Reference Citation Analysis: Find an Article, Find a Category, Find a Journal, Find a Scholar

Download

Total Articles

10
(from Reference Citation Analysis)

Article PDFs (2)

Cited by > 0 (7)

Searched Name

Ian H McHardy

Ranked By

Results Analysis

Year Published Analysis
Article Type Analysis
Publication Title Analysis
Category Analysis

Results Analysis

Indexed Articles

Year Published

Show more Refine

Article Type

Show more Refine

Article Statistics

Refine

MESH Headings

Show more Refine

First Author

Show more Refine

First Author Affiliations

Show more Refine

Authors

Show more Refine

Publication Titles

Show more Refine

Grant Agencies

Show more Refine

Countries/Regions

Show more Refine

Affiliations

Show more Refine

Corresponding Author Affiliations

Show more Refine

Category

Show more Refine

Number

Citation Analysis

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]

Affiliation(s)

Nathaniel L Matteson Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, USA.
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
Elizabeth H Simmons Academic Affairs, 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
Idanya Serafin-Higuera Centro de Diagnostico COVID-19 UABC, 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
Jose L Moreno-Camacho Clinical Laboratory Department, Salud Digna, A.C, Tijuana, Baja California, Mexico
Abraham García-Gil Clinical Laboratory Department, Salud Digna, A.C, Tijuana, Baja California, Mexico
Ashleigh R Murphy Schafer 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
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
Refugio Robles-Sikisaka 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
David Becker Helix, San Mateo, CA, USA
Magnus Isaksson Helix, San Mateo, CA, USA
Nicole L Washington Helix, San Mateo, CA, USA
William Lee Helix, San Mateo, CA, USA
Richard S Garfein Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, CA, USA
Marco A Luna-Ruiz Esparza Innovation and Research Department, Salud Digna, A.C, Tijuana, Baja California, Mexico
Jonathan Alcántar-Fernández Innovation and Research Department, Salud Digna, A.C, Tijuana, Baja California, Mexico
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
Stephen F Kingsmore Rady Children's Institute for Genomic Medicine, San Diego, CA, USA
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
Ian H McHardy Scripps Health, La Jolla, San Diego, CA, USA
Russel A Fielding Scripps Health, La Jolla, San Diego, CA, USA
Laura Nicholson Scripps Health, La Jolla, San Diego, CA, USA
Michael M Quigley Scripps Health, La Jolla, San Diego, CA, USA
Aaron Harding Sharp Healthcare, San Diego, CA, USA
Art Mendoza Sharp Healthcare, San Diego, CA, USA
Omid Bakhtar Sharp Healthcare, San Diego, 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
Alicia Harvey-Vera University of California, San Diego, La Jolla, CA, USA
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.

Collapse

Sasidharan A, Selvarangan R, Konrad K, Faron ML, Shakir SM, Hillyard D, McCall RK, McHardy IH, Goldberg DC, Dunn JJ, Greninger AL, Lansang C, Bogh R, Remillard CV. Multi-center clinical evaluation of the Panther Fusion SARS-CoV-2/Flu A/B/RSV assay in nasopharyngeal swab specimens from symptomatic individuals. J Clin Microbiol 2023;61:e0082723. [PMID: 37902331 PMCID: PMC10662375 DOI: 10.1128/jcm.00827-23] [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: 07/05/2023] [Accepted: 08/26/2023] [Indexed: 10/31/2023] Open

Abstract

The symptomology is overlapping for respiratory infections due to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), influenza A/B viruses, and respiratory syncytial virus (RSV). Accurate detection is essential for proper medical management decisions. This study evaluated the clinical performance of the Panther Fusion SARS-CoV-2/Flu A/B/RSV assay in nasopharyngeal swab (NPS) specimens from individuals of all ages with signs and symptoms of respiratory infection consistent with COVID-19, influenza, or RSV. Retrospective known-positive and prospectively obtained residual NPS specimens were collected during two respiratory seasons in the USA. Clinical performance was established by comparing Panther Fusion SARS-CoV-2/Flu assay results to a three-molecular assay composite comparator interpretation for SARS-CoV-2 and to the FDA-cleared Panther Fusion Flu A/B/RSV assay results for all non-SARS-CoV-2 targets. A total of 1,900 prospective and 95 retrospective NPS specimens were included in the analyses. The overall prevalence in prospectively obtained specimens was 20.7% for SARS-CoV-2, 6.7% for influenza A, and 0.7% for RSV; all influenza B-positive specimens were retrospective specimens. The positive percent agreement of the Panther Fusion assay was 96.9% (378/390) for SARS-CoV-2, 98.0% (121/123) for influenza A virus, 95.2% (20/21) for influenza B virus, and 96.6% (57/59) for RSV. The negative percent agreement was ≥98.5% for all target viruses. Specimens with discordant Panther Fusion SARS/Flu/RSV assay results all had cycle threshold values of ≥32.4 (by comparator or by Panther Fusion SARS/Flu/RSV assay). Only five co-infections were detected in the study specimens. The Panther Fusion SARS-CoV-2/Flu/RSV assay provides highly sensitive and specific detection of SARS-CoV-2, influenza A virus, influenza B virus, and RSV in NPS specimens.

Collapse

McHardy IH, Barker B, Thompson GR. Review of Clinical and Laboratory Diagnostics for Coccidioidomycosis. J Clin Microbiol 2023;61:e0158122. [PMID: 36883820 PMCID: PMC10204634 DOI: 10.1128/jcm.01581-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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] [Indexed: 03/09/2023] Open

Jacobs JP, Goudarzi M, Singh N, Tong M, McHardy IH, Ruegger P, Asadourian M, Moon BH, Ayson A, Borneman J, McGovern DP, Fornace AJ, Braun J, Dubinsky M. A Disease-Associated Microbial and Metabolomics State in Relatives of Pediatric Inflammatory Bowel Disease Patients. Cell Mol Gastroenterol Hepatol 2016;2:750-766. [PMID: 28174747 PMCID: PMC5247316 DOI: 10.1016/j.jcmgh.2016.06.004] [Citation(s) in RCA: 140] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2016] [Accepted: 06/26/2016] [Indexed: 02/07/2023]

Abstract

BACKGROUND & AIMS

Microbes may increase susceptibility to inflammatory bowel disease (IBD) by producing bioactive metabolites that affect immune activity and epithelial function. We undertook a family based study to identify microbial and metabolic features of IBD that may represent a predisease risk state when found in healthy first-degree relatives.

METHODS

Twenty-one families with pediatric IBD were recruited, comprising 26 Crohn's disease patients in clinical remission, 10 ulcerative colitis patients in clinical remission, and 54 healthy siblings/parents. Fecal samples were collected for 16S ribosomal RNA gene sequencing, untargeted liquid chromatography-mass spectrometry metabolomics, and calprotectin measurement. Individuals were grouped into microbial and metabolomics states using Dirichlet multinomial models. Multivariate models were used to identify microbes and metabolites associated with these states.

RESULTS

Individuals were classified into 2 microbial community types. One was associated with IBD but irrespective of disease status, had lower microbial diversity, and characteristic shifts in microbial composition including increased Enterobacteriaceae, consistent with dysbiosis. This microbial community type was associated similarly with IBD and reduced microbial diversity in an independent pediatric cohort. Individuals also clustered bioinformatically into 2 subsets with shared fecal metabolomics signatures. One metabotype was associated with IBD and was characterized by increased bile acids, taurine, and tryptophan. The IBD-associated microbial and metabolomics states were highly correlated, suggesting that they represented an integrated ecosystem. Healthy relatives with the IBD-associated microbial community type had an increased incidence of elevated fecal calprotectin.

CONCLUSIONS

Healthy first-degree relatives can have dysbiosis associated with an altered intestinal metabolome that may signify a predisease microbial susceptibility state or subclinical inflammation. Longitudinal prospective studies are required to determine whether these individuals have a clinically significant increased risk for developing IBD.

Collapse

Affiliation(s)

Jonathan P. Jacobs Division of Digestive Diseases, Department of Medicine, University of California Los Angeles, Los Angeles, California
Maryam Goudarzi Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, District of Columbia
Namita Singh Pediatric Gastroenterology and Inflammatory Bowel Disease, Cedars-Sinai Medical Center, Los Angeles, California
Maomeng Tong Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
Ian H. McHardy Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
Paul Ruegger Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, California
Miro Asadourian Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
Bo-Hyun Moon Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, District of Columbia
Allyson Ayson Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California
James Borneman Department of Plant Pathology and Microbiology, University of California Riverside, Riverside, California
Dermot P.B. McGovern F. Widjaja Foundation Inflammatory Bowel and Immunobiology Research Institute, Cedars-Sinai Medical Center, Los Angeles, California
Albert J. Fornace Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, District of Columbia
Jonathan Braun Department of Pathology and Laboratory Medicine, University of California Los Angeles, Los Angeles, California,∗Correspondence Address correspondence to: Jonathan Braun, MD, PhD, Department of Pathology and Laboratory Medicine, University of California Los Angeles, 924 Westwood Boulevard, Suite 705, Los Angeles, California 90095. fax: (310) 267-4486.Department of Pathology and Laboratory MedicineUniversity of California Los Angeles924 Westwood BoulevardSuite 705Los AngelesCalifornia 90095
Marla Dubinsky Susan and Leonard Feinstein Inflammatory Bowel Disease Center, Department of Pediatrics, Icahn School of Medicine, Mount Sinai, New York,∗∗Marla Dubinsky, MD, Susan and Leonard Feinstein Inflammatory Bowel Disease Center, Department of Pediatrics, Icahn School of Medicine, 17 East 102nd Street, East Tower, 5th Floor, New York, New York 10029. fax: (646) 537-8924.Susan and Leonard Feinstein Inflammatory Bowel Disease CenterDepartment of PediatricsIcahn School of Medicine17 East 102nd StreetEast Tower5th FloorNew YorkNew York 10029

Collapse

Yang S, McHardy IH, Hemarajata P, Wu MT, Garner OB. Microbial recovery from clot-activating Vacutainers®. Diagn Microbiol Infect Dis 2016;85:395-7. [PMID: 27306117 DOI: 10.1016/j.diagmicrobio.2016.05.015] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 05/19/2016] [Accepted: 05/21/2016] [Indexed: 11/29/2022]

Deak E, Charlton CL, Bobenchik AM, Miller SA, Pollett S, McHardy IH, Wu MT, Garner OB. Comparison of the Vitek MS and Bruker Microflex LT MALDI-TOF MS platforms for routine identification of commonly isolated bacteria and yeast in the clinical microbiology laboratory. Diagn Microbiol Infect Dis 2015;81:27-33. [DOI: 10.1016/j.diagmicrobio.2014.09.018] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 09/18/2014] [Accepted: 09/21/2014] [Indexed: 11/27/2022]

Tong M, Jacobs JP, McHardy IH, Braun J. Sampling of intestinal microbiota and targeted amplification of bacterial 16S rRNA genes for microbial ecologic analysis. ACTA ACUST UNITED AC 2014;107:7.41.1-7.41.11. [PMID: 25367129 DOI: 10.1002/0471142735.im0741s107] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]

Sarkar J, McHardy IH, Simanian EJ, Shi W, Lux R. Transcriptional responses of Treponema denticola to other oral bacterial species. PLoS One 2014;9:e88361. [PMID: 24505483 PMCID: PMC3914990 DOI: 10.1371/journal.pone.0088361] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 01/06/2014] [Indexed: 12/16/2022] Open

Abstract

The classic organization by Socransky and coworkers categorized the oral bacteria of the subgingival plaque into different complexes. Treponema denticola, Porphyromonas gingivalis and Tannerella forsythia are grouped into the red complex that is highly correlated with periodontal disease. Socransky's work closely associates red with orange complex species such as Fusobacterium nucleatum and Prevotella intermedia but not with members of the other complexes. While the relationship between species contained by these complexes is in part supported by their ability to physically attach to each other, the physiological consequences of these interactions and associations are less clear. In this study, we employed T. denticola as a model organism to analyze contact-dependent responses to interactions with species belonging to the same complex (P. gingivalis and T. forsythia), the closely associated orange complex (using F. nucleatum and P. intermedia as representatives) and the unconnected yellow complex (using Streptococcus sanguinis and S. gordonii as representatives). RNA was extracted from T. denticola alone as well as after pairwise co-incubation for 5 hrs with representatives of the different complexes, and the respective gene expression profiles were determined using microarrays. Numerous genes related to motility, metabolism, transport, outer membrane and hypothetical proteins were differentially regulated in T. denticola in the presence of the tested partner species. Further analysis revealed a significant overlap in the affected genes and we identified a general response to the presence of other species, those specific to two of the three complexes as well as individual complexes. Most interestingly, many predicted major antigens (e.g. flagella, Msp, CTLP) were suppressed in responses that included red complex species indicating that the presence of the most closely associated species induces immune-evasive strategies. In summary, the data presented here provide an in-depth understanding of the transcriptional responses triggered by contact-dependent interactions between microorganisms inhabiting the periodontal pocket.

Collapse

McHardy IH, Li X, Tong M, Ruegger P, Jacobs J, Borneman J, Anton P, Braun J. HIV Infection is associated with compositional and functional shifts in the rectal mucosal microbiota. Microbiome 2013;1:26. [PMID: 24451087 PMCID: PMC3971626 DOI: 10.1186/2049-2618-1-26] [Citation(s) in RCA: 145] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 10/03/2013] [Indexed: 05/05/2023]

Abstract

BACKGROUND

Regardless of infection route, the intestine is the primary site for HIV-1 infection establishment and results in significant mucosal CD4+ T lymphocyte depletion, induces an inflammatory state that propagates viral dissemination, facilitates microbial translocation, and fosters establishment of one of the largest HIV reservoirs. Here we test the prediction that HIV infection modifies the composition and function of the mucosal commensal microbiota.

RESULTS

Rectal mucosal microbiota were collected from human subjects using a sponge-based sampling methodology. Samples were collected from 20 HIV-positive men not receiving combination anti-retroviral therapy (cART), 20 HIV-positive men on cART and 20 healthy, HIV-negative men. Microbial composition of samples was analyzed using barcoded 16S Illumina deep sequencing (85,900 reads per sample after processing). Microbial metagenomic information for the samples was imputed using the bioinformatic tools PICRUST and HUMAnN. Microbial composition and imputed function in HIV-positive individuals not receiving cART was significantly different from HIV-negative individuals. Genera including Roseburia, Coprococcus, Ruminococcus, Eubacterium, Alistipes and Lachnospira were depleted in HIV-infected subjects not receiving cART, while Fusobacteria, Anaerococcus, Peptostreptococcus and Porphyromonas were significantly enriched. HIV-positive subjects receiving cART exhibited similar depletion and enrichment for these genera, but were of intermediate magnitude and did not achieve statistical significance. Imputed metagenomic functions, including amino acid metabolism, vitamin biosynthesis, and siderophore biosynthesis differed significantly between healthy controls and HIV-infected subjects not receiving cART.

CONCLUSIONS

HIV infection was associated with rectal mucosal changes in microbiota composition and imputed function that cART failed to completely reverse. HIV infection was associated with depletion of some commensal species and enrichment of a few opportunistic pathogens. Many imputed metagenomic functions differed between samples from HIV-negative and HIV-positive subjects not receiving cART, possibly reflecting mucosal metabolic changes associated with HIV infection. Such functional pathways may represent novel interventional targets for HIV therapy if normalizing the microbial composition or functional activity of the microbiota proves therapeutically useful.

Collapse

McHardy IH, Goudarzi M, Tong M, Ruegger PM, Schwager E, Weger JR, Graeber TG, Sonnenburg JL, Horvath S, Huttenhower C, McGovern DPB, Fornace AJ, Borneman J, Braun J. Integrative analysis of the microbiome and metabolome of the human intestinal mucosal surface reveals exquisite inter-relationships. Microbiome 2013;1:17. [PMID: 24450808 PMCID: PMC3971612 DOI: 10.1186/2049-2618-1-17] [Citation(s) in RCA: 196] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2013] [Accepted: 05/12/2013] [Indexed: 05/10/2023]

Abstract

BACKGROUND

Consistent compositional shifts in the gut microbiota are observed in IBD and other chronic intestinal disorders and may contribute to pathogenesis. The identities of microbial biomolecular mechanisms and metabolic products responsible for disease phenotypes remain to be determined, as do the means by which such microbial functions may be therapeutically modified.

RESULTS

The composition of the microbiota and metabolites in gut microbiome samples in 47 subjects were determined. Samples were obtained by endoscopic mucosal lavage from the cecum and sigmoid colon regions, and each sample was sequenced using the 16S rRNA gene V4 region (Illumina-HiSeq 2000 platform) and assessed by UPLC mass spectroscopy. Spearman correlations were used to identify widespread, statistically significant microbial-metabolite relationships. Metagenomes for identified microbial OTUs were imputed using PICRUSt, and KEGG metabolic pathway modules for imputed genes were assigned using HUMAnN. The resulting metabolic pathway abundances were mostly concordant with metabolite data. Analysis of the metabolome-driven distribution of OTU phylogeny and function revealed clusters of clades that were both metabolically and metagenomically similar.

CONCLUSIONS

The results suggest that microbes are syntropic with mucosal metabolome composition and therefore may be the source of and/or dependent upon gut epithelial metabolites. The consistent relationship between inferred metagenomic function and assayed metabolites suggests that metagenomic composition is predictive to a reasonable degree of microbial community metabolite pools. The finding that certain metabolites strongly correlate with microbial community structure raises the possibility of targeting metabolites for monitoring and/or therapeutically manipulating microbial community function in IBD and other chronic diseases.

Collapse