Table 2.
Genotypic and phenotypic characteristics of 44 UPEC belonging to major clonal complexes (CC) or to other sequence types (ST).
| Feature | No. (%) of isolates by ST | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Major UPEC clones | Other STs | ||||||||
| CC10 ST10 (n = 2) | CC69 ST69 (n = 6) | CC73 ST73 (n = 3) | CC95 ST140 (n = 1) | ST127 (n = 1) | CC131 ST131 (n = 6) | ST141 (n = 5) | Singly occurring STsa (n = 20) | Total (%) | |
| VF GENES | |||||||||
| afa | 1 (50) | 1 (16.7) | 0 (0) | 0 (0) | 0 (0) | 4 (66.7) | 0 (0) | 0 (0) | 6 (13.6) |
| papAH | 0 (0) | 3 (50) | 1 (33.3) | 0 (0) | 1 (100) | 2 (33.3) | 3 (60) | 6 (30) | 16 (36.4) |
| papC | 0 (0) | 3 (50) | 1 (33.3) | 0 (0) | 0 (0) | 2 (33.3) | 3 (60) | 6 (30) | 15 (34) |
| papEF | 0 (0) | 4 (66.7) | 1 (33.3) | 0 (0) | 1 (100) | 2 (33.3) | 3 (60) | 5 (25) | 16 (36.4) |
| sfaS | 0 (0) | 0 (0) | 3 (100) | 0 (0) | 1 (100) | 0 (0) | 5 (100) | 4 (20) | 13 (29.5) |
| yfcv | 1 (50) | 0 (0) | 3 (100) | 1 (100) | 1 (100) | 4 (66.7) | 5 (100) | 8 (40) | 23 (52.3) |
| hlyA | 0 (0) | 0 (0) | 3 (100) | 0 (0) | 1 (100) | 1 (16.6) | 3 (60) | 4 (20) | 12 (27.3) |
| vat | 0 (0) | 0 (0) | 3 (100) | 1 (100) | 1 (100) | 0 (0) | 4 (80) | 6 (30) | 15 (34) |
| fyuA | 1 (50) | 4 (66.7) | 3 (100) | 1 (100) | 1 (100) | 6 (100) | 5 (100) | 10 (50) | 31 (70.5) |
| iutA | 2 (100) | 5 (83.3) | 0 (0) | 1 (100) | 0 (0) | 5 (83.3) | 4 (80) | 7 (35) | 24 (54.5) |
| KpsMII | 1 (50) | 5 (83.3) | 3 (100) | 1 (100) | 1 (100) | 5 (83.3) | 4 (80) | 10 (50) | 30 (68.2) |
| PAI | 0 (0) | 0 (0) | 3 (100) | 1 (100) | 1 (100) | 4 (66.7) | 5 (100) | 8 (40) | 22 (50) |
| traT | 1 (50) | 5 (83.3) | 0 (0) | 0 (0) | 0 (0) | 4 (66.7) | 2 (40) | 8 (40) | 20 (45.5) |
| VF score [mean, median, (range)] | 3.5,3.5, (3–4) | 5, 5, (2-7) | 8, 7 (7–10) | 6, 6, (6) | 9, 9, (9) | 6.5, 7, (5–7) | 9.2, 11,(5–12) | 4.1, 3.5 (0–11) | 5.5, 5.5 (0–12) |
| AMR PHENOTYPEb | |||||||||
| Pansusceptible | 2 (100) | 1 (16.6) | 3 (100) | 1 (100) | 0 (0) | 0 (0) | 2 (40) | 13 (65) | 22 (50) |
| Fosfomycin | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) |
| Nitrofurantoin | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) |
| Ciprofloxacin | 0 (0) | 1 (16.6) | 0 (0) | 0 (0) | 0 (0) | 5 (83.3) | 0 (0) | 1 (5) | 7 (15.9) |
| Sulfamethoxazole | 0 (0) | 5 (83.3) | 0 (0) | 0 (0) | 0 (0) | 4 (66.7) | 1 (20) | 4 (20) | 14 (31.8) |
| Trimethoprim | 0 (0) | 4 (66.7) | 0 (0) | 0 (0) | 0 (0) | 3 (50) | 0 (0) | 2 (10) | 9 (20.5) |
| Ampicillin | 0 (0) | 4 (66.7) | 0 (0) | 0 (0) | 0 (0) | 5 (83.3) | 2 (40) | 3 (15) | 14 (31.8) |
| Cefotaxime | 0 (0) | 1 (16.6) | 0 (0) | 0 (0) | 0 (0) | 3 (50) | 0 (0) | 0 (0) | 4 (9) |
| MDR | 0 (0) | 4 (66.7) | 0 (0) | 0 (0) | 0 (0) | 5 (83.3) | 2 (40) | 2 (10) | 13 (29.5) |
| ACQUIRED AMR GENESc | |||||||||
| aac(6′)-Ib-cr | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 1 (16.6) | 0 (0) | 0 (0) | 1 (2.3) |
| blaCTX−M−14 | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 1 (16.6) | 0 (0) | 0 (0) | 1 (2.3) |
| blaCTX−M−15 | 0 (0) | 1 (16.6) | 0 (0) | 0 (0) | 0 (0) | 2 (33.3) | 0 (0) | 0 (0) | 3 (6.8) |
| mph(A) | 0 (0) | 4 (66.7) | 0 (0) | 0 (0) | 0 (0) | 2 (33.3) | 0 (0) | 0 (0) | 6 (13.6) |
Singly occurring ST included ST12 (n = 1), ST14 (n = 1); ST1193 (n = 1); ST59 (n = 1), ST349, (n = 1), ST108 (n = 1), ST841 (n = 1), ST58 (n = 1), ST4628 (n = 1), ST2628 (n = 1), ST1851 (n = 1), ST40 (n = 1), ST720 (n = 1), ST681 (n = 1), ST978 (n = 1), ST1001 (n = 1), ST4299 (n = 1), new ST (n = 3). The new STs were not assigned numerical designations by the E. coli MLST database (http://mlst.warwick.ac.uk/mlst/dbs/Ecoli).
The most important antimicrobials for UTI treatment, as well as ß-lactams are shown. A detailed overview of all resistance profiles is given in Supplementary Table S2.
AMR, antimicrobial resistance; CC, clonal complex; MDR, multidrug resistance; ST, sequence type; UPEC, uropathogenic E. coli; VF, virulence factor.
None of the isolates harbored the plasmid-mediated colistin resistance genes mcr-1 or mcr-2.