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To view a selection of journal articles and posters citing the SmartGene IDNS for research in the public domain, please follow the links below.
2009
Multiplex Strategy for Multilocus Sequence Typing, fla Typing, and Genetic Determination of Antimicrobial Resistance of Campylobacter jejuni and Campylobacter coli Isolates Collected in Switzerland
Bozena M. Korczak,* Monika Zurfluh, Stefan Emler, Jacqueline Kuhn-Oertli, and Peter Kuhnert
Institute of Veterinary Bacteriology, University of Bern, Bern, Switzerland, and SmartGene, Zug, Switzerland
JOURNAL OF CLINICAL MICROBIOLOGY, July 2009, p. 1996-2007
Citation:
(...)The rpoB sequence allowed phylogenetic differentiation between C. coli and C. jejuni, which was not possible by 16S rRNA gene analysis. An online Integrated
Database Network System (SmartGene, Zug, Switzerland)-based platform for MLST data analysis specific to Campylobacter was implemented. This Web-based platform allowed automated allele and ST designation, as well as epidemiological analysis of data, thus streamlining and facilitating the analysis workflow. Data networking facilitates the exchange of information between collaborating centers. The described approach simplifies and improves the genotyping of Campylobacter, allowing cost- and time-efficient routine monitoring.(...)
(click here to request poster).
DNA Sequencing for the Identification of Unusual Yeasts Encountered in a Clinical Mycology Laboratory.
E. Susan Slechta(1), June Inez Pounder(1), Samuel Cohen(2), and Kimberly E Hanson (2),(3)
(1) ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT , (2) Associated Regional and University Pathologists, Inc., Salt Lake City, UT, (3) Department of Pathology, University of Utah, Salt Lake City, UT
Conference "ASM 2009, Philadelphia"
Citation:
(...)The SmartGene Fungal IDNS™ system (SmartGene Inc., Raleigh, NC) is a web-based gene sequencing software and database program with approximately 83,000 quality controlled sequences for the ITS region, and 58,000 sequences for D1/D2, all derived from GenBank.(...)
(click here to request poster).
Analysis of a Large Collection of non-Nocardia Aerobic Actinomycete Clinical Isolates
P. S. King(1), K. E. Simmon(1), A. Croft(1), C. A. Petti(1),(2)
(1)ARUP Laboratories, Salt Lake City, UT, (2)University of Utah, School of Medicine, Salt Lake City, UT.
Citation:
(...)Sequences were compared to related sequences in SmartGene (SmartGene Inc., Raleigh, NC).(...)
(click here to request poster).
Identification of Mixed Infections of Mycobacterium species from Culture with 16S rRNA Gene Sequencing and RipSeq Software
G.L. Smith(1), V. Tesic(1), (2), K.E. Simmon(3), C.A. Petti(1), (2)
(1)ARUP Laboratories, Salt Lake City, UT (2)University of Utah, Salt Lake City, UT (3)ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, UT
Conference "ASM 2009, Philadelphia"
Citation:
(...)Sequences were first analyzed with SmartGene (SmartGene Inc., Raleigh, NC). Electropherograms suggestive of multiple organisms were detected by observing an atypically high number of ambiguous bases (Figure 1) and in some cases an unusual susceptibility patterns.(...)
(click here to request poster).
Direct Detection of Pathogens in Clinical Samples Using Broad Range Bacterial 16S rRNA gene PCR: a Seven Months Prospective Study
G.V. Bloemberg(1), P. Keller(1), S. Rampini(2), G. Dollenmaier(3), R. Speck(2) and E.C. Böttger(1)
(1)Institute of Medical Microbiology and (2) University Hospital Zurich, University of Zurich, 8006 Zurich, SWITZERLAND.
(3)Institute for Clinical Microbiology and Immunology, St. Gallen, SWITZERLAND
Conference "ASM 2009, Philadelphia"
Citation:
(...) homology analysis was performed using Smartgene IDNS™ and Genbank databases. (...)
(click here to request poster).
A diagnostic algorithm combining phenotypic and molecular methods for identification of moulds in the clinical laboratory: report of a five year experience
D.E. Ciardo, A. Imhof, G.V. Bloemberg, E.C. Böttger
Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
Conference "ASM 2009, Philadelphia"
Citation:
(...) sequence comparison with a public database (NCBI) and an in-house established yeasts & moulds ITS database (IMM validated; available through SmartGene IDNS™) containing >1800 high quality sequences (...)
(click here to request poster).
Recognition of Novel Human Disease Associated Pathogens in the Diagnostic Microbiology
P. M. Keller (1), S. Rampini (2), A. B chler (2), R. Speck (2), E.C. Böttger (1), and G.V. Bloemberg (1)
(1) Institute of Medical Microbiology, University of Zurich and (2) Department of Internal Medicine, University Hospital Zurich, 8006 Zurich, SWITZERLAND
Conference "ASM 2009, Philadelphia"
Citation:
(...) Homology analyses were done using SmartGene IDNS™ and NCBI GenBank. (...)
(click here to request poster).
Evaluation of a COBAS Amplicor Based PCR Assay for Direct Detection and Identification of Mycobacterium spp. in Clinical Specimens
S. Peter-Getzlaff, J. Lüthy, A. Voit, G.V. Bloemberg and EC.
Böttger
Institute of Medical Microbiology, University of Zurich, 8006 Zurich, Switzerland
Conference "ASM 2009, Philadelphia"
Citation:
(...) Sequences were analyzed using SmartGene IDNS™ software. (...)
(click here to request poster).
2008
Molecular characterisation of Mycobacterium bovis isolated from cattle
slaughtered at the Bamako abattoir in Mali.
Müller B, Steiner B, Bonfoh B, Fané A, Smith NH, Zinsstag J.
BMC Vet Res. 2008 Jul 17;4:26.
Citation:
"[...] 16S rRNA gene amplification [...]. Species identification was
carried out by comparison with the sequences of the SmartGene Integrated
Database Network System (IDNS™) 3.4.0."
The text is open access at biomedcentral.com
Cross-sectional Versus Cumulative Interpretation of HIV-1 Drug Resistance Mutation
S Yerly 1, P-A Michel 2, S Emler 2, V von Wyl 3, H Günthard 3, B Hirschel 4, L Perrin 1 and L Kaiser 1
1 Laboratory of Virology, Geneva University Hospital and University of Geneva Medical School; 2 SmartGene, Lausanne; 3 University Hospital Zurich; 4 University Hospital Geneva; Switzerland
Poster presented during the XVII International HIV Drug Resistance Workshop held in Sitges (Barcelona), Spain on June 10-14 2008.
(click here to request poster).
2007
Emergence of HIV-1 Drug Resistance in Previously Untreated Patients Initiating Combination Antiretroviral Treatment A Comparison of Different Regimen Types
Viktor von Wyl, MSc; Sabine Yerly, MSc; Jurg Boni, DVM; Philippe Burgisser, PhD; Thomas Klimkait, PhD;
Manuel Battegay, MD; Hansjakob Furrer, MD; Amalio Telenti, MD; Bernard Hirschel, MD; Pietro L. Vernazza, MD;
Enos Bernasconi, MD; Martin Rickenbach, MD; Luc Perrin, MD; Bruno Ledergerber, PhD; Huldrych F. Gunthard, MD; for the Swiss HIV Cohort Study
(click here to request poster).
Improved Multilocus Sequence Typing and Flagelin Gene-based Typing for Online Monitoring of Campylobacter jejuni and Campylobacter coli. B. M. Korczak, M. Fehlmann, P. Kuhnert. Poster presented during the BIOTRACER General Meeting: Athens, Greece, November 14-16, 2007
(click here to request poster).
Detection of Drug Resistance Mutations as a Predictor of Subsequent Virological Failure in Patients With HIV-1 Viral Rebounds of Less Than 1,000 RNA copies/ml.
Chris Verhofstede, Filip Van Wanzeele, Bea Van Der Gucht, Jolanda Pelgrom, Linos Vandekerckhove, Jean Plum, and Dirk Vogelaers. Journal of Medical Virology 79:1254–1260 (2007)
Case report of Curvularia inaequalis detected in tissue sections using ITS sequencing and SmartGene analysis. E. Christensen, M. Nye, V. Creswell, H. Alexander, and B.A. Body. Poster presented during the 107th ASM General Meeting: Toronto, Ontario, Canada, May 21 - 25, 2007
(click here to request poster).
Identification of Yeast by ITS Sequencing June I. Pounder, Keith E. Simmon, Diana E. Ciardo, Philipp P. Bosshard, and Cathy A. Petti, Poster presented during the Focus on Fungal Infections 17 in San Diego, CA March 7-9, 2007.
(click here to request poster).
2006
Application of SmartGene IDNS Software to Partial 16S rRNA Gene Sequences for a Diverse Group of Bacteria in a Clinical Laboratory Keith E. Simmon, Ann C. Croft, and Cathy A. Petti, J. Clin. Microbiol., Dec 2006; 44: 4400 - 4406.
(click here to request article).
Transmission of HIV-1 Drug Resistance in Switzerland: A 10 Year Molecular Epidemiology Survey S. Yerly , V. von Wyl , J. Böni , J. Schüpbach , P. Burgisser , T. Klimkait , M. Rickenbach , B. Ledergerber , H. Günthard, L. Perrin and the Swiss HIV Cohort Study, Poster presented during the Forum for Collaborative HIV Research Standardization & Clinical Relevance of HIV Drug Resistance Working Group Meeting, Sitges, 2006
(click here to request poster).
Identification of Anaerobic Bacteria by 16S rRNA Gene Sequencing with SmartGene
and MicroSeq Software and Databases. K.E. Simmon, S. Mirrett, L.B. Reller2, and C.A. Petti, Poster presented during the annual meeting of the American Society for Microbiology,Orlando, 2006. (click here to request poster).
Identification of Nonsporulating Molds by Sequencing Internal Transcribed Spacer Regions with SmartGene Software and Database
June I. Pounder, Keith E. Simmon, Claudia A. Barton, Sheri L. Hohmann, and Cathy A. Petti, Poster presented during the annual meeting of the American Society for Microbiology, Orlando, 2006. (click here to request poster).
Internal Transcribed Spacer Sequencing versus Biochemical Profiling for Identification of Medically Important Yeasts.D.E. Ciardo, G. Shär, M. Altwegg, E.C. Böttger, P.P. Bosshard. J Clin Microbiol. Jan. 2006, 44(1), 77–84.
2005
Identification of moulds by sequencing of the ITS region: construction and evaluation of a database. D.E. Ciardo, G. Schär, M. Altwegg, E. C. Böttger, P.P. Bosshard. Poster presented during the annual meeting of the Swiss Society for Microbiology, 2005.
(click here to request poster).
2004
Phylogeny of the family Pateurellacea based on rpoB sequences. Korczak et al, Intl. Journal of Systematic and Evol. Microbiol, 2004, 54, 1393-1399.
2003
Ribosomal DNA Sequencing for Identification of Aerobic Gram-Positive Rods in the Clinical Laboratory (an 18-Month Evaluation). P. P. Bosshard, S. Abels, R. Zbinden, E. C. Böttger, and M. Altwegg,
J Clin Microbiol. September 2003, 41(9), 4134-4140.
2001
Mycobacterium doricum sp. nov. Tortoli E, Piersimoni C, Kroppenstedt RM, Montoya-Burgos JI, Reischl U, Giacometti A, Emler S,
Int J Syst Evol Microbiol. November 2001, 51(6), 2007-2012.
Burden of Unidentifiable Mycobacteria in a Reference Laboratory. Enrico Tortoli, Alessandro Bartoloni, Erik C. Böttger, Stefan Emler, Carlo Garzelli, Enrico Magliano, Antonia Mantella, Nalin Rastogi, Laura Rindi, Claudio Scarparo, and Pasquale Urbano, J Clin Microbiol. November 2001, 39(11), 4058–4065.
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