Key survival genes found in non-tuberculous mycobacteria

A research group including Assistant Professor Kotaro Sawai, Associate Professor Yusuke Minato, and Professor Yohei Doi of the Center for Infectious Disease Research at Fujita Health University, in collaboration with Professor Fumito Maruyama of the IDEC Institute at Hiroshima University and Director General Tomotada Iwamoto of the Kobe Institute of Health, successfully comprehensively identified the essential genes indispensable for the survival of non-tuberculous mycobacteria (NTM), which pose a clinical problem in Japan. At the same time, they conducted comparative analyses with other lineages, demonstrating for the first time that gene essentiality differs depending on the bacterial strain. These achievements are expected to contribute to the development of novel antibacterial drugs. The findings were published in Microbial Genomics on June 26.

Pulmonary disease caused by non-tuberculous mycobacteria (NTM-PD) has been increasing globally in recent years, with a particularly high incidence rate reported in Japan. Mycobacterium avium subsp. hominissuis (MAH), a major causative bacterium, is widely present in soil and water environments and is divided into multiple genetic lineages. Among them, the lineage frequently seen in Japan and South Korea is called the "East Asia lineage."

On the other hand, because drug discovery research is centered in Europe and the United States, little was known about the bacterial strains that pose problems in Japan. In particular, regarding the essential genes that serve as targets for antibacterial drugs, the extent of commonality among lineages remained unclear.

Therefore, the research group conducted a gene essentiality analysis using transposon insertion sequencing (Tn-Seq) on MAH strains isolated from patient bathroom environments in Japan. The analysis required the creation of a "transposon mutant library" in which mutations were randomly introduced into genes. However, the efficiency of creating this library in MAH was low, and only two strains had been analyzed worldwide so far. The Tn-Seq method introduces random mutations into genes, allowing the identification of genes required for survival.

As a result, by optimizing conditions and improving protocols across multiple bacterial strains, they succeeded in constructing high-density libraries for three MAH strains and comprehensively identifying essential genes. Furthermore, by performing comparative analysis between the same lineage and existing data from other lineages, they successfully identified 124 core essential genes common across lineages. Additionally, this analysis revealed that the essentiality of each gene changed among strains for more than approximately 200 genes.

This demonstrated that gene essentiality is not fixed but possesses an "essentiality plasticity" that changes depending on the bacterial strain or lineage. It became clear that the number of essential genes common among lineages was smaller than expected, with significant differences existing among strains.

Minato stated: "In this study, we investigated non-tuberculous mycobacteria circulating in Japan. As initially expected, we were able to confirm that Japanese NTM bacteria possess properties different from those reported in Europe and the United States. Furthermore, we found that even among Japanese strains, there are larger differences than expected. Like Mycobacterium tuberculosis, NTM grows slowly, and research takes time. Nevertheless, moving forward, we would like to continue our research in collaboration with our co-researchers to increase the number of strains investigated, aiming to gain insights that will lead to the development of novel therapeutic drugs in particular."

Journal Information
Publication: Microbial Genomics
Title: Integrated analysis of transposon insertion sequencing and pangenome reveals core and lineage-specific essential genes in Mycobacterium avium subsp. hominissuis
DOI: 10.1099/mgen.0.001753