Fig. 5

Loss of pili cluster 1 (csu gene cluster) and gain of siderophore cluster 2 in specific isolates. a Two types of deletion were observed which led to a complete loss of the type I pilus csuAB-E gene cluster. A novel 17 kb deletion was detected in NIPH 335 and OIFC098, whereas a previously reported 42 kb deletion was found in MDR-ZJ06 and nine UH clade B isolates (e.g., UH6207). b Siderophore cluster 2 was detected only in a small subset of isolates across all 249 analyzed. Two apparently independent molecular events were observed among the siderophore cluster 2-positive isolates. In decades-old isolate ATCC 17978, insertion of the gene cluster was detected at a genomic position corresponding to 3.0 Mbp of the ACICU reference genome. c In the remaining siderophore cluster 2-positive modern isolates (e.g., MRSN 3405), insertion was detected at a different location, which corresponds to 3.8 Mbp of the ACICU reference genome. Since ATCC 17978 was isolated in 1951 while other isolates were isolated more recently between 2007 and 2011, the acquiring of siderophore cluster 2 among modern isolates could be an example of the reemergence of a survival mechanism of A. baumannii. The functional significance of siderophore cluster 2 is yet to be determined. Key: pairwise nucleotide identity shown in red to blue (100 % identity) color scale; contig breaks (pink vertical bars); open reading-frames (thick arrows); type I pilus cluster 1 and siderophore cluster 2 genes (green); deleted genes (gray scale); genes bordering insertions/deletions (dark orange and brown); other flanking genes (orange); other genes (light brown)