Table 1.
Genomic studies performed on longitudinal CF isolates of P. aeruginosa
The list of genes or intergenic regions identified in these studies was used to highlight the most mutated regions in Tables 2 and 3. The most representative genomic studies performed on P. aeruginosa CF sequential isolates whose isolations were spaced by at least 1 year were selected.
|
Sequencing type |
No. of patients |
No. of sequenced isolates |
Time span of isolate evolution (years) |
No. of studied lineages or clone types |
Identification of positively selected genes |
Reference |
|---|---|---|---|---|---|---|
|
Whole-genome |
1 |
2 |
7.5 |
1 |
No |
[6] |
|
Gene-targeted |
29 |
58 |
5–20 |
nd |
No |
|
|
Whole-genome |
1 |
45 |
20 |
1 (PA14) |
No |
[7] |
|
1 |
63 |
23 |
1 (C) |
No |
||
|
Whole-genome |
6* |
12* |
35 max.* |
1 (DK2)* |
No |
[13]* |
|
Whole-genome |
21* |
55* |
36* |
1 (DK2)* |
Yes |
[14]* |
|
Whole-genome |
1 |
18 |
32 |
1 (DK1) |
No |
[9] |
|
Whole-genome |
1 |
13 |
6 |
1 |
Yes |
[8] |
|
1 |
14 |
20 |
1 |
|||
|
Whole-genome |
34 |
474 |
1–8 |
53 (36 for PE) |
Yes |
[16] |
|
Whole-genome |
4 |
26 |
17–19 |
6 |
Yes |
[18] |
|
Whole-genome |
1 |
2 |
6.9 |
1 (OC4A) |
No |
[10] |
|
Whole-genome |
1 |
2 |
3 |
1 |
No |
[12] |
|
Whole-genome |
32 (12 for PE) |
262 |
<15–35 |
12 |
Yes |
[17] |
|
Whole-genome |
13 (6 for PE) |
63 |
3–4 |
1 (AUST-02) |
Yes |
[15] |
|
Whole-genome |
1 |
40 |
8 |
1 |
Yes |
[11] |
|
Reanalysis of whole- genome sequencing |
68 |
534 |
nd |
44 |
Yes |
[81] |
nd, Not determined in the study; PE, parallel evolution.
*Isolates sequenced by Yang et al. were also used in the study by Marvig et al., making the results of these two studies interconnected [13, 14].