Background
Methods
Sample collection, isolation, and identification
Antibiotic sensitivity test
DNA extraction and screening for virulence-associated genes
Pathotype | Virulence factor categories | Function | ||
---|---|---|---|---|
Adhesins | Capsule synthesis | Toxins | ||
ExPEC | sfa | S fimbriae (sialic acid-specific) | ||
cnf1 | Cytotoxic necrotizing factor 1 | |||
papC | Pilus associated with pyelonephritis (P fimbriae) | |||
hlyA | α-Hemolysin | |||
rfc | Lipopolysaccharide synthesis | |||
sepA | Secreted serine protease of the auto-transporter family | |||
EAEC | etrA | Component of ETT2 type III secretion system | ||
EIEC | aer | Aerobatin | ||
ETEC | faeG | F4 fimbrial adhesion | ||
fasAb
| Fimbrial adhesion | |||
eltAb
| Heat-labile enterotoxin | |||
estAb
| Heat-stable enterotoxin | |||
EPEC | eaeAa
| Intimin/attaching and effacing | ||
exhAa, b
| Enterohemolysin | |||
EHEC | eaeAa
| Intimin/attaching and effacing | ||
stx1b
stx2b
| Shiga-toxin-I Shiga-toxin-II | |||
exhAa,b
| Enterohemolysin |
Phylogenetic analysis of E. coli strains
Serogrouping
Statistical analysis
Results
Phenotypic antibiotic resistance
Phylogroups (no.) | Resistant phenotypes, no. | |||||||
---|---|---|---|---|---|---|---|---|
AMP (n = 279) | TET (n = 263) | GEN (n = 232) | CHP (n = 221) | CEF (n = 212) | SXT (n = 180) | STR (n = 166) | CIP (n = 128) | |
A (n = 232) | 223 | 204 | 195 | 189 | 166 | 138 | 132 | 99 |
B1 (n = 22) | 22 | 22 | 17 | 6 | 17 | 18 | 14 | 11 |
B2 (n = 12) | 12 | 12 | 3 | 11 | 10 | 9 | 7 | 0 |
D (n = 17) | 17 | 17 | 14 | 14 | 15 | 13 | 13 | 9 |
F (n = 2) | 2 | 2 | 1 | 0 | 2 | 2 | 0 | 2 |
ND (n = 7) | 3 | 6 | 2 | 1 | 2 | 0 | 0 | 7 |
Prevalence of virulence genes
Virulence gene (s)a
| No. (%) of isolates | Phylogenetic group, no. | Serogroup, no. | ||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
A | B1 | B2 | D | F | ß | O2 | O8 | O52 | O60 | O61 | O66 | O91 | O97 | O117 | O139 | O145 | O158 | O159 | O165 | O172 | NDb
| ||
Total no. | 232 | 22 | 12 | 17 | 2 | 7 | 25 | 13 | 9 | 5 | 10 | 11 | 42 | 18 | 24 | 5 | 45 | 10 | 20 | 8 | 21 | 26 | |
sfa | 78 (26.7) | 46 | 12 | 5 | 10 | 1 | 4 | 8 | 6 | 2 | 1 | 1 | 3 | – | 11 | 12 | 3 | – | 6 | 8 | – | 5 | 12 |
eaeA | 5 (1.7) | 5 | – | – | – | – | – | 1 | – | – | – | – | – | 2 | – | – | – | 2 | – | – | – | – | – |
aer, cnf1 | 4 (1.4) | 4 | – | – | – | – | – | – | – | – | 1 | – | – | – | 1 | – | – | – | – | – | 1 | 1 | – |
eaeA, sfa | 63 (21.6) | 51 | 4 | 3 | 3 | 1 | 1 | 3 | 3 | 2 | – | – | 2 | 22 | – | 3 | – | 6 | – | – | 2 | 11 | 9 |
aer, hlyA, sfa | 3 (1.0) | 3 | – | – | – | – | – | – | – | – | – | – | – | 1 | – | – | – | 2 | – | – | – | – | – |
cnf1, eaeA, sfa | 16 (5.5) | 15 | 1 | – | – | – | – | 2 | – | – | 1 | 3 | – | – | – | – | – | – | – | 9 | 1 | – | – |
aer, etrA, hlyA, sfa | 2 (0.7) | 2 | – | – | – | – | – | – | – | 1 | – | – | – | – | – | – | – | – | 1 | – | – | – | – |
cnf1, eaeA, etrA, sfa | 45 (15.4) | 45 | – | – | – | – | – | 2 | 4 | 2 | 1 | 4 | 4 | 6 | 3 | 5 | – | 5 | 1 | – | 3 | 1 | 4 |
cnf1, eaeA, hlyA, sfa | 7 (2.4) | – | 3 | 2 | 2 | – | – | – | – | – | – | – | – | 2 | – | – | – | 2 | – | 1 | 1 | – | 1 |
cnf1, eaeA, papC, sfa | 9 (3.1) | 8 | 1 | – | – | – | – | 2 | – | – | 1 | – | – | – | 1 | 3 | – | – | – | 1 | – | 1 | – |
faeG, hlyA, papC, sfa | 2 (0.7) | 1 | – | – | – | – | 1 | – | – | – | – | – | – | – | – | – | – | 2 | – | – | – | – | – |
faeG, hlyA, rfc, sfa | 1 (0.3) | – | – | 1 | – | – | – | – | – | 1 | – | – | – | – | – | – | – | – | – | – | – | – | – |
faeG, papC, sfa, sepA | 1 (0.3) | 1 | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | 1 | – |
papC, rfc, sfa, sepA | 1 (0.3) | 1 | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | 1 | – |
aer, cnf1, eaeA, papC, sfa | 10 (3.4) | 10 | – | – | – | – | – | 2 | – | – | – | – | – | 1 | – | – | – | 7 | – | – | – | – | – |
cnf1, eaeA, hlyA, papC, sfa | 10 (3.4) | 8 | – | – | 1 | – | 1 | 2 | – | – | – | – | – | 5 | – | – | – | 3 | – | – | – | – | – |
aer, cnf1, eaeA, hlyA, papC, sfa | 9 (3.1) | 9 | – | – | – | – | – | 1 | – | 1 | – | 2 | 2 | – | – | – | – | – | 2 | 1 | – | – | – |
cnf1, eaeA, etrA, hlyA, papC, sfa | 15 (5.1) | 15 | – | – | – | – | – | – | – | – | – | – | – | 1 | – | – | 2 | 12 | – | – | – | – | – |
cnf1, etrA, faeG, papC, rfc, sfa | 1 (0.3) | – | – | – | 1 | – | – | – | – | – | – | – | – | – | 1 | – | – | – | – | – | – | – | – |
eaeA, faeG, hlyA, papC, rfc, sfa | 1 (0.3) | – | 1 | – | – | – | – | – | – | – | – | – | – | – | – | 1 | – | – | – | – | – | – | – |
aer, cnf1, eaeA, hlyA, papC, rfc, sfa | 1 (0.3) | 1 | – | – | – | – | – | – | – | – | – | – | – | – | – | – | – | 1 | – | – | – | – | – |
aer, cnf1, eaeA, etrA, faeG, papC, sfa | 8 (2.7) | 7 | – | 1 | – | – | – | 2 | – | – | – | – | – | 2 | 1 | – | – | 3 | – | – | – | – | – |
Occurrence of E. coli pathotypes
Occurrence of phylogroups
Virulence gene (n) | Associations of gene (OR, 95% confidence interval)*,a
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
No. | AMP | No. | TET | No. | GEN | No. | CHP | No. | CEF | No. | SXT | No. | STR | No. | CIP | |
sfa (223) | 214 | – | 195 | – | 186 | – | 180 | – | 157 | – | 129 | 0.07 (0.0–1.2) | 123 | 0.06 (0.0–0.1) | 90 | 0.03 (0.0–0.6) |
eaeA (174) | 165 | – | 161 | 4.3 (1.9–9.8) | 144 | – | 137 | – | 135 | 3.01 (1.6–5.6) | 120 | 4.9 (2.6–9.4) | 101 | – | 86 | 3.4 (1.7–6.7) |
cnf1 (122) | 122 | 22.9 (1.3–398.8) | 113 | 2.6 (1.1–6.1) | 110 | 2.7 (1.3–5.7) | 79 | 0.008 (0.0–0.1) | 91 | – | 76 | – | 84 | 2.8 (1.7–4.9) | 53 | – |
etrA (69) | 60 | 0.02 (0.0–0.3) | 65 | – | 55 | – | 43 | 0.2 (0.1–0.4) | 56 | 2.1 (1.04–4.1) | 31 | 0.4 (0.2–0.7) | 39 | – | 39 | 2.2(1.2–3.9) |
papC (61) | 52 | 0.02 (0.0–0.3) | 52 | – | 42 | 0.3 (0.1–0.5) | 44 | 0.3 (0.1-0.6) | 40 | – | 37 | – | 42 | 2.0 (1.1–3.7) | 16 | 0.4 (0.2–0.7) |
hlyA (39) | 30 | 0.008 (0.0–0.1) | 29 | 0.3 (0.1–0.7) | 27 | 0.3 (0.1–0.7) | 21 | 0.2 (0.08–0.4) | 27 | – | 12 | 0.2 (0.1-0.5) | 22 | – | 18 | – |
aer (36) | 36 | – | 26 | 0.3 (0.1–0.6) | 24 | 0.3 (0.1–0.6) | 14 | 0.08 (0.03–0.2) | 22 | – | 33 | 9.5 (2.8-32.1) | 26 | 2.2 (1.01–4.8) | 11 | – |
faeG (9) | 09 | – | 07 | – | 02 | 0.04 (0.0–0.2) | 06 | – | 06 | – | 08 | – | 07 | – | 02 | – |
rfc/sepA (2) | 02 | – | 02 | – | 02 | – | 02 | – | 02 | – | 02 | – | 02 | – | 02 | – |
Gene | No. (%) of isolates in phylogroup A (n = 232) | Associations of gene (OR, 95% confidence interval)*,a
| |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|
sfa | eaeA | cnf1 | etrA | papC | hlyA | aer | faeG | rfc | sepA | ||
sfa | 223 | ns |
–
|
–
| 8.5 (0.5–148.9) |
–
|
–
| 0.2 (0.1–0.8) |
–
|
–
|
–
|
eaeA | 174 |
–
| ns | 28.4 (9.8–82.4) | 17.5 (4.1–74.2) | 9.2 (2.7–30.5) |
–
|
–
|
–
|
–
| na |
cnf1 | 122 |
–
| 28.4 (9.8–82.4) | ns | 65.8 (15.5–78.6) | 32.3 (9.7–107.4) | 6.4 (2.6–16.0) | 7.1 (2.71–9.2) |
–
|
–
| na |
etrA | 69 | 8.5 (0.5–148.9) | 17.5 (4.1–74.2) | 65.8 (15.5–278.6) | ns |
–
| 2.1 (1.0–4.2) |
–
| 9.1 (1.8–44.9) | na | na |
papC | 61 |
–
| 9.2 (2.7–30.5) | 32.3 (9.7–107.4) |
–
| ns | 41.8 (15.0–116.3) | 14.3 (6.2–33.1) | 62.1 (3.5–1084.4) | 14.4 (0.7–304.5) | 14.4 (0.7–304.5) |
hlyA | 39 |
–
|
–
| 6.4 (2.6–16.0) | 2.1 (1.0–4.2) | 41.8 (15.0–116.3) | ns | 5.1 (2.3–11.3) |
–
|
–
| na |
aer | 36 | 0.2 (0.1–0.8) |
–
| 7.1 (2.7–19.2) |
–
| 14.3 (6.2–33.1) | 5.1 (2.3–11.3) | ns | 23.4 (4.6–118.2) |
–
| na |
faeG | 9 |
–
|
–
|
–
| 9.1 (1.8–44.9) | 62.1 (3.5–1084.4) |
–
| 23.4 (4.6–118.2) | ns | na | 27.7 (1.6–484.6) |
rfc | 2 |
–
|
–
|
–
|
–
| 14.4 (0.7–304.5) |
–
|
–
|
–
| ns | 229 (7.7–684.3) |
sepA | 2 |
–
|
–
| – |
–
| 14.4 (0.7–304.5) |
–
|
–
| 27.7 (1.6–484.6) | 229 (7.7–684.3) | ns |