Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder

Abstract

Objectives: Antimicrobial resistance (AMR) in clinically relevant bacteria is a growing threat to public health globally. In these bacteria, antimicrobial resistance genes are often associated with mobile genetic elements (MGEs), which promote their mobility, enabling them to rapidly spread throughout a bacterial community.

Methods: The tool MobileElementFinder was developed to enable rapid detection of MGEs and their genetic context in assembled sequence data. MGEs are detected based on sequence similarity to a database of 4452 known elements augmented with annotation of resistance genes, virulence factors and detection of plasmids.

Results: MobileElementFinder was applied to analyse the mobilome of 1725 sequenced Salmonella enterica isolates of animal origin from Denmark, Germany and the USA. We found that the MGEs were seemingly conserved according to multilocus ST and not restricted to either the host or the country of origin. Moreover, we identified putative translocatable units for specific aminoglycoside, sulphonamide and tetracycline genes. Several putative composite transposons were predicted that could mobilize, among others, AMR, metal resistance and phosphodiesterase genes associated with macrophage survivability. This is, to our knowledge, the first time the phosphodiesterase-like pdeL has been found to be potentially mobilized into S. enterica.

Conclusions: MobileElementFinder is a powerful tool to study the epidemiology of MGEs in a large number of genome sequences and to determine the potential for genomic plasticity of bacteria. This web service provides a convenient method of detecting MGEs in assembled sequence data. MobileElementFinder can be accessed at https://cge.cbs.dtu.dk/services/MobileElementFinder/.

Figure 1.

Total number of predicted MGEs and abundance of predicted MGEs per source and country of origin. Putative ComTns are not separated from ComTns.

Figure 2.

The number of iMGEs capable of carrying passenger genes and their genomic location.

Figure 3.

(a) Distributions of the number of predicted MGEs for samples of the 12 most common MLST STs. (b) The number of samples per country with a given MLST ST. (c) Distribution of pairwise core-genome allele differences for the 12 most common MLST STs. The dotted line indicates the threshold used to separate clonal S. enterica. MLST ST19 contained the most diverse isolates, with an average pairwise distance of 403 alleles.

Figure 4.

Samples clustered on the predicted MGE profile using Jaccard distance overlaying meat source, predicted MLST ST and country as overlay. MLST STs occurring less than 12 times were excluded.

Figure 5.

The association of AMR genes with MGEs for five putative TUs. Genes carried on MGEs are located in the relevant element. The figure represents the synteny, not orientation and scale of elements.