Recent journal articles and posters citing the use of SmartGene's technology are listed below. Please use the links to the left to access archived publications, organized by year.
2012
Evaluation of Nucleic Acid Sequencing of the D1/D2 Region of the Large Subunit of the 28S rDNA and the Internal Transcribed Spacer Region Using SmartGene IDNS for Identification of Filamentous Fungi in a Clinical Laboratory. N. Kwiatkowski, W. Babkier, W. Merz, K. Carroll, and S. Zhang. The Johns Hopkins Hospital Microbiology laboratory and the Division of Medical Microbiology, Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland. The Journal of Molecular Diagnostics, Vol. 14, No. 4, July 2012. (Accepted Feb 2012, available online May 2012.) (Click here to request additional information.)
Citation: “... In this study, we evaluated DNA sequencing of the D1/D2 region of the large subunit of the 28S ribosomal RNA gene and the internal transcribed spacer (ITS) region using SmartGene ... for the identification of a broad range of commonly encountered filamentous fungi. The [SmartGene] proofreaders were used to upload, align, and edit fragments, and the resultant sequences were interpreted using the quality-controlled [SmartGene] database. The results were compared with reference identifications using conventional phenotypic methods or ITS DNA sequences obtained from GenBank if phenotypic identifications were inconclusive. ...Correct identification was achieved for 100% ... of the isolates when applying both the D1/D2 and ITS targets. In summary, DNA sequencing using [SmartGene] software provides a rapid, accurate, and reliable tool for the identification of filamentous fungi in a clinical laboratory.”
The Presence of CXCR4-Using HIV-1 in Patients with Recently Diagnosed Infection: Correlates and Evidence for Transmission. K. Chalmet, K. Dauwe, L. Foquet, F. Baatz, C. Seguin-Devaux, B. Van Der Gucht, D. Vogelaers, L. Vandekerckhove, J. Plum, and C. Verhofstede. AIDS Reference Laboratory, AIDS Reference Center, Ghent University, Belgium, and The Laboratory of Retrovirology, CRP-Santé, Luxembourg.
The Journal of Infectious Diseases, 205 (2): 174-184, Jan 2012.
(Click here to request additional information.)
Citation: "HIV-1 subtyping was performed using PR and RT sequences and the Smartgene (IDNS) or REGA subtyping tool. ... Proofreading was performed with Smartgene (IDNS)."
2011
Genotypic Impact of Prolonged Detectable HIV Type 1 RNA Viral Load after HAART Failure in a CRF01_AE-Infected Cohort. M. Zolfo, J.M. Schapiro, V. Phan, O. Koole, S. Thai, M. Vekemans, K. Fransen, and L. Lynen. Institute of Tropical Medicine, Belgium; National Hemophilia Center, Israel; and Sihanouk Hospital Center of HOPE, Cambodia. AIDS Research and Human Retroviruses, Volume 27, Number 7, 2011, pp. 727-735. (Click here to request additional information.)
Citation: "… For viral loads above 1000 copies/ml HIV-1 reverse transcriptase, genotyping was performed using Trugene HIV-1 genotyping (Trugene, Siemens and IDNS, Smartgene). ..."
Internal transcribed spacer region sequence analysis using SmartGene IDNS software for the identification of unusual clinical yeast isolates. E.S. Slechta, S.L. Hohmann, K.E. Simmon, and K.E. Hanson. ARUP Institute for Clinical and Experimental Pathology, Salt Lake City, Utah, USA. Medical Mycology, 2011 November 22 (Epub ahead of print). (Click here to request additional information.)
Citation: “Rapid and accurate identification of clinically important yeasts is essential given their inherent differences in antifungal susceptibility. We implemented nucleic acid sequencing for those species that could not be identified by phenotypic methods. Internal Transcribed Spacer region 1 and 2 (ITS1 and ITS2) sequences were investigated using SmartGene IDNS software … Over a 2.5-year period, 2,938 specimens were evaluated. ... Of the 169 organisms that required molecular analysis, 79% were identified to species level, 19% to genus and 2% remained unresolved. ...”
Identification by 16S rRNA gene sequencing of Negativicoccus succinicivorans recovered from the blood of a patient with hemochromatosis and pancreatitis. D.L. Church, K.E. Simmon, J. Sporina, T. Lloyd, and D.B. Gregson. Calgary Laboratory Services, Alberta, Canada. J Clin Microbiol. 2011 Aug; 49(8):3082-4. (Click here to request additional information.)
Citation: "... The bacterium was identified by 16S rRNA gene sequencing and analysis using the SmartGene Integrated Database Network System software. This is the first published report of the recovery of this organism from a patient with invasive infection."
An Evaluation of the SmartGene Centroid Database for the Identification of Clinically Relevant Anerobic Gram negative Bacteria by 16S rRNA Gene Sequencing M.J. Romagnoli and K.C. Carroll. The Johns Hopkins Medical Institutions, Baltimore, MD, USA. Poster presented during the 111th General Meeting of the American Society for Microbiology, New Orleans, Louisiana, USA, May 2011. (Click here to request additional information.)
Citation: The SmartGene Centroid Database is "easy to use, rapid and simple to interpret."
Three Year Review of Mycobacterial Identification Using Partial 16S Sequence Analysis. F. Lee, K.E. Simmon, G. Smith, K. Hanson. Institute for Clinical and Experimental Pathology, ARUP Laboratories, University of Utah, Department of Pathology, Salt Lake City, Utah, USA. Poster presented during the 111th General Meeting of the American Society for Microbiology, New Orleans, Louisiana, USA, May 2011. (Click here to request additional information.)
Citation: ".... In this study we describe the spectrum of mycobacteria identified by 16S analysis in our laboratory over a 3 year period. Methods: Acid fast mycobacteria (AFB) submitted for ID between Nov 2007 and Nov 2010 were first tested with M. tuberculosis complex (MTBC) and M. avium complex (MAI) AccuProbes. Partial 16S sequence is generated for probe-negative isolates, which are compared to references using SmartGene IDNS software. ..."
Risk for Mycobacterium celatum Infection from Ferret. E. Ludwig, U. Reischl, T. Holzmann, H. Melzl, D. Janik, C. Gilch, and W. Hermanns. Ludwig-Maximilians-Universität München, Munich, Germany (E. Ludwig, D. Janik, W. Hermanns); Universitätsklinik Regensburg, Regensburg, Germany (U. Reischl, T. Holzmann, H. Melzl); and ärztliche Klinik Nürnberg Hafen, Nuremberg, Germany (C. Gilch). Emerging Infectious Diseases, Vol. 17, No. 3, pp. 553-555, March 2011. (Click here to request additional information.)
Citation: "... data were analyzed by using the Integrated Database Network System (SmartGene Services, Lausanne, Switzerland; www.smartgene.com). ..."
Ribosomal RNA Sequence Analysis of Brucella Infection misidentified as Ochrobactrum anthropi. R.T. Horvat, W. El Atrouni, K. Hammound, D. Hawkinson, S. Cowden. University of Kansas, School of Medicine, Department of Pathology and Laboratory Medicine, Department of Medicine, Division of Infectious Diseases, and ViraCor-IBT, Lee's Summit, Missouri, US. Journal of Clinical Microbiology, doi: 10.1128/JCM.01131-10, Jan 2011. (Click here to request additional information.)
Citation: "... After rRNA sequencing, all the isolates were identified as Brucella species. ... The sequences were compared to related sequences in the SmartGene 16S Eubacterial database ... This database is compiled and constantly updated from sequence data in the public domain. The integrity of the data is ensured by using specific profiles to filter out unreliable sequences. The extraction algorithm addresses the variability of the 16S rRNA gene across the bacterial kingdom. The database is frequently updated and takes into account recently described organisms. ... The Genus-level identification of this isolate assigned a 100.0% match to 25 reference Brucella sequences. There are currently 170 Brucella rRNA sequences available in the SmartGene system. ... There was little homology (<50%) to the 133 Ochrobactrum species..."
