Edwardsiella Comparative Phylogenomics Reveal the New Intra/Inter-Species Taxonomic Relationships, Virulence Evolution and Niche Adaptation Mechanisms

Abstract

Edwardsiella bacteria are leading fish pathogens causing huge losses to aquaculture industries worldwide. E. tarda is a broad-host range pathogen that infects more than 20 species of fish and other animals including humans while E. ictaluri is host-adapted to channel catfish causing enteric septicemia of catfish (ESC). Thus, these two species consist of a useful comparative system for studying the intricacies of pathogen evolution. Here we present for the first time the phylogenomic comparisons of 8 genomes of E. tarda and E. ictaluri isolates. Genome-based phylogenetic analysis revealed that E. tarda could be separate into two kinds of genotypes (genotype I, EdwGI and genotype II, EdwGII) based on the sequence similarity. E. tarda strains of EdwGI were clustered together with the E. ictaluri lineage and showed low sequence conservation to E. tarda strains of EdwGII. Multilocus sequence analysis (MLSA) of 48 distinct Edwardsiella strains also supports the new taxonomic relationship of the lineages. We identified the type III and VI secretion systems (T3SS and T6SS) as well as iron scavenging related genes that fulfilled the criteria of a key evolutionary factor likely facilitating the virulence evolution and adaptation to a broad range of hosts in EdwGI E. tarda. The surface structure-related genes may underlie the adaptive evolution of E. ictaluri in the host specification processes. Virulence and competition assays of the null mutants of the representative genes experimentally confirmed their contributive roles in the evolution/niche adaptive processes. We also reconstructed the hypothetical evolutionary pathway to highlight the virulence evolution and niche adaptation mechanisms of Edwardsiella. This study may facilitate the development of diagnostics, vaccines, and therapeutics for this under-studied pathogen.

Type III secretion system genes of Edwardsiella tarda associated with intracellular replication and virulence in zebrafish

“…SPI1 is required for invasion into epithelial cells, while intracellular accumulation of Salmonella in macrophages is dependent on SPI2 function (Hansen-Wester & Hen sel 2001). In contrast, a whole-genome comparison of multiple E. tarda strains revealed that E. tarda genotypes were broadly clustered into 2 major subpopulations: pathogenic E. tarda genotype EdwGI, which represents a genotype of fish pathogens and possesses virulence factor genes such as T3SS and the Type VI secretion system (T6SS); and the nonpathogenic or environmental E. tarda genotype EdwGII (Yang et al 2012). Further, E. tarda isolated from red sea bream had T3SS (Et-LEE) and T6SS (Et-T6SS2) genes, which suggests that the genotype EdwGI could be divided into 2 sub-genotypes, viz.…”

“…Edwardsiella tarda Type III secretion system (T3SS) gene cluster and location of insertional mutations. E. tarda T3SS is composed of 35 genes encoding apparatuses, translocons, effectors, regulators, chaperones, and known-function and hypothetical proteins (Tan et al 2005, Yang et al 2012. The chloramphicol resistance (Cm r ) gene was inserted in the possible effector and hypothetical genes by an allelic exchange method using the suicide vector pRE112 homo logy both to the spiC effector gene and the ssaB T3SS apparatus gene of S. enterica.…”

Transcriptomic dissection of the horizontally acquired response regulator EsrB reveals its global regulatory roles in the physiological adaptation and activation of T3SS and the cognate effector repertoire inEdwardsiella piscicidaduring infection toward turbot

“…5,6 In the T3SS gene cluster, the concomitant 2-component system (TCS) EsrA-EsrB is essential for the bacterium's pathogenesis. 6,31 To better decipher the regulatory roles and the regulatory mechanisms of the response regulator EsrB, we performed RNA-seq analysis with EIB202 and DesrB RNA isolated from LB (n D 3) and DMEM cultures (n D 3) and compared their differential gene expression. DMEM was used to induce the expression of T3SS and T6SS proteins possibly by mimicry of in vivo or intracellular condition.…”

“…3 Elucidating the genes controlled by TCS will facilitate the understanding of the mechanisms underlying TCS scouting of environmental/host cues and switching gene expression and ultimately lead to the development of antibacterial therapies. 4 Edwardsiella piscicida (formerly included in E. tarda), 5,6,7,8 a member of the Enterobacteriaceae, colonizes a broad range of hosts including fish and mammals and causes fatal hemorrhagic septicemia and gastro-and extra-intestinal infections. 9,10,11,12 As a leading pathogen that threats fresh and seawater aquaculture farms, E. piscicida causes huge economic losses to the world aquaculture industry, especially for farmed flatfish (turbot and flounder).…”

“…31 Like their counterparts SsrA, SsrB and SPI-2 in Salmonella, 32,33,34 EsrA and EsrB and the associated T3SS locus may be horizontally acquired and may have evolved to coordinate the expression of virulence and adaptation to host microenvironments by the reprogramming of ancestral genes unlinked to the T3SS locus. 6 Although the exact stimulus recognized by HK EsrA remains elusive, 35 EsrA-EsrB plays a key role in regulating the expression and secretion of T3SS and T6SS by directly binding to the promoters of T3SS genes and to that of EsrC, which further regulates the expression of other T3SS and T6SS genes in the bacterium. 22,36,37 It is still unknown whether other genes, especially those associated with the invasion process, and their regulatory mechanisms are controlled by EsrB during in vivo and in vitro infection of hosts.…”