Document Detail


Evaluation of whole-genome sequencing as a genotyping tool for Campylobacter jejuni in comparison with pulsed-field gel electrophoresis and flaA typing.
MedLine Citation:
PMID:  23300325     Owner:  NLM     Status:  In-Data-Review    
Abstract/OtherAbstract:
Campylobacter jejuni is a leading cause of foodborne illness, with poultry and poultry products being leading sources of infection. Epidemiological efforts to trace Campylobacter can be challenging because of the extreme genetic diversity of this bacterium relative to other foodborne pathogens. To enhance tracking and epidemiological efforts, whole-genome sequencing has been used for other foodborne pathogens but not yet been evaluated for practicality with Campylobacter. Thus, the purpose of this study was to evaluate whole-genome sequencing as a genotyping method for C. jejuni by comparing it with 2 commonly used genotyping methods, namely pulsed-field gel electrophoresis (PFGE) and flaA typing. Whole-genome sequence data were generated using the Roche-454 sequencing platform to map Campylobacter strains (VOL_3, VOL_5, VOL_8, VOL_11, and VOL_20) isolated from conventional and organic poultry. Five additional isolates with published genomes were also compared. The PFGE profiles were created using Sma I digestion. For the flaA short variable region sequencing, standard PCR methods were used and high-quality Sanger reads were generated. The PFGE profiles of strains VOL_3 and VOL_11 were found to be indistinguishable, and strain VOL_20 was found indistinguishable from NCTC 11168. Whole-genome comparisons between strains VOL_20 and 11168 were in agreement with the obtained PFGE profiles, as these 2 isolates had very similar genome sizes, a number of shared genes (1,580), and very similar % G-C content (30.6). Of the 8 strains, 2 strains (VOL_3 and VOL_11) had identical flaA types. Whole-genome sequencing was the most discriminatory of the typing methods. However, the cost and time effort needed to sequence and assemble the genomes may hinder efforts, and therefore, we conclude that more bioinformatics tools need to be developed for whole-genome sequencing to be used as an epidemiological tool.
Authors:
S Pendleton; I Hanning; D Biswas; S C Ricke
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Publication Detail:
Type:  Journal Article    
Journal Detail:
Title:  Poultry science     Volume:  92     ISSN:  0032-5791     ISO Abbreviation:  Poult. Sci.     Publication Date:  2013 Feb 
Date Detail:
Created Date:  2013-01-09     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  0401150     Medline TA:  Poult Sci     Country:  United States    
Other Details:
Languages:  eng     Pagination:  573-80     Citation Subset:  IM    
Affiliation:
Department of Food Science and Technology, and.
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