Comparative genomic analysis of clinical strains of Campylobacter jejuni from South Africa

Abstract

Background: Campylobacter jejuni is a common cause of acute gastroenteritis and is also associated with the post-infectious neuropathies, Guillain-Barré and Miller Fisher syndromes. In the Cape Town area of South Africa, C. jejuni strains with Penner heat-stable (HS) serotype HS:41 have been observed to be overrepresented among cases of Guillain-Barré syndrome. The present study examined the genetic content of a collection of 32 South African C. jejuni strains with different serotypes, including 13 HS:41 strains, that were recovered from patients with enteritis, Guillain-Barré or Miller Fisher syndromes. The sequence-based typing methods, multilocus sequence typing and DNA microarrays, were employed to potentially identify distinguishing features within the genomes of these C. jejuni strains with various disease outcomes.

Methodology/principal findings: Comparative genomic analyses demonstrated that the HS:41 South African strains were clearly distinct from the other South African strains. Further DNA microarray analysis demonstrated that the HS:41 strains from South African patients with the Guillain-Barré syndrome or enteritis were highly similar in gene content. Interestingly, the South African HS:41 strains were distinct in gene content when compared to HS:41 strains from other geographical locations due to the presence of genomic islands, referred to as Campylobacter jejuni integrated elements (CJIEs). Only the integrated element CJIE1, a Campylobacter Mu-like prophage, was present in the South African HS:41 strains whereas this element was absent in two closely-related HS:41 strains from Mexico. A more distantly-related HS:41 strain from Canada possessed both integrated elements CJIE1 and CJIE2.

Conclusion/significance: These findings demonstrate that CJIEs may contribute to the differentiation of closely-related C. jejuni strains. In addition, the presence of bacteriophage-related genes in CJIE1 may contribute to the genomic diversity of C. jejuni strains. This comparative genomic analysis of C. jejuni provides fundamental information that potentially could lead to improved methods for analyzing the epidemiology of disease outbreaks.

Figure 1. Dendrogram of Campylobacter jejuni sequence types, including clinical strains from South Africa, Mexico and Canada.

The dendrogram was constructed by using the neighbor-joining algorithm and the Kimura two-parameter distance estimation method. Bootstrap values of >75%, generated from 500 replicates, are shown at the nodes. The scale bar represents substitutions per site.

Figure 2. Genome comparison of Campylobacter jejuni clinical strains by DNA microarrays analysis.

An average linkage hierarchical clustering of the C. jejuni strains with a distance score scale bar was compiled in GeneSpring version 7.3 with the standard correlation and bootstrapping (see Materials and Methods). The gene status based on cutoff values of absence and presence predictions is shown color-coded: blue, present; light blue, divergent; red, highly divergent or absent; white, no data. C. jejuni strains from South Africa with HS∶41 serotype (yellow), with other serotypes (green), or strains with HS∶41 serotype from Mexico and Canada (white) are designated vertically across the bottom. GBS-associated strains are annotated with stars; MFS-associated strains are annotated with diamonds. The four C. jejuni-integrated elements (CJIEs) and the assigned MLST sequence type (ST) for each strain cluster is indicated.

Figure 3. Patterns of presence, absence or divergence in the 18 hypervariable regions in Campylobacter jejuni strains.

A detailed genomic analysis of the 18 hypervariable regions (Table 2) was compiled in GeneSpring version 7.3 with the standard correlation and bootstrapping (see Materials and Methods). Each panel represents a hypervariable region, and each column corresponds to a C. jejuni strain designated vertically across the bottom, as described in the legend to Figure 2. The gene status based on cutoff values of absence and presence predictions is shown color-coded: blue, present; light blue, divergent; red, highly divergent or absent; white, no data.

Figure 4. Patterns of presence, absence or divergence in the Campylobacter jejuni-integrated elements.

A detailed genomic analysis of the genomic integrated elements CJIE1 (top) and CJIE2 (bottom) was compiled in GeneSpring version 7.3 with the standard correlation and bootstrapping (see Materials and Methods). Each column corresponds to a C. jejuni strain designated vertically across the bottom, as described in the legend to Figure 2. The gene status based on cutoff values of absence and presence predictions is shown color-coded: blue, present; light blue, divergent; red, highly divergent or absent; white, no data.