Differentially Expressed Genes of Pseudomonas aeruginosa Isolates from Eyes with Keratitis and Healthy Conjunctival Sacs

References

• Huang Y, Yang B, Li W. Defining the normal core microbiome of conjunctival microbial communities. Clin Microbiol Infect. 2016;22:643, e7–e12. doi:10.1016/j.cmi.2016.04.008
   PubMed Web of Science ®Google Scholar
• Suzuki T, Okamoto S, Oka N, Hayashi N, Gotoh N, Shiraishi A. Role of pvdE pyoverdine synthesis in Pseudomonas aeruginosa keratitis. Cornea. 2018;37:S99–S105. doi:10.1097/ICO.0000000000001728
   PubMed Web of Science ®Google Scholar
• Oka N, Suzuki T, Ishikawa E, et al. Relationship of virulence factors and clinical features in keratitis caused by Pseudomonas aeruginosa. Invest Ophthalmol Vis Sci. 2015;56:6892–6898. doi:10.1167/iovs.15-17556
   Web of Science ®Google Scholar
• Ma X, Wang Q, Song F, et al. Corneal epithelial injury-induced norepinephrine promotes Pseudomonas aeruginosa keratitis. Exp Eye Res. 2020;195:108048. doi:10.1016/j.exer.2020.108048
   Web of Science ®Google Scholar
• Li J, Ma X, Zhao L, Li Y, Zhou Q, Du X. Extended contact lens wear promotes corneal norepinephrine secretion and Pseudomonas aeruginosa infection in mice. Invest Ophthalmol Vis Sci. 2020;61:17. doi:10.1167/iovs.61.4.17
   Web of Science ®Google Scholar
• Lakhundi S, Siddiqui R, Khan NA. Pathogenesis of microbial keratitis. Microb Pathog. 2017;104:97–109. doi:10.1016/j.micpath.2016.12.013
   PubMed Web of Science ®Google Scholar
• Carnt N, Samarawickrama C, White A, Stapleton F. The diagnosis and management of contact lens-related microbial keratitis. Clin Exp Optom. 2017;100:482–493. doi:10.1111/cxo.12581
   Web of Science ®Google Scholar
• Sharma P, Elofsson M, Roy S. Attenuation of Pseudomonas aeruginosa infection by INP0341, a salicylidene acylhydrazide, in a murine model of keratitis. Virulence. 2020;11:795–804. doi:10.1080/21505594.2020.1776979
   PubMedGoogle Scholar
• Austin A, Lietman T, Rose-Nussbaumer J. Update on the management of infectious keratitis. Ophthalmology. 2017;124:1678–1689. doi:10.1016/j.ophtha.2017.05.012
   PubMed Web of Science ®Google Scholar
• Cunrath O, Meinel DM, Maturana P, et al. Quantitative contribution of efflux to multi-drug resistance of clinical Escherichia coli and Pseudomonas aeruginosa strains. EBioMedicine. 2019;41:479–487. doi:10.1016/j.ebiom.2019.02.061
   PubMed Web of Science ®Google Scholar
• Subedi D, Vijay AK, Willcox M. Overview of mechanisms of antibiotic resistance in Pseudomonas aeruginosa: an ocular perspective. Clin Exp Optomet. 2018;101:162–171. doi:10.1111/cxo.12621
   PubMed Web of Science ®Google Scholar
• Vazirani J, Wurity S, Ali MH. Multidrug-resistant Pseudomonas aeruginosa keratitis: risk factors, clinical characteristics, and outcomes. Ophthalmology. 2015;122:2110–2114. doi:10.1016/j.ophtha.2015.06.007
   PubMed Web of Science ®Google Scholar
• Yamaguchi S, Suzuki T, Kobayashi T, et al. Genotypic analysis of Pseudomonas aeruginosa isolated from ocular infection. J Infect Chemother. 2014;20:407–411. doi:10.1016/j.jiac.2014.02.007
   Web of Science ®Google Scholar
• Lakshmi PJ, Prajna L, Mohankumar V. Genotypic and phenotypic characterization of Pseudomonas aeruginosa isolates from post-cataract endophthalmitis patients. Microb Pathog. 2015;78:67–73. doi:10.1016/j.micpath.2014.11.014
   Web of Science ®Google Scholar
• Doustdar F, Karimi F, Abedinyfar Z, Amoli FA, Goudarzi H. Genetic features of Pseudomonas aeruginosa isolates associated with eye infections referred to Farabi Hospital, Tehran, Iran. Int Ophthalmol. 2019;39:1581–1587. doi:10.1007/s10792-018-0980-5
   Web of Science ®Google Scholar
• Molina Mora JA, Montero-Manso P, García-Batán R, Campos-Sánchez R, Vilar-Fernández J, García F. A first perturbome of Pseudomonas aeruginosa: identification of core genes related to multiple perturbations by a machine learning approach. Biosystems. 2021;205:104411. doi:10.1016/j.biosystems.2021.104411
   Web of Science ®Google Scholar
• Molina-Mora JA, Chinchilla-Montero D, García-Batán R, García F. Genomic context of the two integrons of ST-111 Pseudomonas aeruginosa AG1: a VIM-2-carrying old-acquaintance and a novel IMP-18-carrying integron. Infect Genet Evol. 2021;89:104740. doi:10.1016/j.meegid.2021.104740
   Web of Science ®Google Scholar
• Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10:57–63. doi:10.1038/nrg2484
   PubMed Web of Science ®Google Scholar
• Li S, Dong X, Su Z. Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling. BMC Genom. 2013;14:520. doi:10.1186/1471-2164-14-520
   Web of Science ®Google Scholar
• Perkins TT, Kingsley RA, Fookes MC, et al. A strand-specifc RNA-Seq analysis of the transcriptome of the typhoid bacillus Salmonella typhi. PLoS Genet. 2009;5:e1000569. doi:10.1371/journal.pgen.1000569
   PubMed Web of Science ®Google Scholar
• Sharma CM, Hoffmann S, Darfeuille F, et al. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature. 2010;464:250–255. doi:10.1038/nature08756
   PubMed Web of Science ®Google Scholar
• Molina-Mora JA, Chinchilla-Montero D, Chavarría-Azofeifa M, et al. Transcriptomic determinants of the response of ST-111 Pseudomonas aeruginosa AG1 to ciprofloxacin identified by a top-down systems biology approach. Sci Rep. 2020;10:13717. doi:10.1038/s41598-020-70581-2
   Web of Science ®Google Scholar
• Liu Q, Chen N, Chen H, Huang Y. RNA-Seq analysis of differentially expressed genes of Staphylococcus epidermidis isolated from postoperative endophthalmitis and the healthy conjunctiva. Sci Rep. 2020;10:14234. doi:10.1038/s41598-020-71050-6
   Web of Science ®Google Scholar
• Tjaden B. De novo assembly of bacterial transcriptomes from RNA-seq data. Genome Biol. 2015;16:1. doi:10.1186/s13059-014-0572-2
   PubMed Web of Science ®Google Scholar
• Yoon GS, Dong C, Gao N, Kumar A, Standiford TJ, Yu FS. Interferon regulatory factor-1 in flagellin-induced reprogramming: potential protective role of CXCL10 in cornea innate defense against Pseudomonas aeruginosa infection. Invest Ophthalmol Vis Sci. 2013;54:7510–7521. doi:10.1167/iovs.13-12453
   Web of Science ®Google Scholar
• Li J, Xie L, Qian S, et al. A type VI secretion system facilitates fitness, homeostasis, and competitive advantages for environmental adaptability and efficient nicotine biodegradation. Appl Environ Microbiol. 2021;87(9):e03113–20. doi:10.1128/AEM.03113-20
   Web of Science ®Google Scholar
• Sheldon JR, Laakso HA, Heinrichs DE. Iron acquisition strategies of bacterial pathogens. Microbiol Spectr. 2016;4. doi:10.1128/microbiolspec.VMBF-0010-2015
   Web of Science ®Google Scholar
• Evans DJ, Fleiszig SM. Why does the healthy cornea resist Pseudomonas aeruginosa infection? Am J Ophthalmol. 2013;155:961–970, e2. doi:10.1016/j.ajo.2013.03.001
   Web of Science ®Google Scholar
• Willcox MD. Pseudomonas aeruginosa infection and inflammation during contact lens wear: a review. Optom Vis Sci. 2007;84:273–278. doi:10.1097/OPX.0b013e3180439c3e
   PubMed Web of Science ®Google Scholar
• Naskar S, Hohl M, Tassinari M, Low HH. The structure and mechanism of the bacterial type II secretion system. Mol Microbiol. 2021;115:412–424. doi:10.1111/mmi.14664
   Web of Science ®Google Scholar
• Alarcon I, Evans DJ, Fleiszig SM. The role of twitching motility in Pseudomonas aeruginosa exit from and translocation of corneal epithelial cells. Invest Ophthalmol Vis Sci. 2009;50:2237–2244. doi:10.1167/iovs.08-2785
   PubMed Web of Science ®Google Scholar
• Piepenbrink KH, Sundberg EJ. Motility and adhesion through type IV pili in Gram-positive bacteria. Biochem Soc Trans. 2016;44:1659–1666. doi:10.1042/BST20160221
   Web of Science ®Google Scholar
• Burrows LL. Pseudomonas aeruginosa twitching motility: type IV pili in action. Annu Rev Microbiol. 2012;66:493–520. doi:10.1146/annurev-micro-092611-150055
   PubMed Web of Science ®Google Scholar
• Nieto V, Kroken AR, Grosser MR, et al. Type IV pili can mediate bacterial motility within epithelial cells. mBio. 2019;10:e02880–18. doi:10.1128/mBio.02880-18
   Web of Science ®Google Scholar
• Winstanley C, Kaye SB, Neal TJ, et al. Genotypic and phenotypic characteristics of Pseudomonas aeruginosa isolates associated with ulcerative keratitis. J Med Microbiol. 2005;54:519–526. doi:10.1099/jmm.0.46005-0
   PubMed Web of Science ®Google Scholar
• Thanabalasuriar A, Scott BNV, Peiseler M, et al. Neutrophil extracellular traps confine Pseudomonas aeruginosa ocular biofilms and restrict brain invasion. Cell Host Microbe. 2019;25:526–536, e4. doi:10.1016/j.chom.2019.02.007
   PubMed Web of Science ®Google Scholar
• Sousa AM, Pereira MO. Pseudomonas aeruginosa diversification during infection development in cystic fibrosis lungs-a review. Pathogens. 2014;3:680–703. doi:10.3390/pathogens3030680
   PubMedGoogle Scholar
• Ma L, Wang S, Wang D, Parsek MR, Wozniak DJ. The roles of biofilm matrix polysaccharide Psl in mucoid Pseudomonas aeruginosa biofilms. FEMS Immunol Med Microbiol. 2012;65:377–380. doi:10.1111/j.1574-695X.2012.00934.x
   PubMed Web of Science ®Google Scholar
• Vareechon C, Zmina SE, Karmakar M, Pearlman E, Rietsch A. Pseudomonas aeruginosa effector ExoS inhibits ROS production in human neutrophils. Cell Host Microbe. 2017;21:611–618.e5. doi:10.1016/j.chom.2017.04.001
   PubMed Web of Science ®Google Scholar
• Kaminski A, Gupta KH, Goldufsky JW, Lee HW, Gupta V, Shafikhani SH. Pseudomonas aeruginosa ExoS induces intrinsic apoptosis in target host cells in a manner that is dependent on its GAP domain activity. Sci Rep. 2018;8:14047. doi:10.1038/s41598-018-32491-2
   Web of Science ®Google Scholar
• Mohankumar V, Ramalingam S, Chidambaranathan GP, Prajna L. Autophagy induced by type III secretion system toxins enhances clearance of Pseudomonas aeruginosa from human corneal epithelial cells. Biochem Biophys Res Commun. 2018;503:1510–1515. doi:10.1016/j.bbrc.2018.07.071
   Web of Science ®Google Scholar
• Dave A, Samarth A, Karolia R, et al. Characterization of ocular clinical isolates of Pseudomonas aeruginosa from non-contact lens related keratitis patients from South India. Microorganisms. 2020;8:260. doi:10.3390/microorganisms8020260
   PubMed Web of Science ®Google Scholar
• Li W, Lyte M, Freestone PP, Ajmal A, Colmer-Hamood JA, Hamood AN. Norepinephrine represses the expression of toxA and the siderophore genes in Pseudomonas aeruginosa. FEMS Microbiol Lett. 2009;299:100–109. doi:10.1111/j.1574-6968.2009.01739.x
   PubMed Web of Science ®Google Scholar
• Minandri F, Imperi F, Frangipani E, et al. Role of iron uptake systems in Pseudomonas aeruginosa virulence and airway infection. Infect Immun. 2016;84:2324–2335. doi:10.1128/IAI.00098-16
   PubMed Web of Science ®Google Scholar
• Kang D, Kirienko DR, Webster P, Fisher AL, Kirienko NV. Pyoverdine, a siderophore from Pseudomonas aeruginosa, translocates into C. elegans, removes iron, and activates a distinct host response. Virulence. 2018;9:804–817. doi:10.1080/21505594.2018.1449508
   PubMed Web of Science ®Google Scholar
• Wiens JR, Vasil AI, Schurr MJ, Vasil ML. Iron-regulated expression of alginate production, mucoid phenotype, and biofilm formation by Pseudomonas aeruginosa. mBio. 2014;5:e01010–13. doi:10.1128/mBio.01010-13
   PubMed Web of Science ®Google Scholar
• Kang D, Turner KE, Kirienko NV. PqsA promotes pyoverdine production via biofilm formation. Pathogens. 2017;7:3. doi:10.3390/pathogens7010003
   Web of Science ®Google Scholar
• Molina-Mora JA, García F. Molecular determinants of antibiotic resistance in the Costa Rican Pseudomonas aeruginosa AG1 by a multi-omics approach: a review of 10 years of study. Phenomics. 2021;1:129–142. doi:10.1007/s43657-021-00016-z
   Google Scholar