TABLE 2.
Plasmids involved in AMR gene dissemination.
Plasmid Inc type | AMR genes associated with replicon typea | Other genes found in isolatesb | Conitg size (Kb)c | Matches in NCBI databased (accession number) | Bacterial species for matched plasmidd | Sample origine | % alignmentf | Number of Isolates | Number of farms | Number of MLST STs |
IncQ1 | strAB, sul2 | repAC mobB | 4.4–4.7 | pRSF1010 (NC001740) | E. coli | NK | 53% (50–58%) | 48 | 9 | 9 |
IncI1 | qnrS1 | 18–106 | pSTM2 (KF290378) | Salmonella enterica subsp. enterica serovar Typhimurium | Human | 79% (75–82%) | 19 | 6 | 7 | |
IncFII | strAB, blaTEM–1, sul2, tet(A), and dfrA14 | intI, tra and trb | 48 | pM160133-p2 (CP022166) | E. coli | Human (urine) | 95% (95–96%) | 9 | 2 | ST101 |
Unknown | blaCTX–M–15, blaTEM–1, qnrS1, strAB, and sul2 | 21–36 | pAR0162 (CP021681) pEco-CTXM15 (MF510423) | E. coli | NK Human (bile) | 80% (73–95%) 92% | 3 | 2 | 2 | |
IncI1 | blaCTX–M–1, sul2 | tet(A) | 107 | p369 (IncI) (KT779550) | E. coli | Chicken | 99.7% | 1 | 1 (MSG43) | ST3205 |
unknown | blaCTX–M–1, sul3, dfrA1 | intI | 85 | 91% | 1 | 1 (MSG17) | ST101 | |||
IncA/C2 | blaCMY2, (sul2) | floR, tet(A), strAB | 127-128 | pSN254b (KJ909290) | Aeromonas salmonicida | Fish farm | 92% | 2 | 1 (MSG25) | ST162 |
IncHI2A | strAB, blaCMY2 | Tellurite | 124 | pYD786-1 (KU254578) | E. coli | Human (urine) | 82% (81–84%) | 4 | 1 (MSG25) | ST101 |
IncI1 | blaCMY2 | 86 | p85 (CP023362) | E. coli | Canine | 99% | 1 | 1 (MSG53) | ST156 |
Summary of plasmids contigs present in isolates, as identified from WGS. aAMR genes identified using APHA SeqFinder from WGS. Genes that are variably present are in parenthesis. bOther genes found in isolate but not located on contigs harboring plasmid replicon. cSize of resolved contigs harboring AMR gene and plasmid replicon type. dPlasmid and bacteria with highest BlastN identity in NCBI database. eSample origin of bacterial species harboring matched plasmid. fPercentage of aligned bases to reference calculated using Snippy.