Abstract
Salmonella is one of the primary causes of foodborne disease, especially Salmonella enterica subsp. enterica (I) which has caused ~99% of clinical salmonellosis cases for humans and domestic mammals. The flagella genes, fliC and fljB, which encode the Salmonella phase 1 and phase 2 antigens respectively, are considered as the Salmonella serotype determinant genes, and contribute to the virulence of Salmonella. However, the evolution of the two flagellin genes is still not well-understood. In this study, the fliC and fljB gene clusters were analyzed among 205 S. enterica subspecies I genomes. The dataset covered 87 different serovars of S. enterica subsp. enterica and included 9 genomes (six serovars) of four other Salmonella subspecies. Based on a pan-genome definition and flanked gene linkages, the fliC and fljB gene clusters were identified in 207 (91 serovars) and 138 (61 serovars) genomes, respectively. A phylogenetic tree constructed based on SNPs (Single Nucleotide Polymorphisms) of core genes were used to reflect the essential evolutionary relationships among various serovars. Congruence analysis was performed among the core genome and each gene of fliC and fljB gene clusters, with only fliA and fliS showing congruence to Salmonella core genome. Congruence was also observed among fliB, fliC/fljB, and fliD genes, and their phylogeny revealed a division into two major groups, which strongly corresponded to monophasic and biphasic serovars. Besides, homologous recombination events referring fliB, fliC, and fliD were found to have mainly occurred within each group. These results suggested two distinct evolutionary patterns of Salmonella flagellin gene clusters. Further insight on the evolutionary implication of the two patterns and a framework for phase variation mechanism are needed to be further processed.
Highlights
Salmonella is one of the primary causes of foodborne illness around the world, leading to a huge burden of illness calculated at nearly 93.8 million global cases annually (Majowicz et al, 2010)
Besides the relationship among the genes in the fliC and fljB gene clusters, we further studied their congruence to the core genome using linear regression analysis instead of maximum likelihood (ML) analysis, because datasets of the core genome were too large to calculate -lnL score
With the cost of whole genome sequencing (WGS) decreasing dramatically (Didelot et al, 2012) and the technology becoming available for routine use, WGS is very useful and practical in various bacterial infectious studies including diagnostic and public health microbiology (Koser et al, 2012)
Summary
Salmonella is one of the primary causes of foodborne illness around the world, leading to a huge burden of illness calculated at nearly 93.8 million global cases annually (Majowicz et al, 2010). For understanding the epidemiology of these microorganisms and the investigation of outbreaks caused by Salmonella, serotyping has been greatly facilitated by the characterization of isolates. Enterica (I) strains, the vast majority of Salmonella strains, could be isolated from humans and warm-blooded animals, while all the other subspecies and S. bongori are more frequently isolated from cold-blooded animals (Nataro et al, 2011). Enterica (I) has caused ∼99% of diagnosed salmonellosis cases for humans and domestic mammals (Centers for Disease Control and Prevention (CDC), 2011). Choleraesuis) (Wain and O’Grady, 2017)
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