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Hazan S, Haroon J, Jordan S, Walker SJ. Improvements in Gut Microbiome Composition and Clinical Symptoms Following Familial Fecal Microbiota Transplantation in a Nineteen-Year-Old Adolescent With Severe Autism. J Med Cases 2024; 15:82-91. [PMID: 38715916 PMCID: PMC11073461 DOI: 10.14740/jmc4209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 04/11/2024] [Indexed: 06/11/2024] Open
Abstract
This case report describes a novel therapy for patients with severe autism spectrum disorder (ASD) that is worth further investigation. A 19-year-old male adolescent with ASD, who was not responding to standard treatment received fecal microbiota transplant (FMT) using donor material from his typically developing female sibling. The patient's ASD symptoms were assessed by assessors who were blind to the patient's past ASD symptomatology. Assessors used the Childhood Autism Rating Scale (CARS), an observation-based rating scale to assess developmental delay in children with autism (range of CARS scores is 15 - 60; a score > 28 is indicative of autism; higher score is positively correlated with degree of severity), at baseline and again at six timepoints post-FMT. The patient experienced marked improvements in microbiome diversity and composition over the year and a half period that followed the FMT procedure. Additionally, the patient who was previously nonverbal said his first two words and experienced a reduction in aggression 1-month post-FMT. To the authors' knowledge, this is the first report to demonstrate the use of familial FMT in an adolescent patient with ASD. Given that ASD symptom improvements post-FMT tend to occur in younger patients, the authors hypothesize that the use of a familial donor may be an important factor that contributed to the improved outcomes experienced by this older child.
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Affiliation(s)
- Sabine Hazan
- ProgenaBiome, LLC, Ventura, CA, USA
- Microbiome Research Foundation, Ventura, CA, USA
| | | | | | - Stephen J. Walker
- Wake Forest Institute for Regenerative Medicine, Winston Salem, NC, USA
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2
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Pei XM, Yeung MHY, Wong ANN, Tsang HF, Yu ACS, Yim AKY, Wong SCC. Targeted Sequencing Approach and Its Clinical Applications for the Molecular Diagnosis of Human Diseases. Cells 2023; 12:493. [PMID: 36766834 PMCID: PMC9913990 DOI: 10.3390/cells12030493] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/19/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The outbreak of COVID-19 has positively impacted the NGS market recently. Targeted sequencing (TS) has become an important routine technique in both clinical and research settings, with advantages including high confidence and accuracy, a reasonable turnaround time, relatively low cost, and fewer data burdens with the level of bioinformatics or computational demand. Since there are no clear consensus guidelines on the wide range of next-generation sequencing (NGS) platforms and techniques, there is a vital need for researchers and clinicians to develop efficient approaches, especially for the molecular diagnosis of diseases in the emergency of the disease and the global pandemic outbreak of COVID-19. In this review, we aim to summarize different methods of TS, demonstrate parameters for TS assay designs, illustrate different TS panels, discuss their limitations, and present the challenges of TS concerning their clinical application for the molecular diagnosis of human diseases.
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Affiliation(s)
- Xiao Meng Pei
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Martin Ho Yin Yeung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Alex Ngai Nick Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Hin Fung Tsang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
- Department of Clinical Laboratory and Pathology, Hong Kong Adventist Hospital, Hong Kong, China
| | - Allen Chi Shing Yu
- Codex Genetics Limited, Unit 212, 2/F., Building 16W, No. 16 Science Park West Avenue, The Hong Kong Science Park, Hong Kong 852, China
| | - Aldrin Kay Yuen Yim
- Codex Genetics Limited, Unit 212, 2/F., Building 16W, No. 16 Science Park West Avenue, The Hong Kong Science Park, Hong Kong 852, China
| | - Sze Chuen Cesar Wong
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, China
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3
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Hazan S, Dave S, Papoutsis AJ, Deshpande N, Howell MC, Martin LM. Vitamin C improves gut Bifidobacteria in humans. Future Microbiol 2022. [PMID: 36475828 DOI: 10.2217/fmb-2022-0209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aims: Numerous beneficial effects of vitamin C (ascorbic acid) supplementation have been reported in the literature. However, data on its effects toward the gut microbiome are limited. We assessed the effect of vitamin C supplementation on the abundance of beneficial bacterial species in the gut microbiome. Materials and methods: Stool samples were analyzed for relative abundance of gut microbiome bacteria using next-generation sequencing-based profiling and metagenomic shotgun analysis. Results: Supplementation with vitamin C increased the abundance of bacteria of the genus Bifidobacterium (p = 0.0001) and affected various species. Conclusion: The beneficial effects of vitamin C supplementation may be attributed to modulation of the gut microbiome and the consequent health benefits thereof.
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Affiliation(s)
- Sabine Hazan
- ProgenaBIome, LLC, Ventura, CA 93003, USA
- Mcrobiome Research Foundation, Ventura, CA 93003, USA
| | - Sonya Dave
- Mcrobiome Research Foundation, Ventura, CA 93003, USA
| | | | | | | | - Leisha Ma Martin
- Texas A&M University - Corpus Christi, Department of Life Sciences, Corpus Christi, TX 78412, USA
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4
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He Q, Shi Y, Tang Q, Xing H, Zhang H, Wang M, Chen X. Herbal medicine in the treatment of COVID-19 based on the gut-lung axis. ACUPUNCTURE AND HERBAL MEDICINE 2022; 2:172-183. [PMID: 37808350 PMCID: PMC9746256 DOI: 10.1097/hm9.0000000000000038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/12/2022] [Indexed: 08/18/2023]
Abstract
Respiratory symptoms are most commonly experienced by patients in the early stages of novel coronavirus disease 2019 (COVID-19). However, with a better understanding of COVID-19, gastrointestinal symptoms such as diarrhea, nausea, and vomiting have attracted increasing attention. The gastrointestinal tract may be a target organ of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The intestinal microecological balance is a crucial factor for homeostasis, including immunity and inflammation, which are closely related to COVID-19. Herbal medicine can restore intestinal function and regulate the gut flora structure. Herbal medicine has a long history of treating lung diseases from the perspective of the intestine, which is called the gut-lung axis. The physiological activities of guts and lungs influence each other through intestinal flora, microflora metabolites, and mucosal immunity. Microecological modulators are included in the diagnosis and treatment protocols for COVID-19. In this review, we demonstrate the relationship between COVID-19 and the gut, gut-lung axis, and the role of herbal medicine in treating respiratory diseases originating from the intestinal tract. It is expected that the significance of herbal medicine in treating respiratory diseases from the perspective of the intestinal tract could lead to new ideas and methods for treatment. Graphical abstract http://links.lww.com/AHM/A33.
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Affiliation(s)
- Qiaoyu He
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yumeng Shi
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Qian Tang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Hong Xing
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Han Zhang
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Mei Wang
- LU-European Center for Chinese Medicine and Natural Compounds, Institute of Biology, Leiden University/SU Biomedicine, Leiden, Netherlands
| | - Xiaopeng Chen
- State Key Laboratory of Component-Based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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5
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Beck-Friis T, Kärmander A, Nyström K, Wang H, Gisslén M, Andersson LM, Norder H. Comparison of SARS-CoV-2 spike RNA sequences in feces and nasopharynx indicates intestinal replication. Gut Pathog 2022; 14:35. [PMID: 35987708 PMCID: PMC9392503 DOI: 10.1186/s13099-022-00509-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 07/25/2022] [Indexed: 11/10/2022] Open
Abstract
Background Little is known of possible selection and replication of SARS-CoV-2 in the intestines and if viral load in feces is associated with severity of disease. Therefore, sequence variations of the spike region in strains collected from feces and nasopharynx (NPH) from the same patients were compared. It was also investigated whether viral load in feces related to severity of COVID-19 in hospitalized patients. Results SARS-CoV-2 RNA was found in 88 (79%) fecal samples from 112 patients. The complete spike region could be sequenced in 15 fecal and 14 NPH samples. Fourteen Alpha-variants and one Beta-variant of SARS-CoV-2 were identified. The majority of the viral genetic variants (viral populations) in two fecal samples, but none in NPH, had a reversion of the H69/V70 amino acid deletion normally seen in the Alpha variants. Nine fecal samples contained up to nine minority variants, each which may constitute a separate viral population. Five NPH samples had one genetic variant each, and one NPH sample contained nine minority populations of SARS-CoV-2 spike genes. Conclusions The higher genomic diversity of SARS-CoV-2 in feces compared to NPH, and the reversion of the H69/V70 deletion in Alpha variants from feces indicate a selection of viral strains and replication of SARS-CoV-2 in the gastrointestinal tract. Supplementary Information The online version contains supplementary material available at 10.1186/s13099-022-00509-w.
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Tesauro M, Terraneo M, Consonni M, Fappani C, Colzani D, Stevanin C, Amendola A, Masseroni D, Tanzi E. A Methodological Approach to Water Concentration to Investigate the Presence of SARS-CoV-2 RNA in Surface Freshwaters. Pathogens 2022; 11:845. [PMID: 36014966 PMCID: PMC9415985 DOI: 10.3390/pathogens11080845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/22/2022] [Accepted: 07/26/2022] [Indexed: 02/04/2023] Open
Abstract
During the COVID-19 public health emergency, an increasing number of studies reported the occurrence of SARS-CoV-2 in wastewaters worldwide, but little is known about the presence of the virus in surface freshwaters. The aim of the current study was to develop and validate an appropriate and scalable methodological approach for the concentration and detection of SARS-CoV-2 from surface freshwater samples, collected within the Milan rural network subjected to flood spillways activity. Overall, both surface water and distilled water samples spiked with inactivated SARS-CoV-2 were used to validate the concentration method for pathogens determination. Two pre-filtration systems, filter paper and Sartolab® P20 (Sartorius, Germany) and two concentration methods, two-phase (PEG-dextran method) separation and tangential flow ultrafiltration (UF), were compared. The effects of pre-filtration and concentration on viral nucleic acid recovery were assessed through real time RT-PCR targeting SARS-CoV-2 and the internal viral control PMMoV (Pepper Mild Mottle Virus). Our results showed that UF is more sensitive than the PEG-dextran method in viral acid nucleic recovery from surface water samples. Better results were obtained pre-filtering samples with Sartolab® P20 and extracting the nucleic acids with undiluted silica, rather than diluted as required by the standard protocol. The proposed method will be used for the monitoring of surface waters in the Milan area.
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Affiliation(s)
- Marina Tesauro
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Via Carlo Pascal 36, 20133 Milan, Italy;
- Coordinated Research Center “EpiSoMI”, University of Milan, Via Carlo Pascal 36, 20133 Milan, Italy; (A.A.); (E.T.)
| | - Mara Terraneo
- Department of Health Sciences, University of Milan, Via Carlo Pascal 36, 20133 Milan, Italy; (M.T.); (C.F.); (D.C.); (C.S.)
| | - Michela Consonni
- Department of Biomedical, Surgical and Dental Sciences, University of Milan, Via Carlo Pascal 36, 20133 Milan, Italy;
| | - Clara Fappani
- Department of Health Sciences, University of Milan, Via Carlo Pascal 36, 20133 Milan, Italy; (M.T.); (C.F.); (D.C.); (C.S.)
- Department of Clinical Sciences and Community Health, University of Milan, Via della Commenda 19, 20122 Milan, Italy
| | - Daniela Colzani
- Department of Health Sciences, University of Milan, Via Carlo Pascal 36, 20133 Milan, Italy; (M.T.); (C.F.); (D.C.); (C.S.)
| | - Caterina Stevanin
- Department of Health Sciences, University of Milan, Via Carlo Pascal 36, 20133 Milan, Italy; (M.T.); (C.F.); (D.C.); (C.S.)
| | - Antonella Amendola
- Coordinated Research Center “EpiSoMI”, University of Milan, Via Carlo Pascal 36, 20133 Milan, Italy; (A.A.); (E.T.)
- Department of Health Sciences, University of Milan, Via Carlo Pascal 36, 20133 Milan, Italy; (M.T.); (C.F.); (D.C.); (C.S.)
| | - Daniele Masseroni
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of Milan, Via Celoria 2, 20133 Milan, Italy;
| | - Elisabetta Tanzi
- Coordinated Research Center “EpiSoMI”, University of Milan, Via Carlo Pascal 36, 20133 Milan, Italy; (A.A.); (E.T.)
- Department of Health Sciences, University of Milan, Via Carlo Pascal 36, 20133 Milan, Italy; (M.T.); (C.F.); (D.C.); (C.S.)
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Zaini J, Putra AC, Ridwanuloh AM, Saniyyah Z, Haryanto B, Utomo ARH, Dharmayanthi AB, Prasetyoputri A, Andriani A, Hariyatun H, Nuryana I, Iryanto SB, Saputra S, Wardiana A, Ningrum RA. Possible intraindividual evolution of SARS-CoV-2 in nasopharyngeal and anal swab in an octogenarian: a case report. Germs 2022; 12:298-303. [PMID: 36504602 PMCID: PMC9719385 DOI: 10.18683/germs.2022.1332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 04/30/2022] [Accepted: 05/20/2022] [Indexed: 12/15/2022]
Abstract
Introduction COVID-19 is an emerging infectious disease that remains to be further investigated. Case report Here, we describe a case of COVID-19 in an octogenarian woman with comorbidities who slowly recovered during hospitalization, but died due to sudden cardiac death after 2 weeks of hospitalization. Her nasopharyngeal and anal swabs returned positive for SARS-CoV-2 by RT-PCR on day 7 of hospitalization. The NGS showed possible intraindividual evolution of virus. The sample from the nasopharyngeal swab yielded a B.1470 variant classified as clade GH. This variant showed mutation in the spike gene D614G; N gene; NS3 gene; NSP2 gene and NSP12 gene. The sample from the anal swab showed similar mutation but with additional point mutation in spike gene S12F and was classified as B.1.465 variant. Conclusions The possibility of the gastrointestinal tract that served as reservoir for virus mutation accumulation should also be considered and the potential impact of viral fecal transmission in the environment should be further investigated.
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Affiliation(s)
- Jamal Zaini
- MD, PhD, Department of Pulmonology and Respiratory Medicine, Faculty of Medicine, Universitas Indonesia, Persahabatan National Respiratory Referral Hospital, 13230, Jakarta Timur, Indonesia,Corresponding author: Jamal Zaini,
| | - Andika Chandra Putra
- MD, PhD, Faculty of Medicine, Universitas Yarsi, 10510, Jakarta Pusat, Indonesia, Persahabatan National Respiratory Referral Hospital, 13230, Jakarta Timur, Indonesia
| | - Asep Muhamad Ridwanuloh
- MSc, National Research and Innovation Agency Republic of Indonesia, Jalan Raya Bogor KM 46 Cibinong, Bogor 16911, Jawa Barat, Indonesia
| | - Zahrah Saniyyah
- MD, Faculty of Medicine, Universitas Yarsi, 10510, Jakarta Pusat, Indonesia
| | - Budi Haryanto
- MD, Department of Microbiology, Persahabatan National Respiratory Referral Hospital, 13230, Jakarta Timur, Indonesia
| | - Ahmad Rusdan Handoyo Utomo
- PhD, Graduate School of Biomedical Science Master Program, Universitas Yarsi, 10510, Jakarta Pusat, Indonesia And Dharmais Hospital National Cancer Center, 11480, Jakarta, Indonesia
| | - Anik Budhi Dharmayanthi
- PhD, National Research and Innovation Agency Republic of Indonesia, Jalan Raya Bogor KM 46 Cibinong, Bogor 16911, Jawa Barat, Indonesia
| | - Anggia Prasetyoputri
- PhD, National Research and Innovation Agency Republic of Indonesia, Jalan Raya Bogor KM 46 Cibinong, Bogor 16911, Jawa Barat, Indonesia
| | - Ade Andriani
- PhD, National Research and Innovation Agency Republic of Indonesia, Jalan Raya Bogor KM 46 Cibinong, Bogor 16911, Jawa Barat, Indonesia
| | - Hariyatun Hariyatun
- MSc, National Research and Innovation Agency Republic of Indonesia, Jalan Raya Bogor KM 46 Cibinong, Bogor 16911, Jawa Barat, Indonesia
| | - Isa Nuryana
- MSc, National Research and Innovation Agency Republic of Indonesia, Jalan Raya Bogor KM 46 Cibinong, Bogor 16911, Jawa Barat, Indonesia
| | - Syam Budi Iryanto
- MSc, National Research and Innovation Agency Republic of Indonesia, Jalan Raya Bogor KM 46 Cibinong, Bogor 16911, Jawa Barat, Indonesia
| | - Sugiyono Saputra
- PhD, National Research and Innovation Agency Republic of Indonesia, Jalan Raya Bogor KM 46 Cibinong, Bogor 16911, Jawa Barat, Indonesia
| | - Andri Wardiana
- PhD, National Research and Innovation Agency Republic of Indonesia, Jalan Raya Bogor KM 46 Cibinong, Bogor 16911, Jawa Barat, Indonesia
| | - Ratih Asmana Ningrum
- PhD, National Research and Innovation Agency Republic of Indonesia, Jalan Raya Bogor KM 46 Cibinong, Bogor 16911, Jawa Barat, Indonesia
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Zdenkova K, Bartackova J, Cermakova E, Demnerova K, Dostalkova A, Janda V, Jarkovsky J, Lopez Marin MA, Novakova Z, Rumlova M, Ambrozova JR, Skodakova K, Swierczkova I, Sykora P, Vejmelkova D, Wanner J, Bartacek J. Monitoring COVID-19 spread in Prague local neighborhoods based on the presence of SARS-CoV-2 RNA in wastewater collected throughout the sewer network. WATER RESEARCH 2022. [PMID: 35358873 DOI: 10.1101/2021.07.28.21261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Many reports have documented that the presence of SARS-CoV-2 RNA in the influents of municipal wastewater treatment plants (WWTP) correlates with the actual epidemic situation in a given city. However, few data have been reported thus far on measurements upstream of WWTPs, i.e. throughout the sewer network. In this study, the monitoring of the presence of SARS-CoV-2 RNA in Prague wastewater was carried out at selected locations of the Prague sewer network from August 2020 through May 2021. Various locations such as residential areas of various sizes, hospitals, city center areas, student dormitories, transportation hubs (airport, bus terminal), and commercial areas were monitored together with four of the main Prague sewers. The presence of SARS-CoV-2 RNA was determined by reverse transcription - multiplex quantitative polymerase chain reaction (RT-mqPCR) after the precipitation of nucleic acids with PEG 8,000 and RNA isolation with TRIzol™ Reagent. The number of copies of the gene encoding SARS-CoV-2 nucleocapsid (N1) per liter of wastewater was compared with the number of officially registered COVID-19 cases in Prague. Although the data obtained by sampling wastewater from the major Prague sewers were more consistent than those obtained from the small sewers, the correlation between wastewater-based and clinical-testing data was also good for the residential areas with more than 7,000 registered inhabitants. It was shown that monitoring SARS-CoV-2 RNA in wastewater sampled from small sewers could identify isolated occurrences of COVID-19-positive cases in local neighborhoods. This can be very valuable while tracking COVID-19 hotspots within large cities.
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Affiliation(s)
- Kamila Zdenkova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czechia.
| | - Jana Bartackova
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czechia
| | - Eliska Cermakova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czechia
| | - Katerina Demnerova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czechia
| | - Alzbeta Dostalkova
- Department of Biotechnology, University of Chemistry and Technology Prague, Czechia
| | - Vaclav Janda
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czechia
| | - Jiri Jarkovsky
- Institute of Health Information and Statistics of the Czech Republic, Czechia
| | - Marco Antonio Lopez Marin
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czechia
| | | | - Michaela Rumlova
- Department of Biotechnology, University of Chemistry and Technology Prague, Czechia
| | - Jana Rihova Ambrozova
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czechia
| | - Klara Skodakova
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czechia
| | | | - Petr Sykora
- Prazske vodovody a kanalizace, a.s., Czechia
| | - Dana Vejmelkova
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czechia
| | - Jiri Wanner
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czechia
| | - Jan Bartacek
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czechia
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9
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Zdenkova K, Bartackova J, Cermakova E, Demnerova K, Dostalkova A, Janda V, Jarkovsky J, Lopez Marin MA, Novakova Z, Rumlova M, Ambrozova JR, Skodakova K, Swierczkova I, Sykora P, Vejmelkova D, Wanner J, Bartacek J. Monitoring COVID-19 spread in Prague local neighborhoods based on the presence of SARS-CoV-2 RNA in wastewater collected throughout the sewer network. WATER RESEARCH 2022; 216:118343. [PMID: 35358873 PMCID: PMC8936391 DOI: 10.1016/j.watres.2022.118343] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 03/08/2022] [Accepted: 03/18/2022] [Indexed: 05/12/2023]
Abstract
Many reports have documented that the presence of SARS-CoV-2 RNA in the influents of municipal wastewater treatment plants (WWTP) correlates with the actual epidemic situation in a given city. However, few data have been reported thus far on measurements upstream of WWTPs, i.e. throughout the sewer network. In this study, the monitoring of the presence of SARS-CoV-2 RNA in Prague wastewater was carried out at selected locations of the Prague sewer network from August 2020 through May 2021. Various locations such as residential areas of various sizes, hospitals, city center areas, student dormitories, transportation hubs (airport, bus terminal), and commercial areas were monitored together with four of the main Prague sewers. The presence of SARS-CoV-2 RNA was determined by reverse transcription - multiplex quantitative polymerase chain reaction (RT-mqPCR) after the precipitation of nucleic acids with PEG 8,000 and RNA isolation with TRIzol™ Reagent. The number of copies of the gene encoding SARS-CoV-2 nucleocapsid (N1) per liter of wastewater was compared with the number of officially registered COVID-19 cases in Prague. Although the data obtained by sampling wastewater from the major Prague sewers were more consistent than those obtained from the small sewers, the correlation between wastewater-based and clinical-testing data was also good for the residential areas with more than 7,000 registered inhabitants. It was shown that monitoring SARS-CoV-2 RNA in wastewater sampled from small sewers could identify isolated occurrences of COVID-19-positive cases in local neighborhoods. This can be very valuable while tracking COVID-19 hotspots within large cities.
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Affiliation(s)
- Kamila Zdenkova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czechia.
| | - Jana Bartackova
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czechia
| | - Eliska Cermakova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czechia
| | - Katerina Demnerova
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Czechia
| | - Alzbeta Dostalkova
- Department of Biotechnology, University of Chemistry and Technology Prague, Czechia
| | - Vaclav Janda
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czechia
| | - Jiri Jarkovsky
- Institute of Health Information and Statistics of the Czech Republic, Czechia
| | - Marco Antonio Lopez Marin
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czechia
| | | | - Michaela Rumlova
- Department of Biotechnology, University of Chemistry and Technology Prague, Czechia
| | - Jana Rihova Ambrozova
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czechia
| | - Klara Skodakova
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czechia
| | | | - Petr Sykora
- Prazske vodovody a kanalizace, a.s., Czechia
| | - Dana Vejmelkova
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czechia
| | - Jiri Wanner
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czechia
| | - Jan Bartacek
- Department of Water Technology and Environmental Engineering, University of Chemistry and Technology Prague, Czechia
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10
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Lavania M, Potdar VA, Ranshing S, Vipat V, Saha U, Jadhav SM, Sawant PM, Padbidri V, Chaudhari PA, Patwardhan S. Whole-genome sequencing & mutational analysis of SARS-CoV-2 from patients' faecal samples reveal the possible role in faecal-oral transmission. Indian J Med Res 2022; 155:205-210. [PMID: 35859446 PMCID: PMC9552375 DOI: 10.4103/ijmr.ijmr_1045_21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Mallika Lavania
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Varsha A Potdar
- National Influenza Centre, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Sujata Ranshing
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Veena Vipat
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Ujjayni Saha
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Santosh M Jadhav
- Bioinformatics & Data Management Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Pradeep M Sawant
- Enteric Viruses Group, ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Vikram Padbidri
- Department of Microbiology & Infection Control, Jehangir Hospital, Pune 411 001, Maharashtra, India
| | - Piyush A Chaudhari
- Department of Microbiology & Infection Control, Jehangir Hospital, Pune 411 001, Maharashtra, India
| | - Sampada Patwardhan
- Department of Microbiology and Hospital Infection Control, Deenanath Mangeshkar Hospital and Research Centre, Pune 411 004, Maharashtra, India
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11
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Hazan S, Dave S, Papoutsis AJ, Barrows BD, Borody TJ. Successful Bacterial Engraftment Identified by Next-Generation Sequencing Predicts Success of Fecal Microbiota Transplant for Clostridioides difficile. Gastroenterology Res 2021; 14:304-309. [PMID: 34804275 PMCID: PMC8577596 DOI: 10.14740/gr1434] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/26/2021] [Indexed: 11/11/2022] Open
Abstract
Background The effectiveness of fecal microbiota transplantation (FMT), a treatment for Clostridioides difficile infection (CDI), is dependent on successful engraftment (incorporation) of donor stool. We present a method for evaluating engraftment success based on next-generation sequencing (NGS)-based profiling of bacterial strains present in donor and recipient stool, and we suggest its potential to guide treatment decisions. Methods Bacterial strains in stool samples from three patients from the clinic and one donor were analyzed via NGS and metagenomic sequencing, before and 1 month after FMT for CDI. The similarity of strains present was assessed via relative abundance, principal component analysis, Shannon and Simpson diversity indexes, and Bray-Curtis dissimilarity matrix. A positive outcome was successful engraftment, where the post-FMT sample closely resembled that of the donor and CDI was cured. Results Patients (Pts.) 1 and 2, but not Pt. 3’s stool samples closely resembled the donor specimen post-FMT. Noteworthy, Pt. 3 pre-FMT sample was less similar to the donor than that of Pts. 1 and 2. All methods of assessing similarity and dissimilarity used yielded virtually identical conclusions. Pts. 1 and 2 which closely resembled donor specimen, eradicated CDI giving a surrogate objective measure of engraftment. Conclusions Success of engraftment in FMT can be assessed using NGS and metagenomic analysis and parallels success in curing CDI of the microbiome. The statistical methods we present here are reliable and consistent for such purposes. The dissimilarity of Pt. 3 to the donor combined with the failure of engraftment and failure to cure CDI in Pt. 3 suggests that FMT success may be predictable by comparing pre-FMT samples to donor. There is no clinical trial registry listing this study.
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Affiliation(s)
- Sabine Hazan
- ProgenaBiome, 1845 Knoll Drive, Ventura, CA 93003, USA
| | - Sonya Dave
- Microbiome Research, 1845 Knoll Drive, Ventura, CA 93003, USA
| | | | | | - Thomas J Borody
- Centre for Digestive Diseases, 229 Great North Road, Five Dock, NSW 2046, Australia
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12
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Bozkurt HS, Bilen Ö. Gastrointestinal symptoms in COVID-19 could be associated with severe lung involvement and increased readmission rates. EUR J INFLAMM 2021. [DOI: 10.1177/20587392211048259] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Introduction SARS-CoV-2 virus manifests itself with primary lung damage but also has intestinal involvement. In this study, we aimed to investigate the frequency of gastrointestinal symptoms (GIS) and the relationship of GIS with readmission to the hospital within 30 days in SARS-CoV-2 infected patients who were hospitalized in a specified pandemic hospital. Materials and Methods Symptomatic patients diagnosed with rapid antibody positivity with real-time polymerase chain reaction and typical thorax computed tomography findings were included in this retrospective cohort observational study. Demographic and clinical data were obtained from electronic medical records. Hospital-associated GIS were considered as experiencing at least one of the GIS such as gas, bloating, diarrhea, and constipation developing within72 h after hospital admission. Results The mean age of the patients was 58 ± 14.4 years and 60.7% were men. 82% of hospitalizations were a moderate and severe disease. 71.4% of patients without GIS had at least one of the GIS after hospitalization. As the severity of the disease increased, the frequency of the severity of gastrointestinal symptom increased. GIS bowel disorders were more prominent in patients with moderate and severe disease. Antibiotic and specific treatment (anti-Il-1, anti-Il-6) contributed to the occurrence of gastrointestinal symptom in SARS-CoV-2 inpatients. Conclusion According to our observations of the second wave of the pandemic, the presence, frequency, and severity of gastrointestinal symptom in inpatient is associated with severity of lung disease and increased readmission rate after discharge.
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Affiliation(s)
- Hüseyin S Bozkurt
- Clinic of Gastroenterology, Istanbul Maltepe University Faculty Of Medicine, Istanbul, Turkey
| | - Ömer Bilen
- Bursa Techinical University, Bursa, Turkey
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13
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Simsek C, Erul E, Balaban HY. Role of gastrointestinal system on transmission and pathogenesis of SARS-CoV-2. World J Clin Cases 2021; 9:5427-5434. [PMID: 34307596 PMCID: PMC8281423 DOI: 10.12998/wjcc.v9.i20.5427] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/20/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) continues to pose a significant threat to global health. Primary prevention remains as a major strategy against the pandemic. Current evidence proves that aerosol and droplet-based routes are the main means of transmission of COVID-19 but other ways should be sought in order to prevent possible collateral transmission. The gastrointestinal system may be one such route. Angiotensin converting enzyme 2 is the target entry receptor for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that is abundantly expressed in the gastrointestinal tract. SARS-CoV-2 is able to infect human enterocytes similar to severe acute respiratory syndrome and Middle Eastern respiratory syndrome. Herein this review, we discuss the current knowledge regarding the role of gastrointestinal transmission in transmission and pathophysiology of COVID-19.
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Affiliation(s)
- Cem Simsek
- Department of Gastroenterology, Hacettepe University Faculty of Medicine, Ankara 06100, Turkey
| | - Enes Erul
- Department of Internal Medicine, Hacettepe University Faculty of Medicine, Ankara 06100, Turkey
| | - Hatice Yasemin Balaban
- Department of Gastroenterology, Hacettepe University Faculty of Medicine, Ankara 06100, Turkey
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14
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Rakislova N, Marimon L, Ismail MR, Carrilho C, Fernandes F, Ferrando M, Castillo P, Rodrigo-Calvo MT, Guerrero J, Ortiz E, Muñoz-Beatove A, Martinez MJ, Hurtado JC, Navarro M, Bassat Q, Maixenchs M, Delgado V, Wallong E, Aceituno A, Kim J, Paganelli C, Goco NJ, Aldecoa I, Martinez-Pozo A, Martinez D, Ramírez-Ruz J, Cathomas G, Haab M, Menéndez C, Ordi J. Minimally Invasive Autopsy Practice in COVID-19 Cases: Biosafety and Findings. Pathogens 2021; 10:pathogens10040412. [PMID: 33915771 PMCID: PMC8065952 DOI: 10.3390/pathogens10040412] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/21/2021] [Accepted: 03/27/2021] [Indexed: 12/11/2022] Open
Abstract
Postmortem studies are crucial for providing insight into emergent diseases. However, a complete autopsy is frequently not feasible in highly transmissible diseases due to biohazard challenges. Minimally invasive autopsy (MIA) is a needle-based approach aimed at collecting samples of key organs without opening the body, which may be a valid alternative in these cases. We aimed to: (a) provide biosafety guidelines for conducting MIAs in COVID-19 cases, (b) compare the performance of MIA versus complete autopsy, and (c) evaluate the safety of the procedure. Between October and December 2020, MIAs were conducted in six deceased patients with PCR-confirmed COVID-19, in a basic autopsy room, with reinforced personal protective equipment. Samples from the lungs and key organs were successfully obtained in all cases. A complete autopsy was performed on the same body immediately after the MIA. The diagnoses of the MIA matched those of the complete autopsy. In four patients, COVID-19 was the main cause of death, being responsible for the different stages of diffuse alveolar damage. No COVID-19 infection was detected in the personnel performing the MIAs or complete autopsies. In conclusion, MIA might be a feasible, adequate and safe alternative for cause of death investigation in COVID-19 cases.
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Affiliation(s)
- Natalia Rakislova
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (N.R.); (L.M.); (M.F.); (M.J.M.); (J.C.H.); (Q.B.); (M.M.); (V.D.); (C.M.)
- Department of Pathology, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (P.C.); (M.T.R.-C.); (J.G.); (E.O.); (A.M.-B.); (I.A.); (A.M.-P.); (D.M.); (J.R.-R.)
| | - Lorena Marimon
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (N.R.); (L.M.); (M.F.); (M.J.M.); (J.C.H.); (Q.B.); (M.M.); (V.D.); (C.M.)
| | - Mamudo R. Ismail
- Department of Pathology, Faculty of Medicine, Eduardo Mondlane University, Maputo 1653, Mozambique; (M.R.I.); (C.C.); (F.F.)
- Department of Pathology, Maputo Central Hospital, Maputo 1653, Mozambique
| | - Carla Carrilho
- Department of Pathology, Faculty of Medicine, Eduardo Mondlane University, Maputo 1653, Mozambique; (M.R.I.); (C.C.); (F.F.)
- Department of Pathology, Maputo Central Hospital, Maputo 1653, Mozambique
| | - Fabiola Fernandes
- Department of Pathology, Faculty of Medicine, Eduardo Mondlane University, Maputo 1653, Mozambique; (M.R.I.); (C.C.); (F.F.)
- Department of Pathology, Maputo Central Hospital, Maputo 1653, Mozambique
| | - Melania Ferrando
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (N.R.); (L.M.); (M.F.); (M.J.M.); (J.C.H.); (Q.B.); (M.M.); (V.D.); (C.M.)
| | - Paola Castillo
- Department of Pathology, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (P.C.); (M.T.R.-C.); (J.G.); (E.O.); (A.M.-B.); (I.A.); (A.M.-P.); (D.M.); (J.R.-R.)
| | - Maria Teresa Rodrigo-Calvo
- Department of Pathology, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (P.C.); (M.T.R.-C.); (J.G.); (E.O.); (A.M.-B.); (I.A.); (A.M.-P.); (D.M.); (J.R.-R.)
| | - José Guerrero
- Department of Pathology, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (P.C.); (M.T.R.-C.); (J.G.); (E.O.); (A.M.-B.); (I.A.); (A.M.-P.); (D.M.); (J.R.-R.)
| | - Estrella Ortiz
- Department of Pathology, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (P.C.); (M.T.R.-C.); (J.G.); (E.O.); (A.M.-B.); (I.A.); (A.M.-P.); (D.M.); (J.R.-R.)
| | - Abel Muñoz-Beatove
- Department of Pathology, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (P.C.); (M.T.R.-C.); (J.G.); (E.O.); (A.M.-B.); (I.A.); (A.M.-P.); (D.M.); (J.R.-R.)
| | - Miguel J. Martinez
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (N.R.); (L.M.); (M.F.); (M.J.M.); (J.C.H.); (Q.B.); (M.M.); (V.D.); (C.M.)
- Department of Microbiology, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain;
| | - Juan Carlos Hurtado
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (N.R.); (L.M.); (M.F.); (M.J.M.); (J.C.H.); (Q.B.); (M.M.); (V.D.); (C.M.)
- Department of Microbiology, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain;
| | - Mireia Navarro
- Department of Microbiology, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain;
| | - Quique Bassat
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (N.R.); (L.M.); (M.F.); (M.J.M.); (J.C.H.); (Q.B.); (M.M.); (V.D.); (C.M.)
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo 1929, Mozambique
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
- Pediatrics Department, Hospital Sant Joan de Déu, University of Barcelona, 08950 Barcelona, Spain
- Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain
| | - Maria Maixenchs
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (N.R.); (L.M.); (M.F.); (M.J.M.); (J.C.H.); (Q.B.); (M.M.); (V.D.); (C.M.)
| | - Vima Delgado
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (N.R.); (L.M.); (M.F.); (M.J.M.); (J.C.H.); (Q.B.); (M.M.); (V.D.); (C.M.)
| | - Edwin Wallong
- Department of Pathology, Kenyatta National Hospital (KNH), Nairobi 20723-00202, Kenya;
| | - Anna Aceituno
- RTI International (Research Triangle Institute), Research Triangle Park, NC 12255, USA; (A.A.); (J.K.); (C.P.); (N.J.G.)
| | - Jean Kim
- RTI International (Research Triangle Institute), Research Triangle Park, NC 12255, USA; (A.A.); (J.K.); (C.P.); (N.J.G.)
| | - Christina Paganelli
- RTI International (Research Triangle Institute), Research Triangle Park, NC 12255, USA; (A.A.); (J.K.); (C.P.); (N.J.G.)
| | - Norman J. Goco
- RTI International (Research Triangle Institute), Research Triangle Park, NC 12255, USA; (A.A.); (J.K.); (C.P.); (N.J.G.)
| | - Iban Aldecoa
- Department of Pathology, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (P.C.); (M.T.R.-C.); (J.G.); (E.O.); (A.M.-B.); (I.A.); (A.M.-P.); (D.M.); (J.R.-R.)
- Neurological Tissue Bank of the Biobank-IDIBAPS, Hospital Clínic of Barcelona, 08036 Barcelona, Spain
| | - Antonio Martinez-Pozo
- Department of Pathology, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (P.C.); (M.T.R.-C.); (J.G.); (E.O.); (A.M.-B.); (I.A.); (A.M.-P.); (D.M.); (J.R.-R.)
| | - Daniel Martinez
- Department of Pathology, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (P.C.); (M.T.R.-C.); (J.G.); (E.O.); (A.M.-B.); (I.A.); (A.M.-P.); (D.M.); (J.R.-R.)
| | - José Ramírez-Ruz
- Department of Pathology, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (P.C.); (M.T.R.-C.); (J.G.); (E.O.); (A.M.-B.); (I.A.); (A.M.-P.); (D.M.); (J.R.-R.)
| | - Gieri Cathomas
- Institute of Pathology, Cantonal Hospital Baselland, 4410 Liestal, Switzerland;
| | - Myriam Haab
- Department of Pathology, Saarland University Medical Center, 66421 Homburg/Saar, Germany;
| | - Clara Menéndez
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (N.R.); (L.M.); (M.F.); (M.J.M.); (J.C.H.); (Q.B.); (M.M.); (V.D.); (C.M.)
- Centro de Investigação em Saúde de Manhiça (CISM), Maputo 1929, Mozambique
- Consorcio de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), 28029 Madrid, Spain
| | - Jaume Ordi
- ISGlobal, Barcelona Institute for Global Health, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (N.R.); (L.M.); (M.F.); (M.J.M.); (J.C.H.); (Q.B.); (M.M.); (V.D.); (C.M.)
- Department of Pathology, Hospital Clínic, Universitat de Barcelona, 08036 Barcelona, Spain; (P.C.); (M.T.R.-C.); (J.G.); (E.O.); (A.M.-B.); (I.A.); (A.M.-P.); (D.M.); (J.R.-R.)
- Correspondence:
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