SAGES Magazine

THE SOUTH AFRICAN GASTROENTEROLOGY REVIEW 2021 | VOLUME 19 | ISSUE 2 | 41 An unbiased metaproteomic approach to describe the mucosal microbiome of HIV-exposed African Infant cohort Post Colonoscopy Colorectal Cancer in South Africa S Fortuin 1 , P Khomunala 1 , M Potgieter 3 , J Wendoh 2 , H Jaspan 3 , N Mulder 2 , J Blackburn 1,3 Chemical and Systems Biology, Integrated Biomedical Sciences, Institute for infectious Disease and Molecular Medicine, Faculty Health, University of Cape Town 1 , Computational Biology, Faculty Health, University of Cape Town 2 , Division of Immunology, Faculty Health, University of Cape Town 3 L Fourie, D Bizos Division Surgical Gastroenterology, Charlotte Maxeke Hospital, University of the Witwatersrand Infants born toHIV-infectedmothers have an altered cellular immunity despite being HIV-infected themselves. It is known that the gut microbiome is crucial to immune development. Currently, 16S rRNA sequencing, the gold standard for characterising the microbiome, yields limited information on the function of the microbial community, predicted open reading frames might not be expressed under in vivo conditions. For this study, infant stool samples, both HIV-exposed and unexposed infants collected at birth and at 4-7days were analysed to characterise the metaproteome using mass spectrometry-based proteomics. Briefly, cold stored samples were snap-frozen and ground samples were suspended in organic buffer and precipitated proteinaceous material were subjected to in-solution trypsin digestion. Desalted tryptic peptides were analysed in triplicate on the nLC-MS/MS. An in-house developed pipeline, Metanovo, was used to construct a metaproteomic database using the Universal Reference Database and generated mass spectrometry data. The metaproteomic database was used for protein and organism identification in MaxQuant-suite. Using our unbiased approach, we identified 3943 protein groups for all 55 samples described. The microbial diversity changed dynamically from birth to 4-7 days after birth and the proportion of human proteins identified decreased as the microbial diversity evolved. Using this approach, we identified virus, parasite, bacteria and human proteins in a single sample. The number of proteins belonging to the Bifidobacteriaceae family were significantly different between HEU and HU infants at birth, 1 to 180 respectively. Furthermore, this bacterial family increased dramatically to 1800 proteins within the first week of birth. Members of the Bifidobacteriaceae family are important microbes that colonize the gut of humans and other animals during the early stages of life. Here we demonstrated that using mass spectrometry-based proteomics approach we were able to construct a metaproteomic profile of the microbiota composition of infant stool samples. Figure 1. Dynamic shift in the metaproteome composition of stool samples at birth, 4-7 days after birth HIV-unexposed and HIV- exposed uninfected infants References MetaNovo: a probabilistic approach to peptide and polymorphism discovery in complex mass spectrometry datasets. Thys Potgieter, et.al. 2018 (In Press) Acknowledgements Institute for infectious Disease and Molecular Medicine, University Research Funding, University of Cape Town; National Research Foundation South Africa; National Institutes of Health, USA. Introduction Post-colonoscopy colorectal cancers (PCCRC) are cancers that are diagnosed within 3-5 years of a normal Colonoscopy. Colonoscopy is the current gold standard for the diagnosis of Colorectal cancer. The rate of PCCRC is indicator of the quality of colonoscopy. Objective The primary objective of this study is to calculate the proportion of PCCRC in a privately insured population in South Africa. The secondary objectives are to describe the patient demographics and speciality of the doctor performing the colonoscopy. Method This is a retrospective population-based study. Data was obtained from the largest private health insurance company in South Africa. Patients diagnosed with CRC within the period of 1 January 2013 and 31 December 2019 were included. Patients that were diagnosed with cancer between 6-60 months of index colonoscopy were defined as PCCRC. Results This study investigated the data of 19 538 patients diagnosed with CRC. Exclusions were applied based on membership criteria and predisposing conditions. Following these 4765 patients were included in the study. PCCRC was identified in 8.72% of the study population between 06-60 months and 6.61% of cases between 06-36 months. The average age of patients in this study was 62 years. In this study 1248(26.1%) patients were 50 years and younger. In the subset of patients identified as PCCRC 110 (26.50%) were 50 years and younger. In this study population 51.4% of patients were male and 48.6% were female. In the subset of patients with PCCRC 53% of patients were male and 47% were female. In this study population of 4765 patients 3553 colonoscopies were performed by surgeons. This accounts for 74.5% of colonoscopies. Gastroenterologist performed 7.4% of colonoscopies and 10.07% of Colonoscopies were performed by Physicians 8.1% of colonoscopies were performed by various other specialities including general practitioners. In the PCCRC subset 67.95% of colonoscopies were performed by surgeons 12.53% by gastroenterologists and10.3% by physicians, respectively. Conclusion This study reveals a PCCRC rate of 8.72%. PCCRCmay be used as a surrogate marker for the quality of endoscopy in the country. Further studies need to be done to follow the trend PCCRC over time. SAGES