Search

Figure S3. Synteny analysis of the SPI-7 island between Typhi CT18 and S. diarizonae SBO13 and SBO27. (A) Comparison of the entire island; (B) detail of the rep, pil and tra loci. The vertical grey bars represent BLAST identity of homologous regions (minimal identity for matches 40%). The gradient of the grey colour bars represents BLAST identity (%). (PDF 434 kb)

Figure S1. Subsystem category distribution of the S. diarizonae strain SBO13 genome. The genome of diarizonae SBO13 was annotated using the Rapid Annotation System technology (RAST) server and classified in 27 categories and 571 subsystems. Total proteins annotated with a putative function covered a 56% of the subsystems (green bar). The pie chart represents the percentage distribution of the subsystems categories. (PDF 377 kb)

Table S1. Genes present in the plasmids of S. enterica subsp. diarizonae strains SBO13 and SBO27. (PDF 377 kb)

[Background] Salmonella enterica subsp. diarizonae (IIIb) is frequently isolated from the environment, cold-blooded reptiles, sheep and humans; however only a few studies describe the isolation of this subspecies from invasive human infections. The factors contributing to this unusual behavior are currently unknown., [Results] We report here the genome features of two diarizonae strains, SBO13 and SBO27, isolated from endocervical tissue collected post-abortion and from cerebrospinal fluid of a newborn child, respectively, in the city of Santa Cruz, Bolivia. Although isolated six years apart, SBO27 in 2008 and SBO13 in 2014, both strains belong to the same sequence type 1256 (ST1256) and show a high degree of genome conservation sharing more than 99% of their genes, including the conservation of a ~ 10 kb plasmid. A prominent feature of the two genomes is the presence of 24 genomic islands (GIs), in addition to 10 complete Salmonella pathogenicity islands (SPI) and fragments of SPI-7, a pathogenicity island first reported in the human-adapted serovar Typhi. Some of the GIs identified in SBO13 and SBO27 harbor genes putatively encoding auto-transporters involved in adhesion, lipopolysaccharide modifying enzymes, putative toxins, pili-related proteins, efflux pumps, and several putative membrane cation transport related-genes, among others. These two Bolivian isolates also share genes encoding the type-III secretion system effector proteins SseK2, SseK3 and SlrP with other diarizonae sequence types (ST) mainly-associated with infections in humans. The sseK2, sseK3 and slrP genes were either absent or showing frameshift mutations in a significant proportion of genomes from environmental diarizonae isolates., [Conclusions] The comparative genomic study of two diarizonae strains isolated in Bolivia from human patients uncovered the presence of many genes putatively related to virulence. The statistically-significant acquisition of a unique combination of these functions by diarizonae strains isolated from humans may have impacted the ability of these isolates to successfully infect the human host., This work was supported by grants 215RT-0493 from Programa Iberoamericano de Ciencia y Tecnología para el Desarrollo (CYTED), BIO2016–77639-P (AEI/FEDER, UE) and PCIN-2016-082, from Spanish Ministry of Economy and Competitiveness and European Regional Development Funds (FEDER), awarded to FGdP; and, grants DGAPA IN213516, CONACyT 239659 and FC-2015-2/950, awarded to JLP. PV gratefully acknowledges funding grants DGAPA-PAPIIT IN211814 and IN206318 and CONACyT FC-2015-2/879. Other supporting grants were from Comisión Sectorial de Investigación Científica (CSIC), Universidad de la República (Proyecto Grupos I + D 2014), awarded to LB. CS was supported by CONACyT FC-2015-2/879., We acknowledge support of the publication fee by the CSIC Open Access Support Initiative through its Unit of Information Resources for Research (URICI)

of Genome analysis of Salmonella enterica subsp. diarizonae isolates from invasive human infections reveals enrichment of virulence-related functions in lineage ST1256

Figure S2. Maximum likelihood core-genome phylogeny (species tree) for 76 Salmonella spp. strains. The core-genome was inferred from the 303 top-scoring markers selected of the 1650 consensus clusters computed by GET_HOMOLOGUES. The bar represents the expected number of substitutions per site under the best-fitting GTR + F + ASC + R3 model. Internal nodes are colored by the combined approximate Bayesian support / ultra-fast bootstrap support values, respectively, as indicated on the legend. The inset shows the distribution of Robinson-Foulds gene tree distances to the species-tree. (PDF 1150 kb)