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Investigating a potential infectious cause of death in Sudden Unexpected Death in Infancy and Childhood using 16S rRNA gene sequencing

Gates, Lily; (2022) Investigating a potential infectious cause of death in Sudden Unexpected Death in Infancy and Childhood using 16S rRNA gene sequencing. Doctoral thesis (Ph.D), UCL (University College London). Green open access

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Abstract

Sudden unexpected death in infancy (SUDI) is the most common cause of post-neonatal infant death in the developed world. Following thorough investigation approximately 40% of cases remain unexplained. It has been hypothesised that a subset of these currently unexplained infant deaths are due to infection that could not be diagnosed at post-mortem (PM) examination due to limitations in current diagnostic techniques. The aim of this study was to optimise the 16S rRNA sequencing technique for PM tissue samples from both SUDI cases and their childhood equivalent (collectively referred to as sudden unexpected death in infancy and childhood, or SUDIC) to investigate whether this technique can reliably identify infected tissues and assist in the PM diagnosis of infection. This thesis investigated several aspects of the PM process in order to determine the use of the 16S rRNA gene sequencing technique in routine clinical diagnosis of infection. The process of PM bacterial translocation was investigated using the 16S rRNA gene sequencing technique in two animal models over a 14-day study period in order to determine the effects this process may have on bacteria identified within internal organs in a PM setting. This investigation found no evidence for significant PM bacterial translocation in the mouse model. In the piglet model, low-levels of bacteria were detected in some tissues, but there was no evidence for significant translocation from the gastrointestinal tract or nasal cavity. With this insight into the PM process, a 16S rRNA gene sequencing method was successfully optimised for use in both formalin-fixed paraffin-embedded (FFPE) and frozen tissues from archived cases of SUDI. These investigations included examination of the effects of different sequencing protocols and tissue processing. The optimised 16S rRNA gene sequencing method was then performed on PM tissues from SUDIC cases. These cases were assigned to one of three groups depending on the final cause of death (CoD) as recorded on the autopsy report: (i) infectious, (ii) explained non-infectious, and (iii) unexplained. Results showed that the technique could successfully distinguish between explained non-infectious and infectious cases of SUDIC. The method correctly identified the causative organism in all cases of infectious SUDIC due to a bacterial infection where the pathogen had been identified at PM investigation. In four cases of infectious SUDIC where the causative organism was not identified at PM investigation using current routine techniques, a dominant bacterial pathogen was identified in this study using the sequencing technique. Using control groups a threshold was defined to identify infected PM tissue samples. When applied to the unexplained cohort four cases of SUDIC were identified where overwhelming bacterial colonisation of PM tissues was observed. Considering clinical history and other PM findings, it is possible that these deaths had a potentially unidentified infectious cause. The results of this thesis support the further evaluation and use of 16S rRNA gene sequencing in PM tissues from cases of SUDIC. The technique has the potential to identify infectious agents which are undetected using current techniques. Further work should increase the study cohort and perform this investigation prospectively as a part of routine clinical diagnosis of SUDIC.

Type: Thesis (Doctoral)
Qualification: Ph.D
Title: Investigating a potential infectious cause of death in Sudden Unexpected Death in Infancy and Childhood using 16S rRNA gene sequencing
Open access status: An open access version is available from UCL Discovery
Language: English
Additional information: Copyright © The Author 2022. Original content in this thesis is licensed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) Licence (https://creativecommons.org/licenses/by-nc/4.0/). Any third-party copyright material present remains the property of its respective owner(s) and is licensed under its existing terms. Access may initially be restricted at the author’s request.
UCL classification: UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > UCL GOS Institute of Child Health
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > UCL GOS Institute of Child Health > Infection, Immunity and Inflammation Dept
UCL
URI: https://discovery.ucl.ac.uk/id/eprint/10151141
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