Fungal-bacterial di-kingdom microbial communities associated with chronic pulmonary disease: A cross-sectional study
Authors: Njovu Israel Kiiza , Musinguzi Benson , Akatuhumuriza Mary , Mumbere Brian , Magurusa Rose Charles , Matovu Musa , Mugenyi Jastus Kizito , Nalumaga Pauline Petra , Nuwagira Edwin , Kassaza Kennedy , Ssedyabane Frank , Bazira Joel , Mwesigye James , Iramiot Jacob Stanley , Mukasa James Kiguli , King Jason , Ampaire Lucas , Itabangi Herbert 
Published: July 2024

Background: Fungal-bacterial co-colonization and co-infections are emerging among tuberculosis (TB) suspected patients, yet the underlying mechanisms that enable and arise from their interactions are poorly understood. Understanding how environmental microbes such as fungi and bacteria co-evolve and develop traits to evade host immune responses and resist treatment is critical to controlling opportunistic co-infections. We therefore, hypothesize that cross-kingdom synergistic interactions between environmental fungi and bacteria may influence both fungal and bacterial virulence, antimicrobial resistance patterns and aetiology. We aimed at establishing the prevalence of fungal–bacterial microbial communities associated with chronic primary or opportunistic pulmonary infections.Methods:This was cross sectional study. Sputum samples were collected from 151 study participant. For each sample, both conventional and molecular laboratory methods were performed to isolate and identify the fungal and bacterial aetiologies.Results:Concordantly, through surveilling 302 clinical samples from 151 patients, we established the prevalence of TB (0.7%) to be lower than that of fungi (1.3%) and non-TB bacterial (4.6%) mono-aetiologies. we revealed many di-kingdom aetiological pairings here but their significance remains a question of further examination. Among whichAcremoniumspp +K. pneumoniae(n=5),Acremonium spp+Streptococcus pneumoniae(n=4),Acremoniumspp +C. albicans+K. pneumoniae(n=3) were among the most dominant aetiological pairings observed. Interestingly,Acremonium spp+K. pneumoniaepairings were also seen to be the most commonly associated with pulmonary TB both during and after treatment. Isolation from the same infection niche as seen here calls for further investigations into any interaction signatures that may exist between these organisms.Conclusion:Taken together, our data suggest that fungal-bacterial co-existence may influence their virulence attributes and antimicrobial resistance patterns, with relevance to patient outcomes. Therefore, our data reveals an array of fungal-bacterial pairings that may influence prognosis of chronic pulmonary disease. Importantly, suggesting that the diversity of pulmonary infective fungi and bacteria, and their complex population structures may pose challenges to the analysis and interpretation of conventional data. Thus, there is need to redirect our diagnostic approaches to encompass poly microbial aetiology in order to enhance our suspicion index for better management of opportunistic fungal-bacterial co-infections.Trial registration:The study was registered in the International Standard Randomized Controlled Trail Number (ISRCTN) registry (Ref: ISRCTN 33572982) on 17thNovember, 2021.