Abstract
The Ralstonia solanacearum species complex (RSSC), composed of three species and four phylotypes, are globally distributed soil-borne bacteria with a very broad host range. In 2009, a devastating potato bacterial wilt outbreak was declared in the central highlands of Madagascar, which reduced the production of vegetable crops including potato, eggplant, tomato and pepper. A molecular epidemiology study of Malagasy RSSC strains carried out between 2013 and 2017 identified R. pseudosolanacearum (phylotypes I and III) and R. solanacearum (phylotype II). A previously published population biology analysis of phylotypes II and III using two MultiLocus Variable Number of Tandem Repeats Analysis (MLVA) schemes revealed an emergent epidemic phylotype II (sequevar 1) group and endemic phylotype III isolates. We developed an optimized MLVA scheme (RS1-MLVA14) to characterize phylotype I strains in Madagascar to understand their genetic diversity and structure. The collection included isolates from 16 fields of different Solanaceae species sampled in Analamanga and Itasy regions (highlands) in 2013 (123 strains) and in Atsinanana region (lowlands) in 2006 (25 strains). Thirty-one haplotypes were identified, two of them being particularly prevalent: MT007 (30.14%) and MT004 (16.44%) (sequevar 18). Genetic diversity analysis revealed a significant contrasting level of diversity according to elevation and sampling region. More diverse at low altitude than at high altitude, the Malagasy phylotype I isolates were structured in two clusters, probably resulting from different historical introductions. Interestingly, the most prevalent Malagasy phylotype I isolates were genetically distant from regional and worldwide isolates. In this work, we demonstrated that the RS1-MLVA14 scheme can resolve differences from regional to field scales and is thus suited for deciphering the epidemiology of phylotype I populations.
Highlights
Knowledge of a pathogen’s population biology is a key aspect of disease management [1, 2]
The present study aims to develop and apply an optimized MultiLocus Variable Number of Tandem Repeats Analysis (MLVA) scheme designed for phylotype I isolates in order to: (i) assess the level of genetic diversity and structure of phylotype I populations isolated in Madagascar’s central highlands and lowlands, (ii) compare the population genetic structures of phylotype I with Malagasy phylotypes IIB-1 and III isolates and (iii) analyse the potential genetic links of the Malagasy phylotype I isolates with isolates from other countries
We developed an optimized MLVA scheme capable of characterizing phylotype I isolates with greater reliability and discriminatory power
Summary
Knowledge of a pathogen’s population biology is a key aspect of disease management [1, 2]. VNTR are tandemly repeated DNA sequences, whose copy numbers may vary amongisolates. MLVA has the advantage of being highly discriminatory, robust, reproducible and rapid [6, 7]. It has been widely used in medical microbiology [8] to trace the origin of epidemics or the spread of virulent or antibiotic-resistant variants. Later developed for plant pathogenic bacteria, MLVA schemes have proven to be useful for outbreak analysis, epidemiological surveillance and the study of the genetic diversity and population structure of: Clavibacter michiganensis subsp. Tomato and maculicola [10], Xylella fastidiosa [11], Xanthomonas citri pv. Musacearum [16], Xanthomonas citri pv. Later developed for plant pathogenic bacteria, MLVA schemes have proven to be useful for outbreak analysis, epidemiological surveillance and the study of the genetic diversity and population structure of: Clavibacter michiganensis subsp. michiganensis [9], Pseudomonas syringae pv. tomato and maculicola [10], Xylella fastidiosa [11], Xanthomonas citri pv. citri [12, 13], Xanthomonas oryzae [14], Xanthomonas arboricola pv. pruni [3], Xanthomonas phaseoli pv. manihotis [15], Xanthomonas vasicola pv. musacearum [16], Xanthomonas citri pv. viticola [17], and the Ralstonia solanacearum species complex [18,19,20,21,22]
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