Whole-Genome Sequencing and Comparative Analysis of Mycobacterium brisbanense Reveals a Possible Soil Origin and Capability in Fertiliser Synthesis.

Wei Yee Wee,Siew Woh Choo,Nicholas S Jakubovics,Tze King Tan,Riccardo Manganelli

doi:10.1371/journal.pone.0152682

Wei Yee Wee, Siew Woh Choo + Show 3 more

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https://doi.org/10.1371/journal.pone.0152682

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Abstract

Mycobacterium brisbanense is a member of Mycobacterium fortuitum third biovariant complex, which includes rapidly growing Mycobacterium spp. that normally inhabit soil, dust and water, and can sometimes cause respiratory tract infections in humans. We present the first whole-genome analysis of M. brisbanense UM_WWY which was isolated from a 70-year-old Malaysian patient. Molecular phylogenetic analyses confirmed the identification of this strain as M. brisbanense and showed that it has an unusually large genome compared with related mycobacteria. The large genome size of M. brisbanense UM_WWY (~7.7Mbp) is consistent with further findings that this strain has a highly variable genome structure that contains many putative horizontally transferred genomic islands and prophage. Comparative analysis showed that M. brisbanense UM_WWY is the only Mycobacterium species that possesses a complete set of genes encoding enzymes involved in the urea cycle, suggesting that this soil bacterium is able to synthesize urea for use as plant fertilizers. It is likely that M. brisbanense UM_WWY is adapted to live in soil as its primary habitat since the genome contains many genes associated with nitrogen metabolism. Nevertheless, a large number of predicted virulence genes were identified in M. brisbanense UM_WWY that are mostly shared with well-studied mycobacterial pathogens such as Mycobacterium tuberculosis and Mycobacterium abscessus. These findings are consistent with the role of M. brisbanense as an opportunistic pathogen of humans. The whole-genome study of UM_WWY has provided the basis for future work of M. brisbanense.

Highlights

Mycobacterium is a genus within the Actinobacteria that includes well known human pathogens such as Mycobacterium tuberculosis, the causative agent of tuberculosis, and Mycobacterium leprae, the agent of leprosy
The M. fortuitum complex includes numerous species, M. fortuitum, Mycobacterium peregrinum, Mycobacterium mucogenicum, Mycobacterium mageritense, Mycobacterium farcinogenes, Mycobacterium septicum [4] and an additional taxon with more than one species known as the third biovariant complex
We described the genome of M. brisbanense UM_WWY isolated from the sputum of a 70-year-old Malaysian male patient with a diagnosis of latent tuberculosis

Summary

Introduction

Mycobacterium is a genus within the Actinobacteria that includes well known human pathogens such as Mycobacterium tuberculosis, the causative agent of tuberculosis, and Mycobacterium leprae, the agent of leprosy. The nontuberculous mycobacteria (NTM), known as environmental mycobacteria, are frequently isolated from environmental sources such as soil, water or animal materials [1,2] These organisms tend to be found in the environment, many NTM are opportunistic pathogens, capable of causing human disease among immune-compromised individuals and even sometimes in immune-competent individuals [3]. The M. fortuitum complex includes numerous species, M. fortuitum, Mycobacterium peregrinum, Mycobacterium mucogenicum, Mycobacterium mageritense, Mycobacterium farcinogenes, Mycobacterium septicum [4] and an additional taxon with more than one species known as the third biovariant complex This complex includes Mycobacterium porcinum, Mycobacterium boenickei, Mycobacterium neworleansense, Mycobacterium houstonenense, Mycobacterium conceptionense and M. brisbanense [4,5]. The genome of UM_WWY has been deposited at GenBank with the RefSeq ID of NZ_AUWS00000000.1

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