TY - JOUR
T1 - Comparison of pulsed field gel electrophoresis and repetitive sequence polymerase chain reaction as genotyping methods for detection of genetic diversity and inferring transmission of Salmonella
AU - Weigel, Ronald M.
AU - Qiao, Baozhen
AU - Teferedegne, Belete
AU - Suh, Dong Kyun
AU - Barber, David A.
AU - Isaacson, Richard E.
AU - White, Bryan A.
N1 - Funding Information:
This research was supported by funding from the Illinois Council for Food and Agricultural Research and the Agricultural Experiment Station of the University of Illinois, and from the USDA-NRI program on Epidemiological Approaches to Food Safety. Ping Gao and Svetlana Kocherginskaya provided technical assistance.
Copyright:
Copyright 2008 Elsevier B.V., All rights reserved.
PY - 2004/6/3
Y1 - 2004/6/3
N2 - Pulsed field gel electrophoresis (PFGE) using restriction enzymes AvrII, SpeI, and XbaI, and repetitive sequence polymerase chain reaction (Rep-PCR) using BOX, ERIC, and REP primers, were compared with respect to their ability to detect genetic differences among 68 Salmonella isolates from nine Illinois swine farms. Both genotyping methods had high reproducibility of fragment numbers (reliability>0.9) and sizes (reliability>0.85), and produced approximately the same number of DNA fragments, but Rep-PCR fragment profiles had considerably greater variation. Genetic distances between isolates were calculated from fragment size matching. There was good agreement between the genetic distance matrices for the composite (3-enzyme and 3-primer) methods (Mantel's r=0.83). PFGE detected slightly greater variation in genetic distances among isolates, but failed to differentiate seven pairs of isolates, three of which were sampled at least 1 month apart and therefore unlikely to be truly identical genetically. In contrast, Rep-PCR identified no isolates as genetically identical. In cluster analyses based on genetic distances, there were moderate differences between PFGE and Rep-PCR (about 2/3 agreement in tight cluster membership). Both PFGE and Rep-PCR were able to differentiate isolates of the same serotype. However, some serotypes (Agona, Anatum, Derby, Infantis, Worthington) were distributed across clusters. There was less agreement between individual primer/enzyme and composite results for Rep-PCR than for PFGE. This greater independence of results for individual primers for Rep-PCR accounted in part for the greater discriminative ability of the composite method. Both composite methods indicated that most Salmonella transmission occurred within a farm and that there was no preference for transmission between specific ecological compartments. Given the equally high reliability of both genotyping methods, the greater discriminative ability of Rep-PCR recommends it as the preferred method for precise detection of transmission links.
AB - Pulsed field gel electrophoresis (PFGE) using restriction enzymes AvrII, SpeI, and XbaI, and repetitive sequence polymerase chain reaction (Rep-PCR) using BOX, ERIC, and REP primers, were compared with respect to their ability to detect genetic differences among 68 Salmonella isolates from nine Illinois swine farms. Both genotyping methods had high reproducibility of fragment numbers (reliability>0.9) and sizes (reliability>0.85), and produced approximately the same number of DNA fragments, but Rep-PCR fragment profiles had considerably greater variation. Genetic distances between isolates were calculated from fragment size matching. There was good agreement between the genetic distance matrices for the composite (3-enzyme and 3-primer) methods (Mantel's r=0.83). PFGE detected slightly greater variation in genetic distances among isolates, but failed to differentiate seven pairs of isolates, three of which were sampled at least 1 month apart and therefore unlikely to be truly identical genetically. In contrast, Rep-PCR identified no isolates as genetically identical. In cluster analyses based on genetic distances, there were moderate differences between PFGE and Rep-PCR (about 2/3 agreement in tight cluster membership). Both PFGE and Rep-PCR were able to differentiate isolates of the same serotype. However, some serotypes (Agona, Anatum, Derby, Infantis, Worthington) were distributed across clusters. There was less agreement between individual primer/enzyme and composite results for Rep-PCR than for PFGE. This greater independence of results for individual primers for Rep-PCR accounted in part for the greater discriminative ability of the composite method. Both composite methods indicated that most Salmonella transmission occurred within a farm and that there was no preference for transmission between specific ecological compartments. Given the equally high reliability of both genotyping methods, the greater discriminative ability of Rep-PCR recommends it as the preferred method for precise detection of transmission links.
KW - Genotyping
KW - Salmonella sp.
KW - Swine
KW - Transmission
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U2 - 10.1016/j.vetmic.2004.02.009
DO - 10.1016/j.vetmic.2004.02.009
M3 - Article
C2 - 15145499
AN - SCOPUS:2442555358
SN - 0378-1135
VL - 100
SP - 205
EP - 217
JO - Veterinary Microbiology
JF - Veterinary Microbiology
IS - 3-4
ER -