Bacterial Morphotypes as Important Trait for Uropathogenic E. coli Diagnostic; a Virulence-Phenotype-Phylogeny Study
Abstract
:1. Introduction
2. Materials and Methods
2.1. Urine Samples Collection
2.2. Urinalysis and Detection of UPEC Morphotypes in Urine Sediment
2.3. Urine Cultures and Biochemical Identification of Obtained Bacterial Isolates
2.4. DNA Extraction
2.5. Molecular Identification of E. coli
2.6. Identification of Phylogenetic Groups
2.7. Genotypic Characterization of UPEC Isolates
2.8. Phenotypic Characterization of UPEC Isolates
2.8.1. Motility Test
2.8.2. α-Hemolysin Production
2.8.3. Biofilm Formation Assay
2.8.4. Capsule Production
2.8.5. Adherence Assay
2.8.6. Antibiotic Resistance
2.9. Statistical Analysis
2.10. Ethic Statements
3. Results
3.1. Clinical Characteristics of Adult Women with UTI
3.2. Urine Cultures
3.3. UPEC Morphotypes in Urine Sediment of Patients with UTI
3.4. Prevalence of Virulence Associated Genes
3.5. Virulence Phenotypes of Clinical Isolates of UPEC
3.6. Antibiotic Resistance Phenotypes
3.7. Phylogenetic Groups of Obtained Clinical Isolates
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Acknowledgments
Conflicts of Interest
References
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Gene | Sequence (5′-3′) | Size Product | Tm °C | Reference |
---|---|---|---|---|
fimH | Forward: TTATGGCGGCGTGTTATC Reverse: TCCCTACTGCTCCTAACG | 545 bp | 54 | This study |
sfaD/focC | Forward: AGGCAAATGGACAGGTATGG Reverse: TCACCCAGAACAAACTTTCC | 412 bp | This study | |
papG-II | Forward: ATTCACCATAGAGGCGACTG Reverse: ATCATTATGCGGCTCAGAC | 237 bp | This study | |
papC | Forward: TTCTCTCTCCCTCAATACGG Reverse: TTATAACCTCAACGGGACGG | 926 bp | This study | |
fliCD | Forward: CCGAATCAGAGTTAGTTCCG Reverse: CCCAGCGATGAAATACTTGC | 610 bp | 60 | This study |
sat | Forward: GTTGGCAAACAGGTCAAAC Reverse: CTCGGAGTATTGGCTTCAG | 809 bp | This study | |
hlyA | Forward: GATACGCTGATAGGTGAG Reverse: CCAGGTGTGACTCAATAC | 564 bp | 58 | This study |
kpsM | Forward: CCAGAGTAGATATGACCAG Reverse: CTACGAGAAATACGAACAC | 409 bp | This study | |
agn43 | Forward: CACACAGCCACTAATACC Reverse: CACCTGAATACCCTTACC | 488 bp | 58 | This study |
vat | Forward: ATACAGTCTCGTCTCTGG Reverse GTGACAGTCCCTTTATCC | 670 bp | This study | |
cnf-1 | Forward: CAGACTCATCTTCACTCG Reverse: AGACAGAGACCTTACGAC | 551 bp | This study | |
traT | Forward: TGGTATAGTTCACATCTTCC Reverse: TAAAGCCTACTACTGGATTC | 233 bp | This study | |
fyuA | Forward: CGCCAGTAAACAATCTTCCC Reverse: CCCAAACACCATATCAACGG | 937 bp | 60 | This study |
iucD | Forward: CGTGAGACCCAGTTTATTTCC Reverse: GGGCTGCTGAAGATATGAATAACC | 334 bp | This study | |
iroN | Forward: CAGAATGATGCGGTAACTCC Reverse: CGTGAGACCCAGTTTATTTCC | 435 bp | This study | |
iutA | Forward: GTTCACGCTCTTTGTCAGG Reverse: GGGCTTAATCTCGGGAAAGG | 801 bp | This study | |
feoB | Forward: GTCTAACCTTGAGCGTAACC Reverse: GGCGAGGAAGATAGTCAGC | 736 bp | This study | |
iha | Forward: TGTGCTCTGGTTTGATATGG Reverse: CATTCTGGGTGCCTTATATCC | 594 bp | This study | |
ybbW | Forward: TGATTGGCAAAATCTGGCCG Reverse: ATACTGGCAATCAGTACGCC | 667 bp | [20] |
(a) Included Patients’ Groups (n = 85) | (b) Patients with UTI Caused by UPEC (n = 37) | |||||
---|---|---|---|---|---|---|
With UTI n = 40 (%) | Without UTI n = 45 (%) | p | With Morphotype n = 24 (%) | Without Morphotype n = 13 (%) | p | |
Urinalysis | ||||||
pH: | ||||||
5.0–6.5 | 33 (83) | 39 (87) | 0.55 | 22 (92) | 11 (85) | 0.6 |
7.0–8.0 | 7 (17) | 6 (13) | 2 (8) | 2 (15) | ||
LE: | ||||||
Positive | 25 (63) * | 12 (27) | 0.002 | 16 (67) | 7 (53) | 0.49 |
Negative | 15 (37) | 33 (73) | 8 (33) | 6 (46) | ||
Pyuria: | ||||||
Positive (>5 WBCs/HPF) | 31 (78) * | 13 (29) | <0.0001 | 14 (58) | 10 (85) | 0.72 |
Negative (<5 WBCs/HPF) | 9 (22) | 32 (71) | 10 (42) | 4 (15) | ||
Bacteriuria: | ||||||
>2+ | 23 (58) | 0 (0) | <0.0001 | 7 (29) | 13 (100) | <0.0001 |
<2+ | 17 (42) | 45 (100) * | 17 (71) * | 0 (0) | ||
Comorbidities | ||||||
Diabetes | 11 (28) | 12 (27) | >0.99 | 7 (29) | 4 (31) | >0.99 |
Renal failure | 3 (8) | 3 (7) | >0.99 | 1 (4) | 2 (15) | 0.28 |
Hypertension | 10 (25) | 12 (27) | >0.99 | 5 (20) | 3 (23) | >0.99 |
Diagnosed ITU | 6 (15) | 2 (4) | 0.12 | 3 (13) | 3 (23) | 0.64 |
Vaginal infection | 4 (10) | 4 (9) | >0.99 | 0 (0) * | 3 (23) | 0.037 |
Pregnancy | 3 (8) | 1 (2) | 0.33 | 2 (8) | 1 (8) | >0.99 |
Hypothyroidism | 1 (3) | 5 (11) | 0.2 | 0 (0) | 1 (8) | 0.35 |
Urine culture | ||||||
<100,000 CFU/mL | 17 (43) | 45 (100) * | <0.0001 | 17 (71) | - | <0.0001 |
>100,000 CFU/mL | 20 (50) | 0 (0) | 7 (29) | 13 (100%) |
Virulence Profile | Clinical Isolates |
---|---|
fimH, feoB, fliCD, cnf-1, sfaD/focC | 2,4–6,9–13,16,20,22–24,29,31,33–37,39–40 |
fimH, feoB, fliCD, cnf-1, sfaD/focC, traT, papG-II, kpsM | 2,5,6,9,12,13,20,23,37 |
fimH. feoB, fliCD, cnf-1, sfaD/focC, traT, papG-II, kpsM, vat, sat | 5,6,12,37 |
Gene | % (n = 40) | r | p | Reported PAI a |
---|---|---|---|---|
papG-II: | PAI I, IICFT073, PAI I-V536, PAI I-IIJ96 | |||
papC | 32.5 | 0.49 | 0.001 | PAI I-IICFT073 |
vat | 40 | 0.47 | 0.002 | Not named PAI Ec222 |
iroN | 45 | 0.38 | 0.017 | PAI III536 |
fyuA | 42.5 | 0.39 | 0.012 | PAI IICFT073, PAI III, IV536 |
sfaD/focC | 72.5 | 0.54 | <0.001 | PAI I, IICFT073, PAI I-IVJ96, PAI I-IIJ96, PAI I-III536 |
papC: | PAI IICFT073 | |||
iroN | 30 | 0.38 | 0.0141 | PAI III536 |
fyuA | 30 | 0.45 | 0.003 | PAI IICFT073, PAI III, IV536 |
sat: | PAI IICFT073 | |||
vat | 27.5 | 0.35 | 0.028 | Not named PAI Ec222 |
iroN | 35 | 0.46 | 0.002 | PAI III536 |
fyuA | 35 | 0.53 | <0.001 | PAI IICFT073, PAI III, IV536 |
kpsM | 32.5 | 0.35 | 0.02 | PAI V536 |
iucD | 35 | 0.39 | 0.01 | PAI IICFT073, PAI III-IV536, Not named PAI UMN026 |
hlyA: | PAI ICFT073, PAI I-II536, PAI I-IIJ96 | |||
kpsM | 35 | 0.53 | <0.001 | PAI V536 |
cnf-1 | 35 | 0.33 | 0.04 | PAI IIJ96 |
vat: | Not named PAI Ec222 | |||
cnf-1 | 42.5 | 0.32 | 0.05 | PAI IIJ96 |
cnf-1: | PAI IIJ96 | |||
iha | 37.5 | 0.35 | 0.025 | PAI I, IICFT073, PAI I-IVJ96, PAI I-IIJ96, PAI I-II536 |
KpsM | 52.5 | 0.35 | 0.025 | PAI V536 |
iroN: | PAI III536 | |||
fyuA | 47.5 | 0.59 | <0.001 | PAI IICFT073, PAI III, IV536 |
Gene | NT n = 10 (%) | p | B1 n = 10 (%) | p | B2 n = 11 (%) | p | C n = 3 (%) | p | E n = 6 (%) | p | Total n = 40 (%) |
---|---|---|---|---|---|---|---|---|---|---|---|
fimH | 10 (100) | 1 | 10 (100) | 1 | 11 (100) | 1 | 3 (100) | 1 | 6 (100) | 1 | 14 (35) |
papC | 2 (20) | 0.7 | 2 (20) | 0.7 | 7 (64) | 0.02 | 0 (0) | 0.53 | 3 (50) | 0.64 | 40 (100) |
papG-II | 6 (60) | 1 | 4 (40) | 0.15 | 9 (82) | 0.13 | 3 (100) | 0.26 | 2 (33) | 0.19 | 29 (73) |
sfaD/focC | 8 (80) | 0.69 | 9 (90) | 0.23 | 7 (64) | 0.45 | 3 (100) | 0.54 | 2 (33) | 0.03 | 24 (60) |
fliCD | 10 (100) | 0.55 | 9 (90) | 1 | 10 (91) | 1 | 3 (100) | 1 | 4 (67) | 0.09 | 36 (90) |
cnf-1 | 8 (80) | 1 | 7 (70) | 0.68 | 9 (82) | 0.69 | 2 (67) | 1 | 4 (67) | 0.62 | 16 (40) |
vat | 4 (40) | 0.72 | 4 (40) | 0.72 | 6 (55) | 0.72 | 2 (67) | 0.59 | 3 (50) | 1 | 15 (38) |
sat | 3 (30) | 0.71 | 1 (10) | 0.06 | 7 (64) | 0.08 | 2 (67) | 0.55 | 3 (50) | 0.66 | 24 (60) |
hlyA | 4 (40) | 1 | 4 (40) | 1 | 6 (55) | 0.27 | 0 (0) | 0.27 | 1 (17) | 0.38 | 19 (48) |
feoB | 10 (100) | 1 | 9 (90) | 1 | 11 (100) | 1 | 3 (100) | 1 | 6 (100) | 1 | 30 (75) |
iucD | 4 (40) | 0.12 | 5 (50) | 0.27 | 9 (82) | 0.26 | 2 (67) | 1 | 6 (100) | 0.07 | 29 (73) |
iroN | 4 (40) | 0.15 | 3 (30) | 0.05 | 10 (91) | 0.02 | 3 (100) | 0.26 | 4 (67) | 1 | 11 (28) |
fyuA | 4 (40) | 0.3 | 1 (10) | 0.002 | 11 (100) | 0.0003 | 2 (67) | 0.99 | 4 (67) | 0.67 | 24 (60) |
iha | 1 (10) | 0.03 | 4 (40) | 1 | 6 (55) | 0.29 | 2 (67) | 0.55 | 3 (50) | 0.66 | 26 (65) |
iutA | 0 (0) | 0.55 | 3 (30) | 0.71 | 9 (82) | 1 | 0 (0) | 1 | 0 (0) | 1 | 22 (55) |
traT | 9 (90) | 0.23 | 4 (40) | 0.01 | 8 (73) | 1 | 2 (67) | 1 | 6 (100) | 0.16 | 16 (40) |
kpsM | 5 (50) | 0.48 | 5 (50) | 0.48 | 9 (82) | 0.14 | 1 (33) | 0.55 | 4 (67) | 0.63 | 4 (10) |
agn43 | 2 (20) | 0.69 | 4 (40) | 0.41 | 1 (9) | 0.23 | 2 (67) | 0.17 | 2 (33) | 1 | 39 (98) |
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Ballesteros-Monrreal, M.G.; Arenas-Hernández, M.M.P.; Barrios-Villa, E.; Juarez, J.; Álvarez-Ainza, M.L.; Taboada, P.; De la Rosa-López, R.; Bolado-Martínez, E.; Valencia, D. Bacterial Morphotypes as Important Trait for Uropathogenic E. coli Diagnostic; a Virulence-Phenotype-Phylogeny Study. Microorganisms 2021, 9, 2381. https://doi.org/10.3390/microorganisms9112381
Ballesteros-Monrreal MG, Arenas-Hernández MMP, Barrios-Villa E, Juarez J, Álvarez-Ainza ML, Taboada P, De la Rosa-López R, Bolado-Martínez E, Valencia D. Bacterial Morphotypes as Important Trait for Uropathogenic E. coli Diagnostic; a Virulence-Phenotype-Phylogeny Study. Microorganisms. 2021; 9(11):2381. https://doi.org/10.3390/microorganisms9112381
Chicago/Turabian StyleBallesteros-Monrreal, Manuel G., Margarita M. P. Arenas-Hernández, Edwin Barrios-Villa, Josue Juarez, Maritza Lizeth Álvarez-Ainza, Pablo Taboada, Rafael De la Rosa-López, Enrique Bolado-Martínez, and Dora Valencia. 2021. "Bacterial Morphotypes as Important Trait for Uropathogenic E. coli Diagnostic; a Virulence-Phenotype-Phylogeny Study" Microorganisms 9, no. 11: 2381. https://doi.org/10.3390/microorganisms9112381