Browsing by Author "Cupido, Danielle Tiffany"

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    Investigating pathogens of the gastrointestinal tract in sudden and unexpected death in infancy cases at the Tygerberg medico-legal mortuary, compared to an age-matched healthy control group.
    (Stellenbosch : Stellenbosch University, 2023-07) Cupido, Danielle Tiffany; De Beer, Corena; Whitelaw, Andrew; Dempers, Johan; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology. Medical Virology.
    ENGLISH ABSTRACT: Background: Sudden and unexpected deaths in infancy (SUDI) includes infants under the age of one year that die suddenly and without apparent cause. Childhood diarrhoea is one of the leading causes of death for children under five, with around 1.7 billion cases worldwide each year and is often reported prior to death in SUDI cases. Poor socioeconomic conditions and inadequate water supplies in developing countries contribute to diarrhoea, and diarrhoeagenic Escherichia coli (DEC) were detected in 30-40% of these cases, while acute viral gastroenteritis causes ± 70% of all episodes. The microbiome influences host immunity, infectious susceptibility, and health, disease, and death outcomes. Limited information is available on the gastrointestinal tract (GIT) pathology, as well as the GIT microbiome as contributory factors to SUDI in South Africa. This study aims to investigate the bacterial and viral pathogens and colonisation of the GIT in SUDI cases admitted to the Tygerberg Medico-Legal Mortuary in the Western Cape in the process of determining the cause of death. Finally, the SUDI microbiome was compared to age-matched, apparently healthy infants. Methods: Swabs of the GIT and stool samples were collected from SUDI cases at Tygerberg Medico-legal Mortuary between June 2017 and May 2018. To serve as controls, stool samples were collected from the nappies of 45 healthy and age-matched infants. In stool and swab samples positive for Escherichia coli, DEC were detected using the AllplexTM GI-Bacteria (II) Assay and gastrointestinal viruses were detected in stool samples using the Allplex™ GI-Viral Assay. Positive rotavirus samples were genotyped and the intestinal microbiome was characterised by full-length 16S rRNA sequencing, on the PacBio Sequel IIe System platform. Results: This study included 186 SUDI cases (107 males and 79 females) and 45 controls (24 males and 21 females). Several known demographic factors increase the risk for SUDI, including age between 2-4 months, male sex, cold season, bedsharing, prone and side sleeping positions, as well as informal housing. Enteroaggregative Escherichia coli (EAEC) ) were detected in 87.3% of cases and enteropathogenic Escherichia coli (EPEC) were detected in 78.2% of cases. Co-infections between DEC pathotypes were observed in 85.2% of cases. Rotavirus was detected in 38.6%, of cases followed by norovirus GI and GII (30.0%), whereas norovirus GII was more prevalent in the controls (36.7%). Forty-eight cases had enteric virus co-detections. The association between most viruses and seasons was highly significant. Among the rotavirus genotypes, combinations of the G type and the P type, G1P[8] had the highest prevalence (40%), followed by G2P[4] (30%), while G9P[8] (20%) and G8P[4] (10%) genotypes had the lowest prevalence. Firmicutes, Bacteroidota, Proteobacteria, and Actinobacteria were found to be the most common organisms in the GIT. Significant differences were observed in alpha diversity and beta diversity between cases and controls, as well as the different final diagnoses. Conclusion: This study demonstrated that autopsy sampling procedures should include other sampling sites, e.g., GIT, as these pathogens may contribute to death, particularly with virus and bacterium co-infections. Determining the cause of death based on GIT pathogens, may decrease the number of Sudden Infant Death Syndrome (SIDS) cases reported in the future.