The dissertation primarily aimed to investigate the lung microbiome in patients with bronchiectasis and compare it with that of healthy individuals. It also focused on analyzing microbial dysbiosis and the role of opportunistic pathogens in disease progression. Furthermore, the study evaluated microbial diversity (alpha and beta diversity) to determine differences between patients and controls. It also aimed to detect the presence of Mycobacterium tuberculosis within bronchiectasis patients, assess antimicrobial resistance in tuberculosis isolates particularly multidrug-resistant (MDR) and pre-extensively drug-resistant (Pre-XDR) strains and perform whole-genome sequencing (WGS) to explore genetic mutations, virulence factors, and mobile genetic elements. Overall, the study adopted an integrated approach combining microbiological, genomic, and environmental perspectives.

 The dissertation included several main components. The clinical aspect involved the collection of sputum samples from patients with bronchiectasis, tuberculosis, COPD, and pneumonia. The conventional laboratory aspect included bacterial culture using MacConkey agar, blood agar, and Lowenstein–Jensen medium. Metagenomic analysis was conducted to characterize the entire microbiome without the need for culture and to identify bacterial taxa and their relative abundance. Statistical and ecological analyses included alpha and beta diversity indices, PCA, PCoA, NMDS, heatmaps, and LEfSe analysis. The study also investigated drug-resistant tuberculosis through antimicrobial susceptibility testing to identify MDR and Pre-XDR strains. Advanced genomic analysis using whole-genome sequencing (WGS) was performed to examine mutations, resistance genes, virulence genes, MLST, and lineage classification. In addition, evolutionary and comparative genomic analyses were conducted using BRIG and through the identification of mobile genetic elements.

The most important recommendations which the study has come up with and the average obtained:

1. The study yielded several important findings. At the culture level, positive results were observed only in bronchiectasis and tuberculosis patients, whereas COPD and pneumonia samples were negative, highlighting the limitations of conventional diagnostic methods. At the microbiome level, patients exhibited microbial dysbiosis characterized by an increased abundance of pathogenic genera such as Pseudomonas, Mycobacterium, Nocardia, and Neisseria, while healthy individuals showed a predominance of beneficial genera such as Streptococcus, Prevotella, and Veillonella. Microbial diversity analysis revealed a decrease in diversity among patients, although not statistically significant, along with increased heterogeneity, indicating instability of the microbial environment.

   A strong association between bronchiectasis and tuberculosis was observed, as Mycobacterium tuberculosis was detected in patient samples, suggesting that tuberculosis may be a contributing factor to disease development. A high prevalence of antimicrobial resistance was identified, with approximately 59% of isolates classified as MDR and the presence of Pre-XDR strains. These isolates showed resistance to key antibiotics including rifampicin, isoniazid, amikacin, and levofloxacin.

    Whole-genome sequencing analysis revealed multiple mutations in resistance-associated genes such as rpoB, katG, and gyrA, along with genetic diversity among strains and the presence of globally recognized lineages (Lineage 3 and Lineage 4). Additionally, mobile genetic elements were identified, contributing to gene transfer and the spread of antimicrobial resistance.

   Overall, the study concluded that bronchiectasis is not merely a simple bacterial infection but rather a complex condition driven by microbial dysbiosis, dominance of opportunistic pathogens, and genomic evolution—particularly of drug-resistant tuberculosis.

The final grade: Excellent