Full Text Available
Note: Clicking the button above will open the full text document at the original institutional repository in a new window.
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.
Thesis (PhD)--Stellenbosch University, 2023.
Saved in:
| Main Author: | |
|---|---|
| Other Authors: | |
| Format: | Thesis |
| Language: | en_ZA en_ZA |
| Published: |
Stellenbosch : Stellenbosch University
2023
|
| Subjects: | |
| Tags: |
No Tags, Be the first to tag this record!
|
| _version_ | 1867613821486497792 |
|---|---|
| access_status_str | Open Access |
| author | Cupido, Danielle Tiffany |
| author2 | De Beer, Corena |
| author_browse | Cupido, Danielle Tiffany De Beer, Corena |
| author_facet | De Beer, Corena Cupido, Danielle Tiffany |
| author_sort | Cupido, Danielle Tiffany |
| collection | Thesis |
| dc_rights_str_mv | Stellenbosch University |
| description | Thesis (PhD)--Stellenbosch University, 2023. |
| format | Thesis |
| id | oai:scholar.sun.ac.za:10019.1/128793 |
| institution | Stellenbosch University (South Africa) |
| language | en_ZA en_ZA |
| last_indexed | 2026-06-10T12:42:14.156Z |
| license_str | Other — see source repository |
| provenance_str_mv | Harvested via OAI-PMH from SUNScholar — Stellenbosch University Repository |
| publishDate | 2023 |
| publishDateRange | 2023 |
| publishDateSort | 2023 |
| publisher | Stellenbosch : Stellenbosch University |
| publisherStr | Stellenbosch : Stellenbosch University |
| record_format | dspace |
| source_str | SUNScholar — Stellenbosch University Repository |
| spelling | oai:scholar.sun.ac.za:10019.1/128793 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. Cupido, Danielle Tiffany De Beer, Corena Whitelaw, Andrew Dempers, Johan Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology. Medical Virology. Sudden infant death syndrome -- Western Cape (South Africa) Diarrhea, Infantile -- Western Cape (South Africa) Medical virology -- Western Cape (South Africa) Forensic nursing -- Western Cape (South Africa) Gastroenteritis in children -- Western Cape (South Africa) Thesis (PhD)--Stellenbosch University, 2023. 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. AFRIKAANS OPSOMMING: Agtergrond: Skielike en onverwagte sterftes in babas jonger as een jaar wat skielik en sonder duidelike oorsaak plaasvind word algemeen geag as onverwagte babadood. Diarree is een van die hoofoorsake van dood vir kinders jonger as vyf jaar, met ongeveer 1.7 miljard gevalle wêreldwyd elke jaar en dit word dikwels aangemeld in gevalle van onverwagte babadood. Swak sosio-ekonomiese toestande en onvoldoende watervoorsiening in ontwikkelende lande dra by tot diarree, en diarrogeniese Escherichia coli (DEC) is verantwoordelik vir 30-40% van hierdie gevalle, terwyl akute virale gastro-enteritis ± 70% van alle episodes veroorsaak. Die mikrobioom beïnvloed gasheerimmuniteit, aansteeklike vatbaarheid en gesondheid, siekte en sterftes. Beperkte inligting is beskikbaar oor die spysverteringskanaal patologie, sowel as die spysverteringskanaal-mikrobioom as bydraende faktore tot onverwagte babadood in Suid-Afrika. Hierdie studie het ten doel om die bakteriële en virale patogene en kolonisasie van die spysverteringskanaal in gevalle van onverwagte babadood te ondersoek wat in die Tygerberg Mediesgeregtelike Lykshuis in die Wes-Kaap opgeneem is in die proses om die oorsaak van dood te bepaal. Laastens is die mikrobioom vergelyk tussen gevalle van onverwagte babadood en ʼn groep gesonde babas van dieselfde ouderdom. Metodes: Deppers van die spysverteringskanaal en stoelgangmonsters is van gevalle van onverwagte babadood by Tygerberg Medies-geregtelike Lykshuis ingesamel tussen Junie 2017 en Mei 2018. Om as kontroles te dien, is stoelgangmonsters van die doeke van 45 gesonde en ouderdom-ooreenstemmende babas versamel. In stoelgang- en deppermonsters positief vir Escherichia coli, is DEC opgespoor met behulp van die AllplexTM GI-Bacteria (II) Assay en gastroïntestinale virusse is opgespoor in stoelmonsters met behulp van die Allplex™ GI-Virale Assay. Positiewe rotavirus monsters is genotipeer en die intestinale mikrobioom is gekenmerk deur vollengte 16S rRNA volgordebepaling, op die PacBio Sequel IIe System platform. Resultate: Hierdie studie het 186 gevalle van onverwagte babadood (107 manlik en 79 vroulik) en 45 kontroles (24 manlik en 21 vroulik) ingesluit. Verskeie bekende demografiese faktore verhoog die risiko vir onverwagte babadood, onder andere ouderdom tussen 2-4 maande, manlike geslag, koue seisoen, deel van beddens, buik- en syslaapposisies, sowel as informele behuising. Enteroaggregatiewe Escherichia coli (EAEC) was verantwoordelik vir 87.3% van gevalle en enteropatogene Escherichia coli (EPEC) was verantwoordelik vir 78.2% van gevalle. Koinfeksie is in 85.2% van die gevalle waargeneem. Rotavirus is opgespoor in 38.6% van gevalle, gevolg deur norovirus GI en GII (30.0%), terwyl norovirus GII meer algemeen in die kontroles (36.7%) voorgekom het. Meer as een enteriese virusse is in 48 gevalle bevestig. Die verband tussen die meeste virusse en seisoene was hoogs betekenisvol. Kombinasies van G-tipe en P-tipe, G1P[8] was die algemeenste (40%), gevolg deur G2P[4] (30%), terwyl G9P[8] (20%) en G8P[4] (10%) genotipes het die laagste voorkoms getoon. Firmicutes, Bacteroidota, Proteobacteria en Actinobacteria was die algemeenste organismes in die spysverteringskanaal. Beduidende verskille is waargeneem in alfa-diversiteit en beta-diversiteit tussen gevalle en kontroles, sowel as die verskillende finale diagnoses. Gevolgtrekking: Hierdie studie het getoon dat lykskouingsprosedures ander areas moet insluit, bv. spysverteringskanaal, aangesien hierdie patogene tot die dood kan bydra, veral met virus- en bakteriegepaardgaande infeksies. Die bepaling van die oorsaak van dood gebaseer op spysverteringskaal-patogene kan die aantal wiegiedood gevalle wat in die toekoms aangemeld word, verminder. Doctoral 2023-07-31T12:42:29Z 2024-01-08T11:22:30Z 2023-07-31T12:42:29Z 2024-01-08T11:22:30Z 2023-07 Thesis https://scholar.sun.ac.za/handle/10019.1/128793 en_ZA en_ZA Stellenbosch University xvi, 220 pages application/pdf Stellenbosch : Stellenbosch University |
| spellingShingle | Sudden infant death syndrome -- Western Cape (South Africa) Diarrhea, Infantile -- Western Cape (South Africa) Medical virology -- Western Cape (South Africa) Forensic nursing -- Western Cape (South Africa) Gastroenteritis in children -- Western Cape (South Africa) Cupido, Danielle Tiffany 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. |
| title | 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. |
| title_full | 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. |
| title_fullStr | 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. |
| title_full_unstemmed | 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. |
| title_short | 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. |
| title_sort | 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 |
| topic | Sudden infant death syndrome -- Western Cape (South Africa) Diarrhea, Infantile -- Western Cape (South Africa) Medical virology -- Western Cape (South Africa) Forensic nursing -- Western Cape (South Africa) Gastroenteritis in children -- Western Cape (South Africa) |
| url | https://scholar.sun.ac.za/handle/10019.1/128793 |
| work_keys_str_mv | AT cupidodanielletiffany investigatingpathogensofthegastrointestinaltractinsuddenandunexpecteddeathininfancycasesatthetygerbergmedicolegalmortuarycomparedtoanagematchedhealthycontrolgroup |