If you already have the WGS, you can use the following online tool Article Detection of mobile genetic elements associated with antibio...

Hi Eman,

First check if you have plasmids by finding the plasmid replicon types. This will give you an idea on how many plasmids you have in the bacteria. Although some plasmids are not typable.

You can use starAMR tool on galaxy :

https://toolshed.g2.bx.psu.edu/repository?repository_id=b9822587a6ad2cbf&changeset_revision=4b9a8031ab74

Good luck

Thanks, Mustafa Sadek , for your answer.

As you mentioned the conjugation, If I have different ISs (5, 150) for example, but no plasmid ARGs detected, would you still suggest the conjugation ?!

Have you conjugate any Acinetoacter, before?

Thanks Hazem Ramadan, If I have different insertion sequences (ISs) and Composite transposon, but no plasmid ARGs detected! would it be still a viable option to check the HGT?

Thanks Farah Al-Marzooq , having hard-times registering with the "public name" keep refusing it , any suggestions, considerations?

Yes you can Eman M Taher, however in this case it is preferable to decipher the genetic context for the gene of interest in your isolate.

Hi Eman

You can visualize the fastg files (generated by a de novo assembler like spades or unicycler) on bandage. You may see plasmids as circular contigs.

You can then export the sequences of the circular contigs and analyze using redistance gene identifier on CARD.

Thanks Samira M. Hamed , Will give it a try!

https://cge.food.dtu.dk/services/ResFinderFG/ the best option is this one, you can run the assembled genome here...

RFPlasmid is a good tool that can predict plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers. It can determine if contigs are chromosomal or plasmid with a very high specificity and sensitivity (up to 99%) and can be very useful to analyze WGS data of bacterial genomes and their antimicrobial resistance genes.

http://klif.uu.nl/rfplasmid/

Thanks, Soe Yu Naing I tried to use this tool but it is a little bit confusing any guidance?

Amro Hashish

You can upload the assembled contigs to the web interface, and the output is the table of whether the contigs are likely to be chromosomal or plasmid with the score. If the contig is most likely to be plasmid, you can extract that contig and blast to confirm whether ARGs are present on plasmid or not.

"The tool RFPlasmid supports models for 17 different bacterial taxa, including Campylobacter, Escherichia coli and Salmonella, and has a taxon agnostic model for metagenomic assemblies or unsupported organisms. RFPlasmid is available both as a standalone tool and via a web interface."

Below you can read it in details

https://pubmed.ncbi.nlm.nih.gov/34846288/

Hi,

First of all, you need to make sure that you extracted plasmid DNA (not genomic DNA). plasmid DNA extraction is different and if you didn't do it then your WGS reads will not contain enough reads for assembling plasmid.

second, if you have plasmid DNA reads, you can try assembling it with SPAdes using the flag (--plasimd) so that spades assemble only plasmid DNA. or use PATRIC for the same purpose.

Good luck