ARS | Publication request: Genotyping Campylobacter jejuni by comparative genome indexing: an evaluation with pulsed-field gel electrophoresis and flaA SVR sequencing

Submitted to: Foodborne Pathogens and Disease
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: February 14, 2009
Publication Date: April 1, 2009
Citation: Pittenger, L.G., Englen, M.D., Parker, C., Frye, J.G., Quinones, B., Horn, S.T., Son, I., Cray, P.J., Harrison, M.A. 2009. Genotyping Campylobacter jejuni by comparative genome indexing: an evaluation with pulsed-field gel electrophoresis and flaA SVR sequencing. Foodborne Pathogens and Disease. 6(3):337-349.

Interpretive Summary: Campylobacter jejuni is a common causative agent of bacterial gastroenteritis throughout the world. The development of improved molecular methods for tracing the sources of this ubiquitous pathogen is an essential component in controlling human illness caused by C. jejuni. In this study, a new genetic typing tool called comparative genome indexing (CGI) using DNA microarrays for analyzing the whole genome of test strains was evaluated and compared to two standard methods, pulsed-field gel electrophoresis (PFGE) and flaA short variable region sequencing (flaA SVR typing). A group of geographically diverse C. jejuni strains were selected from a collection of cattle and chicken isolates, and were typed by all three methods. The results were then analyzed using a specialized software program. We found that CGI assigned a unique genotype to each isolate unlike PFGE and flaA SVR which typed some strains as identical. However, there was a high degree of correspondence between the CGI results and the C. jejuni strains typed as identical by PFGE and flaA SVR, indicating the potential value of CGI as a more informative substitute for PFGE or flaA SVR. We conclude that CGI offers a highly effective and informative means of identifying unique strains which enhances our understanding the epidemiology and population genetics of C. jejuni

Technical Abstract: Aims: Comparative genome indexing (CGI) using whole-genome DNA microarrays was evaluated as a means of genotying Campylobacter jejuni relative to two standard methods, pulsed-field gel electrophoresis (PFGE) and flaA short variable region sequencing (flaA SVR typing). Methods and Results: Thirty-six geographically diverse C. jejuni strains were selected from a collection of cattle and chicken isolates. Data from all 36 isolates for each of the three typing methods were analyzed using the BioNumerics® software program. Comparative genome indexing assigned a unique type to each strain while PFGE and flaA SVR identified 29 and 35 different types, respectively. Eleven strains (30.6% of all those tested) showed a high degree of congruence by all three typing methods. Conclusions: The highest discrimination among the isolates was provided by CGI. The congruence of CGI for C. jejuni strains typed as identical by PFGE or flaA SVR indicates the potential value of CGI as a more informative substitute for either method. Significance and Impact of Study: Campylobacter jejuni is a common causative agent of bacterial gastroenteritis throughout the world. The development of CGI as a molecular typing tool for C. jejuni offers a highly effective and informative means of further understanding the epidemiology and population genetics of this ubiquitous pathogen.