RSU Doctoral theses / RSU Disertācijas

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Browsing RSU Doctoral theses / RSU Disertācijas by Subject "16S"

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    Descemet Membrane Endothelial Keratoplasty: NGS Metagenomics-Optimized Tissue Preparation and Surgical Technique. Doctoral Thesis
    (Rīga Stradiņš University, 2021) Borroni, Davide; Krūmiņa, Zita; Giovanni, Porta
    Title: Next-generation sequencing for the detection of microorganisms present in human donor corneal preservation medium. Aim: To detect the presence of microorganisms in the storage media of human donor corneas using next-generation sequencing method. Methods: Seven samples from organ culture (OC) group (Cornea Max, Eurobio, Les Ulis, France) with one control (sterile media without any cornea) and seven samples from hypothermic storage group (Cornea Cold, Eurobio) with one control were used for this study. The corneas were placed in the respective storage media for 14 days before collecting the samples. Storage media (2 mL) from each sample were collected in RNAase-free tubes and shipped for ribosomal RNA sequencing of 16S and 18S. Simultaneously, another 1 mL of media sample was used for conventional diagnostic method (CDM) using Bactec instruments. Results: In both, OC and hypothermic storage and control samples, the most abundant genera were Pseudomonas, Comamonas, Stenotrophomonas, Alcanivorax, Brevundimonas and Nitrobacter. Acidovorax, Acetobacter and Hydrogenophilus were detected mostly in the hypothermic storage group. The most abundant fungal pathogen detected belonged to the genus Malassezia, which was found in both the storage conditions. CDM was negative for microorganisms in all the samples. Conclusion: Metagenomics provides full taxonomic profiling of the detected genomic material of the organisms and thus has the potential to deliver a much wider microbiological diagnostic approach than CDM. The costs and turnaround time need to be reduced, and; the detection of viable organisms would help this technology to be introduced into routine clinical practice.
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    Descemet Membrane Endothelial Keratoplasty: NGS Metagenomics-Optimized Tissue Preparation and Surgical Technique. Summary of the Doctoral Thesis
    (Rīga Stradiņš University, 2021) Borroni, Davide; Krūmiņa, Zita; Giovanni, Porta
    Title: Next-generation sequencing for the detection of microorganisms present in human donor corneal preservation medium. Aim: To detect the presence of microorganisms in the storage media of human donor corneas using next-generation sequencing method. Methods: Seven samples from organ culture (OC) group (Cornea Max, Eurobio, Les Ulis, France) with one control (sterile media without any cornea) and seven samples from hypothermic storage group (Cornea Cold, Eurobio) with one control were used for this study. The corneas were placed in the respective storage media for 14 days before collecting the samples. Storage media (2 mL) from each sample were collected in RNAase-free tubes and shipped for ribosomal RNA sequencing of 16S and 18S. Simultaneously, another 1 mL of media sample was used for conventional diagnostic method (CDM) using Bactec instruments. Results: In both, OC and hypothermic storage and control samples, the most abundant genera were Pseudomonas, Comamonas, Stenotrophomonas, Alcanivorax, Brevundimonas and Nitrobacter. Acidovorax, Acetobacter and Hydrogenophilus were detected mostly in the hypothermic storage group. The most abundant fungal pathogen detected belonged to the genus Malassezia, which was found in both the storage conditions. CDM was negative for microorganisms in all the samples. Conclusion: Metagenomics provides full taxonomic profiling of the detected genomic material of the organisms and thus has the potential to deliver a much wider microbiological diagnostic approach than CDM. The costs and turnaround time need to be reduced, and; the detection of viable organisms would help this technology to be introduced into routine clinical practice.
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    Descemeta membrānas endotēlija keratoplastika: nākamās paaudzes sekvenēšanas metagenomiski optimizētu audu sagatavošana un ķirurģijas tehnika. Promocijas darba kopsavilkums
    (Rīgas Stradiņa universitāte, 2021) Borroni, Davide; Krūmiņa, Zita; Giovanni, Porta
    Pētījumā tika analizēta optimizācija, pielietojot metagenomiku radzenes audu saglabāšanā. Nosaukums: Nākamās paaudzes sekvencēšana mikroorganismu noteikšanai cilvēka donora radzenes audu saglabāšanas vidē. Mērķis: Ar nākamās paaudzes sekvencēšanas metodi noteikt mikroorganismu klātbūtni cilvēka donora radzenes audu uzglabāšanas vidē. Materiāli un metodes: Kopā tika izmantoti septiņi paraugi no orgānu kultūras (no angļu val. – organ culture (OC)) grupas (Cornea Max, Eurobio, Les Ulis, Francija) ar vienu kontroli (sterila barotne bez radzenes audiem) un septiņi paraugi no hipotermiskās uzglabāšanas grupas (Cornea Cold, Eurobio) ar vienu kontroli. Pirms paraugu savākšanas radzenes audus ievietoja attiecīgajās uzglabāšanas vietās uz 14 dienām. Uzglabāšanas vide (2 ml) no katra parauga tika ievietota mēģenēs, kas nesatur RNS-āzi, un tika nosūtīta 16S un 18S ribosomu RNS sekvencēšanai. Vienlaikus 1 ml barotnes parauga tika izmantots konvencionālajai diagnostikas metodei (no angļu val. – conventional diagnostic method (CDM)), izmantojot Bactec instrumentus. Rezultāti: Gan OC, gan hipotermiskās uzglabāšanas un kontroles paraugos visbiežāk novēroja Pseudomonas, Comamonas, Stenotrophomonas, Alcanivorax, Brevundimonas un Nitrobacter ģintis. Acidovorax, Acetobacter un Hydrogenophilus ģintis tika atklātas galvenokārt hipotermiskās uzglabāšanas grupā. Visbiežāk konstatētais sēņu patogēns piederēja Malassezia ģintij, kas tika atrasts abās uzglabāšanas vidēs. Ar CDM visi paraugi bija negatīvi attiecībā uz mikroorganismiem. Secinājumi: Metagenomika nodrošina pilnīgu taksonomisko profilu noteikto organismu genomiskajam materiālam, tādējādi sniedzot daudz plašāku mikrobioloģiskās diagnostikas pieeju nekā CDM. Metodes izmaksu un apgrozījuma laika dzīvotspējīgu organismu noteikšanai samazināšana palīdzētu šo tehnoloģiju ieviest ikdienas klīniskajā praksē.