| Literature DB >> 25807366 |
Willize E van der Starre1, Cees van Nieuwkoop2, Uginia Thomson1, Marleen S M Zijderveld-Voshart1, Jan Pieter R Koopman1, Tanny J K van der Reijden1, Jaap T van Dissel1, Esther van de Vosse1.
Abstract
OBJECTIVE/Entities:
Mesh:
Substances:
Year: 2015 PMID: 25807366 PMCID: PMC4373833 DOI: 10.1371/journal.pone.0121302
Source DB: PubMed Journal: PLoS One ISSN: 1932-6203 Impact factor: 3.240
Primer and probe sequences for the multiplex genotyping assay.
| gene | SNPid | F primer sequence | R primer sequence | Probe sequence |
|---|---|---|---|---|
|
| rs1800629 | ACGTTGGATGGGAGGCAATAGGTTTTGAGG | ACGTTGGATGTTCTGGGCCACTGACTGATT | GGCTGAACCCCGTCC |
|
| rs1800972 | ACGTTGGATGCTGTCAGCTCAGCCTCCAAA | ACGTTGGATGTCATGGCGACTGGCAGGCAA | CAGGAACTGGGGAGA |
|
| rs4293393 | ACGTTGGATGGCTGAGAATGGCTGAAAGTC | ACGTTGGATGTGTTGTACAGAGTGGGTCAG | CAGGTCCAGTGATGTC |
|
| rs8177374 | ACGTTGGATGGTACATGAATCGGAGCTCAG | ACGTTGGATGGCCGAGGGCTGCACCATCC | CACCATCCCCCTGCTGT |
|
| rs1800795 | ACGTTGGATGAGCCTCAATGACGACCTAAG | ACGTTGGATGGATTGTGCAATGTGACGTCC | GTGACGTCCTTTAGCAT |
|
| rs5743618 | ACGTTGGATGTAACTCTGCTGATCGTCACC | ACGTTGGATGTGAGATACCAGGGCAGATCC | CAGGGCAGATCCAAGTAG |
|
| rs2234671 | ACGTTGGATGGAATCTCAGTGGCATCCAGG | ACGTTGGATGTGAGGACCCAGGTGATCC | ggCAGGTGATCCAGGAGA |
|
| rs28661751 | ACGTTGGATGATCACCTCTTGCCTGGAGTG | ACGTTGGATGCAGCCATGAGGATTATCGCC | tAGGATTATCGCCCTCCTC |
|
| rs5743708 | ACGTTGGATGAAAAAAGCCATTCCCCAGCG | ACGTTGGATGCAGGTAGGTCTTGGTGTTCA | TCTTGGTGTTCATTATCTTC |
|
| rs5744168 | ACGTTGGATGTCCTGGAAAAATTACAGACC | ACGTTGGATGAGATATCGGGTATGCTTGG | GGTTGTAAGAGCATTGTCTC |
|
| rs6853 | ACGTTGGATGGCGTACAAAACATGTAGAAG | ACGTTGGATGCACCTGTCCCCCTTTAATAC | ccGGCATTTTAAAGCCATCTC |
|
| rs736227 | ACGTTGGATGGTTCCCAGCATGACATTCTC | ACGTTGGATGGTTTCACATACTGCTGCACG | ggtgaACGCGTGTCGATTAAC |
|
| rs3138060 | ACGTTGGATGTGTGGGAGCTGAGGATTTCT | ACGTTGGATGTCCTCTTCACCTGCTAACTC | CTGCTAACTCCATGTATGAGTG |
|
| rs4073 | ACGTTGGATGGGTACTATGATAAAGTTATCT | ACGTTGGATGCTGAAGCTCCACAATTTGGT | CTCCACAATTTGGTGAATTATCAA |
|
| rs10499563 | ACGTTGGATGAAGCCTGGTCTGGCCTGTAT | ACGTTGGATGACCTGAAAGGAGGTAGCAGA | GATTTCTTAATTATTATACAAGCACA |
Baseline characteristics of the study population.
| controls, | febrile UTI | febrile UTI | |
|---|---|---|---|
| without bacteremia, | with bacteremia, | ||
|
|
|
| |
| Age in years, median [IQR] | 58 [49–75] | 63 [46–75] | 73 [60–82] |
| Male sex | 18 (39) | 16 (36) | 18 (39) |
|
| |||
| Any | 24 (52) | 33 (73) | 36 (78) |
| Urinary tract disorder a | 5 (11) | 10 (22) | 9 (20) |
| Urinary catheter | 0 (0) | 2 (4) | 3 (7) |
| History of nephrolithiasis | 5 (11) | 4 (9) | 5 (11) |
| Recurrent UTIs b | 1 (2) | 16 (36) | 6 (13) |
| Diabetes mellitus | 3 (7) | 5 (11) | 12 (26) |
| Malignancy | 2 (4) | 2 (4) | 4 (9) |
| Hypertension | 17 (37) | 24 (53) | 26 (57) |
| Heart failure | 0 (0) | 5 (11) | 8 (17) |
| Cerebrovascular disease | 1 (2) | 5 (11) | 12 (26) |
| Chronic renal insufficiency | 0 (0) | 3 (7) | 6 (13) |
| COPD | 2 (4) | 7 (16) | 3 (7) |
|
| |||
| Immunosuppressants | 1 (2) | 1 (2) | 4 (9) |
| Vitamin D supplements | 2 (4) | 4 (9) | 4 (9) |
|
| |||
| Winter (Dec—Feb) | 46 (100) | 8 (18) | 5 (11) |
| Spring (Mar—May) | - | 6 (13) | 10 (22) |
| Summer (June—Aug) | - | 11 (24) | 17 (37) |
| Fall (Sept—Nov) | - | 20 (44) | 14 (30) |
|
| |||
| Mean BMI in kg/m2 (sd) | 26.5 (4.6) | 26.6 (4.0) | 27.3 (7.2) |
Data are presented as n (%) unless otherwise stated. UTI = urinary tract infection, IQR = interquartile range, sd = standard deviation, COPD = chronic obstructive pulmonary disease, BMI = body mass index. a Defined as any functional or anatomical abnormality of the urinary tract except urinary catheter and history of nephrolithiasis. b Defined as ≥2 UTIs in the last 6 months or ≥3 UTIs in the last 12 months. c Eight missing BMI data: 2 in controls, 1 in UTI without bacteremia and 5 in UTI with bacteremia.
Plasma 25(OH)D concentrations and vitamin D status.
| controls, | febrile UTI without | febrile UTI with | |
|---|---|---|---|
|
| bacteremia, | bacteremia, | |
| Median 25(OH)D in ng/ml [IQR] | 17.6 [13.9–26.4] | 19.5 [14.1–26.1] | 17.9 [9.4–24.7] |
| vitamin D sufficient | 6 (13%) | 6 (14%) | 8 (18%) |
| vitamin D insufficient | 14 (30%) | 15 (35%) | 11 (25%) |
| vitamin D deficient | 26 (57%) | 22 (51%) | 25 (57%) |
UTI = urinary tract infection, IQR = interquartile range. Vitamin D sufficiency is defined as 25(OH)D of ≥30 ng/ml, vitamin D insufficiency is defined as 25(OH)D >20 and <30 ng/ml, vitamin D deficiency is defined as 25(OH)D of ≤ 20 ng/ml.
Genotypes of genetic variations in controls and UTI patients.
| common name | controls | UTI patients | ||||
|---|---|---|---|---|---|---|
| Gene | SNPid | or location | genotypes | genotypes, n (%) | genotypes, n (%) | p-value |
|
| rs3138060 | 217C>G | CC | 380 (87.6%) | 623 (88.3%) | 0.581 |
| in intron | CG | 52 (12.0%) | 82 (11.6%) | |||
| GG | 2 (0.4%) | 1 (0.1%) | ||||
|
| rs2234671 | 2608 G/C | GG | 379 (87.1%) | 620 (88.0%) | 0.574 |
| Ser276Thr | CG | 54 (12.4%) | 84 (11.9%) | |||
| CC | 2 (0.5%) | 1 (0.1%) | ||||
|
| rs28661751 | A8P | CC | 427 (98.4%) | 700 (99.3%) | 0.373 |
| CG | 7 (1.6%) | 6 (0.7%) | ||||
| GG | 0 | 0 | ||||
|
| rs736227 | in 3’UTR | TT | 196 (45.4%) | 324 (46.1%) | 0.962 |
| CT | 196 (45.4%) | 313 (44.5%) | ||||
| CC | 40 (9.2%) | 66 (9.4%) | ||||
|
| rs1800972 | -44C>G | CC | 264 (60.8%) | 426 (60.4%) | 0.450 |
| -668C>G | CG | 147 (33.9%) | 252 (35.7%) | |||
| GG | 23 (5.3%) | 27 (3.8%) | ||||
|
| rs10499563 | -6331T>C | TT | 277 (63.8%) | 403 (57.4%) | 0.100 |
| CT | 141 (32.5%) | 269 (38.3%) | ||||
| CC | 16 (3.7%) | 30 (4.3%) | ||||
|
| rs1800795 | -174G>C | GG | 147 (33.7%) | 249 (35.2%) | 0.711 |
| CG | 209 (47.9%) | 340 (48.2%) | ||||
| CC | 80 (18.4) | 117 (16.6%) | ||||
|
| rs4073 | -251A/T | TT | 130 (29.9%) | 207 (29.4%) | 0.985 |
| AT | 212 (48.7%) | 346 (49.1%) | ||||
| AA | 93 (21.4%) | 151 (21.5%) | ||||
|
| rs6853 | in 3’UTR | AA | 331 (76.6%) | 551 (78.6%) | 0.120 |
| AG | 92 (21.3%) | 145 (20.7%) | ||||
| GG | 9 (2.1%) | 5 (0.7%) | ||||
|
| rs4293393 | 5’ near gene | TT | 286 (65.9%) | 460 (65.2%) | 0.354 |
| CT | 127 (29.3%) | 220 (31.1%) | ||||
| CC | 21 (4.8%) | 26 (3.7%) | ||||
|
| rs8177374 | S180L | CC | 310 (71.1%) | 498 (70.0%) | 0.995 |
| C539T | CT | 116 (26.6%) | 189 (26.7%) | |||
| TT | 10 (2.3%) | 16 (2.3%) | ||||
|
| rs5743618 | 1805 G/T | GG | 179 (42.0%) | 315 (45.4%) | 0.379 |
| S602I | GT | 193 (45.3%) | 285 (41.1%) | |||
| TT | 54 (12.7%) | 94 (13.5%) | ||||
|
| rs5743708 | Arg753Gln | GG | 408 (93.2%) | 662 (93.8%) | 0.773 |
| R753Q | AG | 30 (6.8%) | 44 (6.2%) | |||
| AA | 0 | 0 | ||||
|
| rs5744168 | R392X | CC | 363 (84.2%) | 626 (89.0%) | 0.072 |
| Arg392Stop | CT | 63 (14.6%) | 72 (10.2%) | |||
| 1174C>T | TT | 5 (1.2%) | 6 (0.8%) | |||
|
| rs1800629 | -308 G/A | GG | 282 (64.6%) | 486 (68.8%) | 0.170 |
| in promoter | AG | 144 (33.0%) | 197 (27.9%) | |||
| AA | 11 (2.5%) | 23 (3.3%) |
* name used in the literature
Genotypes of IL6 variation in UTI patients with and without bacteremia.
| UTI without | UTI with | p-value | |||
|---|---|---|---|---|---|
| Gene | SNPid | genotypes | bacteremia n (%) | bacteremia n (%) | |
|
| rs1800795 | CC | 76 (15.0%) | 37 (23.9%) | 0.009 |
| CG | 257 (50.9%) | 57 (36.8%) | |||
| GG | 172 (34.1%) | 61 (39.3%) |