1
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Keehner J, Abeles SR, Longhurst CA, Horton LE, Myers FE, Riggs-Rodriguez L, Ahmad M, Baxter S, Boussina A, Cantrell K, Cardenas P, De Hoff P, El-Kareh R, Holland J, Ikeda D, Kurashige K, Laurent LC, Lucas A, Pride D, Sathe S, Tran AR, Vasylyeva TI, Yeo G, Knight R, Wertheim JO, Torriani FJ. Integrated Genomic and Social Network Analyses of SARS-CoV-2 Transmission in the Healthcare Setting. Clin Infect Dis 2024; 78:1204-1213. [PMID: 38227643 PMCID: PMC11093679 DOI: 10.1093/cid/ciad738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Indexed: 01/18/2024] Open
Abstract
BACKGROUND Infection prevention (IP) measures are designed to mitigate the transmission of pathogens in healthcare. Using large-scale viral genomic and social network analyses, we determined if IP measures used during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic were adequate in protecting healthcare workers (HCWs) and patients from acquiring SARS-CoV-2. METHODS We performed retrospective cross-sectional analyses of viral genomics from all available SARS-CoV-2 viral samples collected at UC San Diego Health and social network analysis using the electronic medical record to derive temporospatial overlap of infections among related viromes and supplemented with contact tracing data. The outcome measure was any instance of healthcare transmission, defined as cases with closely related viral genomes and epidemiological connection within the healthcare setting during the infection window. Between November 2020 through January 2022, 12 933 viral genomes were obtained from 35 666 patients and HCWs. RESULTS Among 5112 SARS-CoV-2 viral samples sequenced from the second and third waves of SARS-CoV-2 (pre-Omicron), 291 pairs were derived from persons with a plausible healthcare overlap. Of these, 34 pairs (12%) were phylogenetically linked: 19 attributable to household and 14 to healthcare transmission. During the Omicron wave, 2106 contact pairs among 7821 sequences resulted in 120 (6%) related pairs among 32 clusters, of which 10 were consistent with healthcare transmission. Transmission was more likely to occur in shared spaces in the older hospital compared with the newer hospital (2.54 vs 0.63 transmission events per 1000 admissions, P < .001). CONCLUSIONS IP strategies were effective at identifying and preventing healthcare SARS-CoV-2 transmission.
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Affiliation(s)
- Jocelyn Keehner
- Division of Infectious Diseases, Department of Medicine, University of California–SanFrancisco, San Francisco, California, USA
- Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego Health, San Diego, California, USA
| | - Shira R Abeles
- Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego Health, San Diego, California, USA
- Infection Prevention and Clinical Epidemiology Unit, UC San Diego Health, San Diego, California, USA
| | - Christopher A Longhurst
- Division of Biomedical Informatics, Department of Medicine, UC San Diego Health, La Jolla, California, USA
- Department of Pediatrics, University of California–San Diego, La Jolla, California, USA
| | - Lucy E Horton
- Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego Health, San Diego, California, USA
- Infection Prevention and Clinical Epidemiology Unit, UC San Diego Health, San Diego, California, USA
- Vaccine Research and Development Unit, Pfizer Inc, San Diego, California, USA
| | - Frank E Myers
- Infection Prevention and Clinical Epidemiology Unit, UC San Diego Health, San Diego, California, USA
| | - Lindsay Riggs-Rodriguez
- Population Health Services Organization—Programs and Strategy, UC San Diego Health, San Diego, California, USA
| | - Mohammed Ahmad
- Information Services EMR, UC San Diego Health, San Diego, California, USA
| | - Sally Baxter
- Division of Biomedical Informatics at the University of California–San Diego, San Diego, California, USA
| | - Aaron Boussina
- Division of Biomedical Informatics, University of California–San Diego, La Jolla, California, USA
| | - Kalen Cantrell
- Department of Computer Science & Engineering, Jacobs School of Engineering, University of California, San Diego, California, USA
| | - Priscilla Cardenas
- UC San Diego Health's Contact Tracing Team, Infection Prevention and Clinical Epidemiology Unit, UC San Diego Health, San Diego, California, USA
| | - Peter De Hoff
- Sanford Consortium of Regenerative Medicine, University of California–San Diego, La Jolla, California, USA
- Expedited COVID Identification Environment Laboratory, Department of Pediatrics, University of California–San Diego, La Jolla, California, USA
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, UC San Diego Health, San Diego, California, USA
| | - Robert El-Kareh
- Division of Biomedical Informatics, Department of Medicine, UC San Diego Health, La Jolla, California, USA
- Division of Hospital Medicine, Department of Medicine, UC San Diego Health, La Jolla, California, USA
| | - Jennifer Holland
- Analytics and Population Health Department, UC San Diego Health, San Diego, California, USA
| | - Daryn Ikeda
- UC San Diego Health's Contact Tracing Team, Infection Prevention and Clinical Epidemiology Unit, UC San Diego Health, San Diego, California, USA
| | - Kirk Kurashige
- Analytics and Population Health Department, UC San Diego Health, San Diego, California, USA
| | - Louise C Laurent
- Sanford Consortium of Regenerative Medicine, University of California–San Diego, La Jolla, California, USA
- Expedited COVID Identification Environment Laboratory, Department of Pediatrics, University of California–San Diego, La Jolla, California, USA
- Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, UC San Diego Health, San Diego, California, USA
| | - Andrew Lucas
- Information Services EMR, UC San Diego Health, San Diego, California, USA
| | - David Pride
- Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego Health, San Diego, California, USA
- Department of Pathology, UC San Diego Health, La Jolla, California, USA
| | - Shashank Sathe
- Sanford Consortium of Regenerative Medicine, University of California–San Diego, La Jolla, California, USA
- Department of Cellular and Molecular Medicine, University of California–San Diego, La Jolla, California, USA
- Expedited COVID Identification Environment Laboratory, Department of Pediatrics, University of California–San Diego, La Jolla, California, USA
| | - Allen R Tran
- Information Services EMR, UC San Diego Health, San Diego, California, USA
| | - Tetyana I Vasylyeva
- Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego Health, San Diego, California, USA
| | - Gene Yeo
- Sanford Consortium of Regenerative Medicine, University of California–San Diego, La Jolla, California, USA
- Department of Cellular and Molecular Medicine, University of California–San Diego, La Jolla, California, USA
- Expedited COVID Identification Environment Laboratory, Department of Pediatrics, University of California–San Diego, La Jolla, California, USA
| | - Rob Knight
- Department of Pediatrics, University of California–San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California–San Diego, La Jolla, California, USA
- Department of Computer Science and Engineering, University of California–San Diego, La Jolla, California, USA
- Expedited COVID Identification Environment Laboratory, Department of Pediatrics, University of California–San Diego, La Jolla, California, USA
- Center for Microbiome Innovation, University of California–San Diego, La Jolla, California, USA
| | - Joel O Wertheim
- Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego Health, San Diego, California, USA
| | - Francesca J Torriani
- Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego Health, San Diego, California, USA
- Infection Prevention and Clinical Epidemiology Unit, UC San Diego Health, San Diego, California, USA
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2
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Oles RE, Terrazas MC, Loomis LR, Hsu CY, Tribelhorn C, Ferre PB, Ea A, Bryant M, Young J, Carrow HC, Sandborn WJ, Dulai P, Sivagnanam M, Pride D, Knight R, Chu H. Pangenome comparison of Bacteroides fragilis genomospecies unveil genetic diversity and ecological insights. bioRxiv 2023:2023.12.20.572674. [PMID: 38187556 PMCID: PMC10769428 DOI: 10.1101/2023.12.20.572674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Bacteroides fragilis is a Gram-negative commensal bacterium commonly found in the human colon that differentiates into two genomospecies termed division I and II. We leverage a comprehensive collection of 694 B. fragilis whole genome sequences and report differential gene abundance to further support the recent proposal that divisions I and II represent separate species. In division I strains, we identify an increased abundance of genes related to complex carbohydrate degradation, colonization, and host niche occupancy, confirming the role of division I strains as gut commensals. In contrast, division II strains display an increased prevalence of plant cell wall degradation genes and exhibit a distinct geographic distribution, primarily originating from Asian countries, suggesting dietary influences. Notably, division II strains have an increased abundance of genes linked to virulence, survival in toxic conditions, and antimicrobial resistance, consistent with a higher incidence of these strains in bloodstream infections. This study provides new evidence supporting a recent proposal for classifying divisions I and II B. fragilis strains as distinct species, and our comparative genomic analysis reveals their niche-specific roles.
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Affiliation(s)
- Renee E Oles
- Department of Pathology, University of California, San Diego, La Jolla, CA
- Department of Pediatrics, School of Medicine, University of California, La Jolla, CA
| | | | - Luke R Loomis
- Department of Pathology, University of California, San Diego, La Jolla, CA
| | - Chia-Yun Hsu
- Department of Pathology, University of California, San Diego, La Jolla, CA
| | - Caitlin Tribelhorn
- Department of Pediatrics, School of Medicine, University of California, La Jolla, CA
| | - Pedro Belda Ferre
- Department of Pediatrics, School of Medicine, University of California, La Jolla, CA
| | - Allison Ea
- Department of Pathology, University of California, San Diego, La Jolla, CA
| | - MacKenzie Bryant
- Department of Pediatrics, School of Medicine, University of California, La Jolla, CA
| | - Jocelyn Young
- Department of Pediatrics, School of Medicine, University of California, La Jolla, CA
- Rady Children's Hospital, San Diego, CA, United States
| | - Hannah C Carrow
- Department of Pathology, University of California, San Diego, La Jolla, CA
| | - William J Sandborn
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
| | - Parambir Dulai
- Division of Gastroenterology, University of California, San Diego, La Jolla, CA
- Division of Gastroenterology, Northwestern University, Chicago, Illinois
| | - Mamata Sivagnanam
- Department of Pediatrics, School of Medicine, University of California, La Jolla, CA
- Rady Children's Hospital, San Diego, CA, United States
| | - David Pride
- Department of Pathology, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
- Center for Innovative Phage Applications and Therapeutics (IPATH), University of California, San Diego, La Jolla, CA
- Center of Advanced Laboratory Medicine (CALM), University of California, San Diego, La Jolla, CA
| | - Rob Knight
- Department of Pediatrics, School of Medicine, University of California, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
- Shu Chien-Gene Lay Department of Bioengineering, University of California San Diego, La Jolla, CA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA
- Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, CA
| | - Hiutung Chu
- Department of Pathology, University of California, San Diego, La Jolla, CA
- Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA
- Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (cMAV), University of California, San Diego, La Jolla, CA
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3
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Matteson NL, Hassler GW, Kurzban E, Schwab MA, Perkins SA, Gangavarapu K, Levy JI, Parker E, Pride D, Hakim A, De Hoff P, Cheung W, Castro-Martinez A, Rivera A, Veder A, Rivera A, Wauer C, Holmes J, Wilson J, Ngo SN, Plascencia A, Lawrence ES, Smoot EW, Eisner ER, Tsai R, Chacón M, Baer NA, Seaver P, Salido RA, Aigner S, Ngo TT, Barber T, Ostrander T, Fielding-Miller R, Simmons EH, Zazueta OE, Serafin-Higuera I, Sanchez-Alavez M, Moreno-Camacho JL, García-Gil A, Murphy Schafer AR, McDonald E, Corrigan J, Malone JD, Stous S, Shah S, Moshiri N, Weiss A, Anderson C, Aceves CM, Spencer EG, Hufbauer EC, Lee JJ, King AJ, Ramesh KS, Nguyen KN, Saucedo K, Robles-Sikisaka R, Fisch KM, Gonias SL, Birmingham A, McDonald D, Karthikeyan S, Martin NK, Schooley RT, Negrete AJ, Reyna HJ, Chavez JR, Garcia ML, Cornejo-Bravo JM, Becker D, Isaksson M, Washington NL, Lee W, Garfein RS, Luna-Ruiz Esparza MA, Alcántar-Fernández J, Henson B, Jepsen K, Olivares-Flores B, Barrera-Badillo G, Lopez-Martínez I, Ramírez-González JE, Flores-León R, Kingsmore SF, Sanders A, Pradenas A, White B, Matthews G, Hale M, McLawhon RW, Reed SL, Winbush T, McHardy IH, Fielding RA, Nicholson L, Quigley MM, Harding A, Mendoza A, Bakhtar O, Browne SH, Olivas Flores J, Rincon Rodríguez DG, Gonzalez Ibarra M, Robles Ibarra LC, Arellano Vera BJ, Gonzalez Garcia J, Harvey-Vera A, Knight R, Laurent LC, Yeo GW, Wertheim JO, Ji X, Worobey M, Suchard MA, Andersen KG, Campos-Romero A, Wohl S, Zeller M. Genomic surveillance reveals dynamic shifts in the connectivity of COVID-19 epidemics. Cell 2023; 186:5690-5704.e20. [PMID: 38101407 PMCID: PMC10795731 DOI: 10.1016/j.cell.2023.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 08/21/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023]
Abstract
The maturation of genomic surveillance in the past decade has enabled tracking of the emergence and spread of epidemics at an unprecedented level. During the COVID-19 pandemic, for example, genomic data revealed that local epidemics varied considerably in the frequency of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineage importation and persistence, likely due to a combination of COVID-19 restrictions and changing connectivity. Here, we show that local COVID-19 epidemics are driven by regional transmission, including across international boundaries, but can become increasingly connected to distant locations following the relaxation of public health interventions. By integrating genomic, mobility, and epidemiological data, we find abundant transmission occurring between both adjacent and distant locations, supported by dynamic mobility patterns. We find that changing connectivity significantly influences local COVID-19 incidence. Our findings demonstrate a complex meaning of "local" when investigating connected epidemics and emphasize the importance of collaborative interventions for pandemic prevention and mitigation.
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Affiliation(s)
| | - Gabriel W Hassler
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Madison A Schwab
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Sarah A Perkins
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Biomathematics, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA; Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - David Pride
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Peter De Hoff
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Willi Cheung
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Anelizze Castro-Martinez
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium of Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Andrea Rivera
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Anthony Veder
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Ariana Rivera
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Cassandra Wauer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jacqueline Holmes
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Jedediah Wilson
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Shayla N Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Emily R Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rebecca Tsai
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA; Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | | | - Oscar E Zazueta
- Department of Epidemiology, Secretaria de Salud de Baja California, Tijuana, Baja California, Mexico
| | | | - Manuel Sanchez-Alavez
- Centro de Diagnostico COVID-19 UABC, Tijuana, Baja California, Mexico; Department of Molecular Medicine, Scripps Research, La Jolla, CA, USA
| | | | - Abraham García-Gil
- Clinical Laboratory Department, Salud Digna, A.C, Tijuana, Baja California, Mexico
| | | | - Eric McDonald
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Jeremy Corrigan
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - John D Malone
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA
| | - Alana Weiss
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Emily G Spencer
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Emory C Hufbauer
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Justin J Lee
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Alison J King
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Karthik S Ramesh
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Kelly N Nguyen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Kieran Saucedo
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | | | - Kathleen M Fisch
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Steven L Gonias
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Amanda Birmingham
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Smruthi Karthikeyan
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Natasha K Martin
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Robert T Schooley
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA
| | - Agustin J Negrete
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Horacio J Reyna
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Jose R Chavez
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Maria L Garcia
- Facultad de Ciencias de la Salud Universidad Autonoma de Baja California Valle de Las Palmas, Tijuana, Baja California, Mexico
| | - Jose M Cornejo-Bravo
- Facultad de Ciencias Quimicas e Ingenieria, Universidad Autonoma de Baja California, Tijuana, Baja California, Mexico
| | | | | | | | | | - Richard S Garfein
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA
| | | | | | - Benjamin Henson
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Beatriz Olivares-Flores
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Gisela Barrera-Badillo
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Irma Lopez-Martínez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - José E Ramírez-González
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | - Rita Flores-León
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, CDMX, Mexico
| | | | - Alison Sanders
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Allorah Pradenas
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Benjamin White
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Gary Matthews
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Matt Hale
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Ronald W McLawhon
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Sharon L Reed
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | - Terri Winbush
- Return to Learn, University of California, San Diego, La Jolla, CA, USA
| | | | | | | | | | | | | | | | - Sara H Browne
- Division of Infectious Disease and Global Public Health, University of California, San Diego, La Jolla, CA, USA; Specialist in Global Health, Encinitas, CA, USA
| | - Jocelyn Olivas Flores
- Facultad de Ciencias Quimicas e Ingenieria, Universidad Autonoma de Baja California, Tijuana, Baja California, Mexico; University of HealthMx, Tijuana, Baja California, Mexico
| | - Diana G Rincon Rodríguez
- University of HealthMx, Tijuana, Baja California, Mexico; Facultad de Medicina, Universidad Xochicalco, Tijuana, Baja California, Mexico
| | - Martin Gonzalez Ibarra
- University of HealthMx, Tijuana, Baja California, Mexico; Facultad de Medicina, Universidad Xochicalco, Tijuana, Baja California, Mexico
| | - Luis C Robles Ibarra
- University of HealthMx, Tijuana, Baja California, Mexico; Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado, Tijuana, Baja California, Mexico
| | - Betsy J Arellano Vera
- University of HealthMx, Tijuana, Baja California, Mexico; Instituto Mexicano del Seguro Social, Tijuana, Baja California, Mexico
| | - Jonathan Gonzalez Garcia
- University of HealthMx, Tijuana, Baja California, Mexico; SIMNSA, Tijuana, Baja California, Mexico
| | | | - Rob Knight
- Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium of Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Sanford Consortium of Regenerative Medicine, University of California, San Diego, La Jolla, CA, USA; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Joel O Wertheim
- Department of Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Xiang Ji
- Department of Mathematics, School of Science and Engineering, Tulane University, New Orleans, LA, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Marc A Suchard
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
| | - Abraham Campos-Romero
- Innovation and Research Department, Salud Digna, A.C, Tijuana, Baja California, Mexico
| | - Shirlee Wohl
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
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4
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Abstract
Objectives: Breastfeeding and human milk (HM) improve maternal and infant morbidities and mortality. Therefore, monitoring the safety of breastfeeding and access to HM is of critical importance. In this study, we assessed tools to monitor the presence of monkeypox virus (MPXV) in HM and whether standard Holder pasteurization inactivates MPXV. Materials and Methods: Heat-inactivated MPXV was added to HM or viral transport media (VTM) and analyzed using both research and clinical MPXV quantitative polymerase chain reaction (qPCR) tests. Infectious MPXV was added to HM and was exposed to 1 cycle of freeze-thaw, incubation for 1 hour at room temperature, or conditions of Holder pasteurization (62.5°C for 30 minutes) followed by infectious unit quantification by plaque assay. Results: Research and clinical nucleic acid tests detect MPXV that was added to HM but with reduced sensitivity compared with equivalent samples in VTM at low virus inoculum. MPXV added to HM to achieve a starting concentration of 225,000 plaque forming units (pfu)/mL remains infectious after freeze-thaw or 1 hour storage at room temperature. However, Holder pasteurization reduced infectious virus below the limit of detection, >2,000-fold reduction in viral titer. Conclusion: MPXV can be detected when added to HM using a clinical laboratory-developed qPCR test without modification, but the detection limit is reduced compared with equivalent samples in VTM. MPXV remains viable in HM should the virus ever gain access to HM, but Holder pasteurization reduces infectious MPXV to below detection limits and can be used to reduce the risk of MPXV transmission to infants who receive pasteurized (donor) HM.
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Affiliation(s)
- Alex E. Clark
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Annalee Furst
- Department of Pediatrics, and University of California, San Diego, La Jolla, California, USA
| | - Kristija Sejane
- Department of Pediatrics, and University of California, San Diego, La Jolla, California, USA
| | - Lisa Stellwagen
- UC Health Milk Bank, University of California, San Diego, La Jolla, California, USA
- Human Milk Institute (HMI), University of California, San Diego, La Jolla, California, USA
| | - Marissa Proost
- Department of Pathology, University of California, San Diego, La Jolla, California, USA
| | - David Pride
- Department of Pathology, University of California, San Diego, La Jolla, California, USA
| | - Davey M. Smith
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
- VA San Diego Healthcare System, San Diego, California, USA
| | - Aaron F. Carlin
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
- Department of Pathology, University of California, San Diego, La Jolla, California, USA
| | - Lars Bode
- Department of Pediatrics, and University of California, San Diego, La Jolla, California, USA
- Human Milk Institute (HMI), University of California, San Diego, La Jolla, California, USA
- Larsson-Rosenquist Foundation Mother-Milk-Infant Center of research Excellence (MOMI CORE), University of California, San Diego, La Jolla, California, USA
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5
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Knoth P, Herrmannova D, Cancellieri M, Anastasiou L, Pontika N, Pearce S, Gyawali B, Pride D. CORE: A Global Aggregation Service for Open Access Papers. Sci Data 2023; 10:366. [PMID: 37286585 DOI: 10.1038/s41597-023-02208-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 05/03/2023] [Indexed: 06/09/2023] Open
Abstract
This paper introduces CORE, a widely used scholarly service, which provides access to the world's largest collection of open access research publications, acquired from a global network of repositories and journals. CORE was created with the goal of enabling text and data mining of scientific literature and thus supporting scientific discovery, but it is now used in a wide range of use cases within higher education, industry, not-for-profit organisations, as well as by the general public. Through the provided services, CORE powers innovative use cases, such as plagiarism detection, in market-leading third-party organisations. CORE has played a pivotal role in the global move towards universal open access by making scientific knowledge more easily and freely discoverable. In this paper, we describe CORE's continuously growing dataset and the motivation behind its creation, present the challenges associated with systematically gathering research papers from thousands of data providers worldwide at scale, and introduce the novel solutions that were developed to overcome these challenges. The paper then provides an in-depth discussion of the services and tools built on top of the aggregated data and finally examines several use cases that have leveraged the CORE dataset and services.
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Grants
- 739563 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Euratom (H2020 Euratom Research and Training Programme 2014-2018)
- 654021 EC | EU Framework Programme for Research and Innovation H2020 | H2020 Euratom (H2020 Euratom Research and Training Programme 2014-2018)
- CORE, ServiceCORE, DiggiCORE, JDSCORE Joint Information Systems Committee (JISC)
- CORE, ServiceCORE, DiggiCORE, JDSCORE Joint Information Systems Committee (JISC)
- CORE, ServiceCORE, DiggiCORE, JDSCORE Joint Information Systems Committee (JISC)
- CORE, ServiceCORE, DiggiCORE, JDSCORE Joint Information Systems Committee (JISC)
- CORE, ServiceCORE, DiggiCORE, JDSCORE Joint Information Systems Committee (JISC)
- CORE, ServiceCORE, DiggiCORE, JDSCORE Joint Information Systems Committee (JISC)
- DE-AC05-00OR22725 DOE | Advanced Research Projects Agency - Energy (Advanced Research Projects Agency - Energy - U.S. Department of Energy)
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Affiliation(s)
- Petr Knoth
- Knowledge Media Institute, The Open University Walton Hall, Milton Keynes, UK.
| | - Drahomira Herrmannova
- Knowledge Media Institute, The Open University Walton Hall, Milton Keynes, UK
- Oak Ridge National Laboratory Oak Ridge, Oak Ridge, TN, USA
| | - Matteo Cancellieri
- Knowledge Media Institute, The Open University Walton Hall, Milton Keynes, UK
| | - Lucas Anastasiou
- Knowledge Media Institute, The Open University Walton Hall, Milton Keynes, UK
| | - Nancy Pontika
- Knowledge Media Institute, The Open University Walton Hall, Milton Keynes, UK
| | - Samuel Pearce
- Knowledge Media Institute, The Open University Walton Hall, Milton Keynes, UK
| | - Bikash Gyawali
- Knowledge Media Institute, The Open University Walton Hall, Milton Keynes, UK
| | - David Pride
- Knowledge Media Institute, The Open University Walton Hall, Milton Keynes, UK
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6
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Tamma PD, Souli M, Billard M, Campbell J, Conrad D, Ellison DW, Evans B, Evans SR, Greenwood-Quaintance KE, Filippov AA, Geres HS, Hamasaki T, Komarow L, Nikolich MP, Lodise TP, Nayak SU, Norice-Tra C, Patel R, Pride D, Russell J, Van Tyne D, Chambers HF, FowlerJr VG, Schooley RT. Safety and microbiological activity of phage therapy in persons with cystic fibrosis colonized with Pseudomonas aeruginosa: study protocol for a phase 1b/2, multicenter, randomized, double-blind, placebo-controlled trial. Trials 2022; 23:1057. [PMID: 36578069 PMCID: PMC9795609 DOI: 10.1186/s13063-022-07047-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/21/2022] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Bacteriophages (phages) are a promising anti-infective option for human disease. Major gaps remain in understanding their potential utility. METHODS This is a randomized, placebo-controlled, double-blind study of a single dose of intravenous phage in approximately 72 clinically stable adult cystic fibrosis volunteers recruited from up to 20 US sites with Pseudomonas aeruginosa airway colonization. The single dose of phage consists of a mixture of four anti-pseudomonal phages. Six sentinel participants will be sequentially enrolled with dose escalation of the phage mixture by one log10 beginning with 4 × 107 plaque-forming units in an unblinded stage 1. If no serious adverse events related to the study product are identified, the trial will proceed to a double-blinded stage 2. In stage 2a, 32 participants will be randomly assigned to one of three phage dosages or placebo in a 1:1:1:1 allocation. An interim analysis will be performed to determine the phage dosage with the most favorable safety and microbiological activity profile to inform phage dosing in stage 2b. During stage 2b, up to 32 additional volunteers will be randomized 1:1 to the phage or placebo arm. Primary outcomes include (1) the number of grade 2 or higher treatment-emergent adverse events, (2) change in log10 P. aeruginosa total colony counts in sputum, and (3) the probability of a randomly selected subject having a more favorable outcome ranking if assigned to receive phage therapy versus placebo. Exploratory outcomes include (1) sputum and serum phage pharmacokinetics, (2) the impact of phage on lung function, (3) the proportion of P. aeruginosa isolates susceptible to the phage mixture before and after study product administration, and (4) changes in quality of life. DISCUSSION This trial will investigate the activity of phages in reducing P. aeruginosa colony counts and provide insights into the safety profile of phage therapy. TRIAL REGISTRATION ClinicalTrials.gov NCT05453578. Registered on 12 July 2022.
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Affiliation(s)
- Pranita D. Tamma
- grid.21107.350000 0001 2171 9311Department of Pediatrics, Johns Hopkins University School of Medicine, 200 North Wolfe Street, Room 3149, Baltimore, MD 21287 USA
| | - Maria Souli
- grid.189509.c0000000100241216Duke Clinical Research Institute, Duke University Medical Center, Durham, NC USA
| | | | - Joseph Campbell
- grid.419681.30000 0001 2164 9667National Institutes of Health, National Institute of Allergy and Infectious Diseases, Division of Microbiology and Infectious Diseases, Bethesda, MD USA
| | - Douglas Conrad
- grid.266100.30000 0001 2107 4242Department of Medicine, University of California San Diego, San Diego, CA USA
| | - Damon W. Ellison
- grid.507680.c0000 0001 2230 3166Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Beth Evans
- grid.189509.c0000000100241216Duke Clinical Research Institute, Duke University Medical Center, Durham, NC USA
| | - Scott R. Evans
- grid.253615.60000 0004 1936 9510The Biostatistics Center, The George Washington University, Rockville, MD USA
| | | | - Andrey A. Filippov
- grid.507680.c0000 0001 2230 3166Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Holly S. Geres
- grid.189509.c0000000100241216Duke Clinical Research Institute, Duke University Medical Center, Durham, NC USA
| | - Toshimitsu Hamasaki
- grid.253615.60000 0004 1936 9510The Biostatistics Center, The George Washington University, Rockville, MD USA
| | - Lauren Komarow
- grid.253615.60000 0004 1936 9510The Biostatistics Center, The George Washington University, Rockville, MD USA
| | - Mikeljon P. Nikolich
- grid.507680.c0000 0001 2230 3166Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD USA
| | - Thomas P. Lodise
- grid.413555.30000 0000 8718 587XDepartment of Pharmacy Practice, Albany College of Pharmacy and Health Sciences, Albany, NY USA
| | - Seema U. Nayak
- grid.419681.30000 0001 2164 9667National Institutes of Health, National Institute of Allergy and Infectious Diseases, Division of Microbiology and Infectious Diseases, Bethesda, MD USA
| | - Carmelle Norice-Tra
- grid.419681.30000 0001 2164 9667National Institutes of Health, National Institute of Allergy and Infectious Diseases, Division of Microbiology and Infectious Diseases, Bethesda, MD USA
| | - Robin Patel
- grid.66875.3a0000 0004 0459 167XDepartment of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, USA ,grid.66875.3a0000 0004 0459 167XInfectious Diseases and Occupational Medicine, Mayo Clinic, Rochester, MN USA
| | - David Pride
- grid.266100.30000 0001 2107 4242Departments of Medicine and Pathology, University of California San Diego, San Diego, CA USA
| | - Janie Russell
- grid.419681.30000 0001 2164 9667National Institutes of Health, National Institute of Allergy and Infectious Diseases, Division of Microbiology and Infectious Diseases, Bethesda, MD USA
| | - Daria Van Tyne
- grid.21925.3d0000 0004 1936 9000Department of Medicine, University of Pittsburgh, Pittsburgh, PA USA
| | - Henry F. Chambers
- grid.266102.10000 0001 2297 6811Department of Medicine, University of California San Francisco, San Francisco, CA USA
| | - Vance G. FowlerJr
- grid.189509.c0000000100241216Duke Clinical Research Institute, Duke University Medical Center, Durham, NC USA ,grid.189509.c0000000100241216Department of Medicine, Duke University Medical Center, Durham, NC USA
| | - Robert T. Schooley
- grid.266100.30000 0001 2107 4242Departments of Medicine and Pathology, University of California San Diego, San Diego, CA USA
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7
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Chan SK, Zhao Z, Penziner S, Khong E, Pride D, Schooley RT, Steinmetz NF. Isolation of a Peptide That Binds to Pseudomonas aeruginosa Lytic Bacteriophage. ACS Omega 2022; 7:38053-38060. [PMID: 36312416 PMCID: PMC9609082 DOI: 10.1021/acsomega.2c05539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Antimicrobial resistance is a global health threat that is exacerbated by the overuse and misuse of antibiotics in medicine and agriculture. As an alternative to conventional antimicrobial drugs, phage therapy involves the treatment of infected patients with a bacteriophage that naturally destroys bacterial pathogens. With the re-emergence of phage therapy, novel tools are needed to study phages. In this work we set out to screen and isolate peptide candidates that bind to phages and act as affinity tags. Such peptides functionalized with an imaging agent could serves as versatile tools for tracking and imaging of phages. Specifically, we screened a phage display library for peptides that bind to the Good Vibes phage (GV), which lyses the bacterial pathogen Pseudomonas aeruginosa. Isolated monoclonal library phages featured a highly conserved consensus motif, LPPIXRX. The corresponding peptide WDLPPIGRLSGN was synthesized with a GGGSK linker and conjugated to cyanine 5 or biotin. The specific binding of the LPPIXRX motif to GV in vitro was confirmed using an enzyme-linked immunosorbent assay. We demonstrated imaging and tracking of GV in bacterial populations using the fluorescent targeting peptide and flow cytometry. In conclusion, we developed fluorescent labeled peptides that can bind to bacteriophage GV specifically, which may enable real-time analysis of phage in vivo and monitor the efficacy of phage therapy.
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Affiliation(s)
- Soo Khim Chan
- Department
of NanoEngineering, Department of Medicine, Department of Pathology, Department of Bioengineering, Department of Radiology, Center for Nano-ImmunoEngineering, Moores Cancer Center, and Institute for Materials
Discovery and Design, University of California
San Diego, 9500 Gilman Dr., La Jolla, California 92093, United States
| | - Zhongchao Zhao
- Department
of NanoEngineering, Department of Medicine, Department of Pathology, Department of Bioengineering, Department of Radiology, Center for Nano-ImmunoEngineering, Moores Cancer Center, and Institute for Materials
Discovery and Design, University of California
San Diego, 9500 Gilman Dr., La Jolla, California 92093, United States
| | - Samuel Penziner
- Department
of NanoEngineering, Department of Medicine, Department of Pathology, Department of Bioengineering, Department of Radiology, Center for Nano-ImmunoEngineering, Moores Cancer Center, and Institute for Materials
Discovery and Design, University of California
San Diego, 9500 Gilman Dr., La Jolla, California 92093, United States
| | - Ethan Khong
- Department
of NanoEngineering, Department of Medicine, Department of Pathology, Department of Bioengineering, Department of Radiology, Center for Nano-ImmunoEngineering, Moores Cancer Center, and Institute for Materials
Discovery and Design, University of California
San Diego, 9500 Gilman Dr., La Jolla, California 92093, United States
| | - David Pride
- Department
of NanoEngineering, Department of Medicine, Department of Pathology, Department of Bioengineering, Department of Radiology, Center for Nano-ImmunoEngineering, Moores Cancer Center, and Institute for Materials
Discovery and Design, University of California
San Diego, 9500 Gilman Dr., La Jolla, California 92093, United States
| | - Robert T. Schooley
- Department
of NanoEngineering, Department of Medicine, Department of Pathology, Department of Bioengineering, Department of Radiology, Center for Nano-ImmunoEngineering, Moores Cancer Center, and Institute for Materials
Discovery and Design, University of California
San Diego, 9500 Gilman Dr., La Jolla, California 92093, United States
| | - Nicole F. Steinmetz
- Department
of NanoEngineering, Department of Medicine, Department of Pathology, Department of Bioengineering, Department of Radiology, Center for Nano-ImmunoEngineering, Moores Cancer Center, and Institute for Materials
Discovery and Design, University of California
San Diego, 9500 Gilman Dr., La Jolla, California 92093, United States
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8
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Hsu CL, Zhang X, Jiang L, Lang S, Hartmann P, Pride D, Fouts DE, Stärkel P, Schnabl B. Intestinal virome in patients with alcohol use disorder and after abstinence. Hepatol Commun 2022; 6:2058-2069. [PMID: 35368152 PMCID: PMC9315129 DOI: 10.1002/hep4.1947] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 02/22/2022] [Accepted: 03/11/2022] [Indexed: 02/06/2023] Open
Abstract
Alcohol use is a leading cause of chronic liver disease worldwide, and changes in the microbiome associated with alcohol use contribute to patients' risk for liver disease progression. Less is known about the effects of alcohol use on the intestinal viral microbiome (virome) and interactions between bacteriophages and their target bacteria. We studied changes in the intestinal virome of 62 clinically well-characterized patients with alcohol use disorder (AUD) during active alcohol use and after 2 weeks of alcohol abstinence, by extracting virus-like particles and performing metagenomic sequencing. We observed decreased abundance of Propionibacterium, Lactobacillus, and Leuconostoc phages in patients with active AUD when compared with controls, whereas after 2 weeks of alcohol abstinence, patients with AUD demonstrated an increase in the abundance of Propionibacterium, Lactobacillus, and Leuconostoc phages. The intestinal virome signature was also significantly different in patients with AUD with progressive liver disease, with increased abundance of phages targeting Enterobacteria and Lactococcus species phages compared with patients with AUD with nonprogressive liver disease. By performing moderation analyses, we found that progressive liver disease is associated with changes in interactions between some bacteriophages and their respective target bacteria. In summary, active alcohol use and alcohol-associated progressive liver disease are associated with changes in the fecal virome, some of which are partially reversible after a short period of abstinence. Progression of alcohol-associated liver disease is associated with changes in bacteriophage-bacteria interactions.
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Affiliation(s)
- Cynthia L Hsu
- Department of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Xinlian Zhang
- Division of Biostatistics and BioinformaticsDepartment of Family Medicine and Public HealthUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Lu Jiang
- Department of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA.,Department of MedicineVA San Diego Healthcare SystemSan DiegoCaliforniaUSA
| | - Sonja Lang
- Department of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA.,Department of Gastroenterology and HepatologyFaculty of MedicineUniversity of CologneUniversity Hospital CologneCologneGermany
| | - Phillipp Hartmann
- Department of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA.,Department of PediatricsUniversity of California San DiegoLa JollaCaliforniaUSA
| | - David Pride
- Department of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA.,Department of PathologyUniversity of California San DiegoLa JollaCaliforniaUSA.,Center for Innovative Phage Applications and TherapeuticsUniversity of California San DiegoLa JollaCaliforniaUSA
| | | | - Peter Stärkel
- St. Luc University HospitalCatholic University of LouvainBrusselsBelgium
| | - Bernd Schnabl
- Department of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA.,Department of MedicineVA San Diego Healthcare SystemSan DiegoCaliforniaUSA.,Center for Innovative Phage Applications and TherapeuticsUniversity of California San DiegoLa JollaCaliforniaUSA
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9
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Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Schiabor Barrett KM, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission. Nature 2022; 609:101-108. [PMID: 35798029 PMCID: PMC9433318 DOI: 10.1038/s41586-022-05049-6] [Citation(s) in RCA: 140] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 06/29/2022] [Indexed: 11/23/2022]
Abstract
As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing and/or sequencing capacity, which can also introduce biases1–3. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing4,5. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We developed and deployed improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detected emerging variants of concern up to 14 days earlier in wastewater samples, and identified multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission. Emerging SARS-CoV-2 variants of concern were detected early and multiple cases of virus spread not captured by clinical genomic surveillance were identified using high-resolution wastewater and clinical sequencing.
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Affiliation(s)
- Smruthi Karthikeyan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Peter De Hoff
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Amanda Birmingham
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sawyer Farmer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Helena M Tubb
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tommy Valles
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | | | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Shashank Sathe
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Benjamin Henson
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Adam M Mark
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Willi Cheung
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Evelyn S Cresini
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Emily R Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Alma L Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Clarisse A Marotz
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Robert M Neuhard
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA.,Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Angela L Scioscia
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,Student Health and Well-Being, University of California San Diego, La Jolla, CA, USA
| | | | | | - Dismas B Abelman
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - David Brenner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Judith C Bruner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Anne Buckley
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Michael Ellison
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Jeffrey Gattas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Steven L Gonias
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Matt Hale
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Faith Hawkins
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lydia Ikeda
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Hemlata Jhaveri
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ted Johnson
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Vince Kellen
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Brendan Kremer
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Gary Matthews
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ronald W McLawhon
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Pierre Ouillet
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Daniel Park
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Allorah Pradenas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Sharon Reed
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lindsay Riggs
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Alison Sanders
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | | | - Angela Song
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA.,Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Benjamin White
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Terri Winbush
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emory Hufbauer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Justin Lee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sarah A Perkins
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik S Ramesh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Madison A Schwab
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily Spencer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Shirlee Wohl
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | | | | | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | | | | | | | | | | | | | | | | | | | - John D Malone
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | | | - Nikos Gurfield
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA.,Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Richard S Garfein
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Tommi Gaines
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Cheryl Anderson
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Natasha K Martin
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Robert Schooley
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | | | - Duncan R MacCannell
- Office of Advanced Molecular Detection, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Eric McDonald
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Alexander T Yu
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kathleen M Fisch
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Christopher Longhurst
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Biomedical Informatics, University of California, San Diego, La Jolla, California, USA
| | - Patty Maysent
- Office of the UC San Diego Health CEO, University of California, San Diego, USA
| | - David Pride
- Departments of Pathology and Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Pradeep K Khosla
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA.,Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA.,Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA, USA.,Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA. .,Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA. .,Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
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10
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Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Barrett KMS, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission. medRxiv 2022:2021.12.21.21268143. [PMID: 35411350 PMCID: PMC8996633 DOI: 10.1101/2021.12.21.21268143] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples, and identify multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.
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Affiliation(s)
- Smruthi Karthikeyan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Peter De Hoff
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Amanda Birmingham
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sawyer Farmer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Helena M. Tubb
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tommy Valles
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | | | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Shashank Sathe
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Benjamin Henson
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Adam M. Mark
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Willi Cheung
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Evelyn S Cresini
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Emily R Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Alma L Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Clarisse A Marotz
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Robert M Neuhard
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Angela L Scioscia
- Student Health and Well-Being, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | | | | | - Dismas B. Abelman
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - David Brenner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Judith C. Bruner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Anne Buckley
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Michael Ellison
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Jeffrey Gattas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Steven L. Gonias
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Matt Hale
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Faith Hawkins
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lydia Ikeda
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Hemlata Jhaveri
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ted Johnson
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Vince Kellen
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Brendan Kremer
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Gary Matthews
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | | | - Pierre Ouillet
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Daniel Park
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Allorah Pradenas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Sharon Reed
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lindsay Riggs
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Alison Sanders
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | | | - Angela Song
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Benjamin White
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Terri Winbush
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emory Hufbauer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Justin Lee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sarah A Perkins
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik S Ramesh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Madison A Schwab
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily Spencer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Shirlee Wohl
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Laura Nicholson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian H Mchardy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - David P Dimmock
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA
| | | | | | | | | | | | | | | | | | | | | | - John D Malone
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | | | - Nikos Gurfield
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Richard S. Garfein
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Tommi Gaines
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Cheryl Anderson
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Natasha K. Martin
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Robert Schooley
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | | | - Duncan R. MacCannell
- Office of Advanced Molecular Detection, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Eric McDonald
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Alexander T. Yu
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kathleen M Fisch
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Christopher Longhurst
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, California, USA
| | - Patty Maysent
- Office of the UC San Diego Health CEO, University of California, San Diego
| | - David Pride
- Departments of Pathology and Medicine, University of California, San Diego, La Jolla, CA
| | - Pradeep K. Khosla
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Louise C. Laurent
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
| | - Gene W Yeo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
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11
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Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Barrett KMS, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R. Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission. medRxiv 2022. [PMID: 35411350 DOI: 10.1101/2022.01.27.22269965] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
As SARS-CoV-2 continues to spread and evolve, detecting emerging variants early is critical for public health interventions. Inferring lineage prevalence by clinical testing is infeasible at scale, especially in areas with limited resources, participation, or testing/sequencing capacity, which can also introduce biases. SARS-CoV-2 RNA concentration in wastewater successfully tracks regional infection dynamics and provides less biased abundance estimates than clinical testing. Tracking virus genomic sequences in wastewater would improve community prevalence estimates and detect emerging variants. However, two factors limit wastewater-based genomic surveillance: low-quality sequence data and inability to estimate relative lineage abundance in mixed samples. Here, we resolve these critical issues to perform a high-resolution, 295-day wastewater and clinical sequencing effort, in the controlled environment of a large university campus and the broader context of the surrounding county. We develop and deploy improved virus concentration protocols and deconvolution software that fully resolve multiple virus strains from wastewater. We detect emerging variants of concern up to 14 days earlier in wastewater samples, and identify multiple instances of virus spread not captured by clinical genomic surveillance. Our study provides a scalable solution for wastewater genomic surveillance that allows early detection of SARS-CoV-2 variants and identification of cryptic transmission.
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Affiliation(s)
- Smruthi Karthikeyan
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Peter De Hoff
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Amanda Birmingham
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Kristen Jepsen
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sawyer Farmer
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Helena M Tubb
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tommy Valles
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | | | - Rebecca Tsai
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Stefan Aigner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Shashank Sathe
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Niema Moshiri
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Benjamin Henson
- Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
| | - Adam M Mark
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Abbas Hakim
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Nathan A Baer
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tom Barber
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Pedro Belda-Ferre
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Marisol Chacón
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Willi Cheung
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Evelyn S Cresini
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Emily R Eisner
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Alma L Lastrella
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elijah S Lawrence
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Clarisse A Marotz
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Toan T Ngo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Tyler Ostrander
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Ashley Plascencia
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Rodolfo A Salido
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Phoebe Seaver
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Elizabeth W Smoot
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Daniel McDonald
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Robert M Neuhard
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Angela L Scioscia
- Student Health and Well-Being, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | | | | | - Dismas B Abelman
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - David Brenner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Judith C Bruner
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Anne Buckley
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Michael Ellison
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Jeffrey Gattas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Steven L Gonias
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Matt Hale
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Faith Hawkins
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lydia Ikeda
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Hemlata Jhaveri
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ted Johnson
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Vince Kellen
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Brendan Kremer
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Gary Matthews
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Ronald W McLawhon
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Pierre Ouillet
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Daniel Park
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Allorah Pradenas
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Sharon Reed
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Lindsay Riggs
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Alison Sanders
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | | | - Angela Song
- Operational Strategic Initiatives, University of California San Diego, La Jolla, CA, USA
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Benjamin White
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Terri Winbush
- Return to Learn, University of California San Diego, La Jolla, CA, USA
| | - Christine M Aceves
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Catelyn Anderson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik Gangavarapu
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emory Hufbauer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ezra Kurzban
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Justin Lee
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Nathaniel L Matteson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Edyth Parker
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Sarah A Perkins
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karthik S Ramesh
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Refugio Robles-Sikisaka
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Madison A Schwab
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Emily Spencer
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Shirlee Wohl
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Laura Nicholson
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Ian H Mchardy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - David P Dimmock
- Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
| | | | | | | | | | | | | | | | | | | | | | - John D Malone
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | | | - Nikos Gurfield
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Sarah Stous
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Rebecca Fielding-Miller
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Richard S Garfein
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Tommi Gaines
- Division of Infectious Disease and Global Public Health, University of California San Diego, La Jolla, CA, USA
| | - Cheryl Anderson
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Natasha K Martin
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | - Robert Schooley
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California San Diego, La Jolla, CA, USA
| | | | - Duncan R MacCannell
- Office of Advanced Molecular Detection, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | - Seema Shah
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Eric McDonald
- County of San Diego Health and Human Services Agency, San Diego, CA, USA
| | - Alexander T Yu
- COVID-19 Detection, Investigation, Surveillance, Clinical, and Outbreak Response, California Department of Public Health, Richmond, CA, USA
| | - Mark Zeller
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Kathleen M Fisch
- Center for Computational Biology and Bioinformatics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
| | - Christopher Longhurst
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Biomedical Informatics, University of California, San Diego, La Jolla, California, USA
| | - Patty Maysent
- Office of the UC San Diego Health CEO, University of California, San Diego
| | - David Pride
- Departments of Pathology and Medicine, University of California, San Diego, La Jolla, CA
| | - Pradeep K Khosla
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
| | - Louise C Laurent
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Diego, La Jolla, CA, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
| | - Gene W Yeo
- Expedited COVID Identification Environment (EXCITE) Laboratory, Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Sanford Consortium of Regenerative Medicine, University of California San Diego, La Jolla, CA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA
| | - Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Rob Knight
- Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
- Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
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12
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Kunnath SN, Herrmannova D, Pride D, Knoth P. A meta-analysis of semantic classification of citations. Quantitative Science Studies 2021. [DOI: 10.1162/qss_a_00159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Abstract
The aim of this literature review is to examine the current state of the art in the area of citation classification. In particular, we investigate the approaches for characterizing citations based on their semantic type. We conduct this literature review as a meta-analysis covering 60 scholarly articles in this domain. Although we included some of the manual pioneering works in this review, more emphasis is placed on the later automated methods, which use Machine Learning and Natural Language Processing (NLP) for analyzing the fine-grained linguistic features in the surrounding text of citations. The sections are organized based on the steps involved in the pipeline for citation classification. Specifically, we explore the existing classification schemes, data sets, preprocessing methods, extraction of contextual and noncontextual features, and the different types of classifiers and evaluation approaches. The review highlights the importance of identifying the citation types for research evaluation, the challenges faced by the researchers in the process, and the existing research gaps in this field.
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Affiliation(s)
| | | | - David Pride
- Knowledge Media Institute (KMi), The Open University, Milton Keynes, UK
| | - Petr Knoth
- Knowledge Media Institute (KMi), The Open University, Milton Keynes, UK
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13
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Ramirez-Sanchez C, Attai H, Van Tyne D, Shields RK, Yerushalmy O, Hazan R, Nir-Paz R, Pride D, Aslam S. 1276. Assessment of Anti-biofilm Activity of Staphylococcus aureus Bacteriophages Against Clinical Isolates from Patients with Left Ventricular Assist Device Infections. Open Forum Infect Dis 2021. [DOI: 10.1093/ofid/ofab466.1468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Staphylococcus aureus is a common cause of biofilm-mediated left ventricular device (LVAD) infections which are difficult to resolve with antibiotics alone and are associated with substantial morbidity and mortality. Recently, bacteriophages (phage) therapy has been used to resolve LVAD infections in a few cases. Our goal was to assess in vitro susceptibility and anti-biofilm activity of two S. aureus bacteriophages against clinical isolates from patients with S. aureus LVAD infections in order to develop a S. aureus phage cocktail for clinical use.
Methods
Two bacteriophages, OMS1 and OMS2, from the Israeli Phage Bank, were assessed for lytic activity against 15 S.aureus isolates (9 methicillin resistant, MRSA and 6 methicillin susceptible, MSSA) via agar overlay method and plaque forming units (PFU)/mL were enumerated. We then formed bacterial biofilms after overnight incubation at 120 rpm in a 96-well plates in duplicate; experiments were repeated thrice. Wells were then treated with tryptic soy broth (TSB, control) or TSB containing phage at 109 PFU/mL for 24 hours. After washing, biofilms were stained with crystal violet and biomass quantified via optical density at 570mm.
Results
All bacterial isolates were susceptible to both phages via agar overlay to varying degrees as determined by phage titers obtained via serial dilutions (Figure 1a, 1b). OMS1 led to significant reduction in biofilm of 7/9 MRSA and 3/6 MSSA isolates and OMS2 reduced biofilms in 9/9 MRSA and 4/6 MSSA isolates (Figure 1c).
Phage titers and Biofilm Biomass
Figure 1a) Phage titers in PFU/ml obtained from each bacterial isolate via agar overlay method. 1b) Representative agar plate demonstrating lytic plaques from OMS1 and OMS2 on a Staphylococcus aureus LVAD isolate. 1c) Biofilm biomass of Staphylococcus aureus isolates alone (SA) or with individual phage (SA+OMSA1 and SA=OMS2) assessed by optical density readings at 570 nm; error bars represent standard error of the mean.
Conclusion
We demonstrated in vitro lytic and anti-biofilm activity of 2 S. aureus phages against clinical S. aureus isolates from patients with LVAD infection. Our data suggests that phage susceptibility measured with agar overlay does not always correlate with phage susceptibility of S. aureus biofilms, suggesting that more than one method should be used to assess in vitro activity. We plan to assess for synergistic activity with the phage combination.
Disclosures
Ryan K. Shields, PharmD, MS, Shionogi (Consultant, Research Grant or Support) Ran Nir-Paz, MD, BiomX (Consultant)Technophage (Scientific Research Study Investigator, Advisor or Review Panel member) Saima Aslam, MD, MS, BioMx (Consultant)Cystic Fibrosis Foundation (Grant/Research Support)Gilead (Consultant)Johnson and Johnson (Consultant)Merck (Consultant)
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Affiliation(s)
- Claudia Ramirez-Sanchez
- Department of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA, San Diego, California
| | - Hedieh Attai
- Department of Pathology, University of California San Diego, La Jolla, CA, San Diego, California
| | | | | | - Ortal Yerushalmy
- Institute of Biomedical and Oral Research (IBOR), The Hebrew University, Jerusalem, Israel, Jerusalem, Yerushalayim, Israel
| | - Ronen Hazan
- Institute of Biomedical and Oral Research (IBOR), The Hebrew University, Jerusalem, Israel, Jerusalem, Yerushalayim, Israel
| | - Ran Nir-Paz
- Department of clinical Microbiology and Infectious Diseases, Hadassah-Hebrew university medical Center, Jerusalem 91120, Israel, Jerusalem, Yerushalayim, Israel
| | - David Pride
- Department of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA, San Diego, California
| | - Saima Aslam
- Department of Infectious Diseases and Global Public Health, University of California San Diego, La Jolla, CA, San Diego, California
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14
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Keehner J, Horton LE, Binkin NJ, Laurent LC, Pride D, Longhurst CA, Abeles SR, Torriani FJ. Resurgence of SARS-CoV-2 Infection in a Highly Vaccinated Health System Workforce. N Engl J Med 2021; 385:1330-1332. [PMID: 34469645 PMCID: PMC8451183 DOI: 10.1056/nejmc2112981] [Citation(s) in RCA: 109] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Brubaker L, Gourdine JPF, Siddiqui NY, Holland A, Halverson T, Limeria R, Pride D, Ackerman L, Forster CS, Jacobs KM, Thomas-White KJ, Putonti C, Dong Q, Weinstein M, Lukacz ES, Karstens L, Wolfe AJ. Forming Consensus To Advance Urobiome Research. mSystems 2021; 6:e0137120. [PMID: 34282932 PMCID: PMC8409733 DOI: 10.1128/msystems.01371-20] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Urobiome research has the potential to advance the understanding of a wide range of diseases, including lower urinary tract symptoms and kidney disease. Many scientific areas have benefited from early research method consensus to facilitate the greater, common good. This consensus document, developed by a group of expert investigators currently engaged in urobiome research (UROBIOME 2020 conference participants), aims to promote standardization and advances in this field by the adoption of common core research practices. We propose a standardized nomenclature as well as considerations for specimen collection, preservation, storage, and processing. Best practices for urobiome study design include our proposal for standard metadata elements as part of core metadata collection. Although it is impractical to follow fixed analytical procedures when analyzing urobiome data, we propose guidelines to document and report data originating from urobiome studies. We offer this first consensus document with every expectation of subsequent revision as our field progresses.
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Affiliation(s)
- Linda Brubaker
- Department of Obstetrics, Gynecology and Reproductive Sciences, Division of Female Pelvic Medicine and Reconstructive Surgery, University of California, San Diego, San Diego, California, USA
| | - Jean-Philippe F. Gourdine
- Oregon Clinical & Translational Research Institute (OCTRI), Oregon Health & Science University, Portland, Oregon, USA
| | - Nazema Y. Siddiqui
- Department of Obstetrics and Gynecology, Division of Female Pelvic Medicine and Reconstructive Surgery, Duke University, Durham, North Carolina, USA
| | - Amanda Holland
- Department of Obstetrics and Gynecology, Oregon Health & Science University, Portland, Oregon, USA
| | - Thomas Halverson
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - Roberto Limeria
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
| | - David Pride
- Department of Pathology, University of California, San Diego, San Diego, California, USA
- Department of Medicine, University of California, San Diego, San Diego, California, USA
| | - Lenore Ackerman
- Department of Urology, Division of Female Pelvic Medicine and Reconstructive Surgery, University of California, Los Angeles, Los Angeles, California, USA
| | - Catherine S. Forster
- Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Kristin M. Jacobs
- Department of Obstetrics and Gynecology, Division of Female Pelvic Medicine and Reconstructive Surgery, Rush University, Chicago, Illinois, USA
| | - Krystal J. Thomas-White
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, California, USA
| | - Catherine Putonti
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
- Department of Biology, Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
| | - Qunfeng Dong
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
- Center for Biomedical Informatics, Loyola University Chicago, Chicago, Illinois, USA
| | - Michael Weinstein
- Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, California, USA
- Zymo Research, Irvine, California, USA
| | - Emily S. Lukacz
- Department of Obstetrics, Gynecology and Reproductive Sciences, Division of Female Pelvic Medicine and Reconstructive Surgery, University of California, San Diego, San Diego, California, USA
| | - Lisa Karstens
- Department of Clinical Epidemiology and Medical Informatics, Oregon Health & Science University, Portland, Oregon, USA
| | - Alan J. Wolfe
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
- Loyola Genomics Facility, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
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16
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Rakov C, Ben Porat S, Alkalay-Oren S, Yerushalmy O, Abdalrhman M, Gronovich N, Huang L, Pride D, Coppenhagen-Glazer S, Nir-Paz R, Hazan R. Targeting Biofilm of MDR Providencia stuartii by Phages Using a Catheter Model. Antibiotics (Basel) 2021; 10:antibiotics10040375. [PMID: 33918377 PMCID: PMC8065852 DOI: 10.3390/antibiotics10040375] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/21/2021] [Accepted: 03/24/2021] [Indexed: 01/29/2023] Open
Abstract
Providencia spp. are emerging pathogens mainly in nosocomial infections. Providencia stuartii in particular is involved in urinary tract infections and contributes significantly to the high incidence of biofilm-formation in catheterized patients. Furthermore, recent reports suggested a role for multiple drug resistant (MDR) P. stuartii in hospital-associated outbreaks which leads to excessive complications resulting in challenging treatments. Phage therapy is currently one of the most promising solutions to combat antibiotic-resistant infections. However, the number of available phages targeting Providencia spp. is extremely limited, restricting the use of phage therapy in such cases. In the present study, we describe the isolation and characterization of 17 lytic and temperate bacteriophages targeting clinical isolates of Providencia spp. as part of the Israeli Phage Bank (IPB). These phages, isolated from sewage samples, were evaluated for host range activity and effectively eradicated 95% of the tested bacterial strains isolated from different geographic locations and displaying a wide range of antibiotic resistance. Their lytic activity is demonstrated on agar plates, planktonic cultures, and biofilm formed in a catheter model. The results suggest that these bacteriophages can potentially be used for treatment of antibiotic-resistant Providencia spp. infections in general and of urinary tract infections in particular.
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Affiliation(s)
- Chani Rakov
- Institute of Dental Sciences, School of Dentistry, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (C.R.); (S.B.P.); (S.A.-O.); (O.Y.); (N.G.); (S.C.-G.)
| | - Shira Ben Porat
- Institute of Dental Sciences, School of Dentistry, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (C.R.); (S.B.P.); (S.A.-O.); (O.Y.); (N.G.); (S.C.-G.)
| | - Sivan Alkalay-Oren
- Institute of Dental Sciences, School of Dentistry, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (C.R.); (S.B.P.); (S.A.-O.); (O.Y.); (N.G.); (S.C.-G.)
| | - Ortal Yerushalmy
- Institute of Dental Sciences, School of Dentistry, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (C.R.); (S.B.P.); (S.A.-O.); (O.Y.); (N.G.); (S.C.-G.)
| | - Mohanad Abdalrhman
- Hadassah-Hebrew University Medical Center, Department of Clinical Microbiology and Infectious Diseases, The Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (M.A.); (R.N.-P.)
| | - Niv Gronovich
- Institute of Dental Sciences, School of Dentistry, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (C.R.); (S.B.P.); (S.A.-O.); (O.Y.); (N.G.); (S.C.-G.)
| | - Lina Huang
- Department of Pathology, University of California, San Diego, CA 92093, USA; (L.H.); (D.P.)
| | - David Pride
- Department of Pathology, University of California, San Diego, CA 92093, USA; (L.H.); (D.P.)
| | - Shunit Coppenhagen-Glazer
- Institute of Dental Sciences, School of Dentistry, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (C.R.); (S.B.P.); (S.A.-O.); (O.Y.); (N.G.); (S.C.-G.)
| | - Ran Nir-Paz
- Hadassah-Hebrew University Medical Center, Department of Clinical Microbiology and Infectious Diseases, The Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (M.A.); (R.N.-P.)
| | - Ronen Hazan
- Institute of Dental Sciences, School of Dentistry, Hebrew University of Jerusalem, Jerusalem 91120, Israel; (C.R.); (S.B.P.); (S.A.-O.); (O.Y.); (N.G.); (S.C.-G.)
- Correspondence: ; Tel.: +972-26758588
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17
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Jiang L, Lang S, Duan Y, Zhang X, Gao B, Chopyk J, Schwanemann LK, Ventura-Cots M, Bataller R, Bosques-Padilla F, Verna EC, Abraldes JG, Brown RS, Vargas V, Altamirano J, Caballería J, Shawcross DL, Ho SB, Louvet A, Lucey MR, Mathurin P, Garcia-Tsao G, Kisseleva T, Brenner DA, Tu XM, Stärkel P, Pride D, Fouts DE, Schnabl B. Intestinal Virome in Patients With Alcoholic Hepatitis. Hepatology 2020; 72:2182-2196. [PMID: 32654263 PMCID: PMC8159727 DOI: 10.1002/hep.31459] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/15/2020] [Accepted: 06/17/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND AND AIMS Alcoholic hepatitis (AH) is a severe manifestation of alcohol-associated liver disease (ALD) with high mortality. Although gut bacteria and fungi modulate disease severity, little is known about the effects of the viral microbiome (virome) in patients with ALD. APPROACH AND RESULTS We extracted virus-like particles from 89 patients with AH who were enrolled in a multicenter observational study, 36 with alcohol use disorder (AUD), and 17 persons without AUD (controls). Virus-like particles from fecal samples were fractionated using differential filtration techniques, and metagenomic sequencing was performed to characterize intestinal viromes. We observed an increased viral diversity in fecal samples from patients with ALD, with the most significant changes in samples from patients with AH. Escherichia-, Enterobacteria-, and Enterococcus phages were over-represented in fecal samples from patients with AH, along with significant increases in mammalian viruses such as Parvoviridae and Herpesviridae. Antibiotic treatment was associated with higher viral diversity. Specific viral taxa, such as Staphylococcus phages and Herpesviridae, were associated with increased disease severity, indicated by a higher median Model for End-Stage Liver Disease score, and associated with increased 90-day mortality. CONCLUSIONS In conclusion, intestinal viral taxa are altered in fecal samples from patients with AH and associated with disease severity and mortality. Our study describes an intestinal virome signature associated with AH.
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Affiliation(s)
- Lu Jiang
- Department of Medicine, University of California San Diego, La Jolla, CA, USA,Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
| | - Sonja Lang
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Yi Duan
- Department of Medicine, University of California San Diego, La Jolla, CA, USA,Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
| | - Xinlian Zhang
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Bei Gao
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Jessica Chopyk
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | | | - Meritxell Ventura-Cots
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh Liver Research Center, Pittsburgh, PA, USA
| | - Ramon Bataller
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh Liver Research Center, Pittsburgh, PA, USA
| | - Francisco Bosques-Padilla
- Hospital Universitario, Departamento de Gastroenterología, Universidad Autonoma de Nuevo Leon, Monterrey, México
| | - Elizabeth C. Verna
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Juan G. Abraldes
- Division of Gastroenterology (Liver Unit). Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Robert S. Brown
- Division of Gastroenterology and Hepatology, Weill Cornell Medical College, New York, NY, USA
| | - Victor Vargas
- Liver Unit, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain,Centro de Investigación en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Jose Altamirano
- Liver Unit, Hospital Universitari Vall d’Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juan Caballería
- Centro de Investigación en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain,Liver Unit, Hospital Clinic, Barcelona, Spain
| | - Debbie L. Shawcross
- Institute of Liver Studies, King’s College London School of Medicine at King’s College Hospital, King’s College Hospital, London, UK
| | - Samuel B. Ho
- Department of Medicine, University of California San Diego, La Jolla, CA, USA,Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
| | - Alexandre Louvet
- Service des Maladies de L’appareil Digestif et Unité INSERM, Hôpital Huriez, Lille, France
| | - Michael R. Lucey
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Wisconsin School of Medicine and Public Health, WI, USA
| | - Philippe Mathurin
- Service des Maladies de L’appareil Digestif et Unité INSERM, Hôpital Huriez, Lille, France
| | - Guadalupe Garcia-Tsao
- Section of Digestive Diseases, Yale University School of Medicine, New Haven, CT, USA, and Section of Digestive Diseases, VA-CT Healthcare System, West Haven, CT, USA
| | - Tatiana Kisseleva
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - David A. Brenner
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Xin M. Tu
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Peter Stärkel
- St. Luc University Hospital, Université Catholique de Louvain, Brussels, Belgium
| | - David Pride
- Department of Medicine, University of California San Diego, La Jolla, CA, USA,Department of Pathology, University of California San Diego, La Jolla, CA, USA,Center for Innovative Phage Applications and Therapeutics, University of California San Diego, La Jolla, CA, USA
| | | | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA,Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA,Center for Innovative Phage Applications and Therapeutics, University of California San Diego, La Jolla, CA, USA
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18
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Lang S, Demir M, Martin A, Jiang L, Zhang X, Duan Y, Gao B, Wisplinghoff H, Kasper P, Roderburg C, Tacke F, Steffen HM, Goeser T, Abraldes JG, Tu XM, Loomba R, Stärkel P, Pride D, Fouts DE, Schnabl B. Intestinal Virome Signature Associated With Severity of Nonalcoholic Fatty Liver Disease. Gastroenterology 2020; 159:1839-1852. [PMID: 32652145 PMCID: PMC8404510 DOI: 10.1053/j.gastro.2020.07.005] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/10/2020] [Accepted: 07/06/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS Alterations in the gut microbiome have been associated with the severity of nonalcoholic fatty liver disease (NAFLD). Previous studies focused exclusively on the bacteria in the microbiome; we investigated changes in the viral microbiome (virome) in patients with NAFLD. METHODS In a prospective, cross-sectional, observational study, we extracted RNA and DNA virus-like particles from fecal samples from 73 patients with NAFLD: 29 patients had an NAFLD Activity Score (NAS) of 0-4, 44 patients had an NAS of 5-8 or liver cirrhosis (LCI), 37 patients had F0-F1 fibrosis, and 36 patients had F2-F4 fibrosis. As controls, 9 individuals without liver disease and 13 patients with mild primary biliary cholangitis were included in the analysis. We performed shotgun metagenomic sequencing of virus-like particles. RESULTS Patients with NAFLD and NAS 5-8/LCI had a significant decrease in intestinal viral diversity compared with patients with NAFLD and NAS 0-4 or control individuals. The presence of more advanced NAFLD was associated with a significant reduction in the proportion of bacteriophages compared with other intestinal viruses. Using multivariate logistic regression analysis with leave-1-out cross validation, we developed a model, including a viral diversity index and simple clinical variables, that identified patients with NAS 5-8/LCI with an area under the curve of 0.95 (95% confidence interval, 0.91-0.99) and F2-F4 fibrosis with an area under the curve of 0.88 (95% confidence interval, 0.80-0.95). Addition of data on viral diversity significantly improved multivariate models, including those based on only clinical parameters or bacterial diversity. CONCLUSIONS In a study of fecal viromes from patients with NAFLD and control individuals, we associated histologic markers of NAFLD severity with significant decreases in viral diversity and proportion of bacteriophages. We developed a model based on fecal viral diversity and clinical data that identifies patients with severe NAFLD and fibrosis more accurately than models based only on clinical or bacterial data.
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Affiliation(s)
- Sonja Lang
- Department of Medicine, University of California San Diego, La Jolla, CA, USA,University of Cologne, Faculty of Medicine, and University Hospital Cologne, Department of Gastroenterology and Hepatology, Cologne, Germany
| | - Münevver Demir
- Department of Hepatology and Gastroenterology, Campus Virchow Clinic, Charité University Medicine, Berlin, Germany
| | - Anna Martin
- University of Cologne, Faculty of Medicine, and University Hospital Cologne, Department of Gastroenterology and Hepatology, Cologne, Germany
| | - Lu Jiang
- Department of Medicine, University of California San Diego, La Jolla, CA, USA,Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
| | - Xinlian Zhang
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Yi Duan
- Department of Medicine, University of California San Diego, La Jolla, CA, USA,Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
| | - Bei Gao
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Hilmar Wisplinghoff
- Wisplinghoff Laboratories, Cologne, Germany,Institute for Virology and Medical Microbiology, University Witten/Herdecke, Witten, Germany,University of Cologne, Faculty of Medicine, Institute for Medical Microbiology, Immunology and Hygiene, University Hospital of Cologne, Cologne, Germany
| | - Philipp Kasper
- University of Cologne, Faculty of Medicine, and University Hospital Cologne, Department of Gastroenterology and Hepatology, Cologne, Germany
| | - Christoph Roderburg
- Department of Hepatology and Gastroenterology, Campus Virchow Clinic, Charité University Medicine, Berlin, Germany
| | - Frank Tacke
- Department of Hepatology and Gastroenterology, Campus Virchow Clinic, Charité University Medicine, Berlin, Germany
| | - Hans-Michael Steffen
- University of Cologne, Faculty of Medicine, and University Hospital Cologne, Department of Gastroenterology and Hepatology, Cologne, Germany
| | - Tobias Goeser
- University of Cologne, Faculty of Medicine, and University Hospital Cologne, Department of Gastroenterology and Hepatology, Cologne, Germany
| | - Juan G. Abraldes
- Division of Gastroenterology (Liver Unit). Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Xin M. Tu
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Rohit Loomba
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Peter Stärkel
- St. Luc University Hospital, Université Catholique de Louvain, Brussels, Belgium
| | - David Pride
- Department of Medicine, University of California San Diego, La Jolla, CA, USA,Department of Pathology, University of California San Diego, La Jolla, CA, USA,Center for Innovative Phage Applications and Therapeutics, University of California San Diego, La Jolla, CA, USA
| | | | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, California; Department of Medicine, Veterans Affairs San Diego Healthcare System, San Diego, California; Center for Innovative Phage Applications and Therapeutics, University of California San Diego, La Jolla, California.
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19
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Duan Y, Llorente C, Lang S, Brandl K, Chu H, Jiang L, White RC, Clarke TH, Nguyen K, Torralba M, Shao Y, Liu J, Hernandez-Morales A, Lessor L, Rahman IR, Miyamoto Y, Ly M, Gao B, Sun W, Kiesel R, Hutmacher F, Lee S, Ventura-Cots M, Bosques-Padilla F, Verna EC, Abraldes JG, Brown RS, Vargas V, Altamirano J, Caballería J, Shawcross DL, Ho SB, Louvet A, Lucey MR, Mathurin P, Garcia-Tsao G, Bataller R, Tu XM, Eckmann L, van der Donk WA, Young R, Lawley TD, Stärkel P, Pride D, Fouts DE, Schnabl B. Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease. Nature 2019; 575:505-511. [PMID: 31723265 PMCID: PMC6872939 DOI: 10.1038/s41586-019-1742-x] [Citation(s) in RCA: 429] [Impact Index Per Article: 85.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 10/02/2019] [Indexed: 12/14/2022]
Abstract
Chronic liver disease due to alcohol use disorder contributes markedly to the global burden of disease and mortality1–3. Alcoholic hepatitis is a severe and life-threatening form of alcohol-associated liver disease. The gut microbiota promotes ethanol-induced liver disease in mice4, but little is known about microbial factors responsible for this process. We identified cytolysin, a two-subunit exotoxin secreted by Enterococcus faecalis (E. faecalis)5,6, to cause hepatocyte death and liver injury. Compared with controls, patients with alcoholic hepatitis have increased fecal numbers of E. faecalis. The presence of cytolysin-positive (cytolytic) E. faecalis correlated with liver disease severity and mortality in patients with alcoholic hepatitis. Using humanized mice colonized with bacteria from feces of patients with alcoholic hepatitis, we investigated the therapeutic effects of bacteriophages that target cytolytic E. faecalis. We found these phages to decrease cytolysin in the liver and abolish ethanol-induced liver disease in humanized mice. Our findings link cytolysin-positive E. faecalis with worse clinical outcomes and mortality in patients with alcoholic hepatitis. We show that bacteriophages can specifically target cytolytic E. faecalis, providing a method to precisely edit the intestinal microbiota. A prospective clinical trial with a larger cohort is required to validate human relevance of our findings and to test whether this new therapeutic approach is effective for patients with alcoholic hepatitis.
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Affiliation(s)
- Yi Duan
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.,Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
| | - Cristina Llorente
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.,Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
| | - Sonja Lang
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Katharina Brandl
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, USA
| | - Huikuan Chu
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lu Jiang
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.,Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
| | | | | | | | | | - Yan Shao
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Jinyuan Liu
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | | | - Lauren Lessor
- Center for Phage Technology, Texas A & M AgriLife Research and Texas A & M University, College Station, TX, USA
| | - Imran R Rahman
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yukiko Miyamoto
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Melissa Ly
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Bei Gao
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Weizhong Sun
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Roman Kiesel
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Felix Hutmacher
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Suhan Lee
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Meritxell Ventura-Cots
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh Liver Research Center, Pittsburgh, PA, USA
| | - Francisco Bosques-Padilla
- Hospital Universitario, Departamento de Gastroenterología, Universidad Autonoma de Nuevo Leon, Monterrey, Mexico
| | - Elizabeth C Verna
- Division of Digestive and Liver Diseases, Department of Medicine, Columbia University College of Physicians and Surgeons, New York, NY, USA
| | - Juan G Abraldes
- Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Robert S Brown
- Division of Gastroenterology and Hepatology, Weill Cornell Medical College, New York, NY, USA
| | - Victor Vargas
- Liver Unit, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain
| | - Jose Altamirano
- Liver Unit, Hospital Universitari Vall d'Hebron, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Juan Caballería
- Centro de Investigación en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain.,Liver Unit, Hospital Clinic, Barcelona, Spain
| | - Debbie L Shawcross
- Liver Sciences, Department of Inflammation Biology, School of Infectious Diseases and Microbial Sciences, King's College London, London, UK
| | - Samuel B Ho
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.,Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA
| | - Alexandre Louvet
- Service des Maladies de L'appareil Digestif et Unité INSERM, Hôpital Huriez, Lille, France
| | - Michael R Lucey
- Division of Gastroenterology and Hepatology, Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Philippe Mathurin
- Service des Maladies de L'appareil Digestif et Unité INSERM, Hôpital Huriez, Lille, France
| | - Guadalupe Garcia-Tsao
- Section of Digestive Diseases, Yale University School of Medicine, New Haven, CT, USA.,Section of Digestive Diseases, VA Connecticut Healthcare System, West Haven, CT, USA
| | - Ramon Bataller
- Division of Gastroenterology, Hepatology and Nutrition, Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh Liver Research Center, Pittsburgh, PA, USA
| | - Xin M Tu
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California San Diego, La Jolla, CA, USA
| | - Lars Eckmann
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Wilfred A van der Donk
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Howard Hughes Medical Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Ry Young
- Department of Biochemistry and Biophysics, Texas A & M University, College Station, TX, USA.,Center for Phage Technology, Texas A & M AgriLife Research and Texas A & M University, College Station, TX, USA
| | - Trevor D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - Peter Stärkel
- St Luc University Hospital, Université Catholique de Louvain, Brussels, Belgium
| | - David Pride
- Department of Medicine, University of California San Diego, La Jolla, CA, USA.,Department of Pathology, University of California San Diego, La Jolla, CA, USA.,Center for Innovative Phage Applications and Therapeutics, University of California San Diego, La Jolla, CA, USA
| | | | - Bernd Schnabl
- Department of Medicine, University of California San Diego, La Jolla, CA, USA. .,Department of Medicine, VA San Diego Healthcare System, San Diego, CA, USA. .,Center for Innovative Phage Applications and Therapeutics, University of California San Diego, La Jolla, CA, USA.
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20
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Ando T, Peek RM, Pride D, Levine SM, Takata T, Lee YC, Kusugami K, van der Ende A, Kuipers EJ, Kusters JG, Blaser MJ. Polymorphisms of Helicobacter pylori HP0638 reflect geographic origin and correlate with cagA status. J Clin Microbiol 2002; 40:239-46. [PMID: 11773122 PMCID: PMC120108 DOI: 10.1128/jcm.40.1.239-246.2002] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Since the associations between Helicobacter pylori genotype and disease differ in Asia and the West, we investigated the correlation between HP0638, encoding an outer membrane protein, and potential markers of virulence (cagA, vacA, and iceA). For 109 strains from nine countries, the status of cagA, vacA, and iceA was determined by PCR and/or a line probe assay. We also studied 18 strains from 8 patients (parents and 6 daughters) from a Dutch family and paired strains collected on average 8 years apart from 11 patients. When the HP0638 signal sequences were amplified by PCR and DNA sequence determinations were performed, 89 (96%) of 93 cagA-positive strains had HP0638 in frame, versus none (0%) of 16 cagA-negative strains (P < 0.001). Among strains in which HP0638 was in frame, a six-CT dinucleotide repeat pattern was dominant in Western countries (23 of 33 strains [70%]), while a pattern of three CT repeats with another CT after four T's (3 + 1-CT-repeat pattern) was dominant in East Asia (31 of 46 strains [67%]); however, specific CT repeat patterns did not correlate with clinical outcome. HP0638 phylogenetic trees also showed geographic characters. The HP0638 frame status and CT dinucleotide repeat patterns were identical for 9 of 11 pairs of strains obtained on average 8 years apart from individuals and the 15 strains obtained from the mother and all six daughters. Thus, HP0638 frame status and cagA status are strongly correlated. The CT dinucleotide repeat pattern in the putative HP0638 signal sequence has geographic characters and appears stable in particular patients and families over a period of years. Analysis of HP0638 CT polymorphisms may serve as a new typing system to discriminate H. pylori isolates for epidemiological purposes.
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Affiliation(s)
- T Ando
- Department of Medicine, New York University School of Medicine, New York, New York, USA.
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21
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Pride D. Case of Pneumonia with Violent Cerebral Symptoms. Glasgow Med J 1872; 4:404-406. [PMID: 30432900 PMCID: PMC5879406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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22
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Pride D. Notes on the Treatment of Sciatica. Glasgow Med J 1872; 4:378-379. [PMID: 30432910 PMCID: PMC5879421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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23
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Pride D. Notes of a Scarlet Fever Epidemic. Glasgow Med J 1869; 1:440-453. [PMID: 30432668 PMCID: PMC5871503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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24
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Pride D. Remarks on Alcohol. Glasgow Med J 1866; 1:305-312. [PMID: 30432604 PMCID: PMC5867792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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25
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Pride D. On Four Cases of Syphilis, with Remarks. Glasgow Med J 1865; 13:316-319. [PMID: 30432459 PMCID: PMC5799575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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Pride D. Case of Aortic Aneurism with a Spontaneously Curative Tendency, &c., with Remarks. Glasgow Med J 1865; 13:65-70. [PMID: 30432414 PMCID: PMC5799446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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