Escherichia coli Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections
Abstract
:1. Introduction
2. Materials and Methods
2.1. Study Population
2.2. Bacterial Isolates
2.3. Sequencing, Assembly and Annotation
2.4. Phylogeny and Pairwise SNPs
2.5. Accessory Genome Content and Typing
2.6. Ethical Approval
3. Results and Discussion
3.1. Adaptation between First and Second UTI
3.2. Do rUTI Isolates Differ Genetically from Non-rUTI Isolates?
3.3. Limitations
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene Annotation | Function | p-Value | p-Value FDR | Cure n (%) | rUTI n (%) | Isolate_Locus Tag |
---|---|---|---|---|---|---|
Overrepresented in rUTI isolates | ||||||
Fimbria-related genes | ||||||
papB | S/F1C fimbrial transcriptional regulator | 0.0062 | 0.619 | 14 (33) | 28 (62) | 3244-2_K_03164 |
sfaH | S-fimbrial protein subunit | 0.0072 | 0.619 | 2 (5) | 12 (27) | 3244-2_K_03157 |
mprA | Transcriptional repressor | 0.0072 | 0.619 | 26 (60) | 39 (87) | 3244-2_K_03155 |
sfaF | S/F1C fimbrial biogenesis usher protein | 0.0118 | 0.619 | 15 (35) | 28(62) | 3244-2_K_03160 |
sfaE | S/F1C fimbrial biogenesis chaperone | 0.0118 | 0.619 | 15 (35) | 28 (62) | 3244-2_K_03161 |
sfaG | S/F1C fimbrial adhesin minor pilin SfaG/FocF | 0.0118 | 0.619 | 15 (35) | 28 (62) | 3244-2_K_03159 |
sfaD | S/F1C fimbrial minor subunit | 0.0118 | 0.619 | 15 (35) | 28 (62) | 3244-2_K_03162 |
ydiV | Putative anti-FlhC(2)FlhD(4) factor YdiV | 0.0118 | 0.619 | 15 (35) | 28 (62) | 3244-2_K_03156 |
hifA | fimbrial protein | 0.0095 | 0.619 | 11 (26) | 24 (53) | 3244-2_K_02738 |
Other virulence-related genes | ||||||
shlB | Hemolysin transport | 0.0100 | 0.619 | 16 (37) | 30 (67) | 3230-3_K_03314 |
cbeA | Toxin/antitoxin system | 0.0128 | 0.619 | 33 (77) | 43 (96) | 3244-2_K_03419 |
yeeW | Toxin/antitoxin protein | 0.0106 | 0.619 | 28 (65) | 40 (89) | 3244-2_K_03421 |
yeeJ | Adhesin | 0.0079 | 0.619 | 29 (67) | 41 (91) | 3244-2_K_00508 |
wgrG | Type VI secretion system protein | 0.0088 | 0.619 | 4 (9) | 15 (33) | 3244-2_K_04080 |
klcA | Anti-restriction protein | 0.0068 | 0.619 | 34 (79) | 44 (98) | 3014-3_K_04082 |
cbtA | Toxin/antitoxin system | 0.0064 | 0.619 | 32 (74) | 43 (96) | 3244-2_K_04704 |
LPS-biosynthesis | ||||||
gspA_3 | Secretion pathway protein | 0.0015 | 0.619 | 30 (70) | 43 (96) | 3244-2_K_02772 |
gspA_4 | Secretion pathway protein | 0.0015 | 0.619 | 30 (70) | 43 (96) | 3244-2_K_00614 |
rfaY | Lps biosynthesis protein | 0.0015 | 0.619 | 30 (70) | 43 (96) | 3244-2_K_02773 |
epsJ | Glycosyltransferase | 0.0028 | 0.619 | 26 (60) | 40 (89) | 3244-2_K_02775 |
gspA_2 | Secretion pathway protein | 0.0028 | 0.619 | 26 (60) | 40 (89) | 3244-2_K_02774 |
rfaL | Lps biosynthesis protein | 0.0028 | 0.619 | 26 (60) | 40 (89) | 3244-2_K_02776 |
Phage-related genes | ||||||
- | Bacteriophage Replication protein O | 0.0056 | 0.619 | 27 (63) | 40 (89) | 3014-3_K_04219 |
- | Phage replication protein | 0.0057 | 0.619 | 23 (53) | 37 (82) | 3014-3_K_04220 |
alpA | Prophage regulatory protein | 0.0007 | 0.619 | 20 (47) | 37 (82) | 3244-2_K_03100 |
Metabolism-related genes | ||||||
bglA | Metabolism protein | 0.0079 | 0.619 | 29 (67) | 41 (91) | 3244-2_K_00072 |
bglH | Metabolism protein | 0.0079 | 0.619 | 29 (67) | 41 (91) | 3244-2_K_00073 |
yidP | Transcriptional regulator | 0.0079 | 0.619 | 29 (67) | 41 (91) | 3244-2_K_00077 |
yfjR | Transcriptional regulator | 0.0082 | 0.619 | 20 (46) | 34 (76) | 3244-2_K_03712 |
ykfF | Hypothetical protein | 0.0089 | 0.619 | 19 (44) | 33 (73) | 3244-2_K_03710 |
Hypothetical protein | 0.0017 | 0.619 | 20 (47) | 36 (80) | 3244-2_K_03711 | |
rspA | Starvation sensing protein | 0.0038 | 0.619 | 25 (58) | 39 (87) | 3244-2_K_01532 |
yjjL | Inner membrane transport protein | 0.0038 | 0.619 | 25 (58) | 39 (87) | 3244-2_K_01531 |
- | Putative inner membrane protein | 0.0024 | 0.619 | 23 (53) | 38 (84) | 3244-2_K_03387 |
- | Cytoplasmic protein | 0.0047 | 0.619 | 24 (56) | 38 (84) | 3244-2_K_03386 |
rbsK | Ribokinase | 0.0047 | 0.619 | 24 (56) | 38 (84) | 3244-2_K_03385 |
Replication | ||||||
crfC | Replication protein | 0.0122 | 0.619 | 23 (53) | 36 (80) | 3244-2_K_03407 |
Chemotaxis protein | 0.0057 | 0.619 | 23 (53) | 37 (82) | 3244-2_K_03408 | |
Other and unknown function | ||||||
tnpB | Transposase | 0.0098 | 0.619 | 26 (60) | 14 (31) | 3805-3_K_04559 |
ompD | Porin protein | 0.0057 | 0.619 | 23 (53) | 37 (82) | 3244_2_K_00430 |
- | Hypothetical protein | 0.0118 | 0.619 | 15 (35) | 28 (62) | 3244-2_K_03094 |
- | Hypothetical protein | 0.0137 | 0.619 | 22 (51) | 35 (78) | 3244-2_K_03400 |
higA | Toxin/antitoxin system | 0.0122 | 0.619 | 23 (53) | 36 (80) | 3244-2_K_00724 |
Overrepresented in non-rUTI isolates | ||||||
pipB | Type III secretion system protein | 0.0106 | 0.619 | 15 (35) | 5 (11) | 3212-3_K_02120 |
- | Hypothetical protein (prophage) | 0.0112 | 0.619 | 6 (14) | 0 (0) | MN187550_Orf34 |
waaZ | Lps biosynthesis | 0.0112 | 0.619 | 6 (14) | 0 (0) | CP046003_GJD94_01225 |
waaY | Lps biosynthesis | 0.0112 | 0.619 | 6 (14) | 0 (0) | CP046003_GJD94_01220 |
waaJ | Lps biosynthesis | 0.0112 | 0.619 | 6 (14) | 0 (0) | CP046003_GJD94_01215 |
waaO | Lps biosynthesis | 0.0112 | 0.619 | 6 (14) | 0 (0) | CP046003_GJD94_01210 |
yibB | RfaH-regulated high-temperature protein | 0.0032 | 0.619 | 10 | 1 | CP046003_GJD94_01255 |
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Nielsen, K.L.; Stegger, M.; Kiil, K.; Lilje, B.; Ejrnæs, K.; Leihof, R.F.; Skjøt-Rasmussen, L.; Godfrey, P.; Monsen, T.; Ferry, S.; et al. Escherichia coli Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections. Microorganisms 2021, 9, 1416. https://doi.org/10.3390/microorganisms9071416
Nielsen KL, Stegger M, Kiil K, Lilje B, Ejrnæs K, Leihof RF, Skjøt-Rasmussen L, Godfrey P, Monsen T, Ferry S, et al. Escherichia coli Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections. Microorganisms. 2021; 9(7):1416. https://doi.org/10.3390/microorganisms9071416
Chicago/Turabian StyleNielsen, Karen Leth, Marc Stegger, Kristoffer Kiil, Berit Lilje, Karen Ejrnæs, Rikke Fleron Leihof, Line Skjøt-Rasmussen, Paul Godfrey, Tor Monsen, Sven Ferry, and et al. 2021. "Escherichia coli Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections" Microorganisms 9, no. 7: 1416. https://doi.org/10.3390/microorganisms9071416