Masters Degrees (Medical Microbiology)

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Browsing Masters Degrees (Medical Microbiology) by Author "Hamman, Bianca"

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    Investigating the role of respiratory co-infections and the nasopharyngeal microbiome in children with suspected pulmonary tuberculosis
    (Stellenbosch : Stellenbosch University, 2020-12) Hamman, Bianca; Newton-Foot, Mae; Van der Zalm, Marieke; Stellenbosch University. Faculty of Medicine and Health Sciences. Dept. of Pathology: Medical Microbiology.
    Introduction: Tuberculosis (TB) is a global health problem, causing morbidity, mortality and devastating social and economic impacts. Pediatric TB is particularly challenging due to difficulties in diagnosis. Children are particularly susceptible to respiratory infections and this may be influenced by the microbial colonization of the respiratory tract, which may play a role in the clinical presentation and pathogenesis of TB. The nasopharyngeal microbiome is critical for respiratory health and may impact on the development, presentation and diagnosis of TB disease. Antibiotics contribute to microbial dysbiosis which may lead to the development, progression or exacerbation of other diseases. However, there is limited data describing the nasopharyngeal microbiota of children with and without TB, or the effect of TB treatment on the nasopharyngeal microbiome. Methods: Respiratory samples were obtained from pediatric patients with suspected pulmonary TB (PTB) at baseline and follow up visits (2 and 6 months). Participants were classified as having bacteriologically confirmed PTB, clinically diagnosed PTB or unlikely PTB (well-defined ill controls). Respiratory pathogens were detected in all baseline respiratory samples using the Seegene Allplex™ Respiratory Panel 4 and a Pneumocystis jirovecii real-time PCR assay. The nasopharyngeal microbiome of 26 participants was characterized and the effect of TB treatment determined by 16S rRNA sequencing, using the Illumina Miseq platform. Results: Seventy children were included; 27.1% were categorized with bacteriologically confirmed PTB, 32.9% with clinically diagnosed PTB and 40% with unlikely PTB. The most frequently detected bacterial pathogens were Haemophilus influenzae (52/70, 74.2%) and Streptococcus pneumoniae(42/70, 60%). There was no association between the presence of bacterial pathobionts/pathogens and TB disease. Due to poor sequence quality resulting from load shedding during sequencing, the reverse reads were excluded from microbiome analysis. The most commonly detected phyla in all samples were Proteobacteria, Fusobacteria, Firmicutes and Bacteroidetes. Common familia included Streptococcaceae, Pasteurellaceae, Moraxellaceae, Prevotellaceae, Veillonellaceae and Neisseriaceae. There were no significant differences in the microbiome profile or alpha and beta diversity between TB cases and controls at baseline. However, differential abundance testing showed 4-5 fold differences in abundance of Pasteurellaceae and Prevotellaceae between the TB cases and ill controls. There was also no significant difference in microbiota profile or alpha diversity at 2 or 6 months in TB cases, who received TB treatment. However, differential abundance testing identified a reduction in the abundance of Veillonellaceae, Staphylococcaceae, Prevotellaceae, Neisseriaceae, Enterobacteriaceae and Aerococcaceae in TB cases after treatment. Conclusion: This study observed no significant differences between the respiratory pathogens in children with and without PTB. Similarly, no differences in alpha or beta diversity were observed between the respiratory microbiota of TB cases and controls, or after TB treatment. However, differences in abundance of some families, between TB cases and controls at baseline, and before and after TB treatment, suggest that further research on this topic is warranted, considering the numerous limitations which may have impacted the findings of this study. This study contributed to the data available regarding respiratory microbiota in children with suspected PTB in a TB endemic setting and highlighted the challenges of conducting microbiome research in resource limited settings.