Fimbrial phase variation: stochastic or cooperative?

Heterologous expression of the Salmonella enterica serovar Paratyphi A stk fimbrial operon suggests a potential for repeat sequence-mediated low-frequency phase variation

Fimbriae mediate adhesion of Salmonella enterica organisms to the intestinal epithelium, which is an essential step in the pathogenesis process preceding invasion and/or systemic spread. In addition, Salmonella fimbrial genes transcripts were detected in the blood samples from Salmonella infected human patients, which supports the proposal that fimbriae play a role in invasive Salmonella infections. In this study, BlastN-based interrogation of the NCBI bacterial genome database and PCR investigation of Salmonella serovars have shown that the S. Paratyphi A stkF gene and/or the whole stk fimbrial gene cluster is present in about ~30% of S. enterica serovars investigated up to date. Furthermore, bioinformatics and phenotypic characterization have revealed that the stk fimbrial operon belongs to the chaperone/usher-γ4- fimbrial clade and that it encodes a mannose-sensitive hemagglutinating fimbrial structure. The latter trait is typical of type 1 fimbriae, in which fimbrial phase variation is common. The observed intragenic, 26 bp tandem repeat triplication event in stkF would suggest that slipped-strand mispairing and/or recombination within a signature stkF-borne tandem repeat motif as a likely mechanism for a form of low-frequency phase switching at the translational level leading to allelic OFF forms, hence the inability of production and/or absence of fimbriae by EM-examination on E. coli HB101/pUCstk-stkF_OFFv2. The in vitro profile of marked anti-StkF-mediated opsonophagocytosis and complement-mediated killing activity observed coupled with the mice immunogenicity profile strongly supports further investigation of StkF as a potential Salmonella vaccine candidate.

Genome-wide detection of conservative site-specific recombination in bacteria

The ability of clonal bacterial populations to generate genomic and phenotypic heterogeneity is thought to be of great importance for many commensal and pathogenic bacteria. One common mechanism contributing to diversity formation relies on the inversion of small genomic DNA segments in a process commonly referred to as conservative site-specific recombination. This phenomenon is known to occur in several bacterial lineages, however it remains notoriously difficult to identify due to the lack of conserved features. Here, we report an easy-to-implement method based on high-throughput paired-end sequencing for genome-wide detection of conservative site-specific recombination on a single-nucleotide level. We demonstrate the effectiveness of the method by successfully detecting several novel inversion sites in an epidemic isolate of the enteric pathogen Clostridium difficile. Using an experimental approach, we validate the inversion potential of all detected sites in C. difficile and quantify their prevalence during exponential and stationary growth in vitro. In addition, we demonstrate that the master recombinase RecV is responsible for the inversion of some but not all invertible sites. Using a fluorescent gene-reporter system, we show that at least one gene from a two-component system located next to an invertible site is expressed in an on-off mode reminiscent of phase variation. We further demonstrate the applicability of our method by mining 209 publicly available sequencing datasets and show that conservative site-specific recombination is common in the bacterial realm but appears to be absent in some lineages. Finally, we show that the gene content associated with the inversion sites is diverse and goes beyond traditionally described surface components. Overall, our method provides a robust platform for detection of conservative site-specific recombination in bacteria and opens a new avenue for global exploration of this important phenomenon.