Department of Burn and Plastic Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Zhengyong Li
- Department of Burn and Plastic Surgery, West China Hospital, Sichuan University, Chengdu, China
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12
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Mishra V, Singh A, Chen X, Rosenberg AJ, Pearson AT, Zhavoronkov A, Savage PA, Lingen MW, Agrawal N, Izumchenko E. Application of liquid biopsy as multi-functional biomarkers in head and neck cancer. Br J Cancer 2022; 126:361-370. [PMID: 34876674 PMCID: PMC8810877 DOI: 10.1038/s41416-021-01626-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/25/2021] [Accepted: 11/01/2021] [Indexed: 02/06/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a molecularly heterogeneous disease, with a 5-year survival rate that still hovers at ~60% despite recent advancements. The advanced stage upon diagnosis, limited success with effective targeted therapy and lack of reliable biomarkers are among the key factors underlying the marginally improved survival rates over the decades. Prevention, early detection and biomarker-driven treatment adaptation are crucial for timely interventions and improved clinical outcomes. Liquid biopsy, analysis of tumour-specific biomarkers circulating in bodily fluids, is a rapidly evolving field that may play a striking role in optimising patient care. In recent years, significant progress has been made towards advancing liquid biopsies for non-invasive early cancer detection, prognosis, treatment adaptation, monitoring of residual disease and surveillance of recurrence. While these emerging technologies have immense potential to improve patient survival, numerous methodological and biological limitations must be overcome before their implementation into clinical practice. This review outlines the current state of knowledge on various types of liquid biopsies in HNSCC, and their potential applications for diagnosis, prognosis, grading treatment response and post-treatment surveillance. It also discusses challenges associated with the clinical applicability of liquid biopsies and prospects of the optimised approaches in the management of HNSCC.
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Affiliation(s)
- Vasudha Mishra
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | - Alka Singh
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | - Xiangying Chen
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | - Ari J Rosenberg
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | - Alexander T Pearson
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | | | - Peter A Savage
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Mark W Lingen
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Nishant Agrawal
- Department of Surgery, Section of Otolaryngology-Head and Neck Surgery, University of Chicago, Chicago, IL, USA.
| | - Evgeny Izumchenko
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA.
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13
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Mielonen OI, Pratas D, Hedman K, Sajantila A, Perdomo MF. Detection of Low-Copy Human Virus DNA upon Prolonged Formalin Fixation. Viruses 2022; 14:v14010133. [PMID: 35062338 PMCID: PMC8779449 DOI: 10.3390/v14010133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 01/04/2022] [Accepted: 01/08/2022] [Indexed: 02/04/2023] Open
Abstract
Formalin fixation, albeit an outstanding method for morphological and molecular preservation, induces DNA damage and cross-linking, which can hinder nucleic acid screening. This is of particular concern in the detection of low-abundance targets, such as persistent DNA viruses. In the present study, we evaluated the analytical sensitivity of viral detection in lung, liver, and kidney specimens from four deceased individuals. The samples were either frozen or incubated in formalin (±paraffin embedding) for up to 10 days. We tested two DNA extraction protocols for the control of efficient yields and viral detections. We used short-amplicon qPCRs (63–159 nucleotides) to detect 11 DNA viruses, as well as hybridization capture of these plus 27 additional ones, followed by deep sequencing. We observed marginally higher ratios of amplifiable DNA and scantly higher viral genoprevalences in the samples extracted with the FFPE dedicated protocol. Based on the findings in the frozen samples, most viruses were detected regardless of the extended fixation times. False-negative calls, particularly by qPCR, correlated with low levels of viral DNA (<250 copies/million cells) and longer PCR amplicons (>150 base pairs). Our data suggest that low-copy viral DNAs can be satisfactorily investigated from FFPE specimens, and encourages further examination of historical materials.
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Affiliation(s)
- Outi I. Mielonen
- Department of Virology, Helsinki University Hospital, University of Helsinki, 00290 Helsinki, Finland; (O.I.M.); (K.H.)
- Department of Forensic Medicine, University of Helsinki, 00290 Helsinki, Finland;
| | - Diogo Pratas
- Department of Virology, Helsinki University Hospital, University of Helsinki, 00290 Helsinki, Finland; (O.I.M.); (K.H.)
- Department of Electronics, Telecommunications and Informatics, University of Aveiro, 3810-193 Aveiro, Portugal
- Institute of Electronics and Informatics Engineering of Aveiro, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Klaus Hedman
- Department of Virology, Helsinki University Hospital, University of Helsinki, 00290 Helsinki, Finland; (O.I.M.); (K.H.)
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, 00290 Helsinki, Finland;
- Forensic Medicine Unit, Finnish Institute for Health and Welfare, 00271 Helsinki, Finland
| | - Maria F. Perdomo
- Department of Virology, Helsinki University Hospital, University of Helsinki, 00290 Helsinki, Finland; (O.I.M.); (K.H.)
- Correspondence:
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14
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Badran S, Chen M, Coia JE. Multiplex Droplet Digital Polymerase Chain Reaction Assay for Rapid Molecular Detection of Pathogens in Patients With Sepsis: Protocol for an Assay Development Study. JMIR Res Protoc 2021; 10:e33746. [PMID: 34898460 PMCID: PMC8713102 DOI: 10.2196/33746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 10/24/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Blood cultures are the cornerstone of diagnosis for detecting the presence of bacteria or fungi in the blood, with an average detection time of 48 hours and failure to detect a pathogen occurring in approximately 50% of patients with sepsis. Rapid diagnosis would facilitate earlier treatment and/or an earlier switch to narrow-spectrum antibiotics. OBJECTIVE The aim of this study is to develop and implement a multiplex droplet digital polymerase chain reaction (ddPCR) assay as a routine diagnostic tool in the detection and identification of pathogens from whole blood and/or blood culture after 3 hours of incubation. METHODS The study consists of three phases: (1) design of primer-probe pairs for accurate and reliable quantification of the most common sepsis-causing microorganisms using a multiplex reaction, (2) determination of the analytical sensitivity and specificity of the multiplex ddPCR assay, and (3) a clinical study in patients with sepsis using the assay. The QX200 Droplet Digital PCR System will be used for the detection of the following species-specific genes in blood from patients with sepsis: coa (staphylocoagulase) in Staphylococcus aureus, cpsA (capsular polysaccharide) in Streptococcus pneumoniae, uidA (beta-D-glucuronidase) in Escherichia coli, oprL (peptidoglycan-associated lipoprotein) in Pseudomonas aeruginosa, and the highly conserved regions of the 16S rRNA gene for Gram-positive and Gram-negative bacteria. All data will be analyzed using QuantaSoft Analysis Pro Software. RESULTS In phase 1, to determine the optimal annealing temperature for the designed primer-probe pairs, results from a gradient temperature experiment will be collected and the limit of detection (LOD) of the assay will be determined. In phase 2, results for the analytical sensitivity and specificity of the assay will be obtained after an optimization of the extraction and purification method in spiked blood. In phase 3, clinical sensitivity and specificity as compared to the standard blood culture technique will be determined using 301 clinical samples. CONCLUSIONS Successful design of primer-probe pairs in the first phase and subsequent optimization and determination of the LOD will allow progression to phase 3 to compare the novel method with existing blood culture methods. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) PRR1-10.2196/33746.
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Affiliation(s)
- Samir Badran
- Research Unit in Clinical Microbiology, Department of Clinical Diagnostics, Hospital South West Jutland, University Hospital of Southern Denmark, Esbjerg, Denmark.,Department of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Ming Chen
- Department of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark.,Department of Clinical Microbiology, Hospital of Southern Jutland, University Hospital of Southern Denmark, Aabenraa, Denmark
| | - John E Coia
- Research Unit in Clinical Microbiology, Department of Clinical Diagnostics, Hospital South West Jutland, University Hospital of Southern Denmark, Esbjerg, Denmark.,Department of Regional Health Research, Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
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15
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Liu D, Yin H, Wang Y, Cao Y, Yin J, Zhang J, Yin H, Zhao X. Development of a highly sensitive digital PCR assay to quantify long non-coding RNA MYU in urine samples which exhibited great potential as an alternative diagnostic biomarker for prostate cancer. Transl Androl Urol 2021; 10:3815-3825. [PMID: 34804824 PMCID: PMC8575588 DOI: 10.21037/tau-21-820] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 10/21/2021] [Indexed: 12/31/2022] Open
Abstract
Background The diagnostic methods of prostate cancer (PCa) present major drawbacks in that serum prostate specific antigen (PSA) testing lacks specificity for PCa and prostate needle biopsy is a painful and highly invasive procedure for patients. Thus, new alternative screening methods which are specific and non-invasive both in the early detection and in the clinical definitive diagnosis of PCa are in urgent need. Long non-coding RNA MYU has been shown to promote PCa cell proliferation and migration, and is significantly upregulated both at the cellular and tumor tissue level. Therefore, long non-coding RNA MYU may be a new potential diagnostic biomarker for PCa. Methods In the present study, we successfully developed a highly sensitive digital PCR assay to detect long non-coding RNA in clinical urine samples. dPCR was carried out using Qx200 ddPCR EvaGreen Supermix (Bio-Rad) according to the manufacturer’s instructions. Results Our results indicated that the digital PCR assay showed better linearity, repeatability, and reproducibility when compared with real-time quantitative PCR. In addition, we identified the normalized MYU level and used the digital PCR assay to measure it in 100 clinical urine samples. Our study showed that the normalized MYU level is a promising diagnostic biomarker for predicting and evaluating the malignancy of PCa. Conclusions Our findings presented a non-invasive liquid biopsy method to detect an alternative diagnostic parameter which can assist the diagnosis of PCa in clinical practice.
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Affiliation(s)
- Di Liu
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.,JiHua Laboratory, Foshan, China
| | - Huming Yin
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yong Wang
- College of Biomedical Engineering, University of Science and Technology of China, Hefei, China
| | - Yang Cao
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jian Yin
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.,JiHua Laboratory, Foshan, China
| | - Jianping Zhang
- Department of Tuberculosis, The Affiliated Infectious Diseases Hospital of Soochow University, Suzhou, China
| | - Huancai Yin
- CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China.,JiHua Laboratory, Foshan, China
| | - Xiaojun Zhao
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
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16
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Competitiveness of Quantitative Polymerase Chain Reaction (qPCR) and Droplet Digital Polymerase Chain Reaction (ddPCR) Technologies, with a Particular Focus on Detection of Antibiotic Resistance Genes (ARGs). Appl Microbiol 2021. [DOI: 10.3390/applmicrobiol1030028] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
With fast-growing polymerase chain reaction (PCR) technologies and various application methods, the technique has benefited science and medical fields. While having strengths and limitations on each technology, there are not many studies comparing the efficiency and specificity of PCR technologies. The objective of this review is to summarize a large amount of scattered information on PCR technologies focused on the two majorly used technologies: qPCR (quantitative polymerase chain reaction) and ddPCR (droplet-digital polymerase chain reaction). Here we analyze and compare the two methods for (1) efficiency, (2) range of detection and limitations under different disciplines and gene targets, (3) optimization, and (4) status on antibiotic resistance genes (ARGs) analysis. It has been identified that the range of detection and quantification limit varies depending on the PCR method and the type of sample. Careful optimization of target gene analysis is essential for building robust analysis for both qPCR and ddPCR. In our era where mutation of genes may lead to a pandemic of viral infectious disease or antibiotic resistance-induced health threats, this study hopes to set guidelines for meticulous detection, quantification, and analysis to help future prevention and protection of global health, the economy, and ecosystems.
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17
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Sahu R, Vishnuraj MR, Srinivas C, Dadimi B, Megha GK, Pollumahanti N, Malik SS, Vaithiyanathan S, Rawool DB, Barbuddhe SB. Development and comparative evaluation of droplet digital PCR and quantitative PCR for the detection and quantification of Chlamydia psittaci. J Microbiol Methods 2021; 190:106318. [PMID: 34592374 DOI: 10.1016/j.mimet.2021.106318] [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: 07/06/2021] [Revised: 08/28/2021] [Accepted: 08/29/2021] [Indexed: 10/20/2022]
Abstract
Chlamydia psittaci is a zoonotic pathogen mainly transmitted by psittacine birds and poultry. The low shedding rate of the pathogen in the apparently healthy birds and human clinical cases may result in false-negative results. In the present study, a droplet digital PCR (ddPCR) assay was developed and compared with optimized quantitative PCR (qPCR) for the detection of C. psittaci from the clinical samples. The ddPCR assay was found to be comparatively more sensitive than the qPCR, wherein the limit of detection (LOD) of ddPCR was upto 2.4 copies of the DNA template, whereas, the qPCR could detect upto 38 copies of the DNA template in the reaction mixture. Overall, the developed ddPCR assay was found to be robust, specific, and could reliably quantify up to 17.8 copies of the DNA template. Finally, the applicability of the developed ddPCR assay was tested by screening the field samples (n = 124), comprising lung tissues from dead poultry and feral birds; pooled faecal samples from the free-living birds, commercial and backyard poultry farms; pharyngeal and cloacal swabs collected from the duck farms. Of these, a total of seven samples were found to be positive by the ddPCR, whereas, three samples could be detected as positive using the qPCR. The developed ddPCR could serve as a reliable screening tool, particularly in those clinical samples wherein the shedding of C. psittaci is substantially very low.
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Affiliation(s)
- Radhakrishna Sahu
- ICAR-National Research Centre on Meat, Chengicherla, Hyderabad 500092, India; Department of Veterinary Public Health, ICAR- Indian Veterinary Research Institute, Izatnagar 243122, India
| | - M R Vishnuraj
- ICAR-National Research Centre on Meat, Chengicherla, Hyderabad 500092, India
| | - Ch Srinivas
- ICAR-National Research Centre on Meat, Chengicherla, Hyderabad 500092, India
| | - Bhargavi Dadimi
- Department of Veterinary Public Health, ICAR- Indian Veterinary Research Institute, Izatnagar 243122, India
| | - G K Megha
- Department of Veterinary Public Health, ICAR- Indian Veterinary Research Institute, Izatnagar 243122, India
| | | | - Satyaveer S Malik
- Department of Veterinary Public Health, ICAR- Indian Veterinary Research Institute, Izatnagar 243122, India
| | - S Vaithiyanathan
- ICAR-National Research Centre on Meat, Chengicherla, Hyderabad 500092, India
| | - Deepak B Rawool
- ICAR-National Research Centre on Meat, Chengicherla, Hyderabad 500092, India
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18
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Kojabad AA, Farzanehpour M, Galeh HEG, Dorostkar R, Jafarpour A, Bolandian M, Nodooshan MM. Droplet digital PCR of viral DNA/RNA, current progress, challenges, and future perspectives. J Med Virol 2021; 93:4182-4197. [PMID: 33538349 PMCID: PMC8013307 DOI: 10.1002/jmv.26846] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 02/01/2021] [Indexed: 12/18/2022]
Abstract
High-throughput droplet-based digital PCR (ddPCR) is a refinement of the conventional polymerase chain reaction (PCR) methods. In ddPCR, DNA/RNA is encapsulated stochastically inside the microdroplets as reaction chambers. A small percentage of the reaction chamber contains one or fewer copies of the DNA or RNA. After PCR amplification, concentrations are determined based on the proportion of nonfluorescent partitions through the Poisson distribution. Some of the main features of ddPCR include high sensitivity and specificity, absolute quantification without a standard curve, high reproducibility, good tolerance to PCR inhibitor, and high efficacy compared to conventional molecular methods. These advantages make ddPCR a valuable addition to the virologist's toolbox. The following review outlines the recent technological advances in ddPCR methods and their applications in viral identification.
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Affiliation(s)
- Amir Asri Kojabad
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Mahdieh Farzanehpour
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | | | - Ruhollah Dorostkar
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Ali Jafarpour
- Research Center for Clinical VirologyTehran University of Medical SciencesTehranIran
| | - Masoumeh Bolandian
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
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19
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Li H, Chen X, Qiu X, Huang W, Yang C. Comparison of Droplet Digital Polymerase Chain Reaction (ddPCR) and Real-Time Quantitative Polymerase Chain Reaction (qPCR) in Detecting Neonatal Invasive Fungal Infections. J BIOMATER TISS ENG 2021. [DOI: 10.1166/jbt.2021.2408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Invasive fungal infection (IFI) is the leading cause of death in neonatal patients, yet the diagnosis of IFI remains a major challenge. At present, most IFI laboratory diagnostic methods are based on classical, but limited, methods such as fungal isolation and culture and histopathological
examination. Recently, quantitative polymerase chain reaction (qPCR) and droplet digital polymerase chain reaction (ddPCR) technology have been adopted to quantify nucleic-acid identification. In this study, we established qPCR and ddPCR assays for IFI diagnosis and quantification. qPCR and
ddPCR were carried out using identical primers and probe for the amplification of 18S rRNA. Assay results for three fungal strains were positive, whereas ten non-fungal strains had negative results, indicating 100% specificity for both ddPCR and qPCR methods. Genomic DNA of Candida albicans
was tested after a serial dilution to compare the sensitivity of the two PCR methods. The limit of detection of ddPCR was 3.2 copies/L, which was a ten-fold increase compared with that of the qPCR method (32 copies/L). Blood samples from 127 patients with high-risk factors and clinical symptoms
for IFI were collected from a NICU in Shenzhen, China, and analyzed using qPCR and ddPCR. Thirty-four blood samples from neonates had a proven or probable diagnosis of IFI, and 25 of these were positive by qPCR, whereas 30 were positive by ddPCR. Among the 93 blood samples from neonates who
had a possible IFI or no IFI, 24 were positive using qPCR, and 7 were positive using ddPCR. In conclusion, ddPCR is a rapid and accurate pan-fungal detection method and provides a promising prospect for IFI clinical screening.
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Affiliation(s)
- Huitao Li
- Department of Neonatology, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen 518028, Guangdong, PR China
| | - Xueyu Chen
- Department of Neonatology, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen 518028, Guangdong, PR China
| | - Xiaomei Qiu
- Department of Neonatology, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen 518028, Guangdong, PR China
| | - Weimin Huang
- Department of Neonatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, PR China
| | - Chuanzhong Yang
- Department of Neonatology, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen 518028, Guangdong, PR China
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20
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Falzone L, Gattuso G, Lombardo C, Lupo G, Grillo CM, Spandidos DA, Libra M, Salmeri M. Droplet digital PCR for the detection and monitoring of Legionella pneumophila. Int J Mol Med 2020; 46:1777-1782. [PMID: 33000184 PMCID: PMC7521553 DOI: 10.3892/ijmm.2020.4724] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/14/2020] [Indexed: 02/07/2023] Open
Abstract
Legionella pneumophila(L. pneumophila is a harmful pathogen often found in water systems. In hospitals, the absence of L. pneumophila in water systems is mandatory by law, therefore, frequent and effective monitoring of water is of fundamental importance. Molecular methods based on reverse transcription-quantitative polymerase chain reaction (RT-qPCR) have been proposed for the detection of L. pneumophila, however, the sensitivity and accuracy of these methods have not been validated yet. Therefore, it is important to evaluate other strategies able to overcome the limits of culture-based and RT-qPCR methods. On these bases, we compared the sensitivity and accuracy of droplet digital PC (ddPCR) and RT-qPCR in water samples with known concentrations of L. pneumophila and in an in vitro model of water heat treatments. ddPCR showed a higher sensitivity rate and accuracy compared to RT-qPCR in detecting low bacterial load. In addition, ddPCR is not affected by the presence of fragmented DNA and showed higher accuracy than RT-qPC in monitoring the efficacy of heat shock treatments. In conclusion, ddPCR represents an innovative strategy to effectively detect L. pneumophila in water samples. Thanks to its high robustness, ddPCR could be applied also for the detection of L. pneumophila in patients with suspected legionellosis.
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Affiliation(s)
- Luca Falzone
- Epidemiology Unit, IRCCS Istituto Nazionale Tumori 'Fondazione G. Pascale', I‑80131 Naples, Italy
| | - Giuseppe Gattuso
- Department of Biomedical and Biotechnological Sciences, Section of General Pathology, University of Catania, I‑95123 Catania, Italy
| | - Cinzia Lombardo
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, I‑95123 Catania, Italy
| | - Gabriella Lupo
- Department of Biomedical and Biotechnological Sciences, Section of Biochemistry, University of Catania, I‑95123 Catania, Italy
| | - Caterina Maria Grillo
- Department of Medical Sciences, Surgical and Advanced Technologies, GF Ingrassia, University of Catania, I‑95123 Catania, Italy
| | - Demetrios A Spandidos
- Laboratory of Clinical Virology, Medical School, University of Crete, 71003 Heraklion, Greece
| | - Massimo Libra
- Department of Biomedical and Biotechnological Sciences, Section of General Pathology, University of Catania, I‑95123 Catania, Italy
| | - Mario Salmeri
- Department of Biomedical and Biotechnological Sciences, Section of Microbiology, University of Catania, I‑95123 Catania, Italy
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21
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Kutti T, Johnsen IA, Skaar KS, Ray JL, Husa V, Dahlgren TG. Quantification of eDNA to Map the Distribution of Cold-Water Coral Reefs. FRONTIERS IN MARINE SCIENCE 2020. [PMID: 0 DOI: 10.3389/fmars.2020.00446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
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22
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Csoboz B, Rasheed K, Sveinbjørnsson B, Moens U. Merkel cell polyomavirus and non-Merkel cell carcinomas: guilty or circumstantial evidence? APMIS 2020; 128:104-120. [PMID: 31990105 DOI: 10.1111/apm.13019] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/02/2019] [Indexed: 12/11/2022]
Abstract
Merkel cell polyomavirus (MCPyV) is the major causative factor of the rare but aggressive cancer, Merkel cell carcinoma (MCC). Two characteristics of MCPyV-positive MCCs are integration of the viral genome and expression of a truncated version of one of its oncogenic proteins, namely large T antigen. The strong association of MCPyV with MCC development has incited researchers to further investigate a possible role of this virus in other cancers. However, many of the examples displaying the presence of the virus in the various non-MCC cancers are not able to clearly demonstrate a direct connection between cellular transformation and the presence of the virus. The prevalence of the virus is significantly lower in non-MCC cancers compared to MCCs, with a lower level of viral load and sparse viral protein expression. Moreover, the state of the viral genome, and whether a truncated large T antigen is expressed, has rarely been investigated. Nonetheless, considering the strong oncogenic potential of MCPyV proteins in MCC, the plausible contribution of MCPyV to transformation and cancer growth in non-MCC tumors cannot be ruled out. Furthermore, the absence of MCPyV in cancers does not exclude a hit-and-run mechanism, or the oncoproteins of MCPyV may potentiate the neoplastic process mediated by co-infecting oncoviruses such as high-risk human papillomaviruses and Epstein-Barr virus. The current review is focusing on the available data describing the presence of MCPyV in non-MCC tumors, with an aim to provide a comprehensive overview of the corresponding literature and to discuss the potential contribution of MCPyV to non-MCC cancer in light of this.
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Affiliation(s)
- Balint Csoboz
- Molecular Inflammation Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Kashif Rasheed
- Molecular Inflammation Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Baldur Sveinbjørnsson
- Molecular Inflammation Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
| | - Ugo Moens
- Molecular Inflammation Research Group, Department of Medical Biology, University of Tromsø - The Arctic University of Norway, Tromsø, Norway
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23
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Salipante SJ, Jerome KR. Digital PCR—An Emerging Technology with Broad Applications in Microbiology. Clin Chem 2019; 66:117-123. [DOI: 10.1373/clinchem.2019.304048] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 09/18/2019] [Indexed: 01/10/2023]
Abstract
Abstract
BACKGROUND
The PCR and its variant, quantitative PCR (qPCR), have revolutionized the practice of clinical microbiology. Continued advancements in PCR have led to a new derivative, digital PCR (dPCR), which promises to address certain limitations inherent to qPCR.
CONTENT
Here we highlight the important technical differences between qPCR and dPCR, and the potential advantages and disadvantages of each. We then review specific situations in which dPCR has been implemented in clinical microbiology and the results of such applications. Finally, we attempt to place dPCR in the context of other emerging technologies relevant to the clinical laboratory, including next-generation sequencing.
SUMMARY
dPCR offers certain clear advantages over traditional qPCR, but these are to some degree offset by limitations of the technology, at least as currently practiced. Laboratories considering implementation of dPCR should carefully weigh the potential advantages and disadvantages of this powerful technique for each specific application planned.
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Affiliation(s)
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington, Seattle, WA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA
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24
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Zakrzewska K, Arvia R, Torcia MG, Clemente AM, Tanturli M, Castronovo G, Sighinolfi G, Giuggioli D, Ferri C. Effects of Parvovirus B19 In Vitro Infection on Monocytes from Patients with Systemic Sclerosis: Enhanced Inflammatory Pathways by Caspase-1 Activation and Cytokine Production. J Invest Dermatol 2019; 139:2125-2133.e1. [DOI: 10.1016/j.jid.2019.03.1144] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 03/22/2019] [Accepted: 03/22/2019] [Indexed: 01/28/2023]
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25
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Frías M, Rivero-Juárez A, Téllez F, Palacios R, Jiménez-Arranz Á, Pineda JA, Merino D, Gómez-Vidal MA, Pérez-Camacho I, Camacho Á, Rivero A. Evaluation of hepatitis C viral RNA persistence in HIV-infected patients with long-term sustained virological response by droplet digital PCR. Sci Rep 2019; 9:12507. [PMID: 31467339 PMCID: PMC6715682 DOI: 10.1038/s41598-019-48966-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 08/13/2019] [Indexed: 12/12/2022] Open
Abstract
Several studies have reported the persistence of HCV RNA in liver and/or peripheral blood mononuclear cells (PBMCs) in spite of undetectable viremia in patients who have achieved sustained virological response (SVR). This event, defined as occult HCV infection, remains controversial and low titers of persistent virus may be underestimated because it has not yet been analyzed by a highly sensitive test such as droplet digital PCR (ddPCR). This method provides an alternate ultra-sensitive detection technique for very low numbers of copies of viral RNA or DNA. The aim of this study was to evaluate the persistence of HCV in HIV-coinfected patients with long-term SVR using ddPCR. For each patient, the presence of HCV RNA in serum and PBMCs at baseline was determined by nested RT-ddPCR. Patients with HCV RNA in PBMCs at baseline were followed until the end of the study. One hundred and twenty-three patients were analyzed for persistence of HCV RNA in serum and PBMCs. Persistence of HCV was not found in serum in any patient. HCV RNA was detected in PBMCs in one patient (0.81%; 95% CI: 0.04–3.94) and resolved spontaneously during follow-up. Persistence of HCV RNA in PBMCs is not a common event in HIV/HCV co-infected patients with long-term SVR evaluated by RT-ddPCR.
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Affiliation(s)
- Mario Frías
- Unidad de Enfermedades Infecciosas. Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía de Córdoba, Universidad de Córdoba, Córdoba, Spain
| | - Antonio Rivero-Juárez
- Unidad de Enfermedades Infecciosas. Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía de Córdoba, Universidad de Córdoba, Córdoba, Spain.
| | - Francisco Téllez
- Unidad Gestión Clínica Enfermedades Infecciosas, Hospital La Línea, AGS Campo de Gibraltar, Cádiz, Spain
| | - Rosario Palacios
- Unidad de Enfermedades Infecciosas. Hospital Universitario Virgen de la Victoria, Complejo Hospitalario Provincial de Málaga, Málaga, Spain
| | - Álvaro Jiménez-Arranz
- Unidad de Genómica. Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía, Universidad de Córdoba, Córdoba, Spain
| | - Juan A Pineda
- Unidad de Enfermedades Infecciosas y Microbiología, Hospital Universitario de Valme, Instituto de Biomedicina de Sevilla (iBiS), Sevilla, Spain
| | - Dolores Merino
- Unidad de Enfermedades Infecciosas, Hospitales Juan Ramón Jiménez e Infanta Elena de Huelva, Huelva, Spain
| | | | - Inés Pérez-Camacho
- Unidad de Enfermedades Infecciosas, Hospital de Poniente, El Ejido, Spain
| | - Ángela Camacho
- Unidad de Enfermedades Infecciosas. Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía de Córdoba, Universidad de Córdoba, Córdoba, Spain
| | - Antonio Rivero
- Unidad de Enfermedades Infecciosas. Instituto Maimónides de Investigación Biomédica de Córdoba (IMIBIC), Hospital Universitario Reina Sofía de Córdoba, Universidad de Córdoba, Córdoba, Spain
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26
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Schibler M, Brito F, Zanella MC, Zdobnov EM, Laubscher F, L'Huillier AG, Ambrosioni J, Wagner N, Posfay-Barbe KM, Docquier M, Schiffer E, Savoldelli GL, Fournier R, Lenggenhager L, Cordey S, Kaiser L. Viral Sequences Detection by High-Throughput Sequencing in Cerebrospinal Fluid of Individuals with and without Central Nervous System Disease. Genes (Basel) 2019; 10:genes10080625. [PMID: 31431002 PMCID: PMC6723360 DOI: 10.3390/genes10080625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/12/2019] [Accepted: 08/14/2019] [Indexed: 12/16/2022] Open
Abstract
Meningitis, encephalitis, and myelitis are various forms of acute central nervous system (CNS) inflammation, which can coexist and lead to serious sequelae. Known aetiologies include infections and immune-mediated processes. Despite advances in clinical microbiology over the past decades, the cause of acute CNS inflammation remains unknown in approximately 50% of cases. High-throughput sequencing was performed to search for viral sequences in cerebrospinal fluid (CSF) samples collected from 26 patients considered to have acute CNS inflammation of unknown origin, and 10 patients with defined causes of CNS diseases. In order to better grasp the clinical significance of viral sequence data obtained in CSF, 30 patients without CNS disease who had a lumbar puncture performed during elective spinal anaesthesia were also analysed. One case of human astrovirus (HAstV)-MLB2-related meningitis and disseminated infection was identified. No other viral sequences that can easily be linked to CNS inflammation were detected. Viral sequences obtained in all patient groups are discussed. While some of them reflect harmless viral infections, others result from reagent or sample contamination, as well as index hopping. Altogether, this study highlights the potential of high-throughput sequencing in identifying previously unknown viral neuropathogens, as well as the interpretation issues related to its application in clinical microbiology.
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Affiliation(s)
- Manuel Schibler
- Laboratory of Virology, Laboratory Medicine Division, Diagnostic Department, Geneva University Hospitals, 1205 Geneva, Switzerland.
| | - Francisco Brito
- Swiss Institute of Bioinformatics, 1206 Geneva, Switzerland
- Department of Genetic Medicine and Development, Faculty of Medicine of Geneva, 1206 Geneva, Switzerland
| | - Marie-Céline Zanella
- Laboratory of Virology, Laboratory Medicine Division, Diagnostic Department, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Evgeny M Zdobnov
- Swiss Institute of Bioinformatics, 1206 Geneva, Switzerland
- Department of Genetic Medicine and Development, Faculty of Medicine of Geneva, 1206 Geneva, Switzerland
| | - Florian Laubscher
- Laboratory of Virology, Laboratory Medicine Division, Diagnostic Department, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Arnaud G L'Huillier
- Paediatric Infectious Diseases Unit, Department of Women-Children-Teenagers, Geneva University Hospitals and Medical School, 1205 Geneva, Switzerland
| | - Juan Ambrosioni
- Infectious Diseases Service, Hospital Clinic-IDIBAPS, University of Barcelona, 08036 Barcelona, Spain
| | - Noémie Wagner
- Paediatric Infectious Diseases Unit, Department of Women-Children-Teenagers, Geneva University Hospitals and Medical School, 1205 Geneva, Switzerland
| | - Klara M Posfay-Barbe
- Paediatric Infectious Diseases Unit, Department of Women-Children-Teenagers, Geneva University Hospitals and Medical School, 1205 Geneva, Switzerland
| | - Mylène Docquier
- iGE3 Genomics Platform, University of Geneva, 1206 Geneva, Switzerland
| | - Eduardo Schiffer
- Anaesthesiology Division, Department of Anaesthesiology, Pharmacology, Intensive Care and Emergency Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland
- Faculty of Medicine of Geneva, University of Geneva, 1205 Geneva, Switzerland
| | - Georges L Savoldelli
- Anaesthesiology Division, Department of Anaesthesiology, Pharmacology, Intensive Care and Emergency Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland
- Faculty of Medicine of Geneva, University of Geneva, 1205 Geneva, Switzerland
| | - Roxane Fournier
- Anaesthesiology Division, Department of Anaesthesiology, Pharmacology, Intensive Care and Emergency Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Lauriane Lenggenhager
- Laboratory of Virology, Laboratory Medicine Division, Diagnostic Department, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Samuel Cordey
- Laboratory of Virology, Laboratory Medicine Division, Diagnostic Department, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Laurent Kaiser
- Laboratory of Virology, Laboratory Medicine Division, Diagnostic Department, Geneva University Hospitals, 1205 Geneva, Switzerland
- Faculty of Medicine of Geneva, University of Geneva, 1205 Geneva, Switzerland
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27
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Dupas E, Legendre B, Olivier V, Poliakoff F, Manceau C, Cunty A. Comparison of real-time PCR and droplet digital PCR for the detection of Xylella fastidiosa in plants. J Microbiol Methods 2019; 162:86-95. [DOI: 10.1016/j.mimet.2019.05.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/20/2019] [Accepted: 05/20/2019] [Indexed: 12/14/2022]
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28
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Pinheiro-de-Oliveira TF, Fonseca-Júnior AA, Camargos MF, Laguardia-Nascimento M, Giannattasio-Ferraz S, Cottorello ACP, de Oliveira AM, Góes-Neto A, Barbosa-Stancioli EF. Reverse transcriptase droplet digital PCR to identify the emerging vesicular virus Senecavirus A in biological samples. Transbound Emerg Dis 2019; 66:1360-1369. [PMID: 30864242 DOI: 10.1111/tbed.13168] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 03/05/2019] [Accepted: 03/06/2019] [Indexed: 12/13/2022]
Abstract
Senecavirus A (SVA) belonging to the family Picornaviridae, genus Senecavirus was incidentally isolated in 2002 from the PER.C6 (transformed foetal retinoblast) cell line. However, currently, this virus is associated with vesicular disease in swine and it has been reported in countries such as the United States of America, Canada, China, Thailand and Colombia. In Brazil, the SVA was firstly reported in 2015 in outbreaks of vesicular disease in swine, clinically indistinguishable of Foot-and-mouth disease, a contagious viral disease that generates substantial economic losses. In the present work, it was standardized a diagnostic tool for SVA based on RNA reverse transcriptase droplet digital PCR (RT-ddPCR) using one-step and two-step approaches. Analytical sensitivity and specificity were done in parallel with real-time PCR, RT-qPCR (one-step and two-step) for comparison of sensitivity and specificity of both methods. In the standardization of RT-ddPCR, the double-quenched probe and the temperature gradient were crucial to reduce background and improve amplitude between positive and negative droplets. The limit of detection and analytical specificity of techniques of one-step techniques showed superior performance than two-step methods described here. Additionally, the results showed 94.2% concordance (p < 0.001) for RT-ddPCR and RT-qPCR using the one-step assay approach and biological samples from Brazilian outbreaks of Senecavirus A. However, ddRT-PCR had a better performance than RT-PCR when swine serum pools were tested. According to the results, the one-step RT-ddPCR and RT-qPCR is highlighted to be used as an auxiliary diagnostic tool for Senecavirus A and for viral RNA absolute quantification in biological samples (RT-ddPCR), being a useful tool for vesicular diseases control programs.
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Affiliation(s)
| | - A A Fonseca-Júnior
- Ministério da Agricultura, Pecuária e Abastecimento, Pedro Leopoldo, Minas Gerais, Brazil
| | - M F Camargos
- Ministério da Agricultura, Pecuária e Abastecimento, Pedro Leopoldo, Minas Gerais, Brazil
| | - M Laguardia-Nascimento
- Ministério da Agricultura, Pecuária e Abastecimento, Pedro Leopoldo, Minas Gerais, Brazil
| | | | - A C P Cottorello
- Ministério da Agricultura, Pecuária e Abastecimento, Pedro Leopoldo, Minas Gerais, Brazil
| | - A M de Oliveira
- Ministério da Agricultura, Pecuária e Abastecimento, Pedro Leopoldo, Minas Gerais, Brazil
| | - A Góes-Neto
- Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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29
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Powell EA, Babady NE. Digital PCR in the Clinical Microbiology Laboratory: Another Tool on the Molecular Horizon. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.clinmicnews.2018.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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30
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Auvré F, Coutier J, Martin MT, Fortunel NO. Quantitative Detection of Low-Abundance Transcripts at Single-Cell Level in Human Epidermal Keratinocytes by Digital Droplet Reverse Transcription-Polymerase Chain Reaction. Methods Mol Biol 2018; 1879:31-41. [PMID: 29736807 DOI: 10.1007/7651_2018_149] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Genetic and epigenetic characterization of the large cellular diversity observed within tissues is essential to understanding the molecular networks that ensure the regulation of homeostasis, repair, and regeneration, but also pathophysiological processes. Skin is composed of multiple cell lineages and is therefore fully concerned by this complexity. Even within one particular lineage, such as epidermal keratinocytes, different immaturity statuses or differentiation stages are represented, which are still incompletely characterized. Accordingly, there is presently great demand for methods and technologies enabling molecular investigation at single-cell level. Also, most current methods used to analyze gene expression at RNA level, such as RT-qPCR, do not directly provide quantitative data, but rather comparative ratios between two conditions. A second important need in skin biology is thus to determine the number of RNA molecules in a given cell sample. Here, we describe a workflow that we have set up to meet these specific needs, by means of transcript quantification in cellular micro-samples using flow cytometry sorting and reverse transcription-digital droplet polymerase chain reaction. As a proof-of-principle, the workflow was tested for the detection of transcription factor transcripts expressed at low levels in keratinocyte precursor cells. A linear correlation was found between quantification values and keratinocyte input numbers in a low quantity range from 40 cells to 1 cell. Interpretable signals were repeatedly obtained from single-cell samples corresponding to estimated expression levels as low as 10-20 transcript copies per keratinocyte or less. The present workflow may have broad applications for the detection and quantification of low-abundance nucleic acid species in single cells, opening up perspectives for the study of cell-to-cell genetic and molecular heterogeneity. Interestingly, the process described here does not require internal references such as house-keeping gene expression, as it is initiated with defined cell numbers, precisely sorted by flow cytometry.
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Affiliation(s)
- Frédéric Auvré
- Laboratoire de Génomique et Radiobiologie de la Kératinopoïèse, CEA/DRF/IBFJ/IRCM, Evry, France.,INSERM U967, Fontenay-aux-Roses, France.,Université Paris-Diderot, Paris 7, France.,Université Paris-Saclay, Paris 11, France
| | - Julien Coutier
- Laboratoire de Génomique et Radiobiologie de la Kératinopoïèse, CEA/DRF/IBFJ/IRCM, Evry, France.,INSERM U967, Fontenay-aux-Roses, France.,Université Paris-Diderot, Paris 7, France.,Université Paris-Saclay, Paris 11, France
| | - Michèle T Martin
- Laboratoire de Génomique et Radiobiologie de la Kératinopoïèse, CEA/DRF/IBFJ/IRCM, Evry, France.,INSERM U967, Fontenay-aux-Roses, France.,Université Paris-Diderot, Paris 7, France.,Université Paris-Saclay, Paris 11, France
| | - Nicolas O Fortunel
- Laboratoire de Génomique et Radiobiologie de la Kératinopoïèse, CEA/DRF/IBFJ/IRCM, Evry, France. .,INSERM U967, Fontenay-aux-Roses, France. .,Université Paris-Diderot, Paris 7, France. .,Université Paris-Saclay, Paris 11, France.
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31
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Characterization of oseltamivir-resistant influenza virus populations in immunosuppressed patients using digital-droplet PCR: Comparison with qPCR and next generation sequencing analysis. Antiviral Res 2017; 145:160-167. [DOI: 10.1016/j.antiviral.2017.07.021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 07/28/2017] [Accepted: 07/31/2017] [Indexed: 01/27/2023]
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32
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Vynck M, Vandesompele J, Thas O. Quality control of digital PCR assays and platforms. Anal Bioanal Chem 2017; 409:5919-5931. [PMID: 28799053 DOI: 10.1007/s00216-017-0538-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/11/2017] [Accepted: 07/17/2017] [Indexed: 10/19/2022]
Abstract
Digital polymerase chain reaction (digital PCR, dPCR) is a direct nucleic acid quantification method, thus requiring no standard curves unlike quantitative real-time PCR (qPCR). Nevertheless, evaluation of the linear dynamic range, accuracy, and precision of an assay or platform is recommended, as there are several potential causes of important non-linearity, bias, and imprecision. Ignoring these quality issues may lead to erroneous quantification. This necessitates an approach akin to the construction of standard curves. We study the pitfalls associated with the evaluation of such an experiment, and provide guidelines for the assessment of linearity, accuracy, and precision in dPCR experiments. We present simulation results and a case study supporting the importance of a thorough evaluation. Further, typically presented plots and statistics may not reveal problems with linearity, accuracy, or precision. We find that a robust weighted least-squares approach is highly advisable, yet may also suffer from an inflated false-positive rate. The proposed assessments are also applicable to other analyses, such as the comparison of results obtained from qPCR and dPCR. A web tool for quality evaluation, dPCalibRate, is available.
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Affiliation(s)
- Matthijs Vynck
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
| | - Jo Vandesompele
- Center for Medical Genetics, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium.,Bioinformatics Institute Ghent: from Nucleotides to Networks (BIG N2N), Ghent University, De Pintelaan 185, 9000, Ghent, Belgium.,Biogazelle, Technologiepark 3, 9052, Zwijnaarde, Belgium
| | - Olivier Thas
- Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Coupure Links 653, 9000, Ghent, Belgium.,Bioinformatics Institute Ghent: from Nucleotides to Networks (BIG N2N), Ghent University, Coupure Links 653, 9000, Ghent, Belgium.,National Institute for Applied Statistics Research Australia (NIASRA), School of Mathematics and Applied Statistics, University of Wollongong, NSW, 2522, Australia
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Gil BM, Valero D. NUEVAS TECNOLOGÍAS PARA EL DIAGNÓSTICO GENÉTICO. REVISTA MÉDICA CLÍNICA LAS CONDES 2017. [DOI: 10.1016/j.rmclc.2017.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
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