Large-Scale Comparative Genomics Meta-Analysis of Campylobacter jejuni Isolates Reveals Low Level of Genome Plasticity

Abstract

We have used comparative genomic hybridization (CGH) on a full-genome Campylobacter jejuni microarray to examine genome-wide gene conservation patterns among 51 strains isolated from food and clinical sources. These data have been integrated with data from three previous C. jejuni CGH studies to perform a metaanalysis that included 97 strains from the four separate data sets. Although many genes were found to be divergent across multiple strains (n ‫؍‬ 350), many genes (n ‫؍‬ 249) were uniquely variable in single strains. Thus, the strains in each data set comprise strains with a unique genetic diversity not found in the strains in the other data sets. Despite the large increase in the collective number of variable C. jejuni genes (n ‫؍‬ 599) found in the meta-analysis data set, nearly half of these (n ‫؍‬ 276) mapped to previously defined variable loci, and it therefore appears that large regions of the C. jejuni genome are genetically stable. A detailed analysis of the microarray data revealed that divergent genes could be differentiated on the basis of the amplitudes of their differential microarray signals. Of 599 variable genes, 122 could be classified as highly divergent on the basis of CGH data. Nearly all highly divergent genes (117 of 122) had divergent neighbors and showed high levels of intraspecies variability. The approach outlined here has enabled us to distinguish global trends of gene conservation in C. jejuni and has enabled us to define this group of genes as a robust set of variable markers that can become the cornerstone of a new generation of genotyping methods that use genome-wide C. jejuni gene variability data.Campylobacter jejuni is a human pathogen, a commensal inhabitant of many domestic animals, and globally, the most common cause of acute bacterial enteritis (for a review, see reference 31). Two well-established serotyping methods, namely, Penner typing based on heat-stable antigens and Lior typing based on heat-labile antigens, have been in use for more than two decades to study species diversity, to track epidemiological trends, and to determine important epidemiological correlations (15,23). Technical limitations on the production of high-quality typing sera have limited the availability of these reagents. Culturing conditions can affect the expression of serotyping determinants, which affects serotyping results, and several strains are nontypeable (32). Additionally, serotype relatedness is not always indicative of genetic relatedness since members of different serotypes of C. jejuni are genetically related, despite differences in heat-stable antigen expression (16).The need for alternative subtyping schemes has been recognized, leading to the development of a number of different methods based on differences at the DNA level (i.e., genotyping). The techniques used at present range from analysis of polymorphisms in groups of housekeeping genes (multilocus sequence typing [5,26]), amplified fragment length polymorphism analysis (28), restriction fragment length polymorphism analysi...

Comparative phylogenomics of the food-borne pathogen Campylobacter jejuni reveals genetic markers predictive of infection source

“…Thus Taboada et al (14) propose large regions of the C. jejuni genome are genetically stable. Of the highly divergent genes that were identified 117 of 122 genes had divergent neighbors and showed high levels of intraspecies variability (14). Another recent study used DNA microarrays to address the issue of whether genetic markers specific to strains causing GBS could be identified.…”

“…In this particular study, algorithms were used that selected a dynamic boundary between the conserved and variable genes similar to the GACK algorithm (13). More recently, genomic comparisons of 51 strains isolated from food and clinical sources have been integrated with data from the three previous C. jejuni DNA microarray studies (10)(11)(12) to perform a metaanalysis that included 97 strains from the four separate data sets (14). In that study (14), a large proportion of the variable genes were found to be absent or divergent in single strains only, and these uniquely variable genes could be mapped to previously defined variable loci.…”

Comparative Genomics of Host-Specific Virulence in Pseudomonas syringae

“…The relative hybridization intensity at each arrayed locus corresponds to the likelihood that the gene is present in the tester strains. Bacterial CGH studies have been extraordinarily successful in quantifying genome variability 1 and characterizing the differences between pathogenic and nonpathogenic strains, but to date this approach has not been used for the large-scale identification of host-associated virulence factors (Behr et al 1999;Salama et al 2000;Hakenbeck et al 2001;Israel et al 2001;Malloff et al 2001;Perrin et al 2002;Saunders et al 2004;Taboada et al 2004;Tsolaki et al 2004;Zhong et al 2004;Lindroos et al 2005;Porwollik et al 2005;Taboada et al 2005;van Leeuwen et al 2005;Yao et al 2005).…”

Comparison of Molecular Typing Methods Useful for Detecting Clusters of Campylobacter jejuni and C. coli Isolates through Routine Surveillance

“…Full details of the CGF typing method outlined here will be published elsewhere (53a). Prospective typing markers for inclusion into the CGF typing scheme were identified by microarray-based comparative genomics (51)(52)(53) and were selected based on a binary distribution (presence or absence) in microarray data from many isolates. Of the genes that exhibited variable carriage in these isolates, 43 were subsequently selected for the development of the CGF typing method.…”

“…In this work, we have compared the results from the typing of Campylobacter isolates using PFGE; the Oxford MLST method; the Oxford flaA SVR typing method; combined MLST and flaA SVR typing (MLST ϩ flaA SVR); porA sequence typing (6,28) (http://pubmlst .org/campylobacter/); combined MLST, flaA SVR, and porA sequence typing (MLST ϩ flaA SVR ϩ porA); and comparative genomic fingerprinting (CGF), a newly developed multiplex PCR method designed to detect Campylobacter genes that were identified as having a high degree of intraspecies variability in comparative genomic hybridizations using DNA microarrays (33,51). Each method or combination of methods appeared to group isolates at different levels within the population and therefore was useful for a different purpose.…”