Predicting Salmonella enterica serotypes by repetitive sequence-based PCR

Wise, Mark G.; Siragusa, Gregory R.; Plumblee, Jodie R.; Healy, Mimi; Fedorka–Cray, Paula J.; Seal, Bruce S.

doi:10.1016/j.mimet.2008.09.006

Cited by 61 publications

(50 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For banding-pattern-based subtyping methods, the ability to correctly predict serovars ranged from 65% to 76% for isolates representing the 40 most common Salmonella serovars, and by comparison, MLST correctly predicted the serovars of 91% of these isolates. Previous studies typically only tested the ability of one or a few subtyping methods to predict serovars in isolates representing limited diversity and a small number of serovars (19,21,22,(46)(47)(48). For example, Gaul et al (47) compared one banding-pattern method, PFGE, to traditional serotyping on a collection of 674 swine Salmonella isolates.…”

Section: Discussionmentioning

confidence: 99%

“…All DNA samples were amplified using the DiversiLab Salmonella kit for DNA fingerprinting (bioMérieux, Inc., Durham, NC), according to the manufacturer's instructions. Analysis of rep-PCR patterns was conducted as described previously (21), using DiversiLab software version 3.4. The "top match" feature of the software was utilized, and a query sample that matched a serovar library entry at Ͼ85% was considered to represent a positive identification.…”

Section: Methodsmentioning

confidence: 99%

“…In addition to PFGE (16,17), different ribotyping approaches (18)(19)(20), repetitive extragenic palindromic sequencebased PCR (rep-PCR) (21,22), multilocus sequence typing (MLST) (23,24), and molecular typing based on genomic markers (25)(26)(27)(28) have been investigated for their abilities to replace or complement traditional serotyping. While many of these methods have been able to reliably predict a limited set of serovars, they still lack widespread adoption, likely due to the requirements for specialized equipment, as well as a lack of proven reliability for predicting Salmonella serovars.…”

mentioning

confidence: 99%

See 2 more Smart Citations

Comparison of Typing Methods with a New Procedure Based on Sequence Characterization for Salmonella Serovar Prediction

et al. 2013

View full text Add to dashboard Cite

bAs the development of molecular serotyping approaches is critical for Salmonella spp., which include >2,600 serovars, we performed an initial evaluation of the ability to identify Salmonella serovars using (i) different molecular subtyping methods and (ii) a newly implemented combined PCR-and sequencing-based approach that directly targets O-and H-antigen-encoding genes. Initial testing was performed using 46 isolates that represent the top 40 Salmonella serovars isolated from human and nonhuman sources, as reported by the U.S. Centers for Disease Control and Prevention and the World Health Organization. Multilocus sequence typing (MLST) was able to accurately predict the serovars for 42/46 isolates and showed the best ability to predict serovars among the subtyping methods tested. Pulsed-field gel electrophoresis (PFGE), ribotyping, and repetitive extragenic palindromic sequence-based PCR (rep-PCR) were able to accurately predict the serovars for 35/46, 34/46, and 30/46 isolates, respectively. Among the methods, S. enterica subsp. enterica serovars 4,5,12:i:؊, Typhimurium, and Typhimurium var. 5؊ were frequently not classified correctly, which is consistent with their close phylogenetic relationship. To develop a PCR-and sequence-based serotyping approach, we integrated available data sources to implement a combination PCR-based O-antigen screening and sequencing of internal fliC and fljB fragments. This approach correctly identified the serovars for 42/46 isolates in the initial set representing the most common Salmonella serovars, as well as for 54/63 isolates representing less common Salmonella serovars. Our study not only indicates that different molecular approaches show the potential to allow for rapid serovar classification of Salmonella isolates, but it also provides data that can help with the selection of molecular serotyping methods to be used by different laboratories.

show abstract

Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

See 1 more Smart Citation

Comparison of Typing Methods with a New Procedure Based on Sequence Characterization for Salmonella Serovar Prediction

et al. 2013

View full text Add to dashboard Cite

show abstract

“…Repetitive extragenic palindromic sequence-based PCR (REP-PCR), has also been used to investigate Salmonella diversity (21,22). In the pres- (28,29).…”

mentioning

confidence: 99%

Salmonella enterica Diversity in Central Californian Coastal Waterways

Walters

González-Escalona

Son

et al. 2013

Appl Environ Microbiol

View full text Add to dashboard Cite

bSalmonella enterica is one of the most important bacterial enteric pathogens worldwide. However, little is known about its distribution and diversity in the environment. The present study explored the diversity of 104 strains of Salmonella enterica isolated over 2 years from 12 coastal waterways in central California. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing were used to probe species diversity. Seventy-four PFGE patterns and 38 sequence types (STs) were found, including 18 newly described STs. Nineteen of 25 PFGE patterns were indistinguishable from those of clinical isolates in PulseNet. The most common ST was consistent with S. enterica serovar Typhimurium, and other frequently detected STs were associated with the serovars Heidelberg and Enteritidis; all of these serovars are important etiologies of salmonellosis. An investigation into S. enterica biogeography was conducted at the level of ST and subspecies. At the ST and subspecies level, we found a taxon-time relationship but no taxon-area or taxon-environmental distance relationships. STs collected during wet versus dry conditions tended to be more similar; however, STs collected from waterways adjacent to watersheds with similar land covers did not tend to be similar. The results suggest that the lack of dispersal limitation may be an important factor affecting the diversity of S. enterica in the region.

show abstract

“…Wise et al (21) developed a laboratory method utilizing repetitive sequence-based PCR to predict Salmonella enterica serotypes, while several others have reported a good correlation between PFGE patterns and Salmonella serotypes (2, 7, 13). Gaul et al (7) suggested using hierarchical cluster analysis of PFGE with XbaI restriction as a possible alternative method for screening and identifying Salmonella serotypes.…”

Section: Discussionmentioning

confidence: 99%

Evaluation of Pulsed-Field Gel Electrophoresis Profiles for Identification of Salmonella Serotypes

Zou¹,

Lin²,

Foley

et al. 2010

J Clin Microbiol

View full text Add to dashboard Cite

Pulsed-field gel electrophoresis (PFGE) is a standard typing method for isolates from Salmonella outbreaks and epidemiological investigations. Eight hundred sixty-six Salmonella enterica isolates from eight serotypes, including Heidelberg (n ‫؍‬ 323), Javiana (n ‫؍‬ 200), Typhimurium (n ‫؍‬ 163), Newport (n ‫؍‬ 93), Enteritidis (n ‫؍‬ 45), Dublin (n ‫؍‬ 25), Pullorum (n ‫؍‬ 9), and Choleraesuis (n ‫؍‬ 8), were subjected to PFGE, and their profiles were analyzed by random forest classification and compared to conventional hierarchical cluster analysis to determine potential predictive relationships between PFGE banding patterns and particular serotypes. Cluster analysis displayed only the underlying similarities and relationships of the isolates from the eight serotypes. However, for serotype prediction of a nonserotyped Salmonella isolate from its PFGE pattern, random forest classification provided better accuracy than conventional cluster analysis. Discriminatory DNA band class markers were identified for distinguishing Salmonella serotype Heidelberg, Javiana, Typhimurium, and Newport isolates.

show abstract

Predicting Salmonella enterica serotypes by repetitive sequence-based PCR

Cited by 61 publications

References 31 publications

Comparison of Typing Methods with a New Procedure Based on Sequence Characterization for Salmonella Serovar Prediction

Comparison of Typing Methods with a New Procedure Based on Sequence Characterization for Salmonella Serovar Prediction

Salmonella enterica Diversity in Central Californian Coastal Waterways

Evaluation of Pulsed-Field Gel Electrophoresis Profiles for Identification of Salmonella Serotypes

Contact Info

Product

Resources

About