Loss of resistance within clade IC1. (A) Loss of erythromycin and tetracycline resistance in group 3 isolates. (i) Plot of coverage calculated by mapping sequence reads from group 3 isolate IC210 to the reference genome Tn916-type element, showing no coverage across the transposon. This suggests it has been lost from the genome. (ii) Comparison of de novo assembly of isolate IC210 with the reference sequence. The red bands between the two sequences indicate BLAT matches between sequences in the same orientation. The annotation of the reference sequence is at the top; protein coding sequences (CDSs) are indicated by pink boxes, except for those that encode resistance determinants, which are coloured blue. The brown boxes indicate the fragments of a CDS that is reformed by the apparent excision of the transposon, as seen in the assembled sequence of isolate IC210 at the bottom of the diagram. (B) Loss of tetracycline resistance in group 2 isolates. The figure shows the structure of the tetM gene, including the positions of the promoter elements, leader peptide and ribosome binding sites (RBS). A 58 bp deletion within the leader peptide, at the bases indicated by the shaded bar, appears to result in the inactivation of the gene. (C) Loss of erythromycin resistance in group 4 isolates. The structure of the ermB gene is displayed as described for (B), with the position of the sequence alteration leading to a frameshift mutation indicated by the shaded bar. (D) Loss of chloramphenicol resistance within some group 5 isolates through deletion of the cat chloramphenicol acetyltransferase gene on the Ωcat(pC194) element. (i) Plot of mapped sequence read coverage and (ii) comparison of de novo assembly with the reference genome for group 5 isolate 0301 + 23540, displayed as in (A). BLAT, BLAST-like alignment tool.