Repeatability and reproducibility of ribotyping and its computer interpretation.
Many molecular typing methods are difficult to interpret because their repeatability (within-laboratory variance) and reproducibility (between-laboratory variance) have not been thoroughly studied. In the present work, ribotyping of coryneform bacteria was the basis of a study involving within-gel and between-gel repeatability and between-laboratory reproducibility (two laboratories involved). The effect of different technical protocols, different algorithms, and different software for fragment size determination was studied. Analysis of variance (ANOVA) showed, within a laboratory, that there was no significant added variance between gels. However, between-laboratory variance was significantly higher than within-laboratory variance. This may be due to the use of different protocols. An experimental function was calculated to transform the data and make them compatible (i.e., erase the between-laboratory variance). The use of different interpolation algorithms (spline, Schaffer and Sederoff) was a significant source of variation in one laboratory only. The use of either Taxotron (Institut Pasteur) or GelCompar (Applied Maths) was not a significant source of added variation when the same algorithm (spline) was used. However, the use of Bio-Gene (Vilber Lourmat) dramatically increased the error (within laboratory, within gel) in one laboratory, while decreasing the error in the other laboratory; this might be due to automatic normalization attempts. These results were taken into account for building a database and performing automatic pattern identification using Taxotron. Conversion of the data considerably improved the identification of patterns irrespective of the laboratory in which the data were obtained.
Lefresne
Gwénola
G
UMR Génie et Microbiologie des Procédés Alimentaires INRA-INAPG, Institut National de la Recherche Agronomique, 78850 Thiverval-Grignon, France.
Latrille
Eric
E
Irlinger
Françoise
F
Grimont
Patrick A D
PA
D000465:Algorithms; D001173:Arthrobacter / Q000235:genetics; D002954:Citrobacter / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D003627:Data Interpretation, Statistical; D004587:Electrophoresis, Agar Gel; D009693:Nucleic Acid Hybridization; D012335:RNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D015203:Reproducibility of Results; D021521:Ribotyping / Q000379:methods* / Q000592:standards; D012984:Software / Q000592:standards
D004269:DNA, Bacterial; D012335:RNA, Ribosomal