Comparative Genomic Analysis of Campylobacter jejuni Strains Reveals Diversity Due to Genomic Elements Similar to Those Present in C. jejuni Strain RM1221

Abstract

Analysis of the complete genomic sequence of Campylobacter jejuni strain RM1221 identified four large genomic elements, Campylobacter jejuni-integrated elements (CJIEs), that were absent from C. jejuni strain NCTC 11168. To further investigate the genomic diversity of Campylobacter, we conducted a comparative genomic analysis from a collection of 67 C. jejuni and 12 Campylobacter coli strains isolated from various geographical locations and clinical and veterinary sources. Utilizing PCR, we demonstrated that 55% of the C. jejuni strains examined were positive for at least one RM1221-like genomic element and 27% were positive for two or more of these CJIEs. Furthermore, many C. coli strains were positive for either genomic element CJIE1 or CJIE3. To simultaneously assess for the presence or absence of several genes that comprise the various CJIEs, we developed a multistrain C. jejuni DNA microarray that contained most of the putative coding sequences for strains NCTC 11168 and RM1221. A comparative genomic hybridization (CGH) analysis of 35 of the 67 C. jejuni strains confirmed the presence of genomic elements similar to those in strain RM1221. Interestingly, the DNA microarray analysis demonstrated that these genomic elements in the other C. jejuni strains often exhibited modular patterns with some regions of the CJIEs present and other regions either absent or highly divergent compared to strain RM1221. Our CGH method also identified 18 other intraspecies hypervariable regions, such as the capsule and lipooligosaccharide biosynthesis regions. Thus, the inclusion of genes from these integrated genomic elements and the genes from the other intraspecies hypervariable regions contributes to a better assessment of the diversity in C. jejuni and may increase the usefulness of DNA microarrays as an epidemiological genotyping tool. Finally, we also showed that in CJIE1, a Campylobacter Mu-like phage, is located differentially in other strains of C. jejuni, suggesting that it may integrate essentially randomly.

Temperate Bacteriophages Affect Pulsed-Field Gel Electrophoresis Patterns of Campylobacter jejuni

“…These results were not unexpected, given that isolates 00-2544 and 00-2856 have different PFGE patterns and that Southern blots of PFGE gels indicate that the bacteriophage was present in a different band. The results are also consistent with those of Parker et al, who determined that CMLP1 is differentially located in a number of C. jejuni isolates (16). Altogether, these data suggest that CMLP1 inserts randomly into the chromosome and may have the potential to translocate.…”

Nucleases Encoded by the Integrated Elements CJIE2 and CJIE4 Inhibit Natural Transformation of Campylobacter jejuni

“…Nine genes hybridized with genes of CJIE4; seven of these genes are located on a module also present in CJIE2 and are indistinguishable by comparative genomic hybridization (25).…”

“…Briefly, a whole C. jejuni genome open reading frame (ORF)-based DNA array, consisting of 1,530 ORFs (94%) from the naturally transformable strain NCTC 11168 and 227 unique ORFs from the nonnaturally transformable strain RM1221, was hybridized with chromosomal DNA isolated from six naturally transformable C. jejuni strains and 20 nonnaturally transformable strains. The microarrays were scanned and analyzed as described previously, and the status of a gene (present, divergent, or absent) was defined using comparative genomic indexing (13,25).…”

Functional Characterization of Excision Repair and RecA-Dependent Recombinational DNA Repair in Campylobacter jejuni

“…At the population level, C. jejuni is genetically highly diverse (11,60,62), which may facilitate bacterial environmental adaptation. Genetic diversity in C. jejuni is generated via horizontal gene transfer (9,10,51), intragenomic rearrangements (9), and the presence of numerous stretches of nucleotide repeats that are prone to mispairing during DNA replication (26,41,42,46). In addition, the genomic DNA is probably subject to various types of damage caused by a range of endogenous and environmental factors which may cause single-or double-strand breaks, nucleotide modifications, abasic sites, bulky adducts, and mismatches (14).…”