Tools
Tools
Johansson, Markus H K, Bortolaia, Valeria, Tansirichaiya, Supathep, Aarestrup, Frank M, Roberts, Adam 
ORCID: https://orcid.org/0000-0002-0760-3088 and Petersen, Thomas N
(2021)
'Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder'. Journal of Antimicrobial Chemotherapy, Vol 76, Issue 1, pp. 101-109.
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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/.
| Item Type: | Article |
|---|---|
| Subjects: | QW Microbiology and Immunology > QW 45 Microbial drug resistance. General or not elsewhere classified. WC Communicable Diseases > Infection. Bacterial Infections > Enteric Infections > WC 260 Enterobacteriaceae and other enteric infections WC Communicable Diseases > Infection. Bacterial Infections > Enteric Infections > WC 269 Salmonella infections |
| Faculty: Department: | Biological Sciences > Department of Tropical Disease Biology |
| Digital Object Identifer (DOI): | https://doi.org/10.1093/jac/dkaa390 |
| Depositing User: | Stacy Murtagh |
| Date Deposited: | 07 Oct 2020 11:55 |
| Last Modified: | 14 Dec 2020 13:35 |
| URI: | https://archive.lstmed.ac.uk/id/eprint/15778 |
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