Mobilization of Antimicrobial Resistance Genes

Each resistance gene was classified as either being iMGE-associated, carried by an MGE or having an unknown association. The AMR was considered associated if it was located within 31 kb of an iMGE. The threshold corresponds to the longest ComTn (Tn6108) from S. enterica in the database and is intended to reflect which genes have the potential to be mobilized by surrounding iMGEs.
The iMGE-associated AMR genes were grouped on MGE type and distance to the closest MGE. Groups with 10 or more members were investigated further as they could be putative TUs. The level of conservation of the sequence spanning between the iMGE and the associated AMR gene was estimated by calculating the average nucleotide identity (ANI) with FastANI (v1.3).³⁸ (link) Translocatability was indicated by a particular MGE and AMR gene combination being located on multiple different plasmids across several unrelated isolates.
Integrons located in association with these putative TUs were detected using Integron Finder v2-2020-04-28 with the local-max option.³⁹ (link)

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Johansson M.H., Bortolaia V., Tansirichaiya S., Aarestrup F.M., Roberts A.P, & Petersen T.N. (2020). Detection of mobile genetic elements associated with antibiotic resistance in Salmonella enterica using a newly developed web tool: MobileElementFinder. Journal of Antimicrobial Chemotherapy, 76(1), 101-109.

Publication 2020

Gene Integron Nucleotide Plasmids

Corresponding Organization : Technical University of Denmark

Other organizations : UiT The Arctic University of Norway, Liverpool School of Tropical Medicine

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Variable analysis

independent variables

Classification of resistance genes as either being iMGE-associated, carried by an MGE, or having an unknown association

dependent variables

Whether the AMR was considered associated (located within 31 kb of an iMGE)
Grouping of iMGE-associated AMR genes by MGE type and distance to the closest MGE
Level of conservation of the sequence spanning between the iMGE and the associated AMR gene (average nucleotide identity)
Identification of translocatable MGE and AMR gene combinations (located on multiple different plasmids across several unrelated isolates)
Identification of integrons located in association with the putative transcriptional units (TUs)

control variables

The threshold of 31 kb, corresponding to the longest ComTn (Tn6108) from S. enterica in the database, to reflect which genes have the potential to be mobilized by surrounding iMGEs

Annotations

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