Saudi Cultural Missions Theses & Dissertations
Permanent URI for this communityhttps://drepo.sdl.edu.sa/handle/20.500.14154/10
Browse
4 results
Search Results
Item Restricted Diversity and vector biology of ectoparasites of small mammals in Saudi Arabia: implications for bacterial zoonoses(University of Liverpool, 2024-06) Alkathiry, Hadil; Makepeace, BenjaminGlobally, rodents are a major reservoir for many vector-borne bacterial diseases that are important for public and veterinary health. Due to their widespread distribution across ecological niches and their capacity to host a vast array of ectoparasites, including ticks, mites, and fleas, rodents are considered important hosts that aid in the persistence and spread of zoonotic illnesses such as scrub typhus (caused by Orientia spp.), Lyme disease and rickettsioses. The objectives of the current study were to (i) investigate the chigger mite fauna and other ectoparasites on rodents in two regions: Asir and Al-Bahah provinces (Saudi Arabia); (ii) determine the identity and prevalence of bacterial pathogens and symbionts in ectoparasites and hosts in these regions, with a special focus of on Orientia; and (iii) analyse the metagenome of the chigger Pentidionis agamae, identified here as a potential vector of Orientia in Saudi Arabia. Small mammals were trapped in southwest Saudi Arabia and in total, 7,392 chiggers, 368 ticks of various stages, 146 mesostigmatid mites, and 53 fleas (Parapulex chephrensis) were collected from 82 hosts. Internal rodent organs were also harvested and stored in 70% ethanol. Chiggers comprised 20 species belonging to nine genera, including a newly described species (Odontacarus thesigeri) and five species that constituted new records for the Arabian Peninsula. The most prevalent chigger species in Asir were Ericotrombidium kazeruni and Ericotrombidium caucasicum, while Schoutedenichia zarudnyi and P. agamae were dominant in Al-Bahah. Phylogenetic analysis of COI fragments of eight chigger species revealed a monophyletic grouping for each chigger genus. Phylogenetic analysis and ASAP (“assemble species by automatic partitioning”) analysis of COI sequences of mesostigmatid mites showed a distinct operational taxonomic unit that may represent a new Dermanyssus spp. The morphology of immature ticks assigned the specimens to Rhipicephalus spp. and Haemaphysalis spp., while phylogenetic trees were constructed based on COI, 12S rRNA, and 16S rRNA sequences, revealing novel clades of Rhipicephalus and Haemaphysalis ticks in Asir. Thirty-two per cent of tested Rhipicephalus spp. and Haemaphysalis spp. were found to be infected with Ehrlichia spp., forming two distinct clades separated by geographical regions. Wolbachia symbiont detection using the wsp gene was conducted on 53 flea samples and 17 chigger pools from Asir and sequences matched supergroups A, B, and V, while two clusters were distinct from known supergroups. The amplification of traD and htrA for Orientia screening was conducted for rodent organs and 165 chigger pools. Seven rodents and two chigger pools of Microtrombicula muhaylensis and P. agamae (sample R9P) were found to be Orientia positive. Phylogenetic analysis of the R9P htrA sequence revealed a single clade shared with Candidatus (Ca.) O. chuto htrA sequences from A. dimidiatus tissues collected in Asir. This is the first time that DNA from Ca. O. chuto has been found in potential vector species from this region, where it is geographically distant from a reported human case in Dubai. Metagenomic assembly and phylogenetic analysis of Wolbachia detected in P. agamae positioned a novel strain, designated as wPaga, within its own distinct clade, namely supergroup X, which segregated with other divergent supergroups. Moreover, the analysis of contigs from all three P. agamae pools identified sequences assigned to Spirochaetes. Based on 16S rRNA and sequence typing genes, these were found to represent a Borrelia clade associated with rodents that has not been detected in arthropods previously. Finally, the metagenomic analysis allowed for the assembly of three mitochondrial genomes from different P. agamae pools, enabling intraspecific comparisons. In summary, these findings highlight the hidden biology of rodent ectoparasites, zoonotic agents, and arthropod symbionts in a highly neglected biogeographical region.20 0Item Restricted Comparison of long-read and short-read bacterial DNA sequencing(King's College London, 2024-08-30) Alqirnas, Mohammed; Carpenter, Guy; Cleaver, LeanneThis study aimed to compare long-read (Oxford Nanopore) and short-read (Illumina) sequencing technologies for characterizing the diversity and composition of in vitro oral biofilms. An oral biofilm model was established using hydroxyapatite discs to mimic the tooth surface. Saliva samples from six healthy participants were pooled and used to inoculate the discs, which underwent aerobic and anaerobic incubation phases. Biofilm formation was assessed using confocal microscopy with LIVE/DEAD staining, revealing heterogeneous growth patterns with coverage ranging from 17% to 47%. DNA extraction was carried out using the GenElute Bacterial Genomic DNA Kit, with yields showing significant variations across experiments (0-5 ng/μL). Interestingly, gel electrophoresis showed no difference in DNA fragment lengths between samples prepared for short-read and long-read sequencing. The experiment also highlighted the potential benefits of CO2-rich environments for early colonizer growth, particularly Streptococcus species. While the biofilm model was successfully established, the results underline the need for protocol optimization, particularly in DNA extraction and biofilm cultivation. This research provides insights into the complexity of oral microbiome analysis and sets the stage for future comparative studies on advanced sequencing technologies in oral microbiome. The findings also emphasize the importance of refining the in vitro experimental protocol, from biofilm cultivation to DNA sequencing and data analysis.13 0Item Restricted Comparison of long-read and short-read bacterial DNA sequencing(King's College London, 2024-08) Alqirnas, Mohammed; Carpenter, Guy; Cleaver, LeanneThis study aimed to compare long-read (Oxford Nanopore) and short-read (Illumina) sequencing technologies for characterizing the diversity and composition of in vitro oral biofilms. An oral biofilm model was established using hydroxyapatite discs to mimic the tooth surface. Saliva samples from six healthy participants were pooled and used to inoculate the discs, which underwent aerobic and anaerobic incubation phases. Biofilm formation was assessed using confocal microscopy with LIVE/DEAD staining, revealing heterogeneous growth patterns with coverage ranging from 17% to 47%. DNA extraction was carried out using the GenElute Bacterial Genomic DNA Kit, with yields showing significant variations across experiments (0-5 ng/μL). Interestingly, gel electrophoresis showed no difference in DNA fragment lengths between samples prepared for short-read and long-read sequencing. The experiment also highlighted the potential benefits of CO2-rich environments for early colonizer growth, particularly Streptococcus species. While the biofilm model was successfully established, the results underline the need for protocol optimization, particularly in DNA extraction and biofilm cultivation. This research provides insights into the complexity of oral microbiome analysis and sets the stage for future comparative studies on advanced sequencing technologies in oral microbiome. The findings also emphasize the importance of refining the in vitro experimental protocol, from biofilm cultivation to DNA sequencing and data analysis.29 0Item Restricted Field Cancerization and Microbiome Effects on Lung Cancer: A Source of Early Detection Biomarkers to Improve Patients’ Outcome(George Mason University, 2024-08-16) Alhammad, Rayan; Luchini, AlessandraLung cancer results in more deaths than any other cancer in the United States and worldwide, with non-small cell lung cancer (NSCLC) accounting for most cases. Diagnosis typically involves chest imaging, molecular testing, and biopsy. However, most patients are diagnosed at advanced stages, with only a 6% chance of a 5-year survival rate. In contrast, early-stage diagnosis and treatment can result in a favorable prognosis, with a high 5-year survival rate of 70-90%. The concept of tumor field cancerization describes a phenomenon where exposure to carcinogens can cause histologic changes in large areas of tissue, creating a field of pre-malignant cells that can eventually develop into tumors. Additionally, microbiota dysbiosis might influence tumor development. Studies have identified several commensal bacteria present in the lower airway tracts, such as Streptococcus, Prevotella, and Veillonella. The high mortality rate of lung cancer is often attributed to i) its late-stage diagnosis, ii) aggressive nature given its ability to metastasize early in the disease process complicating treatment and reducing survival rates, and iii) significant therapeutic challenges despite current treatments such as surgery, chemotherapy, radiation therapy, targeted therapy and immunotherapy. Despite advancements, the survival rate for advanced lung cancer remains low. To address this challenge, our research focuses on identifying risk protein biomarkers that are associated with the earliest molecular changes indicative of an ongoing tumorigenic process, thus offering significant potential for early intervention. Our study investigates the phenotypic molecular changes in the bronchial tree of NSCLC patients in light of the field cancerization theory and correlates these findings with blood biomarkers to support the future development of a non-invasive risk assessment test. Using enhanced liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomic analysis and two independent cohorts of lung cancer patients (N=18, and N=263) with matched plasma and bronchial tree tissue specimens, we identified a set of 6 and 13 candidate risk plasma biomarkers with tissue origin. Additionally, we explored the microbiome proteome composition in NSCLC patient tissue and plasma to support future characterization of its potential role in cancer development. Risk biomarkers will enable the evaluation of individuals at high risk, guiding necessary lifestyle adjustments and facilitating the development of personalized prevention plans and therapies.48 0