Abstract
BackgroundSalmonella enterica is a significant foodborne pathogen, which can be transmitted via several distinct routes, and reports on acquisition of antimicrobial resistance (AMR) are increasing. To better understand the association between human Salmonella clinical isolates and the potential environmental/animal reservoirs, whole genome sequencing (WGS) was used to investigate the epidemiology and AMR patterns within Salmonella isolates from two adjacent US states.ResultsWGS data of 200 S. enterica isolates recovered from human (n = 44), swine (n = 32), poultry (n = 22), and farm environment (n = 102) were used for in silico prediction of serovar, distribution of virulence genes, and phylogenetically clustered using core genome single nucleotide polymorphism (SNP) and feature frequency profiling (FFP). Furthermore, AMR was studied both by genotypic prediction using five curated AMR databases, and compared to phenotypic AMR using broth microdilution. Core genome SNP-based and FFP-based phylogenetic trees showed consistent clustering of isolates into the respective serovars, and suggested clustering of isolates based on the source of isolation. The overall correlation of phenotypic and genotypic AMR was 87.61% and 97.13% for sensitivity and specificity, respectively. AMR and virulence genes clustered with the Salmonella serovars, while there were also associations between the presence of virulence genes in both animal/environmental isolates and human clinical samples.ConclusionsWGS is a helpful tool for Salmonella phylogenetic analysis, AMR and virulence gene predictions. The clinical isolates clustered closely with animal and environmental isolates, suggesting that animals and environment are potential sources for dissemination of AMR and virulence genes between Salmonella serovars.
Highlights
Salmonella enterica is a significant foodborne pathogen, which can be transmitted via several distinct routes, and reports on acquisition of antimicrobial resistance (AMR) are increasing
Salmonella serotyping based on whole genome sequencing (WGS) The 200 Salmonella sequences in this study selected from human clinical cases, swine, poultry, and environmental samples were serotyped using the Salmonella in silico typing resource (SISTR) platform for confirmation [26], and showed a high level of serotype diversity (Table 1)
Our results suggest that the refinement of WGS-based AMR prediction could be beneficial and can definitely enhance the monitoring of AMR strains and determinants detected in humans, foods, animals, and environment
Summary
Salmonella enterica is a significant foodborne pathogen, which can be transmitted via several distinct routes, and reports on acquisition of antimicrobial resistance (AMR) are increasing. The U.S Department of Health and Human Services reported an increase in Salmonella infections from 13.6 to 16.4 cases per 100,000 population, which represented a 17.1% increase from 1997 to 2011 [4]. Inappropriate use of antimicrobials in livestock production and the association to resistant Salmonella infection in humans are a growing concern to public health agencies, and have led to the rise of new multidrug resistant (MDR) bacteria and transferable genetic loci, such as colistin resistance mediated by the MCR-1 gene [5, 6]. The selection pressure on Salmonella is created by antimicrobial use in human health and food animal production leading to development and potential spread of antimicrobial resistance [8,9,10,11]. Our previous studies reported the persistence and dissemination of multiple resistant Salmonella serovars along with their determinants in the environment of commercial swine operation due to the manure application on land [12, 13]
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