Genomic characterization and phylogenetic analysis of Salmonella enterica serovar Javiana

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Microbiology

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Introduction

Materials & Methods

Sequencing, preprocessing, and genome assembly of TN isolates

SNP detection and phylogenetic analyses

Genome annotation and pan-GWAS

In silico identification of genomic features and genes

Global phylogenetic analysis

Comparison to polyphyletic serovars

Results

Tennessee Salmonella ser. Javiana population structure

High-quality single nucleotide polymorphism (hqSNP) analysis for cluster detection

Epidemiological trends

Geographical and temporal distribution

Identification of mobile genetic elements (MGEs)

Identification of virulence factors and pathogenicity islands

Identification of antibiotic resistance genes

Clade-enriched genes

Global population structure

Discussion

Conclusions

Supplemental Information

Neighbor-joining KSNP tree of global clinical Salmonella ser. Javiana strains

Tree was constructed based on core SNPs determined by KSNP3 (Gardner, Slezak & Hall, 2015). The optimal tree with the sum of branch length of 31,777.6 is shown. The percentage of replicate trees in which the associated taxa clustered together in the bootstrap test are represented by branch color (maximum as green, midpoint as yellow, and minimum as red). The tree is drawn to scale, with branch lengths (above branches) representing the number of base differences at core SNP positions per isolate (SNP distance). The analysis involved 161 isolates and 30,657 total SNP positions. The three major clades are labeled. HC900 (ceBG) clusters are indicated (590 is not shaded and 204 is shaded in gray). TN isolates belonging to TN clades I, II, and III from our original analysis (Fig. 1) are highlighted in purple, green, and blue, respectively. Metadata, including HC100 cluster designations, country, region/state, and collection year are listed to the right of node labels.

DOI: 10.7717/peerj.10256/supp-1

Minimal spanning trees of Salmonella ser. Javiana and polyphyletic serovar strains

Minimal spanning trees were constructed from cgMLST data using GrapeTree on Enterobase with the improved minimal spanning tree algorithm (MSTree V2). Separate trees were constructed for each (A) Salmonella ser. Javiana, (B) ser. Derby, (C) ser. Kentucky, (D) ser. Mississippi, (E) ser. Montevideo, (F) ser. Newport, (G) ser. Saintpaul, and (H) ser. Senftenberg. Nodes are color coded by ceBG designations (see legend in each panel) and ceBG designations associated with each serovar are in red boxes. Branch lengths (representing cgMLST allelic differences) are shown in red above branches between ceBG clusters.

DOI: 10.7717/peerj.10256/supp-2

Map of incidence rates

DOI: 10.7717/peerj.10256/supp-3

Tennessee clade II plasmid

Circular representation of the 87.5 kb found in TN clade II isolate SRS2822480. Genes in green signify over-represented Clade II genes and their corresponding Prokka annotations. RASTtk annotations that differ from the Prokka annotations are in gray. Figure was created using Geneious Prime 2019.1.1 ( https://www.geneious.com ).

DOI: 10.7717/peerj.10256/supp-4

Tennessee isolate details, IDs, and Assembly Statistics

DOI: 10.7717/peerj.10256/supp-5

Global Salmonella ser. Javiana Clinical Strains Dataset

Strain dataset used to evaluate the global population structure of Salmonella ser. Javiana clinical isolates. The original dataset included 526 isolates and the final dataset consisted of 161 isolates (indicated in the third column from the right). Includes strain identifiers, metadata (e.g., source, location), experimental data (e.g., in silico serotyping, MLST, cgMLST, wgMLST, and assembly stats), TN clade (for TN isolates included in the first KSNP analysis), and lineage (determined from the KSNP analysis of this dataset).

DOI: 10.7717/peerj.10256/supp-6

Polyphyletic Serovar Datasets

Isolate datasets used to construct minimal spanning trees for the following serovars: (A) Javiana, (B) Derby, (C) Kentucky, (D) Mississippi, (E) Montevideo, (F) Newport, (G) Saintpaul, and (H) Senftenberg. Includes strain identifiers, metadata (e.g., source, location), and experimental data (e.g., in silico serotyping, MLST, cgMLST, wgMLST, and assembly stats). Datasets are also publicly available on EnteroBase.

DOI: 10.7717/peerj.10256/supp-7

Clustered hqSNP Distance Matrix Heatmaps (TN Clades I, II, and III and all isolates)

Clustered matrices contain hqSNP distances between isolates as determined by the CFSAN SNP Pipeline (Davis et al., 2015) . The seven tabs (A, B, B2, C, C2, D, and D2) contain the results from when isolates from when all isolates were analyzed together with the external reference or the three internal references and the last six tabs (E, F, G, H, I, and J) from when the clades were analyzed independently with the external reference or the respective internal reference. Cells are colored to reflect hqSNP distances (low are white, high are dark red). Potential clusters at various hqSNP distance thresholds are indicated (£25 hqSNPs with dashed lines, ≤10 hqSNPs with dotted lines, and £5 hqSNPs with solid lines).

DOI: 10.7717/peerj.10256/supp-8

Prophage regions present in the representative subset of TN isolates, as determined by Phaster (Arndt et al., 2016; Zhou et al., 2011)

DOI: 10.7717/peerj.10256/supp-9

Virulence Factors and Salmonella Pathogenicity Islands (PAIs)

(A) Virulence factors determined by VFanalyzer and (B) Salmonella pathogenicity islands determined by SPIfinder.

DOI: 10.7717/peerj.10256/supp-10

Scoary Results (full)

DOI: 10.7717/peerj.10256/supp-11

Additional Information and Declarations

Competing Interests

The authors declare there are no competing interests.

Author Contributions

Lauren K. Hudson conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

Lisha Constantine-Renna performed the experiments, prepared figures and/or tables, authored or reviewed drafts of the paper, and approved the final draft.

Linda Thomas, Christina Moore and Xiaorong Qian performed the experiments, authored or reviewed drafts of the paper, and approved the final draft.

Katie Garman, John R. Dunn and Thomas G. Denes conceived and designed the experiments, authored or reviewed drafts of the paper, and approved the final draft.

Data Availability

The following information was supplied regarding data availability:

The data is available in the Supplemental Files.

Funding

This work was supported by Epidemiology and Laboratory Capacity for Infectious Diseases (ELC) grant 6 NU50CK000528-01 funded by the Centers for Disease Control and Prevention (CDC) and multistate project S1077 “Enhancing Microbial Food Safety by Risk Analysis.” The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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