title: Comparison of Biolog GEN III MicroStation semi-automated bacterial identification system with matrix-assisted laser desorption ionization-time of flight mass spectrometry and 16S ribosomal RNA gene sequencing for the identification of bacteria of veterinary interest.
abstract: Recent advances in phenotypic and chemotaxonomic methods have improved the ability of systems to resolve bacterial identities at the species level. Key to the effective use of these systems is the ability to draw upon databases which can be augmented with new data gleaned from atypical or novel isolates. In this study we compared the performance of the Biolog GEN III identification system (hereafter, GEN III) with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and 16S rRNA gene sequencing in the identification of isolates of veterinary interest. The use of strains that had proven more difficult to identify by routine methods was designed to test the systems' abilities at the extremes of their performance range. Over an 18month period, 100 strains were analysed by all three methods. To highlight the importance of identification to species level, a weighted scoring system was devised to differentiate the capacity to identify at genus and species levels. The overall relative weighted scores were 0.869:0.781:0.769, achieved by 16S rRNA gene sequencing, GEN III and MALDI-TOF MS respectively, when compared to the 'gold standard'. Performance to the genus level was significantly better using 16S rRNA gene sequencing; however, performance to the species level was similar for all three systems.
authors.affiliation: Animal Health and Veterinary Laboratories Agency-Penrith Regional Laboratory, Penrith, Cumbria CA11 9RR, United Kingdom. Electronic address: peter.wragg@ahvla.gsi.gov.uk.
authors.forename: P
authors.initials: P
authors.lastname: Wragg
authors.affiliation: Department of Bacteriology, Animal Health and Veterinary Laboratories Agency-Weybridge, New Haw, Addlestone, Surrey KT15 3NB, United Kingdom.
authors.forename: L
authors.initials: L
authors.lastname: Randall
authors.affiliation: Department of Bacteriology, Animal Health and Veterinary Laboratories Agency-Weybridge, New Haw, Addlestone, Surrey KT15 3NB, United Kingdom.
authors.forename: A M
authors.initials: AM
authors.lastname: Whatmore
mesh_terms: D000818:Animals; D057205:Automation, Laboratory / Q000379:methods; D001419:Bacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification* / Q000378:metabolism; D001424:Bacterial Infections / Q000175:diagnosis / Q000662:veterinary*; D001431:Bacteriological Techniques / Q000379:methods*; D005838:Genotype; D055432:Metabolomics / Q000379:methods*; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D010641:Phenotype; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA / Q000379:methods; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization / Q000379:methods*; D014730:Veterinary Medicine / Q000379:methods*
chemical_list: D012336:RNA, Ribosomal, 16S
keywords: 16S ribosomal RNA; Biolog GEN III; MALDI-TOF MS; Veterinary clinical bacteriology