Multi-locus sequence typing of Ehrlichia ruminantium strains from geographically diverse origins and collected in Amblyomma variegatum from Uganda

Abstract

BackgroundThe rickettsial bacterium Ehrlichia ruminantium is the causative agent of heartwater in ruminants. A better understanding of the population genetics of its different strains is, however, needed for the development of novel diagnostic tools, therapeutics and prevention strategies. Specifically, the development of effective vaccination policies relies on the proper genotyping and characterisation of field isolates. Although multi-locus sequence typing (MLST) has been recently developed, only strains from geographically restricted collections have been analysed so far. The expansion of the MLST database to include global strains with different geographic origins is therefore essential. In this study, we used a panel of reference strains from geographically diverse origins and field samples of E. ruminantium detected from its vector, Amblyomma variegatum, in heartwater-endemic areas in Uganda.ResultsA total of 31 novel alleles (six, four, six, three, two, five, three, and two for gltA, groEL, lepA, lipA, lipB, secY, sodB, and sucA loci, respectively) and 19 novel sequence types (STs) were identified. Both neighbour-joining and minimum spanning tree analyses indicated a high degree of genetic heterogeneity among these strains. No association was observed between genotypes and geographic origins, except for four STs from West African countries. When we performed six different tests for recombination (GeneConv, Bootscan, MaxChi, Chimaera, SiScan, and 3Seq) on concatenated sequences, four possible recombination events were identified in six different STs. All the recombination breakpoints were located near gene borders, indicating the occurrence of intergenic recombination. All four STs that localized to a distinct group in clustering analysis showed evidence of identical recombination events, suggesting that recombination may play a significant role in the diversification of E. ruminantium.ConclusionsThe compilation of MLST data set across the African continent will be particularly valuable for the understanding of the existing genetic diversity of field isolates in African countries. Comprehensive information on the degree of cross-protection between strains and further understanding of possible relationships between genotypes and phenotypes such as vaccine efficacy are expected to lead to the development of region-specific vaccination strategies.

Development and implementation of a highly-multiplexed SNP array for genetic mapping in maritime pine and comparative mapping with loblolly pine

“…Comparative mapping was already investigated between P . taeda and other Pinus species using putatively orthologous markers [17,58-60]. Macro-synteny was also reported between maritime and loblolly pines [6] and 32 shared EST-Ps made it possible to identify 10 homologous LGs.…”

Recombination Is a Major Driving Force of Genetic Diversity in the Anaplasmataceae Ehrlichia ruminantium

“…In order to construct E. ruminantium phylogeny and elucidate genetic population structure, a multilocus sequence typing (MLST) analysis based on housekeeping genes (Adakal et al, 2009 , 2010a ; Nakao et al, 2011 ) and a multilocus variable number of tandem repeats based on mini-satellites were developed for E. ruminantium (Pilet et al, 2012 ). The apparent advantages of these techniques are based on a perceived lack of ambiguity, portability, reproducibility, good discriminatory powers to differentiate isolates and ability to be automated (Lindstedt, 2005 ; Sullivan et al, 2005 ).…”

Development of a Quantitative PCR Assay for Differentiating the Agent of Heartwater Disease, Ehrlichia ruminantium , from the Panola Mountain Ehrlichia

“…Additionally, because of the limited number of sequences available for PME, the close homology between PME and ER, and lack of awareness of this emerging organism, multilocus sequence typing based on housekeeping genes may erroneously include PME as a ‘strain’ of ER. This is possible because some contemporary analysis of genetic variation of ER in Africa is based on sequences amplified from ticks, not from isolates obtained from infected ruminants (Nakao et al., ). In particular, strain 623 () has a higher per cent identity with PME (94%) than with any other accessioned strain of ER (91%), over the region for which sequences are available for all taxa.…”