1
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Mendes de Almeida V, Engel DF, Ricci MF, Cruz CS, Lopes ÍS, Alves DA, d’ Auriol M, Magalhães J, Machado EC, Rocha VM, Carvalho TG, Lacerda LSB, Pimenta JC, Aganetti M, Zuccoli GS, Smith BJ, Carregari VC, da Silva Rosa E, Galvão I, Dantas Cassali G, Garcia CC, Teixeira MM, André LC, Ribeiro FM, Martins FS, Saia RS, Costa VV, Martins-de-Souza D, Hansbro PM, Marques JT, Aguiar ERGR, Vieira AT. Gut microbiota from patients with COVID-19 cause alterations in mice that resemble post-COVID symptoms. Gut Microbes 2023; 15:2249146. [PMID: 37668317 PMCID: PMC10481883 DOI: 10.1080/19490976.2023.2249146] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/19/2023] [Accepted: 08/14/2023] [Indexed: 09/06/2023] Open
Abstract
Long-term sequelae of coronavirus disease (COVID)-19 are frequent and of major concern. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection affects the host gut microbiota, which is linked to disease severity in patients with COVID-19. Here, we report that the gut microbiota of post-COVID subjects had a remarkable predominance of Enterobacteriaceae strains with an antibiotic-resistant phenotype compared to healthy controls. Additionally, short-chain fatty acid (SCFA) levels were reduced in feces. Fecal transplantation from post-COVID subjects to germ-free mice led to lung inflammation and worse outcomes during pulmonary infection by multidrug-resistant Klebsiella pneumoniae. transplanted mice also exhibited poor cognitive performance. Overall, we show prolonged impacts of SARS-CoV-2 infection on the gut microbiota that persist after subjects have cleared the virus. Together, these data demonstrate that the gut microbiota can directly contribute to post-COVID sequelae, suggesting that it may be a potential therapeutic target.
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Affiliation(s)
- Viviani Mendes de Almeida
- Laboratory of Microbiota and Immunomodulation - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Daiane F. Engel
- Department of Clinical Analysis, School of Pharmacy, Universidade Federal de Ouro Preto - UFOP, Ouro Preto, Brazil
| | - Mayra F. Ricci
- Laboratory of Microbiota and Immunomodulation - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Clênio Silva Cruz
- Laboratory of Microbiota and Immunomodulation - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Ícaro Santos Lopes
- Laboratory of Virus Bioinformatics - Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz - UESC, Ilhéus, Brazil
| | - Daniele Almeida Alves
- Laboratory of RNA Interference and Antiviral Immunity - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Mirna d’ Auriol
- Laboratory of Toxicology - Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - João Magalhães
- Laboratory of Microbiota and Immunomodulation - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Elayne C. Machado
- Laboratory of Microbiota and Immunomodulation - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Victor M. Rocha
- Laboratory of Microbiota and Immunomodulation - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Toniana G. Carvalho
- Laboratory of Neurobiochemistry - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Larisse S. B. Lacerda
- Center for Research and Development of Drugs - Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Jordane C. Pimenta
- Center for Research and Development of Drugs - Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Mariana Aganetti
- Laboratory of Microbiota and Immunomodulation - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Giuliana S. Zuccoli
- Laboratory of Neuroproteomics - Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade do Estado de Campinas - UNICAMP, Campinas, Brazil
| | - Bradley J. Smith
- Laboratory of Neuroproteomics - Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade do Estado de Campinas - UNICAMP, Campinas, Brazil
| | - Victor C. Carregari
- Laboratory of Neuroproteomics - Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade do Estado de Campinas - UNICAMP, Campinas, Brazil
| | - Erika da Silva Rosa
- Laboratory of Microbiota and Immunomodulation - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Izabela Galvão
- Laboratory of Microbiota and Immunomodulation - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Geovanni Dantas Cassali
- Laboratory of Comparative Pathology - Department of Pathology, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Cristiana C. Garcia
- Laboratory of Respiratory Viruses and Measles, Instituto Oswaldo Cruz - Fiocruz, Rio de Janeiro, Brazil
| | - Mauro Martins Teixeira
- Center for Research and Development of Drugs - Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Leiliane C. André
- Laboratory of Toxicology - Department of Clinical and Toxicological Analysis, Faculty of Pharmacy, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Fabiola Mara Ribeiro
- Laboratory of Neurobiochemistry - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Flaviano S. Martins
- Laboratory of Biotherapeutic Agents - Department of Microbiology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Rafael Simone Saia
- Laboratory of Intestinal Physiology - Department of Physiology, Ribeirão Preto Medical School, Universidade de São Paulo, Ribeirão Preto, Brazil
| | - Vivian Vasconcelos Costa
- Center for Research and Development of Drugs - Department of Morphology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics - Department of Biochemistry and Tissue Biology, Institute of Biology, Universidade do Estado de Campinas - UNICAMP, Campinas, Brazil
- D’Or Institute for Research and Education, São Paulo, Brazil
- Experimental Medicine Research Cluster, Universidade do Estado de Campinas - UNICAMP, Campinas, Brazil
- National Institute of Biomarkers in Neuropsychiatry, National Council for Scientific and Technological Development, São Paulo, Brazil
| | - Philip M. Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Sydney, Australia
| | - João Trindade Marques
- Laboratory of RNA Interference and Antiviral Immunity - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
- CNRS UPR9022, University of Strasbourg, Strasbourg, France
| | - Eric R. G. R. Aguiar
- Laboratory of Virus Bioinformatics - Department of Biological Science, Center of Biotechnology and Genetics, Universidade Estadual de Santa Cruz - UESC, Ilhéus, Brazil
| | - Angélica T. Vieira
- Laboratory of Microbiota and Immunomodulation - Department of Biochemistry and Immunology, Institute of Biological Sciences, Universidade Federal de Minas Gerais - UFMG, Belo Horizonte, Brazil
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2
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Thapar I, Langan LM, Davis H, Norman RS, Bojes HK, Brooks BW. Influence of storage conditions and multiple freeze-thaw cycles on N1 SARS-CoV-2, PMMoV, and BCoV signal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 896:165098. [PMID: 37392884 PMCID: PMC10307669 DOI: 10.1016/j.scitotenv.2023.165098] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/03/2023]
Abstract
Wastewater-based epidemiology/wastewater-based surveillance (WBE/WBS) continues to serve as an effective means of monitoring various diseases, including COVID-19 and the emergence of SARS-CoV-2 variants, at the population level. As the use of WBE expands, storage conditions of wastewater samples will play a critical role in ensuring the accuracy and reproducibility of results. In this study, the impacts of water concentration buffer (WCB), storage temperature, and freeze-thaw cycles on the detection of SARS-CoV-2 and other WBE-related gene targets were examined. Freeze-thawing of concentrated samples did not significantly affect (p > 0.05) crossing/cycle threshold (Ct) value for any of the gene targets studied (SARS-CoV-2 N1, PMMoV, and BCoV). However, use of WCB during concentration resulted in a significant (p < 0.05) decrease in Ct for all targets, and storage at -80 °C (in contrast to -20 °C) appeared preferable for wastewater storage signal stability based on decreased Ct values, although this was only significantly different (p < 0.05) for the BCoV target. Interestingly, when Ct values were converted to gene copies per influent sample, no significant differences (p > 0.05) were observed in any of the targets examined. Stability of RNA targets in concentrated wastewater against freeze-thaw degradation supports archiving of concentrated samples for use in retrospective examination of COVID-19 trends and tracing SARS-CoV-2 variants and potentially other viruses, and provides a starting point for establishing a consistent procedure for specimen collection and storage for the WBE/WBS community.
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Affiliation(s)
- Isha Thapar
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA
| | - Laura M Langan
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA.
| | - Haley Davis
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Harbor Branch Oceanographic Institute, Florida Atlantic University, 5600 US-1, Fort Pierce, FL 34946, USA
| | - R Sean Norman
- Department of Environmental Health Sciences, Arnold School of Public Health, South Carolina, 921 Assembly St., Columbia, SC 29208, USA
| | - Heidi K Bojes
- Environmental Epidemiology and Disease Registries Section, Texas Department of State Health Services, Austin, TX 78756, USA
| | - Bryan W Brooks
- Department of Environmental Science, Baylor University, One Bear Place #97266, Waco, TX 76798, USA; Center for Reservoir and Aquatic Systems Research, Baylor University, One Bear Place #97178, Waco, TX 76798, USA; Institute of Biomedical Studies, Baylor University, One Bear Place #97224, Waco, TX 76798, USA
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3
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Gao J, Lin D, Hou C, Shen Y, Li Y, Wu D, Xu Y. The clinical value of anal swabs for microbial detection in allogeneic haematopoietic stem cell transplantation. Transplant Cell Ther 2023; 29:619.e1-619.e9. [PMID: 37499872 DOI: 10.1016/j.jtct.2023.07.018] [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: 05/16/2023] [Revised: 07/17/2023] [Accepted: 07/18/2023] [Indexed: 07/29/2023]
Abstract
The intestinal microbiota plays critical roles in allogeneic hematopoietic stem cell transplantation (allo-HSCT). Rapid and effective microbial detection methods have important guiding value for the selection of intervention strategies for allo-HSCT recipients. We evaluated the application of the anal swab test before transplantation in allo-HSCT recipients. A total of 120 patients who underwent anal swab testing before allo-HSCT were retrospectively analyzed and divided into 3 groups: sterile (aseptic growth-negative), G+ (gram-positive bacterial colonization), and G- (gram-negative bacterial colonization). On 16S rRNA sequencing, gram-negative bacteria predominated in the G- group before and after transplantation. Compared with the sterile group, the percentage of natural killer cells was higher and the percentage of T cells was lower after transplantation in the G- group at 1 month after transplantation. The percentage of CD4+ and CD4+CD8+ T cells was lower and the percentage of regulatory T cells was higher in the G- group. The plasma levels of proinflammatory cytokines (TNF-α, IFN-γ, IL-6, and IL-17A) at 2 weeks post-transplantation were lower in the G- group than in the sterile group, as was the cumulative incidence of grade III-IV acute graft-versus-host disease (GVHD). Gram-negative bacterial colonization before allo-HSCT was associated with low rates of bloodstream infections within 100 days post-transplantation and cytomegalovirus reactivation at 100 days to 2 years post-transplantation. Moreover, patients in the G- group had a higher rate of 2-year GVHD-free, relapse-free survival compared with patients in the sterile group. The detection results using anal swabs were consistent with the gram-negative or gram-positive bacteria abundance of 16S rRNA sequencing results and associated with immune homeostasis and clinical outcomes after allo-HSCT. Anal swab testing may have potential advantages as a simple and effective method for microbial detection in allo-HSCT.
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Affiliation(s)
- Jun Gao
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China; Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Dandan Lin
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China; Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Chang Hou
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China; Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Ying Shen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China; Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Yangzi Li
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China; Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Depei Wu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China; Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China
| | - Yang Xu
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, China; Institute of Blood and Marrow Transplantation, Collaborative Innovation Center of Hematology, Soochow University, Suzhou, China.
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4
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Espira LM, Gessese B, Kassa BA, Wu CC, Riley J, Bedru S, Sahilu G, Desta A, Baye K, Jones AD, Love NG, Eisenberg JNS. Multiscalar Evaluation of the Water Distribution System and Diarrheal Disease Risk in Addis Ababa, Ethiopia. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2023; 57:13313-13324. [PMID: 37642551 PMCID: PMC10501120 DOI: 10.1021/acs.est.2c08976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/31/2023]
Abstract
Despite growing urbanization, our understanding of the impacts of water and sanitation on human health has largely come from studies in rural sectors. To this end, we collected data at both regional (water quality measures from water treatment systems) and community (cross-sectional surveys) scales to examine determinants of enteric pathogen infection and diarrheal disease among infants in Addis Ababa, Ethiopia. Regionally, the Legedadi water treatment plant had significantly lower heterotrophic plate counts, total coliform counts, and fecal coliform counts compared with the Gefersa water treatment plant. The number of pathogen types in infant stool also differed by plant. Decreases in chlorine levels and increases in the relative abundance of Gammaproteobacteria with distance from treatment plants suggest a compromised water distribution system. In communities, infants in households that obtained water from yard pipes or public taps had significantly lower odds of diarrhea compared to households that had water piped into their dwellings (OR = 0.35, 95% CI 0.16, 0.76, and OR = 0.39, 95% CI 0.15, 1.00, respectively). Similarly, infants in households that boiled or filtered water had significantly lower odds of diarrhea compared to households that did not treat water (OR = 0.40, 95% CI 0.19, 0.86 and OR = 0.23, 95% CI 0.06, 0.84, respectively). Integrating multiscalar data better informs the health impacts of water in urban settings.
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Affiliation(s)
- Leon M. Espira
- Department
of Epidemiology, University of Michigan
School of Public Health, Ann Arbor, Michigan 48109, United States
| | - Brook Gessese
- Ethiopian
Institute of Water Resources, Addis Ababa
University, Addis
Ababa 150461, Ethiopia
| | - Bayable A. Kassa
- Institute
of Biotechnology, Addis Ababa University, Addis Ababa 1176, Ethiopia
| | - Chia-Chen Wu
- Institute
of Environmental Engineering, National Yang
Ming Chiao Tung University, Hsinchu City 30010, Taiwan
| | - Joshua Riley
- Department
of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Seifedin Bedru
- School of
Civil and Environmental Engineering, Addis
Ababa University, Addis Ababa 1176, Ethiopia
| | - Geremew Sahilu
- School of
Civil and Environmental Engineering, Addis
Ababa University, Addis Ababa 1176, Ethiopia
| | - Adey Desta
- Department
of Microbial and Cellular Biology, Addis
Ababa University, Addis Ababa 1176, Ethiopia
| | - Kaleab Baye
- Center
for
Food Science and Nutrition, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa 1176, Ethiopia
| | - Andrew D. Jones
- Department
of Nutritional Sciences, University of Michigan
School of Public Health, Ann Arbor, Michigan 48109, United States
| | - Nancy G. Love
- Department
of Civil and Environmental Engineering, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Joseph N. S. Eisenberg
- Department
of Epidemiology, University of Michigan
School of Public Health, Ann Arbor, Michigan 48109, United States
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SER-109: An Oral Investigational Microbiome Therapeutic for Patients with Recurrent Clostridioides difficile Infection (rCDI). Antibiotics (Basel) 2022; 11:antibiotics11091234. [PMID: 36140013 PMCID: PMC9495252 DOI: 10.3390/antibiotics11091234] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
Abstract
Clostridioides difficile infection (CDI) is classified as an urgent health threat by the Centers for Disease Control and Prevention (CDC), and affects nearly 500,000 Americans annually. Approximately 20−25% of patients with a primary infection experience a recurrence, and the risk of recurrence increases with subsequent episodes to greater than 40%. The leading risk factor for CDI is broad-spectrum antibiotics, which leads to a loss of microbial diversity and impaired colonization resistance. Current FDA-approved CDI treatment strategies target toxin or toxin-producing bacteria, but do not address microbiome disruption, which is key to the pathogenesis of recurrent CDI. Fecal microbiota transplantation (FMT) reduces the risk of recurrent CDI through the restoration of microbial diversity. However, FDA safety alerts describing hospitalizations and deaths related to pathogen transmission have raised safety concerns with the use of unregulated and unstandardized donor-derived products. SER-109 is an investigational oral microbiome therapeutic composed of purified spore-forming Firmicutes. SER-109 was superior to a placebo in reducing CDI recurrence at Week 8 (12% vs. 40%, respectively; p < 0.001) in adults with a history of recurrent CDI with a favorable observed safety profile. Here, we discuss the role of the microbiome in CDI pathogenesis and the clinical development of SER-109, including its rigorous manufacturing process, which mitigates the risk of pathogen transmission. Additionally, we discuss compositional and functional changes in the gastrointestinal microbiome in patients with recurrent CDI following treatment with SER-109 that are critical to a sustained clinical response.
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McChalicher C, Abdulaziz A, Zhou SS, Lombardo MJ, Hasson B, Auniņš JG, McGovern B, Ege DS. Manufacturing Process of SER-109, a Purified Investigational Microbiome Therapeutic, Reduces Risk of Coronavirus Transmission from Donor Stool. Open Forum Infect Dis 2022; 9:ofac448. [PMID: 36158136 PMCID: PMC9492665 DOI: 10.1093/ofid/ofac448] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/31/2022] [Indexed: 11/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may present risk to patients treated with donor-derived microbiome therapies when appropriate manufacturing controls and inactivation processes are lacking. We report that the manufacturing steps for SER-109, a purified investigational microbiome therapeutic developed to reduce risk of Clostridioides difficile recurrence, inactivate porcine epidemic diarrhea virus, a model coronavirus for SARS-CoV-2.
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Affiliation(s)
| | - Ahmad Abdulaziz
- Seres Therapeutics 200 Sidney Street Cambridge, MA 02139 USA
| | - S Steve Zhou
- Microbac Laboratories, Inc. 105 Carpenter Dr Sterling, VA 20164 USA
| | | | - Brooke Hasson
- Seres Therapeutics 200 Sidney Street Cambridge, MA 02139 USA
| | - John G Auniņš
- Seres Therapeutics 200 Sidney Street Cambridge, MA 02139 USA
| | | | - David S Ege
- Seres Therapeutics 200 Sidney Street Cambridge, MA 02139 USA
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7
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Li D, Zhou Z, Sun J, Mei X. Prospects of NIR fluorescent nanosensors for green detection of SARS-CoV-2. SENSORS AND ACTUATORS. B, CHEMICAL 2022; 362:131764. [PMID: 35370362 PMCID: PMC8964475 DOI: 10.1016/j.snb.2022.131764] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 02/22/2022] [Accepted: 03/21/2022] [Indexed: 05/02/2023]
Abstract
The pandemic of the novel coronavirus disease 2019 (COVID-19) is continuously causing hazards for the world. Effective detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can relieve the impact, but various toxic chemicals are also released into the environment. Fluorescence sensors offer a facile analytical strategy. During fluorescence sensing, biological samples such as tissues and body fluids have autofluorescence, giving false-positive/negative results because of the interferences. Fluorescence near-infrared (NIR) nanosensors can be designed from low-toxic materials with insignificant background signals. Although this research is still in its infancy, further developments in this field have the potential for sustainable detection of SARS-CoV-2. Herein, we summarize the reported NIR fluorescent nanosensors with the potential to detect SARS-CoV-2. The green synthesis of NIR fluorescent nanomaterials, environmentally compatible sensing strategies, and possible methods to reduce the testing frequencies are discussed. Further optimization strategies for developing NIR fluorescent nanosensors to facilitate greener diagnostics of SARS-CoV-2 for pandemic control are proposed.
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Key Words
- 5 G, the fifth generation technology standard for broadband cellular networks
- ACE2, Angiotensin-converting enzyme 2
- AIE, aggregation-induced emission
- AIE810NP, an aggregation-induced emission (AIE) nanoparticle (λem = 810 nm)
- AIEgens, AIE luminogens
- ASOs, antisense oligonucleotides
- AuNP, Gold nanoparticle
- CF647, a cyanine-based far-red fluorescent dye
- COVID-19, The pandemic of the novel coronavirus disease 2019
- CP-MNB, capture probe-conjugated magnetic bead particle
- CdS, core/shell lead sulfide/cadmium sulfide
- CoPhMoRe, corona phase molecular recognition
- Cy7Cl, a cationic cyanine dye
- DCNPs, Down-conversion nanoparticles
- DPV, Differential pulse voltammetry
- DSNP, down shifting nanoparticles
- DSNP@MY-1057-GPC-3, active targeting antibody glypican-3 (GPC-3) was conjugated with DSNP@MY-1057
- E, envelope
- EB-NS, prepared by the layered pigment CaCuSi4O10 (Egyptian Blue, EB) via ball milling and facile tip sonication into NIR fluorescent nanosheets
- ENMs, electrospun nanofibrous membranes
- Environmental-friendly
- FLU, an infectious disease caused by influenza viruses
- FRET, fluorescence resonance energy transfer
- Green synthesis
- HA1, hemagglutinin subunit.
- HA1., hemagglutinin subunit
- HAS, serum albumin
- HCC, hepatocellular carcinoma
- IONPs, iron oxide nanoparticles.
- IONPs., iron oxide nanoparticles
- IgG A, IgG aggregation
- IgG, immunoglobulin G
- IgM, immunoglobulin M
- LED, light emitting diode
- LICOR, IRDye-800CW
- Low-toxic
- M, membrane
- MCU, microcontroller unit
- MERS, Middle East respiratory syndrome coronavirus
- N protein, nucleocapsid protein
- N, nucleocapsid
- NIR
- NIR, Near-Infrared
- NIR775, an H2S-inert fluorophore
- Nanosensor
- P, FITC-labelled GzmB substrate peptides
- PBS, Phosphate-buffered saline
- PCR, Polymerase Chain Reaction
- PEG, branched by Polyethylene glycol
- PEG1000 PE, 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)− 1000]
- PEG2000 PE, (1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-[methoxy(polyethylene glycol)− 2000);
- POC, point-of-care
- PS, polystyrene
- Pb-Ag2S ODs, lead doped Ag2S quantum dots
- QDs, quantum dots
- QY, quantum yield
- R, R represents a common recognition element for the target
- RCA, rolling circle amplification
- RNA, ribonucleic acid
- S RBD, SARS-CoV-2 spike receptor-binding domain
- S protein, spike protein
- S, spike
- SAM, self-assembled monolayer
- SARS-CoV-2
- SARS-CoV-2, Severe acute respiratory syndrome coronavirus
- SPNs, semiconducting polymer nanoparticles.
- SPNs., semiconducting polymer nanoparticles
- SWCNTs, single-walled carbon nanotubes
- Si-RP, silica-reporter probe
- VIS, visible
- VTM, viral transport medium
- pGOLD, plasmonic gold
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Affiliation(s)
- Dan Li
- Department of Basic Science, Jinzhou Medical University, 40 Songpo Road, Jinzhou 121001, China
| | - Zipeng Zhou
- Department of Key Laboratory of Medical Tissue Engineering of Liaoning, Jinzhou Medical University, 40 Songpo Road, Jinzhou 121001, China
| | - Jiachen Sun
- Department of Key Laboratory of Medical Tissue Engineering of Liaoning, Jinzhou Medical University, 40 Songpo Road, Jinzhou 121001, China
| | - Xifan Mei
- Department of Key Laboratory of Medical Tissue Engineering of Liaoning, Jinzhou Medical University, 40 Songpo Road, Jinzhou 121001, China
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Coryell MP, Carlson PE. Longitudinal sampling sheds light on SARS-CoV-2 fecal shedding dynamics. MED 2022; 3:351-352. [PMID: 35690052 PMCID: PMC9185873 DOI: 10.1016/j.medj.2022.05.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
Persistent fecal shedding of SARS-CoV-2 viral RNA has remained a clinical feature of interest throughout the COVID-19 pandemic. In this issue of Med, Natarajan et al. report fecal shedding dynamics of individuals diagnosed with mild-to-moderate COVID-19 disease and sampled longitudinally for up to 10 months1
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Affiliation(s)
- Michael P Coryell
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial, Parasitic, and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Paul E Carlson
- Laboratory of Mucosal Pathogens and Cellular Immunology, Division of Bacterial, Parasitic, and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
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9
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Natarajan A, Zlitni S, Brooks EF, Vance SE, Dahlen A, Hedlin H, Park RM, Han A, Schmidtke DT, Verma R, Jacobson KB, Parsonnet J, Bonilla HF, Singh U, Pinsky BA, Andrews JR, Jagannathan P, Bhatt AS. Gastrointestinal symptoms and fecal shedding of SARS-CoV-2 RNA suggest prolonged gastrointestinal infection. MED (NEW YORK, N.Y.) 2022; 3:371-387.e9. [PMID: 35434682 PMCID: PMC9005383 DOI: 10.1016/j.medj.2022.04.001] [Citation(s) in RCA: 165] [Impact Index Per Article: 82.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 03/01/2022] [Accepted: 04/05/2022] [Indexed: 02/01/2023]
Abstract
Background COVID-19 manifests with respiratory, systemic, and gastrointestinal (GI) symptoms.1, SARS-CoV-2 RNA is detected in respiratory and fecal samples, and recent reports demonstrate viral replication in both the lung and intestinal tissue.2, 3, 4 Although much is known about early fecal RNA shedding, little is known about long-term shedding, especially in those with mild COVID-19. Furthermore, most reports of fecal RNA shedding do not correlate these findings with GI symptoms.5. Methods We analyzed the dynamics of fecal RNA shedding up to 10 months after COVID-19 diagnosis in 113 individuals with mild to moderate disease. We also correlated shedding with disease symptoms. Findings Fecal SARS-CoV-2 RNA is detected in 49.2% [95% confidence interval, 38.2%-60.3%] of participants within the first week after diagnosis. Whereas there was no ongoing oropharyngeal SARS-CoV-2 RNA shedding in subjects at 4 months, 12.7% [8.5%-18.4%] of participants continued to shed SARS-CoV-2 RNA in the feces at 4 months after diagnosis and 3.8% [2.0%-7.3%] shed at 7 months. Finally, we found that GI symptoms (abdominal pain, nausea, vomiting) are associated with fecal shedding of SARS-CoV-2 RNA. Conclusions The extended presence of viral RNA in feces, but not in respiratory samples, along with the association of fecal viral RNA shedding with GI symptoms suggest that SARS-CoV-2 infects the GI tract and that this infection can be prolonged in a subset of individuals with COVID-19. Funding This research was supported by a Stanford ChemH-IMA grant; fellowships from the AACR and NSF; and NIH R01-AI148623, R01-AI143757, and UL1TR003142.
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Affiliation(s)
- Aravind Natarajan
- Department of Genetics, Stanford University, 269 Campus Dr, CCSR 1155b, Stanford, CA, USA,Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Soumaya Zlitni
- Department of Genetics, Stanford University, 269 Campus Dr, CCSR 1155b, Stanford, CA, USA,Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Erin F. Brooks
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Summer E. Vance
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Alex Dahlen
- Quantitative Science Unit, Stanford University, Stanford, CA, USA
| | - Haley Hedlin
- Quantitative Science Unit, Stanford University, Stanford, CA, USA
| | - Ryan M. Park
- Department of Genetics, Stanford University, 269 Campus Dr, CCSR 1155b, Stanford, CA, USA,Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Alvin Han
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Danica T. Schmidtke
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Renu Verma
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA
| | - Karen B. Jacobson
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA
| | - Julie Parsonnet
- Department of Medicine (Infectious Diseases), Stanford University, Stanford, CA, USA,Department of Medicine (Epidemiology and Population Health), Stanford University, Stanford, CA, USA
| | - Hector F. Bonilla
- Department of Medicine (Infectious Diseases), Stanford University, Stanford, CA, USA
| | - Upinder Singh
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA
| | - Benjamin A. Pinsky
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA,Department of Pathology, Stanford University, Stanford, CA, USA
| | - Jason R. Andrews
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA
| | - Prasanna Jagannathan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA,Department of Medicine (Infectious Diseases), Stanford University, Stanford, CA, USA
| | - Ami S. Bhatt
- Department of Genetics, Stanford University, 269 Campus Dr, CCSR 1155b, Stanford, CA, USA,Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA,Corresponding author
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10
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Natarajan A, Han A, Zlitni S, Brooks EF, Vance SE, Wolfe M, Singh U, Jagannathan P, Pinsky BA, Boehm A, Bhatt AS. Standardized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA. Nat Commun 2021; 12:5753. [PMID: 34599164 PMCID: PMC8486790 DOI: 10.1038/s41467-021-25576-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/18/2021] [Indexed: 12/28/2022] Open
Abstract
Patients with COVID-19 shed SARS-CoV-2 RNA in stool, sometimes well after their respiratory infection has cleared. This may be significant for patient health, epidemiology, and diagnosis. However, methods to preserve stool, and to extract and quantify viral RNA are not standardized. We test the performance of three preservative approaches at yielding detectable SARS-CoV-2 RNA: the OMNIgene-GUT kit, Zymo DNA/RNA shield kit, and the most commonly applied, storage without preservative. We test these in combination with three extraction kits: QIAamp Viral RNA Mini Kit, Zymo Quick-RNA Viral Kit, and MagMAX Viral/Pathogen Kit. We also test the utility of ddPCR and RT-qPCR for the reliable quantification of SARS-CoV-2 RNA from stool. We identify that the Zymo DNA/RNA preservative and the QiaAMP extraction kit yield more detectable RNA than the others, using both ddPCR and RT-qPCR. Taken together, we recommend a comprehensive methodology for preservation, extraction and detection of RNA from SARS-CoV-2 and other coronaviruses in stool.
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Affiliation(s)
- Aravind Natarajan
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Alvin Han
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Soumaya Zlitni
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Erin F Brooks
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Summer E Vance
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Marlene Wolfe
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Upinder Singh
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA
| | - Prasanna Jagannathan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA
| | - Benjamin A Pinsky
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Alexandria Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Ami S Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA.
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA.
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11
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Updates and Challenges in Fecal Microbiota Transplantation for Clostridioides difficile Infection in Children. J Pediatr Gastroenterol Nutr 2021; 73:430-432. [PMID: 34238831 PMCID: PMC8455422 DOI: 10.1097/mpg.0000000000003229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Fecal microbiota transplantation (FMT) is currently the most effective but loosely regulated therapy, for recurrent Clostridioides difficile infection (rCDI) in pediatrics. Over the last 2 years, there have been mounting challenges in the ability to provide FMT to pediatric patients. Firstly, an Food and Drug Administration (FDA) safety alert in 2019 reported transmission of a multidrug resistant organism from FMT donor to recipient resulting in the death of 1 patient. Secondly, the coronavirus disease 2019 (COVID-19) pandemic induced further safety and regulatory challenges. Biotherapeutics are promising and more readily regulated treatment options for rCDI, which may replace FMT in the near future for adults upon regulatory agency approvals. Such approvals, however, are expected to be significantly delayed for children, raising concerns for limited access to effective treatment for children with rCDI. In this commentary, we discuss the recent challenges and future directions of FMT and microbial therapeutics in children with rCDI.
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12
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The Role of Fecal Microbiota Transplantation in the Treatment of Inflammatory Bowel Disease. J Clin Med 2021; 10:jcm10184055. [PMID: 34575166 PMCID: PMC8465860 DOI: 10.3390/jcm10184055] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/02/2021] [Accepted: 09/03/2021] [Indexed: 12/12/2022] Open
Abstract
The exact pathogenesis of inflammatory bowel disease (IBD) is still not completely understood. It is hypothesized that a genetic predisposition leads to an exaggerated immune response to an environmental trigger, leading to uncontrolled inflammation. As there is no known causative treatment, current management strategies for inflammatory bowel disease focus on correcting the excessive immune response to environmental (including microbial) triggers. In recent years, there has been growing interest in new avenues of treatment, including targeting the microbial environment itself. Fecal microbiota transplantation (FMT) is a novel treatment modality showing promising results in early studies. The article discusses the rationale for the use of FMT in inflammatory bowel disease and the yet-unresolved questions surrounding its optimal use in practice.
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13
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Li T, Garcia-Gutierrez E, Yara DA, Scadden J, Davies J, Hutchins C, Aydin A, O'Grady J, Narbad A, Romano S, Sayavedra L. An optimised protocol for detection of SARS-CoV-2 in stool. BMC Microbiol 2021; 21:242. [PMID: 34488633 PMCID: PMC8419809 DOI: 10.1186/s12866-021-02297-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 08/18/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND SARS-CoV-2 has been detected in stool samples of COVID-19 patients, with potential implications for faecal-oral transmission. Compared to nasopharyngeal swab samples, the complexity of the stool matrix poses a challenge in the detection of the virus that has not yet been solved. However, robust and reliable methods are needed to estimate the prevalence and persistence of SARS-CoV-2 in the gut and to ensure the safety of microbiome-based procedures such as faecal microbiota transplant (FMT). The aim of this study was to establish a sensitive and reliable method for detecting SARS-CoV-2 in stool samples. RESULTS Stool samples from individuals free of SARS-CoV-2 were homogenised in saline buffer and spiked with a known titre of inactivated virus ranging from 50 to 750 viral particles per 100 mg stool. Viral particles were concentrated by ultrafiltration, RNA was extracted, and SARS-CoV-2 was detected via real-time reverse-transcription polymerase chain reaction (RT-qPCR) using the CDC primers and probes. The RNA extraction procedure we used allowed for the detection of SARS-CoV-2 via RT-qPCR in most of the stool samples tested. We could detect as few as 50 viral particles per 100 mg of stool. However, high variability was observed across samples at low viral titres. The primer set targeting the N1 region provided more reliable and precise results and for this primer set our method had a limit of detection of 1 viral particle per mg of stool. CONCLUSIONS Here we describe a sensitive method for detecting SARS-CoV-2 in stool samples. This method can be used to establish the persistence of SARS-CoV-2 in stool and ensure the safety of clinical practices such as FMT.
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Affiliation(s)
- Tianqi Li
- Gut Health and Microbes, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, China
| | | | - Daniel A Yara
- Gut Health and Microbes, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Jacob Scadden
- Gut Health and Microbes, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Jade Davies
- Gut Health and Microbes, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Chloe Hutchins
- Gut Health and Microbes, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Alp Aydin
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Justin O'Grady
- Microbes in the Food Chain, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Arjan Narbad
- Gut Health and Microbes, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Stefano Romano
- Gut Health and Microbes, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
| | - Lizbeth Sayavedra
- Gut Health and Microbes, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
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14
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A rapid and simple protocol for concentration of SARS-CoV-2 from sewage. J Virol Methods 2021; 297:114272. [PMID: 34454988 PMCID: PMC8388153 DOI: 10.1016/j.jviromet.2021.114272] [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: 05/27/2021] [Revised: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 11/21/2022]
Abstract
The aim of this study was to set up a simple protocol to concentrate SARS-CoV-2 from sewage, which can be implemented in laboratories with minimal equipment resources. The method avoids the need for extensive purification steps and reduces the concentration of potential inhibitors of RT-qPCR contained in sewage. The concentration method consists of a single step, in which a small volume (40 mL) of sewage sample is incubated with polyaluminum chloride (PAC)(0.00045 N Al3+ final concentration). Virus particles adsorbed to the precipitate are collected by low-speed centrifugation, after which the recovered pellet is resuspended with a saline buffer. PAC-concentrated samples are stable for at least one week at 4 °C. Therefore, they may be sent refrigerated to a diagnosis center for RNA extraction and RT-qPCR for SARS-CoV-2 RNA detection if the lab does not have such capabilities. The PAC concentration method produced an average shift of 4.5-units in quantification cycle (Cq) values compared to non-concentrated samples, indicating a 25-fold increase in detection sensitivity. The lower detection limit corresponded approximately to 100 viral copies per ml. Kappa index indicated substantial agreement between PAC and polyethylene glycol (PEG) precipitation protocols (k = 0.688, CI 0.457-0.919). This low-cost concentration protocol could be useful to aid in the monitoring of community circulation of SARS-CoV-2, especially in low- and middle-income countries, which do not have massive access to support from specialized labs for sewage surveillance.
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15
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Tozaki T, Ohnuma A, Kikuchi M, Ishige T, Kakoi H, Hirota KI, Kusano K, Nagata SI. Robustness of digital PCR and real-time PCR against inhibitors in transgene detection for gene doping control in equestrian sports. Drug Test Anal 2021; 13:1768-1775. [PMID: 34270866 DOI: 10.1002/dta.3131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/11/2021] [Accepted: 07/13/2021] [Indexed: 12/17/2022]
Abstract
Gene doping is a threat to fair competition in sports, both human and equestrian. One method of gene doping is to administer exogenous genetic materials, called transgenes, into the bodies of postnatal humans and horses. Polymerase chain reaction (PCR)-based transgene detection methods such as digital PCR and real-time PCR have been developed for gene doping testing in humans and horses. However, the significance of PCR inhibitors in gene doping testing has not been well evaluated. In this study, we evaluated the effects of PCR inhibitors on transgene detection using digital PCR and real-time PCR against gene doping. Digital PCR amplification was significantly inhibited by high concentrations of proteinase K (more than 0.1 μg/μl), ethylenediaminetetraacetic acid (more than 5 nmol/μl), and heparin (more than 0.05 unit/μl) but not by ethanol or genomic DNA. In addition, phenol affected droplet formation in the digital PCR amplification process. Real-time PCR amplification was inhibited by high concentrations of phenol (more than 1% v/v), proteinase K (more than 0.001 μg/μl), ethylenediaminetetraacetic acid (more than 1 nmol/μl), heparin (more than 0.005 unit/μl), and genomic DNA (more than 51.9 ng/μl) but not by ethanol. Although both PCR systems were inhibited by nearly the same substances, digital PCR was more robust than real-time PCR against the inhibitors. We believe that our findings are important for the development of better methods for transgene detection and prevention of false negative results in gene doping testing.
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Affiliation(s)
- Teruaki Tozaki
- Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Tochigi, Japan
| | - Aoi Ohnuma
- Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Tochigi, Japan
| | - Mio Kikuchi
- Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Tochigi, Japan
| | - Taichiro Ishige
- Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Tochigi, Japan
| | - Hironaga Kakoi
- Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Tochigi, Japan
| | - Kei-Ichi Hirota
- Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Tochigi, Japan
| | - Kanichi Kusano
- Equine Department, Japan Racing Association, Minato, Tokyo, Japan
| | - Shun-Ichi Nagata
- Genetic Analysis Department, Laboratory of Racing Chemistry, Utsunomiya, Tochigi, Japan
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16
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Natarajan A, Han A, Zlitni S, Brooks EF, Vance SE, Wolfe M, Singh U, Jagannathan P, Pinsky BA, Boehm A, Bhatt AS. Standardized and optimized preservation, extraction and quantification techniques for detection of fecal SARS-CoV-2 RNA. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.04.10.21255250. [PMID: 33880485 PMCID: PMC8057253 DOI: 10.1101/2021.04.10.21255250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
COVID-19 patients shed SARS-CoV-2 viral RNA in their stool, sometimes well after they have cleared their respiratory infection. This feature of the disease may be significant for patient health, epidemiology, and diagnosis. However, to date, methods to preserve stool samples from COVID patients, and to extract and quantify viral RNA concentration have yet to be optimized. We sought to meet this urgent need by developing and benchmarking a standardized protocol for the fecal detection of SARS-CoV-2 RNA. We test three preservative conditions for their ability to yield detectable SARS-CoV-2 RNA: OMNIgene-GUT, Zymo DNA/RNA shield kit, and the most common condition, storage without any preservative. We test these in combination with three extraction kits: the QIAamp Viral RNA Mini Kit, Zymo Quick-RNA Viral Kit, and MagMAX Viral/Pathogen Kit. Finally, we also test the utility of two detection methods, ddPCR and RT-qPCR, for the robust quantification of SARS-CoV-2 viral RNA from stool. We identify that the Zymo DNA/RNA shield collection kit and the QiaAMP viral RNA mini kit yield more detectable RNA than the others, using both ddPCR and RT-qPCR assays. We also demonstrate key features of experimental design including the incorporation of appropriate controls and data analysis, and apply these techniques to effectively extract viral RNA from fecal samples acquired from COVID-19 outpatients enrolled in a clinical trial. Finally, we recommend a comprehensive methodology for future preservation, extraction and detection of RNA from SARS-CoV-2 and other coronaviruses in stool.
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Affiliation(s)
- Aravind Natarajan
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Alvin Han
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Soumaya Zlitni
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Erin F. Brooks
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Summer E. Vance
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
| | - Marlene Wolfe
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Upinder Singh
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA
| | - Prasanna Jagannathan
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
- Department of Medicine (Infectious Diseases), Stanford University, Stanford, CA, USA
| | - Benjamin A. Pinsky
- Department of Medicine (Infectious Diseases and Geographic Medicine), Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Alexandria Boehm
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, USA
| | - Ami S. Bhatt
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Medicine (Hematology, Blood and Marrow Transplantation), Stanford University, Stanford, CA, USA
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