TABLE 1 

Obtained ampliconsa align with 100% identity in colocalized groups within known sequencesc

Example no.Species and strain (accession no.)Island or plasmidAmpliconLocation (kb)
1Acinetobacter baumannii strain AYE (CU459141.1)Resistance islandqacEΔ13621.2
aadA3622.0
intI13624.9
IS263626.6
aphA13627.6
IS263628.9
IS263633.2
tetR3643.7
IS61003649.0
qacEΔ13651.7
qacEΔ13655.8
aadA3656.6
strA3658.1
tetG3672.3
qacEΔ13676.1
dfrA13677.3
intI13677.9
strB3679.4
2Proteus mirabilis strain PmGUE (JX121641.1)Genomic islandintI126.3
qacEΔ128.4
IS610030.4
tetR35.9
strB42.1
IS2645.3
blaTEM46.7
IS2648.4
aphA149.4
IS2650.3
intI151.7
qacEΔ153.0
tetG56.9
qacEΔ162.5
IS610065.2
3Salmonella enterica strain ST06-53 (KT334335.1)Plasmid pHK0653IS2672.1
IS2678.2
IS2680.6
IS2684.3
aadA285.0
IS2687.0
aphA187.9
IS2688.8
aadA94.1
cmlA194.6
aadA296.4
intI198.9
Tn21102.8
sul2106.9
IS4110.6
IS26114.5
qacEΔ1118.2
IS26120.1
4Klebsiella pneumoniae strain JM45 (CP006657.1)Plasmid p1Tn2141.9
incN51.0b
IS2663.9b
IS610067.9
intI169.8
dfrA270.5
aadA271.6
qacEΔ172.3
tetRb76.9
Tn23129.4
IS26140.5
blaTEM141.9
tetG148.0
qacEΔ1151.8
IS6100154.0
IS26154.8
aphA1155.8
IS26156.7
IS26158.6
5Escherichia coli (NC_010558.1)Plasmid pIP1206IS2690.9
tetB96.1
Tn21101.5
IS26104.8
qacEΔ1107.9
aadA5108.4
intI1110.1
IS26111.5
IS26112.9
blaTEM115.8
intI1123.0
IS26123.7
IS26b135.0
6Escherichia coli strain 2009C-3133 (CP013027.1)Plasmid unnamed3sul2123.1
IS26125.5
strAb137.1
aadA138.2
IS4142.4
IS26144.7
blaTEM148.1
IS26148.9
IS26b172.7
blaTEM173.4
  • a The most abundant of each allele of each primer was included in the query.

  • b Indicates a single mismatch between the most abundant amplicon and its local alignment with the NCBI sequence.

  • c Six examples from the NCBI database of the obtained amplicons aligning in clusters within genomes. Examples 1 to 5 include genes from the intI1-IS6100 cluster and some intercluster genes, while example 6 includes genes from the blaTEM-sul2 cluster (IS26, while found in the sequence, was not cooccurring with this cluster in the swine samples). Co-localization of genes within 10 kb from another alignment position is common as indicated by the differences in genomic locations. Sequences from the NCBI database with the highest numbers of total alignments are shown. Examples from the IS1216-tet cluster are discussed in the text.