A novel multilocus variable number tandem repeat analysis typing scheme for African phylotype III strains of theRalstonia solanacearumspecies complex

Abstract

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.

New Multilocus Variable-Number Tandem-Repeat Analysis (MLVA) Scheme for Fine-Scale Monitoring and Microevolution-Related Study of Ralstonia pseudosolanacearum Phylotype I Populations

“…It is important that all these studies analyzed the genetic diversity in areas that were larger than ours (continent, country, and regional scales, respectively). Interestingly, our values were higher than that reported for an R. pseudosolanacearum phylotype III field population sampled in Cameroon (H E ϭ 0.03; G/N ϭ 0.235) (52). An explanation for the low genetic diversity detected, apart from a possible sampling bias effect, might be that the RSSC is capable of surviving in plants and in soil in a viable but not cultivable (VBNC) state (58).…”

“…within the Ivory Coast and Africa (41), addressed the global surveillance of phylotype III (52), and identified sources of contamination of the Thames by phylotype IIB-1 (17). These studies improved the comprehension of RSSC epidemiology, its spread, its structuration on different scales, and its colonization pattern.…”

“…The proposed new MLVA scheme is the fourth one developed for the RSSC, after the initial work of N=Guessan et al (including the phylotype I-specific MLVA-13 scheme) (20), the phylotype IIB-1-specific scheme of Parkinson et al (17), and the phylotype III-specific scheme of Ravelomanantsoa et al (52). These three schemes, used on regional scales, allowed the inference of possible dissemination routes of phylotype I and Vallon 2012 (n ϭ 319) collections were genotyped using the MLVA-7 scheme (left), and their distribution within the three collections was determined using the table.value tool (right).…”

“…To date, three MLVA schemes have already been developed, to decipher RSSC population genetics on different scales (41), to investigate sources of water contamination by Ralstonia solanacearum (phylotype IIB) (17), and to characterize African R. pseudosolanacearum phylotype III strains on local and global scales (52). The MLVA phylotype I-specific scheme of N=Guessan et al (20) (13 loci; MLVA-13) and the MLVA phylotype III-specific scheme of Ravelomanantsoa et al (52) gave promising results in discriminating populations on scales ranging from cropping areas to continents (41).…”

Isolation and characterization of Ralstonia solanacearum strains causing bacterial wilt of potato in Nakuru County of Kenya

“…For instance, in Cameroon and Ivory Coast, phylotypes I, II and III have been reported (Mahbou et al, 2009;N'Guessan et al, 2012) while in Ethiopia phylotypes I and II have been identified (Lemessa and Zeller, 2007). Phylotype I was also previously reported in Madagascar and eastern African countries bordering the Indian Ocean including Kenya and South Africa (Wicker et al, 2012;Ravelomanantsoa et al, 2016;Carstensen et al, 2017). This is the first report of phylotype IV in Kenya which could have been introduced in the country through imported potato seed with latent infection (Kaguongo et al, 2010).…”