Whole genome sequencing-based detection of antimicrobial resistance and virulence in non-typhoidal Salmonella enterica isolated from wildlife

Abstract

The aim of this study was to generate a reference set of Salmonella enterica genomes isolated from wildlife from the United States and to determine the antimicrobial resistance and virulence gene profile of the isolates from the genome sequence data. We sequenced the whole genomes of 103 Salmonella isolates sampled between 1988 and 2003 from wildlife and exotic pet cases that were submitted to the Oklahoma Animal Disease Diagnostic Laboratory, Stillwater, Oklahoma. Among 103 isolates, 50.48% were from wild birds, 0.9% was from fish, 24.27% each were from reptiles and mammals. 50.48% isolates showed resistance to at least one antibiotic. Resistance against the aminoglycoside streptomycin was most common while 9 isolates were found to be multi-drug resistant having resistance against more than three antibiotics. Determination of virulence gene profile revealed that the genes belonging to csg operons, the fim genes that encode for type 1 fimbriae and the genes belonging to type III secretion system were predominant among the isolates. The universal presence of fimbrial genes and the genes encoded by pathogenicity islands 1-2 among the isolates we report here indicates that these isolates could potentially cause disease in humans. Therefore, the genomes we report here could be a valuable reference point for future traceback investigations when wildlife is considered to be the potential source of human Salmonellosis.

Keywords: Antimicrobial resistance; Foodborne pathogen; Salmonella virulence; Salmonellosis; Whole genome sequencing; Wildlife.

Fig. 1

Phenotypic and genotypic anti-microbial resistance of 103 wildlife salmonella isolates. a Heatmap of phenotypic resistance against 12 antibiotics was measured using Sensititre NARMS gram-negative plate. The CLSI breakoff points for resistance against various antibiotics was used for determining the antimicrobial susceptibility of 103 salmonella strains. Legend description: 0 = susceptible, 1 = intermediate, and 2 = resistant. b Heatmap of genotypic resistance against antimicrobials detected using CLC workbench 9.0 by BLAST against ResFinder 2.1 and CARD database. Legend description: 0 = absent, 1 = present. The golS, mdsABC complex, and mdtK genes associated with multidrug resistance was present in all except 16 isolates. Similarly, multidrug efflux pump regulator gene sdiA was absent in 14 isolates. Complete data used to generate b is given in Additional file 2: Table S2

Fig. 2

Heatmap of virulence genes present in 103 wildlife salmonella isolates. Salmonella genome Assemblies were searched against a local copy of the Virulence Factor Database using BLAST. In the figure, each row represents a virulence gene and each column denotes a sample. Legend on the left side of the figure denotes the following categories of virulence genes: (I) Fimbrial adherence determinants, (II) Macrophage inducible genes, (III) Magnesium uptake, (IV) Non-fimbrial adherence determinants, (V) Secretion system, (VI) Serum resistance, (VII) Stress protein, (VIII) Toxin, and (IX) Two-component system. The virulence genes belonged 5 categories—PSLT, SeHA, SEN, SeSA, and STM. Seventeen isolates had fewer virulence genes compared to others and this correlated with the absence of genes associated with multidrug resistance. Legend description: 0 = absent, 1 = present. Data underlying this figure is given in Additional file 3: Table S3