Diarrhea
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- ItemRestrictedCharacterization of multi-drug resistant salmonella using long read genome sequencing(Kamuzu University of Health Sciences, 2022-01-19) Nyambi, PhillipIntroduction Salmonella Typhimulium is a Gram negative bacteria of the Enterobacteriaceae family that has been reported to cause an epidemic of invasive non-typhoidal Salmonella disease. The strain responsible is reported to be sequence type ST313. From the data gathered ST313 encodes the gene ctx-m-15 which is responsible for production of an extended spectrum beta lactamase enzyme. Since the introduction of sequencing technologies the data about bacterial genomes has been generated at a rapid pace owing to the fact that second and third generation sequencing technologies have improved and enhanced the analysis of bacterial genome sequence data. Third generation sequencing technologies have provided long reads which have enabled whole genome sequencing for both prokarytotes which includes Salmonella Typhimurium and eukaryotic genomes. Methodology This is a retrospective study that’s looking at one sample and sample analysis will begin with genome assembly, then polishing and annotation of the gene of interest will be done. The data in the form of gff files will be visualized on artemis and location of the gene will be established. Objectives Providing the location of the ctx-m-15 will tell us whether the production of the enzyme ESBL has been established and stabilized within the pathogen. Research has shown this Salmonella Typhimurium ST313 to have ctx-m-15 gene with illumna sequencing, however; the location is not known. Therefore the aim of this study is to locate the position of the gene with regard to its stability within the genome of the pathogen. Specific objectives 1. To perform assembly of Salmonella Typhimurium ST313 disjointigs through De novo genome assembly using the long reads to come up with contigs that facilitate a complete genome from the disjointigs.Identify drug resistant genes for Salmonella Typhimurium ST313 through database that will locate points of mutations within the long reads genome. 3. Identify the location of ctx-m-15 gene for Salmonella Typhimurium ST313 genome through annotation of the genome by using a database that will allow the location of the gene to be identified on the contigs of the pathogen. Expected Outcomes The study will help in understanding of the evolution of the strain of Salmonella Typhimurium ST313 and be able to trace evolution of new clade of the organism since it is suggested that the organism is going through a phase of evolutionary bottleneck. Though the results of the project may not be conclusive, but they will provide insightful knowledge on how ST313 is evolving of which this could be used by big projects on a larger scale.
- ItemRestrictedComparison of the occurrence and degree of E.COLI antibiotic resistance between excreta of broiler chickens from commercial intensive farms and local free range chickens from rural villages in Malawi’s Lilongwe district by Chifundo Soko(Kamuzu University of Health Sciences, 2022-03-16) Soko, Chifundo
- ItemRestrictedEnterics for Global Health (Efgh): Shigella Surveillance Study(Kamuzu University of Health Sciences, 2022-01-19) Cornick, JeniferStudy type: The Enterics for Global Health (EFGH) Shigella surveillance study will employ crosssectional and longitudinal study designs to establish updated incidence rates and document consequences of Shigella diarrhea within 7 country sites in Africa, Asia, and Latin America. Problem: Diarrhea remains a leading cause of death among young children, with most diarrhea deaths occurring in low- and middle-income countries. Diarrhea caused by the bacterium Shigella is responsible for an estimated 60,000 deaths each year and may cause particularly severe illness among children. In low- and middle-income countries, nearly one third of children experience at least one episode of Shigella-attributable diarrhea during their first 2 years of life. In addition to it being a leading cause of diarrhea, this enteric bacterium is also associated with linear growth faltering, a precursor to stunting. Stunting is a marker of vulnerability to childhood infection, decreased vaccine efficacy and lifelong morbidity. Currently, there are several promising vaccines to prevent Shigella diarrhea in development, but key information is still needed to inform future vaccine studies. Broad objective: To determine the incidence of Shigella-attributed MAD in children 6 to 35 months of age. Specific objectives: 1) To determine the incidence of Shigella MAD by serotype, severity definition, laboratory method (culture vs. qPCR), age, and by season. 2) To describe the prevalence of resistance to commonly used antibiotics in Shigella isolates in each EFGH country site. 3) To determine the risk of death, hospitalization, persistent diarrhea, diarrhea recurrence, and linear growth faltering in the 3 months following an episode of Shigella MAD. 4) To compare various severity definitions in their ability to distinguish Shigella from non- Shigella attributable diarrhea, and their ability to predict risk of death or hospitalization in the subsequent 3 months following discharge from the health facility. 5) To qcuantify the cost incurred by families and health care systems due to Shigella morbidity and mortality. 6) To identify optimal laboratory methods for Shigella culture by comparing the isolation rate of Shigella between two transport media for rectal swabs (Cary-Blair and modified Buffered Glycerol Saline [BGS]) 7) To determine the serum immune responses to Shigella infection, utilizing acute and convalescent blood samples. Methodology: Over a two-year period, the EFGH study will enroll 9,800 children (1,400 per country site) between 6-35 months of age with MAD. In Malawi, the population under surveillance will comprise residents of Ndirande Township, with children recruited from Ndirande District Health Centre. and the Queen Elizabeth Central Hospital, Blantyre. Population enumeration and healthcare utilization studies will be undertaken to inform Shigella-attributed MAD incidence estimates. A stool sample will be obtained from each child on enrolment and examined for Shigella by culture and qPCR. Acute and convalescent dried blood spot samples will be examined for Shigella antibody using ELISA. Children will be followed following discharge for three months to allow assessment of clinical outcomes, growth, and costs attributed to Shigella infection. Expected Results and Dissemination: Eventual Phase 2b/3 Shigella vaccine trials will require a consortium of potential vaccine trial sites in settings with a high incidence of Shigella-attributed MAD, high participant retention, and the laboratory capacity to confirm Shigella infection. Through this multi-country surveillance network, selected EFGH sites will be ready to quickly implement rigorous and efficient vaccine trials and provide critical data to policy makers about the relative importance of this vaccine-preventable disease, accelerating the time to vaccine availability and uptake among children in high Shigella burden settings. The study findings will be shared with the College of Medicine Research Ethics Committee (COMREC), the Ministry of Health (MoH), published in peer reviewed journals and will be disseminated to the public through the annual College of Medicine Research dissemination conference.