Background
Methods
Sample collection and antibiotic susceptibility testing
Phylogeny, serotyping, and fumC/fimH typing
Detection of β-lactamases and virulence factor genes
Statistical analysis
Results
Phylogeny and sequence typing
Numbers and percentagesof isolates and their respective traits (n = 155) | ||||||
---|---|---|---|---|---|---|
Resistance traits | Total Isolates (n = 155)n (%) | Group A (n = 8)n(%) | Group B1 (n = 12) n(%) | Group B2 (n = 92) n(%) | Group D (n = 43)n(%) | p value |
ESBL phenotypes | 65(42) | 1(13) | 3(25) | 36(39) | 25(58) | 0.0268 |
blaCTX-M-15 | 57(37) | 1(13) | 3(25) | 32(35) | 21(49) | 0.1333 |
blaTEM | 23(15) | 1(13) | 3(25) | 13(14) | 6(14) | 0.7823 |
blaSHV | 6(4) | 00 | 00 | 3(3) | 3(7) | 0.0907 |
blaOXA | 10(6) | 00 | 1(8) | 4(4) | 5(12) | 0.3610 |
blaPSE | 1(0.6) | 00 | 00 | 1(1) | 00 | 0.8783 |
Piperacillin tazobactam | 7(5) | 00 | 1(8) | 4(4) | 2(5) | 0.8514 |
Ceftazidime | 96(62) | 3(38) | 7(58) | 54(59) | 32(74) | 0.1483 |
Cefotaxime | 101(65) | 3(38) | 7(58) | 59(64) | 32(74) | 0.2028 |
Ceftriaxone | 99(64) | 3(38) | 8(67) | 59(64) | 29(67) | 0.4001 |
Ciprofloxacin | 95(61) | 6(75) | 7(58) | 56(90) | 26(60) | 0.4001 |
Levofloxacin | 97(63) | 7(88) | 8(67) | 56(90) | 26(60) | 0.4929 |
Amikacin | 7(5) | 1(13) | 00 | 5(5) | 1(2) | 0.4920 |
Gentamicin | 47(30) | 4(50) | 6(50) | 24(26) | 13(30) | 0.2171 |
Amoxicillin-clavulanic acid | 111(72) | 5(63) | 7(58) | 66(72) | 26(60) | 0.5224 |
Trimethoprim sulfonamides | 130(84) | 7(88) | 11(92) | 77(84) | 35(81) | 0.8461 |
Nitrofurantoin | 9(6) | 1(13) | 1(8) | 6(7) | 1(2) | 0.6075 |
Fosfomycin | 15(10) | 1(13) | 2(17) | 8(9) | 4(9) | 0.8370 |
fimH
| 155 (100) | 8 (100) | 12 (100) | 92 (100) | 43 (100) | > 0.9999 |
papA
| 20 (13) | 1 (13) | 1 (8) | 12 (13) | 6 (14) | 0.9659 |
papC
| 75 (48) | 2 (25) | 8 (67) | 43 (47) | 22 (51) | 0.3092 |
papEF
| 37 (24) | 0 | 6 (50) | 19 (21) | 12 (28) | 0.0476 |
papGI
| 6 (4) | 0 | 0 | 3 (3) | 3 (7) | 0.5699 |
papGII
| 70 (45) | 2 (25) | 7 (58) | 37 (40) | 24 (53) | 0.1695 |
papGIII
| 6 (4) | 0 | 0 | 4 (4) | 2 (5) | 0.8177 |
sfa/foc
| 20 (13) | 2 (25) | 1 (8) | 13 (14) | 4 (9) | 0.5968 |
Afa
| 15 (10) | 0 | 1 (8) | 10 (11) | 4 (9) | 0.7919 |
bmaE
| 2 (1) | 0 | 1 (8) | 1 (1) | 0 | 0.1466 |
fyuA
| 37 (24) | 1 (13) | 2 (17) | 21 (23) | 13 (30) | 0.5882 |
iutA
| 86 (55) | 5 (63) | 5 (42) | 52 (57) | 24 (56) | 0.7701 |
feoB
| 76 (49) | 3 (38) | 6 (50) | 40 (43) | 27 (63) | 0.1852 |
kpsmtII
| 40 (26) | 0 | 4 (33) | 21 (23) | 15 (35) | 0.1438 |
kpsmtIII
| 4 (3) | 0 | 1 (8) | 3 (3) | 0 | 0.3765 |
Usp
| 22 (14) | 2 (25) | 2 (17) | 14 (15) | 4 (9) | 0.6256 |
hlyA
| 18 (12) | 1 (13) | 3 (25) | 6 (7) | 8 (19) | 0.0908 |
cdtB
| 11 (7) | 0 | 3 (25) | 6 (7) | 2 (5) | 0.0758 |
Numbers and percentages of the sequence typed isolates (n = 155) | |||
---|---|---|---|
No of isolates in group n (%) | No of MDR isolates n (%) | ESBL+FQR-MDR isolates n (%) | p value |
Group A 8(5) | 7(88) | 2(25) | 0.0117 |
Group B112(8) | 10(83) | 5(42) | 0.0350 |
Group B2 92(59) | 71(77) | 33(36) | < 0.0001 |
Group D 43(28) | 36(84) | 11(26) | < 0.0001 |
ST131 71(46) | 57(82) | 22(31) | < 0.0001 |
H30 35(49) | 28(80) | 10(29) | < 0.0001 |
Non H30 36(51) | 29(81) | 12(33) | < 0.0001 |
ST405 28(18) | 24(86) | 10(36) | 0.0001 |
ST168 16(10) | 14(88) | 7(44) | 0.0092 |
ST2913(8) | 9(69) | 5(38) | 0.1156 |
ST69 5(3) | 5(100) | 2(40) | 0.0384 |
ST95 2(1) | 2(100) | 00 | |
ST31 2(1) | 00 | 00 | |
ST10 2(1) | 1(50) | 00 | |
ST4482(1) | 1(50) | 00 | |
ST892(1) | 2(100) | 1(50) | 0.2482 |
ST7032(1) | 2(100) | 00 | |
ST910 1(1) | 1(100) | 00 | |
ST5451(1) | 00 | 00 | |
ST9711(1) | 00 | 00 | |
ST1531(1) | 00 | 00 | |
ST1521(1) | 1(100) | 00 | |
ST121(1) | 1(100) | 00 | |
ST8381(1) | 0(100) | 00 | |
NSC3(2) | 2(67) | 2(67) | > 0.9999 |
MDR among ST131 strains
No (%) of the isolates | ||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ST131; n(%) | Other STs; n (%) | |||||||||||||||||||||
Resistance traits | All isolates (n = 155) | All ST131 (n = 71) | Non H30 (n = 35) | H30 (n = 36) | ST405 (n = 28) | ST168 (n = 16) | ST29 (n = 13) | ST69 (n = 5) | ST95 (n = 2) | ST31 (n = 2) | ST10 (n = 2) | ST448 (n = 2) | ST89 (n = 2) | ST703 (n = 2) | ST910 (n = 1) | ST545 (n = 1) | ST971 (n = 1) | ST153 (n = 1) | ST152 (n = 1) | ST12 (n = 1) | ST838 (n = 1) | NSC (n = 3) |
ESBL phenotypes | 65(42) | 30(42) | 15(43) | 15(42) | 13(46) | 8(50) | 7(54) | 2(40) | 00 | 00 | 1(50) | 00 | 1(50) | 00 | 00 | 00 | 00 | 00 | 1(100) | 00 | 00 | 2(67) |
blaCTX-M-15 | 57(39) | 27(38) | 12(34) | 15(42) | 11(39) | 8(50) | 6(46) | 2(40) | 00 | 00 | 1(50) | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 2(67) |
blaTEM | 23(15) | 8(11) | 5(14) | 3(8) | 5(18) | 5(31) | 3(23) | 2(40) | 00 | 00 | 1(50) | 00 | 1(50) | 00 | 00 | 00 | 00 | 00 | 1(100) | 00 | 00 | 00 |
blaSHV | 6(4) | 3(4) | 1(3) | 2(6) | 1(4) | 2(13) | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 |
blaOXA | 10(6) | 6(8) | 3(9) | 3(8) | 3(11) | 1(6) | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 |
blaPSE | 1(0.6) | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 1(100) | 00 | 00 | 00 | 00 | 00 | 00 | 00 |
Piperacillin tazobactam | 7(5) | 3(4) | 2(6) | 0(0) | 3(11) | 2(13) | 00 | 00 | 1(50) | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 |
Ceftazidime | 96(62) | 43(61) | 20(57)7 | 23(64) | 20(71) | 10(63) | 9(69) | 5(100) | 1(50) | 00 | 00 | 00 | 1(50) | 2(100) | 1(100) | 00 | 00 | 00 | 00 | 1(100) | 00 | 00 |
Cefotaxime | 101(65) | 46(65) | 22(63) | 24(67) | 20(71) | 10(63) | 9(69) | 5(100) | 2(100) | 00 | 1(50) | 1(50) | 1(50) | 2(100) | 1(100) | 00 | 00 | 00 | 1(100) | 00 | 00 | 00 |
Ceftriaxone | 99(64) | 46(65) | 25(71) | 21(58) | 21(75) | 10(63) | 9(69) | 2(40) | 1(50) | 00 | 00 | 1(50) | 1(50) | 1(50) | 1(100) | 1(100) | 00 | 00 | 1(100) | 1(100) | 1(100) | 2(67) |
Ciprofloxacin | 95(61) | 45(63) | 23(66) | 22(61) | 18(64) | 13(81) | 6(46) | 4(80) | 2(100) | 1(50) | 1(50) | 1(50) | 00 | 2(100) | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 2(67) |
Levofloxacin | 97(63) | 45(63) | 24(69) | 21(58) | 19(68) | 14*(88) | 6(46) | 4(80) | 2(100) | 1(50) | 2(100) | 00 | 2(100) | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 2(67) |
Amikacin | 7(5) | 4(6) | 2(6) | 2(6) | 00 | 1(6) | 1(8) | 1(20) | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 |
Gentamicin | 47(30) | 21(30) | 11(31) | 10(28) | 10(36) | 5(31) | 3(23) | 1(20) | 2(100) | 00 | 1(50) | 1(50) | 00 | 2(100) | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 1(33) |
Amoxicillin-clavulanic acid | 111(72) | 48(68) | 25(71) | 23(64) | 22(79) | 10(63) | 9(69) | 2(40) | 00 | 00 | 00 | 1(50) | 1(50) | 1(50) | 1(100) | 1(100) | 00 | 00 | 1(100) | 1(100) | 1(100) | 2(67) |
Trimethoprim sulfonamides | 130(84) | 61(86) | 30(86) | 31(86) | 24(86) | 13(81) | 10(77) | 4(80) | 2(100) | 1(50) | 1(50) | 1(50) | 2(100) | 2(100) | 1(100) | 1(100) | 1(100) | 1(100) | 1(100) | 1(100) | 00 | 3(100) |
Nitrofurantoin | 9(6) | 9(13)*** | 6(17)*** | 3(8) | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 | 00 |
Fosfomycin | 15(10) | 9(13) | 3(9) | 6(17) | 00 | 2(13) | 00 | 00 | 00 | 1(50) | 00 | 1(50) | 1(50) | 00 | 00 | 00 | 00 | 00 | 1(100) | 00 | 00 | 00 |
Occurrence of β-lactamases among ST131
Numbers and percentages of the isolates andtheir respective traits | ||||
---|---|---|---|---|
Resistance traits | All isolates (n = 155); n(%) | Non ESBL producers (n = 90) n(%) | ESBL producers (n = 65) n(%) | p value |
Piperacillin tazobactam | 7(5) | 4(4) | 3(5) | > 0.9999 |
Ceftazidime | 96(62) | 36(40) | 60(92) | < 0.0001 |
Cefotaxime | 101(65) | 40(44) | 61(94) | < 0.0001 |
Ceftriaxone | 99(64) | 49(54) | 50(77) | 0.0040 |
Ciprofloxacin | 95(61) | 45(50) | 50(77) | 0.000684 |
Levofloxacin | 97(63) | 48(53) | 49(75) | 0.0051 |
Amikacin | 7(5) | 4(4) | 3(5) | 0.9597 |
Gentamicin | 47(30) | 30(33) | 17(26) | 0.3373 |
Amoxicillin-clavulanic acid | 111(72) | 50(56) | 61(94) | < 0.0001 |
Trimethoprim sulfonamides | 130(84) | 67(74) | 63(97) | 0.0002 |
Nitrofurantoin | 9(6) | 6(7) | 3(5) | 0.5900 |
Fosfomycin | 15(10) | 8(9) | 7(11) | 0.6960 |
fimH
| 155 (100) | 90 (100) | 65 (100) | > 0.9999 |
papA
| 20 (13) | 12 (13) | 8 (12) | 0.8509 |
papC
| 75 (48) | 42 (47) | 33 (51) | 0.6140 |
papEF
| 37 (24) | 18 (20) | 19 (29) | 0.1834 |
papGI
| 6 (4) | 3 (3) | 3 (5) | 0.6831 |
papGII
| 70 (45) | 33 (37) | 37 (57) | 0.0124 |
papGIII
| 6 (4) | 4 (4) | 2 (3) | 0.6632 |
sfa/foc
| 20 (13) | 11 (12) | 9 (14) | 0.7660 |
Afa
| 15 (10) | 7 (8) | 8 (12) | 0.3466 |
bmaE
| 2 (1) | 1 (1) | 1 (2) | 0.8246 |
fyuA
| 37 (24) | 20 (22) | 17 (26) | 0.5710 |
iutA
| 86 (55) | 45 (50) | 41 (63) | 0.1060 |
feoB
| 76 (49) | 40 (44) | 36 (55) | 0.1788 |
kpsmtII
| 40 (26) | 19 (21) | 21 (32) | 0.1160 |
kpsmtIII
| 4 (3) | 2 (2) | 2 (3) | 0.4729 |
Usp
| 22 (14) | 10 (9) | 12 (18) | 0.1957 |
hlyA
| 18 (12) | 7 (8) | 11 (17) | 0.0795 |
cdtB
| 11 (7) | 6 (7) | 5 (8) | 0.8062 |
Distribution of VF genes among different sequence types
Number of the isolates with traits n(%) | ||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Traits | Total n = 155 | ST-131 n = 71 | NonH30 n = 35 | H30 n = 36 | ST-05 n = 28 | ST-168 n = 16 | ST-29 n = 13 | ST-69 n = 5 | ST-95 n = 2 | ST-31 n = 2 | ST-10 n = 2 | ST-448 n = 2 | ST-89 n = 2 | ST-703 n = 2 | ST-910 n = 1 | ST-545 n = 1 | ST-971 n = 1 | ST-153 n = 1 | ST-152 n = 1 | ST-12 n = 1 | ST-838 n = 1 | NSC n = 3 |
fimH
| 155 (100) | 71 (100) | 35 (100) | 36 (100) | 28 (100) | 16 (100) | 13 (100) | 5 (100) | 2 (100) | 2 (100) | 2 (100) | 2 (100) | 2 (100) | 2 (100) | 1 (100) | 1 (100) | 1 (100) | 1 (100) | 1 (100) | 1 (100) | 1 (100) | 3 (100) |
papA
| 20 (13) | 12 (17) | 5 (14) | 7 (19) | 4 (14) | 1 (6) | 0 | 0 | 0 | 0 | 0 | 1 (50) | 0 | 0 | 0 | 0 | 0 | 1(100) | 0 | 0 | 0 | 1 (33) |
papC
| 75 (48) | 33 (46) | 17 (49) | 16 (44) | 15 (54) | 9 (56) | 5 (38) | 3 (60) | 1 (50) | 1 (50) | 0 | 0 | 1 (50) | 1 (50) | 1 (100) | 0 | 1 (100) | 1 (100) | 0 | 0 | 1 (100) | 2 (67) |
papEF
| 37 (24) | 20 (28) | 7 (20) | 13* (36) | 7 (25) | 3 (19) | 3 (23) | 1 (20) | 0 | 0 | 0 | 1 (50) | 0 | 0 | 0 | 1 (100) | 1 (100) | 0 | 0 | 0 | 0 | 1 (33) |
papGI
| 6 (4) | 2 (3) | 0 | 2 (6) | 1 (4) | 1 (6) | 0 | 1 (20) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 (33) |
papGII
| 70 (45) | 32 (45) | 17 (49) | 15 (42) | 12 (43) | 6 (38) | 4 (31) | 4 (80) | 2 (100) | 0 | 2 (100) | 1 (50) | 2 (100) | 1 (50) | 0 | 1 (100) | 0 | 0 | 0 | 1 (100) | 0 | 2 (67) |
papGIII
| 6 (4) | 4 (6) | 1 (3) | 3 (8) | 1 (4) | 1 (6) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
sfa/foc
| 20 (13) | 13* (18) | 4 (11) | 9* (25) | 2 (7) | 1 (6) | 1 (8) | 0 | 1 (50) | 0 | 1 (50) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 (33) |
afa
| 15 (10) | 7 (10) | 4 (11) | 3 (8) | 6*(21) | 1 (6) | 1 (8) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
bmaE
| 2 (1) | 1 (1) | 1 (3) | 0 | 0 | 1 (6) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
fyuA
| 37 (24) | 12*(17) | 7 (20) | 5 (14) | 10 (36) | 6 (38) | 2 (15) | 2 (40) | 0 | 0 | 2(100) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 (100) | 1 (100) | 0 | 1 (33) |
iutA
| 86 (55) | 41 (58) | 22*** (63) | 19 (53) | 14 (50) | 10 (63) | 5 (38) | 3 (60) | 2 (100) | 1 (50) | 2 (100) | 1 (50) | 1 (50) | 1 (50) | 1 (100) | 0 | 1 (100) | 0 | 1 (100) | 0 | 0 | 2 (67) |
feoB
| 76 (49) | 28* (39) | 13 (37) | 15 (42) | 12 (43) | 10 (63) | 6 (46) | 4 (80) | 2 (100) | 1 (50) | 2 (100) | 1 (50) | 2 (100) | 2 (100) | 1 (100) | 0 | 1 (100) | 0 | 1 (100) | 1 (100) | 0 | 2 (67) |
kpsmtII
| 40 (26) | 20 (28) | 9 (26) | 11 (31) | 8 (29) | 2 (13) | 2 (15) | 2 (40) | 0 | 0 | 0 | 1 (50) | 0 | 0 | 0 | 0 | 0 | 0 | 1 (100) | 1 (100) | 1 (100) | 2 (67) |
kpsmtIII
| 4 (3) | 2 (3) | 0 | 2 (6) | 0 | 0 | 0 | 1 (20) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 (100) | 0 | 0 | 0 | 0 | 0 | 0 |
usp
| 22 (14) | 13 (18) | 5 (14) | 8 (22) | 2 (7) | 3 (19) | 1 (8) | 0 | 0 | 0 | 1 (50) | 0 | 0 | 0 | 0 | 1(100) | 0 | 0 | 0 | 0 | 0 | 1 (33) |
hlyA
| 18 (12) | 8 (11) | 1 (3) | 7* (32) | 5 (18) | 1 (6) | 1 (8) | 0 | 1 (50) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 (100) | 0 | 1 (33) |
cdtB
| 11 (7) | 4 (6) | 1 (3) | 3 (8) | 4 (14) | 1 (6) | 0 | 0 | 1(50) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 (33) |