Ngeow Yun Fong, Wong Yan Ling, Tan Joon Liang, Hong Kar Wai, Ng Hien Fuh, Ong Bee Lee, Chan Kok Gan
Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.
PLoS One. 2015 Apr 1;10(4):e0120789. doi: 10.1371/journal.pone.0120789. eCollection 2015.
Members of the Mycobacterium terrae complex are slow-growing, non-chromogenic acid-fast bacilli found in the natural environment and occasionally in clinical material. These genetically closely-related members are difficult to differentiate by conventional phenotypic and molecular tests. In this paper we describe the use of whole genome data for the identification of four strains genetically similar to Mycobacterium sp. JDM601, a newly identified member of the M. terrae complex. Phylogenetic information from the alignment of genome-wide orthologous genes and single nucleotide polymorphisms show consistent clustering of the four strains together with M. sp. JDM601 into a distinct clade separate from other rapid and slow growing mycobacterial species. More detailed inter-strain comparisons using average nucleotide identity, tetra-nucleotide frequencies and analysis of synteny indicate that our strains are closely related to but not of the same species as M. sp. JDM601. Besides the 16S rRNA signature described previously for the M. terrae complex, five more hypothetical proteins were found that are potentially useful for the rapid identification of mycobacterial species belonging to the M. terrae complex. This paper illustrates the versatile utilization of whole genome data for the delineation of new bacterial species and introduces four new genomospecies to add to current members in the M. terrae complex.
地分枝杆菌复合群的成员是在自然环境中发现的生长缓慢、不产色素的抗酸杆菌，偶尔也在临床材料中发现。这些遗传关系密切的成员很难通过传统的表型和分子检测进行区分。在本文中，我们描述了如何使用全基因组数据来鉴定四株与分枝杆菌属JDM601基因相似的菌株，JDM601是地分枝杆菌复合群新鉴定的成员。来自全基因组直系同源基因比对和单核苷酸多态性的系统发育信息显示，这四株菌株与分枝杆菌属JDM601一起一致聚类成一个与其他快速和缓慢生长的分枝杆菌物种不同的独特进化枝。使用平均核苷酸同一性、四核苷酸频率和共线性分析进行更详细的菌株间比较表明，我们的菌株与分枝杆菌属JDM601密切相关，但不是同一物种。除了先前描述的地分枝杆菌复合群的16S rRNA特征外，还发现了另外五种假定蛋白，它们可能有助于快速鉴定属于地分枝杆菌复合群的分枝杆菌物种。本文阐述了全基因组数据在新细菌物种划分中的广泛应用，并引入了四个新的基因组种，以增加地分枝杆菌复合群的现有成员。
