JMIR Publications

ABSTRACT

Background:

Fungal-bacterial co-colonization and co-infections is an emerging challenge among patients suspected for pulmonary tuberculosis (PTB), yet the underlying pathogenic mechanisms and microbiome 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 pulmonary fungal co-infections. In this project, we propose to study the co-existence of fungal and bacterial microbial communities during chronic pulmonary disease with a keen interest in underpinning fungal etiological evolution and establishing the predominating interaction relationships that may exist.

Objective:

This is a protocol for a study aimed at investigating the metabolic and molecular ecological evolution of opportunistic pulmonary fungal co-infections through determining and characterizing the burden, etiological profiles, microbial communities, and; interaction relationships established between fungi and bacteria as implicated among patients with presumptive PTB.

Methods:

This will be a laboratory-based cross-sectional study, with a sample size of 406 participants. From each participant, two sputa (an on-spot and early morning) samples will be collected. These will then be analyzed for both fungal and bacterial aetiology using conventional metabolic and molecular (ITS and 16S rDNA based PCR) approaches. We shall also attempt to design a genome-scale metabolic model (GSMM) for pulmonary microbial communities to infer whole microbiome (fungi and bacteria) and; host-microbial interactions under different patient conditions. This will be based on the interplays of genes (identified by metagenomics and inferred from amplicon data and metabolites (identified by metabolomics) by analyzing the full data set and by employing specific computational tools. We will also collect baseline data including, demographic and clinical history using a patient-reported questionnaire. Altogether, this will be a diagnostic-based observational study. The primary outcome will be an overall fungal and bacterial diagnostic profile of the study participants. Other diagnostic factors associated with the etiological profile such as incidence and prevalence will also be analyzed in univariate and multivariate schemes. Odds ratios with 95% confidence intervals (CIs) will be presented with a statistical significance at p<0.0.5.

Results:

The study has been approved by the Mbarara University Research Ethic Committee (MUREC1/7-07/09/20) and the Uganda National Council of Science and Technology (HS1233ES). Following careful scrutiny, the protocol was designed to enable patient enrollment which began in March 2022 at Mbarara University Teaching Hospital. Data collection is expected to be completed by July 2023, manuscripts submitted for publication thereafter.

Conclusions:

Through this protocol, we shall explore the metabolic and molecular ecological evolution of opportunistic pulmonary fungal co-infections among presumptive PTB cases. Establishing key fungal-bacterial cross kingdom synergistic relationships crucial for instituting fungal bacterial co-infecting aetiology. Clinical Trial: International Standard Randomized Controlled Trial Number (ISRCTN) registry (Ref: ISRCTN33572982).