Ravelomanantsoa Santatra, Robène Isabelle, Chiroleu Frédéric, Guérin Fabien, Poussier Stéphane, Pruvost Olivier, Prior Philippe
BIOS UMR PVBMT, CIRAD, Saint-Pierre, La Réunion, France; UMR PVBMT, Université de la Reunion, Saint-Denis, La Réunion, France; Faculty of Sciences, University of Antananarivo, Antananarivo, Madagascar.
BIOS UMR PVBMT, CIRAD , Saint-Pierre, La Réunion , France.
PeerJ. 2016 May 5;4:e1949. doi: 10.7717/peerj.1949. eCollection 2016.
Background. Reliable genotyping that provides an accurate description of diversity in the context of pathogen emergence is required for the establishment of strategies to improve disease management. MultiLocus variable number tandem repeat analysis (MLVA) is a valuable genotyping method. It can be performed at small evolutionary scales where high discriminatory power is needed. Strains of the Ralstonia solanacearum species complex (RSSC) are highly genetically diverse. These destructive pathogens are the causative agent of bacterial wilt on an unusually broad range of host plants worldwide. In this study, we developed an MLVA scheme for genotyping the African RSSC phylotype III. Methods. We selected different publicly available tandem repeat (TR) loci and additional TR loci from the genome of strain CMR15 as markers. Based on these loci, a new phylotype III-MLVA scheme is presented. MLVA and multiLocus sequence typing (MLST) were compared at the global, regional, and local scales. Different populations of epidemiologically related and unrelated RSSC phylotype III strains were used. Results and Discussion. Sixteen polymorphic TR loci, which included seven microsatellites and nine minisatellites, were selected. These TR loci were distributed throughout the genome (chromosome and megaplasmid) and located in both coding and intergenic regions. The newly developed RS3-MLVA16 scheme was more discriminative than MLST. RS3-MLVA16 showed good ability in differentiating strains at global, regional, and local scales, and it especially highlighted epidemiological links between closely related strains at the local scale. RS3-MLVA16 also underlines genetic variability within the same MLST-type and clonal complex, and gives a first overview of population structure. Overall, RS3-MLVA16 is a promising genotyping method for outbreak investigation at a fine scale, and it could be used for outbreak investigation as a first-line, low-cost assay for the routine screening of RSSC phylotype III.
背景。在病原体出现的背景下，为制定改善疾病管理的策略，需要可靠的基因分型来准确描述多样性。多位点可变数目串联重复序列分析（MLVA）是一种有价值的基因分型方法。它可在需要高鉴别力的小进化尺度上进行。青枯雷尔氏菌复合种（RSSC）的菌株具有高度的遗传多样性。这些具有破坏性的病原体是全球范围内异常广泛的寄主植物上细菌性枯萎病的病原体。在本研究中，我们开发了一种用于非洲RSSC III型基因分型的MLVA方案。方法。我们选择了不同的公开可用串联重复（TR）位点以及来自菌株CMR15基因组的额外TR位点作为标记。基于这些位点，提出了一种新的III型MLVA方案。在全球、区域和局部尺度上对MLVA和多位点序列分型（MLST）进行了比较。使用了流行病学相关和不相关的RSSC III型菌株的不同群体。结果与讨论。选择了16个多态性TR位点，其中包括7个微卫星和9个小卫星。这些TR位点分布在整个基因组（染色体和大质粒）中，位于编码区和基因间区域。新开发的RS3 - MLVA16方案比MLST更具鉴别力。RS3 - MLVA16在全球、区域和局部尺度上区分菌株方面表现出良好的能力，尤其突出了局部尺度上密切相关菌株之间的流行病学联系。RS3 - MLVA16还强调了同一MLST型和克隆复合体中的遗传变异性，并给出了种群结构的初步概述。总体而言，RS3 - MLVA16是一种用于精细尺度爆发调查的有前景的基因分型方法，可作为RSSC III型常规筛查的一线低成本检测方法用于爆发调查。
