Publications about RipSeq

Please find all articles, posters and more about RipSeq below.

(Click any heading below to expand and collapse)

2016 Open Microbiology Journal

Aerococcus christensenii as Part of Severe Polymicrobial Chorioamnionitis in a Pregnant Woman
Catrine Carlstein 1 Lillian Marie Søes 2 and Jens Jørgen Christensen 2,*

1 Department of Gynaecology and Obstetrics, Næstved Hospital, Ringstedgade 61, 4700 Næstved, Denmark

2 Department of Clinical Microbiology, Slagelse Hospital, Ingemannsvej 18, 4200 Slagelse, Denmark

 

2016 European Journal of Gastroenterology & Hepatology

Detection of molecular bacterascites in decompensated cirrhosis defines a risk with decreased survival
Engelmann, Cornelius; Krohn, Sandra; Prywerek, Delia; Hartmann, Jan; Herber, Adam; Boehlig, Albrecht; Zeller, Katharina; Boehm, Stephan; Berg, Thomas

Department of Internal Medicine, Neurology, Dermatology, Section of Hepatology, University Hospital Leipzig, Leipzig bDepartment of Gastroenterology and Hepatology, Hospital and Outpatient Clinic for Internal Medicine A, Ernst Moritz Arndt University of Greifswald, Greifswald, Germany.

 

2016 Journal of Diagnostic Microbiology and Infectious Disease

Bordetella trematum sepsis with shock in a diabetic patient with rapidly developing soft tissue infection

Lorrance L. Majewskia, Masayuki Nogia, Matthew J. Bankowskibcd, Heath H. Chunga

a Department of Medicine, John A. Burns School of Medicine, University of Hawaii at Manoa, 1356 Lusitana Street, 7th floor, Honolulu, HI, 96813, USA

b Department of Pathology, John A. Burns School of Medicine, University of Hawaii at Manoa, 651 Ilalo Street, Medical Education Building, Honolulu, HI, 96813, USA

c Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, 651 Ilalo Street, Biosciences Building, 3rd Floor, Honolulu, HI, 96813, USA

d Diagnostic Laboratory Services, Inc. (The Queen’s Medical Center), 99–859 Iwaiwa Street, Aiea, HI, 96701, USA

 

2016 Journal of Clinical Microbiology (JCM)
Mycobacterium arupenseMycobacterium heraklionense, and a Newly Proposed Species, “Mycobacterium virginiense” sp. nov., but Not Mycobacterium nonchromogenicum, as Species of the Mycobacterium terrae Complex Causing Tenosynovitis and Osteomyelitis

Ravikiran Vasireddya, Sruthi Vasireddya, Barbara A. Brown-Elliotta, Nancy L. Wengenackb, Uzoamaka A. Ekec*, Jeana L. Benwilla, Christine Turenned*and Richard J. Wallace Jr.a

aMycobacteria/Nocardia Research Laboratory, Department of Microbiology, The University of Texas Health Science Center at Tyler, Tyler, Texas, USA

bMayo Clinic, Rochester, Minnesota, USA

cDivision of Infectious Disease, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA

dSaskatchewan Disease Control Laboratory, Regina, Saskatchewan, Canada

 

2016 International Journal of Food Microbiology

Diversity of the microbiota involved in wine and organic apple cider submerged vinegar production as revealed by DHPLC analysis and next-generation sequencing

Janja Trčeka, b, , , Aleksander Mahničc, Maja Rupnikc, d, e

a University of Maribor, Faculty of Natural Sciences and Mathematics, Department of Biology, Maribor, Slovenia

b University of Maribor, Faculty of Chemistry and Chemical Engineering, Maribor, Slovenia

c National Laboratory for Health, Environment and Food, NLZOH, Maribor, Slovenia

d University of Maribor, Faculty of Medicine, Maribor, Slovenia

e Centre of Excellence for Integrated Approaches in Chemistry and Biology of Proteins, Ljubljana, Slovenia

 

2016 Emerging Infectious Diseases, CDC (EID)

Wohlfahrtiimonas chitiniclastica Infections in 2 Elderly Patients, Hawaii, USA

Masayuki Nogi,corresponding author Matthew J. Bankowski, and Francis D. Pien

University of Hawaii at Manoa John A. Burns School of Medicine, Honolulu, Hawaii, USA (M. Nogi, M.J. Bankowski, F.D. Pien);

University of Hawaii at Manoa, Honolulu (M. Nogi, M.J. Bankowski, F.D. Pien);

Diagnostic Laboratory Services, Inc., Aiea, Hawaii, USA (M.J. Bankowski)

 

2016 SpringerPlus

Cultivation-independent approach for the direct detection of bacteria in human clinical specimens as a tool for analysing culture-negative samples: a prospective study

Ma. Guadalupe Aguilera-Arreola,corresponding author Marcos Daniel Martínez-Peña, Fabiola Hernández-Martínez, Sara R. Juárez Enriques, Beatriz Rico Verdín, Cristina Majalca-Martínez, Graciela Castro-Escarpulli, Enrique Albarrán-Fernández, and S. Cecilia Serrano-López

Department of Microbiology, Instituto Politécnico Nacional (IPN), Escuela Nacional de Ciencias Biológicas (ENCB), Mexico City, D.F. Mexico

Special Test Laboratory, Centro Médico Nacional (CMN) 20 de Noviembre - Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico City, D.F. Mexico

Department of Epidemiology, Centro Médico Nacional (CMN) 20 de Noviembre del Instituto de Seguridad y Servicios Sociales de los Trabajadores del Estado (ISSSTE), Mexico City, D.F. Mexico

Microbial Genetic Resources Laboratory, Centro Nacional de Recursos Genéticos (CNRG)-INIFAP, Tepatitlán de Morelos, Jalisco Mexico

Department of Zoology, Escuela Nacional de Ciencias Biológicas - Instituto Politécnico Nacional, Mexico City, D.F. Mexico

Ma. Guadalupe Aguilera-Arreola

 

2016 Case Reports in Infectious Diseases

Subacute Bacterial Endocarditis with Leptotrichia goodfellowii in a Patient with a Valvular Allograft: A Case Report and Review of the Literature

Wilfredo R. Matias, 1 , * Daniel L. Bourque, 1 , 2 Tomoko Niwano, 3 Andrew B. Onderdonk, 1 , 4 and Joel T. Katz 1 , 5

1Harvard Medical School, Boston, MA, USA

2Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA

3Tokyo Medical and Dental University, Tokyo, Japan

4Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA

5Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, USA

 

2016 Annals of Clinical & Laboratory Science

Comparison between a Broad-Range Real-Time and a Broad-Range End-Point PCR Assays for the Detection of Bacterial 16S rRNA in Clinical Samples

Mariam Meddeb, Christelle Koebel, Benoît Jaulhac and Frédéric Schramm

Faculty of Medicine, University of Strasbourg, Strasbourg, France

 

2015 Infectious Diseases

Time window for positive cerebrospinal fluid broad-range bacterial PCR and Streptococcus pneumoniae immunochromatographic test in acute bacterial meningitis

Brink M, Welinder-Olsson C, Hagberg L.

From the Institute of Biomedicine, Department of Infectious Diseases , University of Gothenburg , Gothenburg , Sweden.

 

2015 Emerging Infectious Diseases, CDC (EID)

Infections with Candidatus Neoehrlichia mikurensis and Cytokine Responses in 2 Persons Bitten by Ticks, Sweden

Anna Grankvist,1 Lisa Labbé Sandelin,1 Jennie Andersson, Linda Fryland, Peter Wilhelmsson, Per-Eric Lindgren, Pia Forsberg, and Christine Wennerås

University of Gothenburg, Göteborg, Sweden (A. Grankvist, J. Andersson, C. Wennerås);

Sahlgrenska University Hospital, Göteborg (A. Grankvist, J. Andersson, C. Wennerås);

Kalmar County Hospital, Kalmar, Sweden (L.L. Sandelin); Uppsala University, Uppsala, Sweden (L.L. Sandelin);

Linköping University, Linköping, Sweden (L. Fryland, P. Wilhelmsson, P.-E. Lindgren, P. Forsberg);

County Hospital Ryhov, Jönköping, Sweden (P.-E. Lindgren)

 

2015 Journal of Clinical Microbiology (JCM)

First Report of Wohlfahrtiimonas chitiniclastica Isolation from a Patient with Cellulitis in the United States

Angel de Dios,a Seby Jacob,a Amit Tayal,a Mark A. Fisher,b Tanis C. Dingle,a Camille L. Hamulaa

Department of Pathology, Icahn School of Medicine at Mount Sinai, New York, New York, USAa ; ARUP Laboratories and University of Utah Department of Pathology, Salt Lake City, Utah, USAb


2015 Molecular and Cellular Probes

Rapid prediction of inducible clarithromycin resistance in Mycobacterium abscessus

Yan Chun Zhu, Kara K. Mitchell, Elizabeth J. Nazarian, Vincent E. Escuyer, Kimberlee A. Musser,

Wadsworth Center, New York State Department of Health, Albany, NY, USA

 

2015 Clinical Microbiology Newsletter

Cardiobacterium valvarum, an Emerging New HACEK Organism, as the Causative Agent of Infective Endocarditis: Case Report and Review of the Literature

Tobias Pusch, M.D.a, b, Mark A. Fisher, Ph.D.c, Rita M. Gander, Ph.D.b, ,

a Infectious Diseases and Clinical Microbiology, Providence Medical Group, Infectious Disease Consultants West/The Traveler's Clinic, Portland, Oregon

b Department of Pathology, University of Texas Southwestern Medical Center, Dallas, Texas

c Department of Pathology, Division of Microbiology, University of Utah School of Medicine and ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah

 

2015 Ticks and Tick-borne Diseases

Borrelia burgdorferi sensu lato-infected Ixodes ricinus collected from vegetation near the Arctic Circle

Dag Hvidstena, , , Frode Stordalb, Malin Lagerc, Bjørg Rognerudb, Bjørn-Erik Kristiansend, Andreas Matussekc, Jeremy Graye, Snorre Stuenf

a Department of Microbiology and Infection Control, University Hospital of North Norway, Sykehusveien 1, 9038 Tromsø, Norway

b Department of Geosciences, University of Oslo, P.O. Box 1047 Blindern, 0316 Oslo, Norway

c Department of Laboratory Services, Division of Medical Services, County Hospital Ryhov, Sjukhusvägen 1, 55185 Jönköping, Sweden

d Research Group of Host–Microbe Interactions, Department of Medical Biology, Faculty of Health Sciences, UiT – The Arctic University of Norway, P.O. Box 6050 Langnes, 9037 Tromsø, Norway

e UCD School of Biology and Environmental Science, University College Dublin, Dublin 4, Ireland

f Norwegian University of Life Sciences, Department of Production Animal Clinical Sciences, Kyrkjevegen 332/334, 4325 Sandnes, Norway

 

2015 Journal of Clinical Microbiology (JCM)

Nocardia thailandica Pulmonary Nocardiosis in a Post-Solid Organ Transplant Patient

Joseph Canterino,a Alberto Paniz-Mondolfi,b Barbara A. Brown-Elliott,c Wilson Vientos,d Ravikiran Vasireddy,c Richard J. Wallace, Jr.,c Sheldon Campbellb,d

Division of Infectious Diseases, Yale School of Medicine/Yale-New Haven Hospital, New Haven, Connecticut, USAa

Microbiology Laboratory, Department of Laboratory Medicine, Yale School of Medicine/Yale-New Haven Hospital, New Haven, Connecticut, USAb

Department of Microbiology, The University of Texas Health Science Center, Mycobacteria/Nocardia Laboratory, Tyler, Texas, USAc

Laboratory of Microbiology, VA Connecticut Healthcare, West Haven, Connecticut, USAd

 

2015 PLOS ONE

Genetic Diversity of Circulating Rotavirus Strains in Tanzania Prior to the Introduction of Vaccination

Sabrina J. Moyo1,2*, Bjørn Blomberg1,3, Kurt Hanevik1,3, Oyvind Kommedal4, Kirsti Vainio5, Samuel Y. Maselle2, Nina Langeland1,6

1 Department of Clinical Science, University of Bergen, Bergen, Norway, 2 Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania, 3 Centre for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway, 4 Department of Microbiology, Haukeland University Hospital, Bergen, Norway, 5 Division of Infectious Disease Control, Norwegian Institute of Public Health, Oslo, Norway, 6Department of Medicine, Haukeland University Hospital, Bergen, Norway

 

2014 Journal of Acquired Immune Deficiency Syndromes (JAIDS)

On the Usefulness of Circulating Bacterial 16S rDNA as a Marker of Microbial Translocation in HIV-1Infected Patients

Svärd, Jenny PhD*; Sönnerborg, Anders MD, PhD*,†; Vondracek, Martin PhD‡,§; Mölling, Paula PhD; Nowak, Piotr MD, PhD*

*Unit of Infectious Diseases and Dermatology, Department of Medicine Huddinge, Karolinska Institutet, Stockholm, Sweden

Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden

Department of Clinical Microbiology, Karolinska University Hospital, Stockholm, Sweden

  • Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden

Department of Laboratory Medicine, Clinical Microbiology, Örebro University Hospital, Örebro, Sweden.

 

2014 Journal of Clinical Microbiology (JCM)

Massive parallel sequencing provides new perspectives on bacterial brain abscesses.

Øyvind Kommedal1, Marianne Thulin Wilhelmsen1, Steinar Skrede2,3, Roger Meisal4 ,

Aleksandra Jakovljev5, Peter Gaustad6, Nils Olav Hermansen6, Einar Vik-Mo7, Ole Solheim8,9

Ole Herman Ambur4, Øystein Sæbø10, Christina Teisner Høstmælingen11, Christian Helland12,13**

1Department of Microbiology, Haukeland University Hospital, Bergen, Norway

2Department of Medicine, Haukeland University Hospital, Bergen, Norway

3Department of Clinical Science, University of Bergen, Norway

4Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway

5Department of Microbiology, St. Olav’s University Hospital, Trondheim, Norway

6Department of Microbiology, Oslo University Hospital, Oslo, Norway

7Departments of Neurosurgery, Oslo University Hospital, Oslo, Norway

8Department of Neurosurgery, St. Olav’s University Hospital, Trondheim, Norway

9Department of Neuroscience, Norwegian University of Science and Technology, Trondheim, Norway

10Department of Neurosurgery, University of North Norway, Tromsø, Norway

11Isentio Inc., Palo Alto, California, USA

12Department of Neurosurgery, Haukeland University Hospital, Bergen, Norway

13Department of Clinical Medicine, University of Bergen, Bergen, Norway

 

2014 Journal of Clinical Microbiology (JCM)

The Capnocytophaga canimorsus Isolate That Caused Sepsis in an Immunosufficient Man Was Transmitted by the Large Pine Weevil Hylobius abietis

Tamara Tuuminen,a,b Heli Viiri,c Sakari Vuorinend

Eastern Finland Laboratory Centre Joint Authority Enterprise (ISLAB), Mikkeli District Laboratory, Porrassalmenkatu, Mikkeli, Finlanda

Haartman Institute, University of Helsinki, Department of Bacteriology and Immunology, Helsinki, Finlandb

Finnish Forest Research Institute, Joensuu Unit, Joensuu, Finlandc

Mikkeli Central Hospital, Etelä-Savo Hospital District, Porrassalmenkatu, Mikkeli, Finlandd

 

2014 Medical Mycology

Complexities associated with the molecular and proteomic identification of Paecilomyces species in the clinical mycology laboratory

Adam P. Barker1,, Jennifer L. Horan2, E. Susan Slechta3, Barbara D. Alexander2 and Kimberly E. Hanson4

1 Department of Pathology, University of Utah, ARUP Institute for Clinical and Experimental Pathology,

Salt Lake City, UT, USA,

2 Department of Medicine/Infectious Diseases, Duke University Medical Center,

Durham, NC, USA,

3 ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT, USA

4 Department of Medicine and Department of Pathology, University of Utah, Salt Lake City, UT, USA

 

2014 Journal of Clinical Microbiology (JCM)

Septic Arthritis and Osteomyelitis Due to Bordetella petrii

Masayuki Nogi,a Matthew J. Bankowski,b,c Francis D. Piena

Departments of Internal Medicinea and Pathology,b John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, USA; Diagnostic Laboratory Services, Inc. (The Queen’s Medical Center), Aiea, Hawaii, USAc

 

2014 Journal of Clinical Microbiology (JCM)

Application of Qualitative and Quantitative Real-Time PCR, Direct Sequencing, and Terminal Restriction Fragment Length Polymorphism Analysis for Detection and Identification of Polymicrobial 16S rRNA Genes in Ascites

Sandra Krohn,a,b Stephan Böhm,a Cornelius Engelmann,a Jan Hartmann,c Annika Brodzinski,a Antonis Chatzinotas,b Katharina Zeller,a Delia Prywerek,a Ingo Fetzer,b,d Thomas Berga

University Hospital Leipzig, Division of Gastroenterology and Hepatology, Leipzig, Germanya

; Helmholtz Centre for Environmental Research—UFZ, Department of

Environmental Microbiology, Leipzig, Germanyb

; Department of Medicine A, University Medicine Greifswald, Greifswald, Germanyc

; Stockholm University, Stockholm Resilience Centre, Stockholm, Swedend

 

2014 Journal of Antimicrobial Chemotherapy

Molecular techniques for diagnosing prosthetic joint infections

John C. Hartley* and Kathryn A. Harris

Department of Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital for Children NHS Foundation

Trust

 

2014 PLOS ONE

Genetic Diversity of Circulating Rotavirus Strains in Tanzania Prior to the Introduction of Vaccination

Sabrina J. Moyo1,2*, Bjørn Blomberg1,3, Kurt Hanevik1,3, Oyvind Kommedal4, Kirsti Vainio5, Samuel Y. Maselle2

, Nina Langeland1,6

1 Department of Clinical Science, University of Bergen, Bergen, Norway,
2 Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
3 Centre for Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway,
4 Department of Microbiology, Haukeland University Hospital, Bergen, Norway,
5 Division of Infectious Disease Control, Norwegian Institute of Public Health, Oslo, Norway,
6 Department of Medicine, Haukeland University Hospital, Bergen, Norway

 

2014 European Journal of Clinical Microbiology & Infectious Diseases

Purification of DNA eluates from the ProbeTec GC Qxassay on BD Viper™ XTR allows for further analysis and confirmation of gonorrhea

  1. S. Tunsjø 1, E. Smedsrud 1, P. C. Holm 1, K. Rokvam 1, C. Schie 1, V. Rognlien 1, I. Augustin 1, A. Fostervold 1,2
    1.Unit of Gene Technology and Department of Microbiology, Division of Diagnostics and TechnologyAkershus University HospitalNordbyhagenNorway

2.Department of Medical MicrobiologyStavanger University HospitalStavangerNorway

 

2014 Infection, Genetics and Evolution

Genetic diversity of norovirus in hospitalised diarrhoeic children and asymptomatic controls in Dar es Salaam, Tanzania

Sabrina Moyoa, b, Kurt Hanevika, c, Bjørn Blomberga, c, Oyvind Kommedald, Kirsti Vainioe, Samuel Maselleb, Nina Langelanda, f

a Department of Clinical Science, University of Bergen, N-5021 Bergen, Norway

b Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Tanzania

c Centre for Tropical Infectious Diseases, Department of Medicine, Haukeland University Hospital, Bergen, Norway

d Department of Microbiology, Haukeland University Hospital, Bergen, Norway

e Division of Infectious Disease Control, Norwegian Institute of Public Health, Oslo, Norway

f Department of Medicine, Haukeland University Hospital, Bergen, Norway

 

2014 Clinics in Laboratory Medicine

Nontuberculous Mycobacteria in Respiratory Infections: Advances in Diagnosis and Identification

Akos Somoskovi, MD, PhD, DSca, Max Salfinger, MDb, ,

a Institute of Medical Microbiology, Swiss National Reference Center for Mycobacteriology, University of Zuirch, Gloriastrasse 30/32, CH-8006, Zurich, Switzerland

b Department of Medicine, National Jewish Health, K420, 1400 Jackson Street, Denver, CO 80206, USA

 

2014 MASARYKOVA UNIVERZITA

Molekulárně-biologická detekce patogenů u pacientů s polymikrobiálními infekcemi močových katétrů

Bc. Iva Kotásková

Přírodovědecká fakulta, Masarykova univerzita. Ústav experimentální biologie

 

2013 Journal of Clinical Microbiology (JCM)

Culture-Negative Prosthetic Valve Endocarditis with Concomitant Septicemia Due to a Nontoxigenic Corynebacterium diphtheriae Biotype Gravis Isolate in a Patient with Multiple Risk Factors.

Keith D. Tardif1, Keith E. Simmon2, Øyvind Kommedal3,4, Michael T. Pyne1 and Robert Schlaberg1,5

1ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT

2Isentio US, Sunnyvale, CA, 3University of Bergen, Norway

4Isentio AS, Bergen, Norway

5University of Utah School of Medicine, Department of Pathology, Salt Lake City, UT

 

2013 Journal of Clinical Microbiology (JCM). Vol. 51 no. 4.

Sequencing-Based Genotyping of Mixed Human Papillomavirus Infections Using RipSeq Software.

Keith D. Tardif1, Keith E. Simmon2, Øyvind Kommedal3,4, Michael T. Pyne1 and Robert Schlaberg1,5

1ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT

2Isentio US, Sunnyvale, CA, 3University of Bergen, Norway

4Isentio AS, Bergen, Norway

5University of Utah School of Medicine, Department of Pathology, Salt Lake City, UT

  

2013 Journal of Clinical Microbiology (JCM). Vol. 51 no. 4.

Direct sequencing and RipSeq interpretation as a tool for identification of polymicrobial infections.

Wolff T Y1, Eickhardt S2,3, Björnsdottir M K2, Moser C2, Bjarnsholt T2,3, Høiby N2 and Thomsen T R1,4

1The Danish Technological Institute, Life Science Division, Aarhus, Denmark

2Department of Clinical Microbiology, Rigshospitalet, University hospital of Copenhagen, Copenhagen, Denmark 3Department of International Health, Immunology and Microbiology, University of Copenhagen, Denmark,

4Department of Biotechnology, Chemistry, and Environmental Engineering, Aalborg University, Aalborg, Denmark

 

2013 Mycoses: Diagnosis, Therapy and Prophylaxis of Fungal Diseases (M).

Deciphering the aetiology of a mixed fungal infection by broad-range PCR with sequencing and fluorescence in situ hybridization.

  1. Rickerts1, I. McCormick Smith1, S. Mousset2, O. Kommedal3 and D. N. Fredricks4

1Robert Koch Institut, FG 16, Berlin, Germany

2University Hospital, Haematology, Frankfurt, Germany

3Isentio AS, Bergen, Norway

4Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Devision, Seattle, USA

 

2013 Infect Dis Clin Pract
A Lethal Case of Pseudomonas putida Bacteremia Due to Soft Tissue Infection

Benjamin S. Thomas, MD* , Koh Okamoto, MD* , Matthew J. Bankowski, PhD†,‡,§, and Todd B. Seto, MD, MPH*,‡,∥

*Department of Medicine, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI
†Department of Pathology, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI
‡The Queen’s Medical Center, Honolulu, HI §Diagnostic Services, Inc, Aiea, HI
∥Native Hawaiian Health, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI

 

2013 Journal of Clinical Microbiology (JCM)

Monitoring of patients supported by extracorporeal membrane oxygenation for systemic infections by broad-range rRNA gene PCR amplification and sequence analysis

Peter Orszaga, Claudia Disquéb , Sonja Keimb , Michael G. , Lorenzb , Olaf Wiesnerc , Johannes Hademd , Meike Stiesche , Axel Havericha , Christian Kühna

Department of Thoracic, Transplant, and Cardiovascular Surgery, Hannover Medical School, Hannover, Germanya

Molzym GmbH & Co. KG, Bremen, Germanyb

Department of Respiratory Medicine, Hannover Medical School, Hannover, Germanyc

Department of Gastroenterology, Hepatology, and Endocrinology, Hannover

Medical School, Hannover, Germanyd

Department of Prosthetic Dentistry, Hannover Medical School, Hannover, Germanye

 

2013 Advances in Microbiology

How Liquid Based Microbiology Can Change the Workflow in the Microbiology Laboratories

Carla Fontana1,2*, Marco Favaro1, Cartesio Favalli1,2

1 Department of Experimental Medicine and Surgery, “Tor Vergata” University of Rome, Rome, Italy
2 Clinical Microbiology Laboratories, Foundation Polyclinic Tor Vergata, Rome, Italy

 

2013 Journal of Clinical Microbiology (JCM)

First Report of Mycobacterium canariasense Catheter-Related Bacteremia in the Americas.

Alberto Paniz-Mondolfi,a Lynn Ladutko,b Barbara A. Brown-Elliott,c Ravikiran Vasireddy,c Sruthi Vasireddy,c Richard J. Wallace, Jr.,c, Wesley Jakubiec,b Stephen Brecher,d,e Sheldon Campbella,b

Department of Laboratory Medicine, Yale School of Medicine/Yale-New Haven Hospital, New Haven, Connecticut, USAa

VA Connecticut Healthcare, West Haven, Connecticut, USAb

Department of Microbiology, The University of Texas Health Science Center, Mycobacteria/Nocardia Laboratory, Tyler, Texas, USAc

VA Boston Healthcare, West Roxbury, Massachusetts, USAd

Boston University School of Medicine, Boston, Massachusetts, USA

 

2013 Diagnostic Microbiology and Infectious Disease

Molecular diagnosis of microbial aetiologies using SepsiTest™ in the daily routine of a diagnostic laboratory

Heike Haag 1, Franziska Locher, Oliver Nolte

1 Labor Dr. Brunner, Mainaustraße 48 a/b, DE-78464, Konstanz, Germany.

 

2013 Ticks and Tick-borne Diseases

Ixodes ricinus and Borrelia prevalence at the Arctic Circle in Norway

Dag Hvidstena,, Snorre Stuenb, Andrew Jenkins c, Olaf Dienus d, Renate S. Olsene, Bjørn-Erik Kristiansenf, Reidar Mehl g, Andreas Matussek d

a Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
b Department of Production Animal Clinical Sciences, Norwegian School of Veterinary Science, Sandnes, Norway
c Department of Environmental and Health Studies, Telemark University College, Bø, Norway
d Department of Laboratory Services, Division of Medical Services, County Hospital Ryhov, Jönköping, Sweden
e Host-Microbe Interactions, Institute of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
f Institute of Medical Biology, UiT The Arctic University of Norway, Tromsø, Norway
g Institute of Microbiology, Armed Forces Medical Services, Oslo, Norway

 

2013 European Journal of Microbiology and Immunology

Non-Culture-based methods to diagnose bloodstream infection: Does it work?

Miha Skvarc1 , David Stubljar1 , Petra Rogina2 and Achim J. Kaasch3*

1 Institute of Microbiology and Immunology, Faculty of Medicine, Ljubljana, Slovenia
2 General Hospital, Novo Mesto, Slovenia
3 Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, 50935 Cologne, Germany

 

2013 PLOS ONE

Prevalence, Diversity, and Load of Borrelia species in Ticks That Have Fed on Humans in Regions of Sweden and Åland Islands, Finland with Different Lyme Borreliosis Incidences

Peter Wilhelmsson1*, Pontus Lindblom1, Linda Fryland2, Jan Ernerudh2, Pia Forsberg3,4, Per-Eric, Lindgren1,5

1 Division of Medical Microbiology, Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, Linköping, Sweden,

2 Division of Clinical Immunology, Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, Linköping, Sweden,

3 Division of Infectious Diseases, Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, Linköping, Sweden,

4 Clinic of Infectious Diseases, County Council of Östergötland, Linköping, Sweden,

5 Medical Services, Department of Microbiology, Ryhov County Hospital, Jönköping, Sweden

 

2012 Journal of Clinical Microbiology (JCM).

Prosthetic Joint Infection Diagnosis using Broad-Range PCR of Biofilms Dislodged from Knee and Hip Arthroplasty Surfaces using Sonication.

Gomez E, Cazanave C, Cunningham SA, Greenwood-Quaintance KE, Steckelberg JM, Uhl JR, Hanssen AD, Karau MJ, Schmidt SM, Osmon DR, Berbari EF, Mandrekar J, Patel R.

Mayo Clinic, Rochester, USA. Division of Infectious Diseases, Department of Medicine.

 

2012 Journal of Clinical Microbiology (JCM)

Nocardia neocaledoniensis as a cause of human skin and soft tissue infection.

Travea McGhie1, Robert Fader2, John Carpenter1, Barbara A. Brown-Elliott3, Ravikiran Vasireddy3, Richard J. Wallace Jr.

1Department of Medicine, Division of Infectious Disease

2Department of Pathology, Scott & White Healthcare; Texas A&M School of Medicine, Temple, TX 76508 3Mycobacteria/Nocardia Laboratory, The University of Texas Health Science Center, Tyler, TX 75708

 

2012 Journal of Clinical Microbiology (JCM)

Dual-priming oligonucleotides for broad-range amplification of the bacterial 16S rRNA gene directly from human clinical specimens.

Kommedal O1, Simmons K2, Karaca D3, Langeland N3, Wiker HG1,4

1Section for Microbiology and Immunology, the Gade Institute, University of Bergen, Bergen, Norway

2Isentio US LLC, Sunnyvale, California, USA

3Institute of Medicine, University of Bergen, Bergen, Norway

4Department of Microbiology, Haukeland University Hospital, Bergen, Norway

 

2012 Emerging Infectious Diseases, CDC (EID)

Emergence of Unusual G6P[6] Rotaviruses in Children, Burkina Faso, 2009–2010.

J Nordgren1, L W Nitiema2, S Sharma1, D Ouermi2, A S Traore2, J Simpore2, L Svensson1

1Linköping University, Linköping, Sweden

2Université de Ouagadougou, Ouagadougou, Burkina Faso

 

2012 Experimental Applied Acarology (EAA)

Borrelia burgdorferi sensu lato in Ixodes ricinus ticks from Norway: evaluation of a PCR test targeting the chromosomal flaB gene.

Andrew Jenkins1, Dag Hvidsten2, Andreas Matussek3, Per-Eric Lindgren4, Snorre Stuen5, Bjørn-Erik Kristiansen6

1 Unilabs Telelab, Skien, Norway

2 Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway

3 Clinical Microbiology Laboratory, Division of Medical Services, Department of Laboratory Medicine, Sweden

4 Division of Medical Microbiology, Department of Clinical and Experimental Medicine, Sweden,

5 Department of Production Animal Clinical Sciences, Norwegian School of Veterinary Science, Norway,

6 Department of Microbiology and Virology, University of Tromsø, Norway

 

2012 Zeitschrift für Gastroenterologie

Identifizierung polybakterieller DNA im Aszites mittels Nachweis und Charakterisierung von 16S rRNA Gensequenzen

S Krohn 1, 2, J Hartmann 1, A Brodzinski 1, A Chatzinotas 2, I Fetzer 2, S Böhm 1, T Berg 1

1 Universitätsklinikum Leipzig, Abteilung für Gastroenterologie und Rheumatologie, Sektion Hepatologie, Leipzig, Germany

2 Helmholtz-Zentrum für Umweltforschung – UFZ, Department für Umweltmikrobiologie, Leipzig, Germany

 

2012 Journal of Clinical Microbiology (JCM).
Rapid Molecular Microbiologic Diagnosis of Prosthetic Joint Infection

Charles Cazanave,a Kerryl E. Greenwood-Quaintance,a, Arlen D. Hanssen,b, Melissa J. Karau,a, Suzannah M. Schmidt,a, Eric O. Gomez Urena,a, Jayawant N. Mandrekar,d, Douglas R. Osmon,c, Lindsay E. Lough,a, Bobbi S. Pritt,a, James M. Steckelberg,c, Robin Patela,c

Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology,a
Department of Orthopedic Surgery,b
Division of Infectious Diseases, Department of Medicine,c

Division of Biomedical Statistics and Informatics, Department of Health Science Research,d

All: Mayo Clinic, Rochester, Minnesota, USA

 

2012 Journal of Clinical Microbiology (JCM).

Identification of Anaerobic Bacteria by Bruker Biotyper Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry with On-Plate Formic Acid Preparation

Bryan H. Schmitt, a, Scott A. Cunningham, a, Aaron L. Dailey, a, Daniel R. Gustafson, a, Robin Patela,b

Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology,a
Division of Infectious Diseases, Department of Medicine,b
All: Mayo Clinic, Rochester, Minnesota, USA

 

2012 Journal of Clinical Microbiology (JCM).

Isolation and Identification of Kroppenstedtia eburnea Isolates from Multiple Patient Samples

Adam P. Barker,a, Keith E. Simmon,b,*, Sam Cohen,c, E. Susan Slechta,b, Mark A. Fisher,a,b and Robert Schlaberga,b

University of Utah School of Medicine, Salt Lake City, Utah, USAa

ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah, USAb

ARUP Laboratories, Salt Lake City, Utah, USAc

 

2012 Culture Negative Orthopedic Biofilm Infections

Improved Diagnosis of Biofilm Infections Using Various Molecular Methods

Trine Rolighed Thomsen 1,2, Yijuan Xu 1,2, Jan Lorenzen 2, Per Halkjær Nielsen 1, Henrik Carl Schønheyder 3

1 Department of Biotechnology, Chemistry, and Environmental Engineering, Aalborg University
2 Life Science Division, The Danish Technological Institute

3 Department of Clinical Microbiology, Aalborg Hospital, Aarhus University Hospital

2012 Aalborg Universitet

Detection, identification and quantification of microorganisms in selected infections

Rudkjøbing, Vibeke Børsholt

Aalborg University, Denmark

 

2011 Journal of Medical Microbiology (JMM), Vol. 60, No. 7.

Characterization of polybacterial clinical samples using a set of group-specific broad-range primers targeting the 16S rRNA gene followed by DNA sequencing and RipSeq analysis.

Øyvind Kommedal 1 Katrine Lekang,2 Langeland N3, Wiker HG1,4

1Section for Microbiology and Immunology, The Gade Institute, University of Bergen, Norway

2Institute of Biology, University of Bergen, Norway

3Institute of Medicine, University of Bergen, Norway

4Department of Microbiology, Haukeland University Hospital, Norway

 

2011 Ornamental Plants: Types, Cultivation and Nutrition (OPTCN).

Watery varieties: Aquarium plant diversity from aesthetic, commercial and systematic perspectives

Lehtonen S, Falck D.

University of Turku, Department. of Biology, Turku, Finland.

 

2011 Enfermedades Infecciosas y Microbiología Clínica

Métodos de identificación bacteriana en el laboratorio de microbiología (Bacterial identification methods in the microbiology laboratory)

Germán Boua, , , Ana Fernández-Olmosb, Celia Garcíac, Juan Antonio Sáez-Nietod, Sylvia Valdezated

a Servicio de Microbiología, Complejo Hospitalario Universitario, La Coruña, España

b Servicio de Microbiología, Hospital Ramón y Cajal, Madrid, España

c Servicio de Microbiología, Hospital Universitario Marqués de Valdecilla, Santander, España

d Servicio de Bacteriología, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, España

 

2010 Journal of Infection (JOI), Vol 60, Issue 6.

Shuttleworthia satelles Endocarditis: Evidence of Non-Dental Human Disease.

Neel B. Shahe1, Rakesh M. Suri2, Rowlens M. Melduni2, Robin Patel3, Øyvind Kommedal4, Øystein Sæbø4, Daniel R. Gustafson5, Walter R. Wilson3, Larry M. Baddour3

1 Mayo Clinic College of Medicine, Department of Internal Medicine, Mayo Clinic School of Graduate Medical Education, Rochester, USA

2 Mayo Clinic College of Medicine, Department of Cardiovascular Surgery, Mayo Clinic School of Graduate Medical Education, Rochester, USA

3 Mayo Clinic College of Medicine, Division of Infectious Diseases, Mayo Clinic School of Graduate Medical Education, Rochester, USA

4 iSentio AS, Bergen, Norway

5 Mayo Clinic College of Medicine, Division of Clinical Microbiology, , Mayo Clinic School of Graduate Medical Education, Rochester, USA

 

2010 Respiration

Identification of Bacterial DNA in Noninfectious Pleural Fluid with a Highly Sensitive PCR Method.

Rosa Cremades a Antonio Galiana a Juan Carlos Rodriguez a Ana Santos a Pilar Lopez a Montserrat Ruiz a Eduardo Garcia-Pachon b Gloria Royo a

Sections of a Microbiology and b Respiratory Medicine, Hospital General Universitario, Elche , Spain

 

2010 Journal of Medical Microbiology (JMM). Vol. 59, No. 4.

Direct 16S rRNA gene sequencing of polymicrobial culture-negative samples with analysis of mixed chromatograms.

Hartmeyer G N, Justesen U S

Department of Clinical Microbiology, Odense University Hospital, Odense, Denmark

 

2010 Journal of Clinical Microbiology (JCM). Vol. 48, No. 9.

Simultaneous Sequencing Analysis of The 16S rRNA and rpoB Genes Using RipSeq Software to Identify Mycobacterium Species.

Keith E. Simmon1, Øyvind Kommedal2,3, Øystein Saebo3, Bjarte Karlsen3 and Cathy A. Petti1,4

1 Associated Regional and University Pathologists (ARUP), Institute for Clinical and Experimental Pathology, Salt Lake City, Utah

2 University of Bergen, The Gade Institute, Section for Microbiology and Immunology, Bergen, Norway

3 iSentio AS, Bergen, Norway

4 University of Utah School of Medicine, Departments of Medicine and Pathology, Salt Lake City, Utah

 

2010 Emerging Infectious Diseases, CDC (EID)

Emergence of Unusual G6P[6] Rotaviruses in Children, Burkina Faso, 2009–2010

  1. Nordgren 1, S. Sharma 1, L. Svensson 1, L.W. Nitiema 2, D., Ouermi 2, A.S. Traore 2, J. Simpore 2

1 Linköping University, Linköping, Sweden

2 Université de Ouagadougou, Ouagadougou, Burkina Faso

 

2009 Journal of Clinical Microbiology (JCM). Vol 47, No. 11.

Direct 16S rRNA Gene Sequencing from Clinical Specimens, with Special Focus on Polybacterial Samples and Interpretation of Mixed DNA Chromatograms

Kommedal Ø1,2, Kvello K2, Skjåstad R1, Langeland N3,4, Wiker H G1,2

1Department of Microbiology and Immunology, Haukeland University Hospital, Bergen, Norway

2Section for Microbiology and Immunology, the Gade Institute, University of Bergen, Bergen, Norway

3Institute of Medicine, University of Bergen, Bergen, Norway

4Department of Medicine, Haukeland University Hospital, Bergen, Norway

 

2008 Journal of Clinical Microbiology (JCM). Vol. 46, No. 11.

Analysis of Mixed Sequencing Chromatograms and Its Application in Direct 16S rRNA Gene Sequencing of Polymicrobial Samples.

Kommedal Ø, Karlsen B, Sæbø Ø

iSentio AS, Bergen, Norway

2017 ASM - Session: Culture-Independent Testing

Validation of a Clinical 16S Metagenomics Assay for the Identification of Bacterial Infections

Shaun Yang, PhD, D(ABMM), MLS(ASCP)CMMBCM
University of New Mexico Health Sciences Center, TriCore Reference Laboratories

 

2015 Wiley Blackwell

Modern Techniques for Pathogen Detection

Jürgen Popp, Michael Bauer

 

2014 ASM - Clinical Microbiology Reviews

Prosthetic Joint Infection

Aaron J. Tande,a Robin Patela,b

Division of Infectious Diseases, Department of Internal Medicine,a
Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology,b
All: Mayo Clinic, Rochester, Minnesota, USA

 

2012 Molzym GmbH (White paper)

Direct Eubacterial PCR Diagnosis of Primary Sterile Body Fluids and Tissues

Michael Lustig

Molzym GmbH & Co. KG, Bremen, Germany

 

2012 Ninth International Symposium on Molecular Diagnostics (White paper)

Microbial DNA enrichment combined with broad-range real-time PCR – a tool for the diagnosis of culture-negative infections

Detmers J.

Molzym, Bremen, Germany

 

2012 ECCMID
Direct sequencing and RipSeq analysis as a tool for identification of polymicrobial bactaeremia

Wolff T Y, Eickhardt S, Moser C, Bjarnsholt T, Nielsen P H, Høiby N, Lorenzen J, Thomsen T R.

Aarhus, Copenhagen, Aalborg, Denmark

 

2012 ECCMID
How Liquid Based Microbiology can change the workflow in the Microbiology laboratories.

Fontana C, Favaro M, Favalli C

1 Università Tor Vergata, Biochimiche, , Roma, Italy

2 Università Tor Vergata, Lab Microbiologia, Policlinico, Roma, Italy

 

2012 ECCMID
RipSeq® Single, advancing the quality of a bacterial reference database through social curation.

Cathy A. Petti1, Keith E. Simmon2, Bjarte Karlsen2, Øystein Sæbø2, Øyvind Kommedal2

1TriCore Reference Laboratories, Albuquerque, NM, USA

2Isentio AS, Bergen, Norway

 

2011 ECCMID
Molecular pathogen detection (16S rDNA-PCR/sequencing) in culture-negative infections

Nolte O, Labor Dr. Brunner

Konstanz, Germany

 

2010 ECCMID
Dissection of polybacterial clinical samples using group specific broad-range primers and DNA sequencing followed by RipSeq analysis.

Kommedal Ø.

University of Bergen, The Gade Institute Section for Microbiology and Immunology, Norway and Isentio AS, Bergen, Norway

 

2010 ASM
Application of RipSeq Mixed Software in Identification of Bacteria by 16S ribosomal RNA Gene Sequencing.

Hall L, Connelly B J1, Kommdal Ø2, Sæbø Ø F2, Patel F, Ihde S M1, Gustafson D R1, Rosenblatt J E1, Wengenack N L1,

1 Mayo Clinic, Rochester, USA

2 Isentio, Bergen, Norway

 

2010 ASMCM
Evaluation of the GenBank BLAST and RipSeq by Isentio for sequence comparisons of DNA obtained from Corneal scrapings in patients with suspected ophthalmic infections.

Grankvist A, Kjellin E, Welinder-Olsson.

Sahlgrenska University Hospital, Clinical Bacteriology Laboratory, Gothenburg, Sweden

 

2009 ICCAC
Identification of Polymicrobial Bacteremia by 16S rRNA Sequencing with RipSeq(TM) Software.

Tesic V 1,2, Simmon K E3, Petti A 1,2,

1 ARUP Laboratories, Salt Lake City, USA

2 University of Utah, USA

3 ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, USA

 

2009 ASM
Identification of Mixed Infections of Mycobacterium species from Culture with 16S rRNA Gene Sequencing and RipSeq Software.

Smith G L1, Tesic V 1,2, Simmon K E3, Petti A 1,2.

1ARUP Laboratories, Salt Lake city, USA

2Univ of Utah, Salt Lake City, ARUP, USA

3ARUP Inst for Clinical and Experimental Pathology, Salt Lake City, USA

 

2008 ICCAC
Simultaneous Sequence Analysis of Two Loci to Identify Mycobacterium spp.

Simmon K E 1, Kommedal Ø 2, Karlsen B 2, Sæbø Ø 2, Petti A 1,3.

1 ARUP, Institute for Clinical and Experimental Pathology, Salt Lake City, USA

2 Isentio, Bergen, Norway,

3 University of Utah School of Medicine, Department of Medicin and Pathology, Salt Lake City, USA

 

RipSeq Mixed

RipSeq Mixed is an online software tool for rapid bacterial identification, with focus on analyzing mixed clinical samples. Through the use of advanced algorithms, we remove the need for manual isolation and re-cultivation of colonies from poly-microbial samples prior to 16S rDNA sequencing. This makes direct sequencing relevant for a broader range of clinical samples, including abscesses and pleural fluids.
Pathogenomix RipSeq Mixed (PDF)
RipSeq Single

DNA target sequencing is the prevailing method for accurate identification of human pathogens. With the introduction of RipSeq Single and the already established RipSeq Mixed, Isentio now makes RipSeq software the complete package for DNA target sequence based identification.
Pathogenomix RipSeq Single (PDF)
RipSeq NGS

Using our novel algorithms RipSeq will process your targeted NGS sequence file locally, and reduce the information needed to upload by a factor of 1000:1, while still retaining resolution and specificity. This means no lengthy file upload, and no costly big data file storage. After upload, the cloud based RipSeq will analyze the uploaded reads against any of our curated Ripseq DB databases - no matter the target. All this in less than 5 minutes! Including reporting!
Pathogenomix RipSeq Single (PDF)
RipSeq Mixed Examples

RipSeq Mixed is a computer program able to read and interpret mixed chromatograms containing up to three individual sequences (ref. JCM, Nov. 2009). Through the use of advanced algorithms we remove the need for culture and manual separation of the present bacteria prior to sequencing.
Pathogenomix RipSeq Mixed Examples (PDF)
RipSeq Mixed handles InDels

RipSeq Mixed is an online application able to read and interpret mixed sequencing chromatograms through the use of advanced algorithms. The RipSeq Mixed module can automatically handle and identify indel copy variants in DNA sequences obtained from pure bacterial isolates.
Pathogenomix RipSeq Mixed InDels (PDF)

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