Multilaboratory validation study of standardized multiple-locus variable-number tandem repeat analysis protocol for shiga toxin-producing Escherichia coli O157: a novel approach to normalize fragment size data between capillary electrophoresis platforms.
The PulseNet USA subtyping network recently established a standardized protocol for multiple-locus variable-number tandem repeat analysis (MLVA) to characterize Shiga toxin-producing Escherichia coli O157. To enable data comparisons from different laboratories in the same database, reproducibility and high quality of the data must be ensured. The aim of this study was to test the robustness and reproducibility of the proposed standardized protocol by subjecting it to a multilaboratory validation process and to address any discrepancies that may have arisen from the study. A set of 50 strains was tested in 10 PulseNet participating laboratories that used capillary electrophoresis instruments from two manufacturers. Six out of the 10 laboratories were able to generate correct MLVA types for 46 (92%) or more strains. The discrepancies in MLVA type assignment were caused mainly by difficulties in optimizing polymerase chain reactions that were attributed to technical inexperience of the staff and suboptimal quality of reagents and instrumentation. It was concluded that proper training of staff must be an integral part of technology transfer. The interlaboratory reproducibility of fragment sizing was excellent when the same capillary electrophoresis platform was used. However, sizing discrepancies of up to six base pairs for the same fragment were detected between the two platforms. These discrepancies were attributed to different dye and polymer chemistries employed by the manufacturers. A novel software script was developed to assign alleles based on two platform-specific (Beckman Coulter CEQ8000 and Applied Biosystems Genetic Analyzer 3130xl) look-up tables containing fragment size ranges for all alleles. The new allele assignment method was validated at the PulseNet central laboratory using a diverse set of 502 Shiga toxin-producing Escherichia coli O157 isolates. The validation confirmed that the script reliably assigned the same allele for the same fragment regardless of the platform used to size the fragment.
Hyytia-Trees
Eija
E
Centers for Disease Control and Prevention, Atlanta, Georgia 30333, USA. ehyytia-trees@cdc.gov
Lafon
Patricia
P
Vauterin
Paul
P
Ribot
Efrain M
EM
D000483:Alleles; D001483:Base Sequence; D053938:DNA Fragmentation; D004269:DNA, Bacterial / Q000032:analysis*; D019075:Electrophoresis, Capillary / Q000295:instrumentation / Q000379:methods / Q000592:standards*; D004927:Escherichia coli Infections / Q000382:microbiology*; D019453:Escherichia coli O157 / Q000145:classification* / Q000235:genetics* / Q000378:metabolism; D005516:Food Microbiology; D006801:Humans; D007753:Laboratories / Q000592:standards; D010802:Phylogeny; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D022603:Shiga Toxins / Q000096:biosynthesis; D020080:Tandem Repeat Sequences
D004269:DNA, Bacterial; D022603:Shiga Toxins