Comparative Genomics and Transcriptomic Profiling of Mycobacterium avium’s morphotypes

Abstract

Mycobacterium avium complex (MAC) infections are still prevalent in humans, more prominent in immunocompromised individuals. These environmental mycobacteria are widely distributed in soil and water sources, making their exposure very common.
In various organisms, phase variation enables reversible switches between avirulent and virulent states. Some strains of M. avium exhibit this visible phase variation, transitioning between two colony types with different virulence and antibiotic resistance. The virulent form, smooth transparent (SmT), evades immune responses and when grown repeatedly under laboratory conditions gives rise to the avirulent smooth opaque (SmO) form, susceptible to antibiotics.
The underlying mechanism behind this switch is still unknown and, in this project, we sought to perform genomic and transcriptomic analyses of these two colony morphotypes as a first step to answer this question, using the M. avium subsp. hominissuis strains LU439 and TH135.
Genomic analysis confirmed the genetic similarity between the two morphologies in both strains, except for two small hypothetical proteins in each, although short-read sequencing limited our insights. Functional analysis using the COG classification system identified many genes related to lipid transportation and transcription regulator.
This project was successful in developing a functional protocol for the RNA-seq data analysis, validated by comparison with an outsource analysis of the same data set. At this point, it is premature to draw definitive conclusions from the transcriptomic data available, as additional analysis is required, although the Principal Component Analysis (PCA) plot showed that the morphologies present different patterns in gene expression with a tendency for metal-related genes over-expressed in the SmT genome.
Immediate next steps include Oxford Nanopore sequencing and RNA-seq analysis for two additional strains. Looking further ahead, we plan to look at DNA methylation, analyze metabolic pathways and developing markers to track virulence, for a better understanding of the bacteria and identify the mechanism behind this bacterial switch.

Popular Abstract

In the ongoing battle against Mycobacterium avium complex (MAC) infections, a team of researchers has delved into the intricate world of these bacteria's behavior, particularly their ability to switch between harmless and harmful states. MAC infections pose a significant threat, especially to individuals with weakened immune systems, and understanding the mechanisms behind the bacteria's transitions could pave the way for more effective treatments.

M. avium bacteria are widespread in the environment, residing in soil and water sources. The infections they cause are notorious for their persistence and resistance to treatment, making them a challenging medical concern. The focus of this research has been on the two distinct colony types of M. avium—smooth transparent (SmT) and smooth opaque (SmO). The former, SmT, demonstrates an adept ability to evade the immune system, while the latter, SmO, is more vulnerable to antibiotic interventions.

The scientific community has long been intrigued by the phenomenon of phase variation, wherein bacteria can undergo reversible switches between avirulent and virulent states. In the case of M. avium, this visible phase variation is manifested in the transition between SmT and SmO colony types.

The researchers conducted genomic and transcriptomic analyses on two strains of M. avium subsp. hominissuis—LU439 and TH135. While genetic similarities were identified between the two morphologies, the investigation uncovered intriguing differences in two small hypothetical proteins. Additionally, functional analysis using the COG classification system pointed towards genes associated with lipid transportation and transcription regulators, shedding light on potential factors contributing to the bacteria's behavior.

A significant achievement of this project was the development of a functional protocol for RNA-seq data analysis. The reliability of this methodology was validated through external analysis verification, marking a crucial step towards gaining insights into the bacteria's genetic activity during phase variation. Although conclusive findings are still in the early stages, the Principal Component Analysis (PCA) plot revealed distinct gene expression patterns, with a noteworthy tendency for metal-related genes to be overexpressed in the SmT genome.

Looking ahead, the research team plans to employ Oxford Nanopore sequencing and conduct RNA-seq analysis on additional strains of M. avium. These endeavors are expected to provide a more comprehensive understanding of the genetic and molecular factors influencing the bacteria's behavior. Furthermore, the researchers aim to explore DNA methylation, analyze metabolic pathways, and develop markers for tracking virulence—steps that will contribute to a holistic understanding of M. avium and, ultimately, uncover the elusive mechanism behind the bacterial switch.

In summary, this research represents a significant step forward in unraveling the complexities of M. avium infections. By combining genomic and transcriptomic analyses, the team is laying the groundwork for future investigations that could lead to innovative approaches in the prevention and treatment of MAC infections, benefiting individuals at risk and the broader healthcare landscape.

• author: Moreira, Joel
• supervisor: Julia Lienard; Courtney Stairs
• organization: Degree Projects in Bioinformatics
• course: BINP52 20222
• year: 2023
• type: H2 - Master's Degree (Two Years)
• subject: Biology and Life Sciences
• language: English
• id: 9145041
• date added to LUP: 2024-01-15 14:40:17
• date last changed: 2024-01-15 14:40:17