A whole-genome worldwide molecular epidemiology approach for contagious caprine pleuropneumonia

Abstract

Contagious caprine pleuropneumonia is an infectious and contagious disease affecting goats and wildlife ruminants, mostly in Africa and Asia. It is caused by a mycoplasma, Mycoplasma capricolum susbp. capripneumoniae, which is very fastidious. This may be the reason why there are few reports of its isolation and characterization. This study describes the development of a whole genome typing strategy based on sequencing reads assemblies on a reference genome (Abomsa, GenBank accession LM995445) and extraction of informative single nucleotide polymorphism. FASTA sequences inferred from the variant calling files were used to establish a comprehensive phylogenetic tree based on 2880 SNPs. This tree included a total of 34 strains originating from all the regions where CCPP has been detected, as well as strains isolated from wildlife. A recent isolate from West-Niger was positioned closely to another 1995 East-Niger isolate, an indication that CCPP may be extending westward in Africa. Six 2013 Tanzanian isolates had identical sequences in spite of diverse geographical origins. This could be explained by the clonal expansion of a virulent strain at that time in East Africa. Although all strains isolated from wildlife in the Middle East were in the same phylogenetic group, this may not sign an adaptation to new hosts. The most probable explanation for wildlife contamination remains the contact with goats. This strategy will easily accommodate new data in the near future and should become a gold-standard high-resolution typing procedure for the surveillance of contagious caprine pleuropneumonia.

Keywords: Bioinformatics; Contagious caprine pleuropneumonia; Evolutionary biology; Genetics; Microbiology; Mycoplasma capricolum subsp. capripneumoniae; Veterinary medicine; Whole genome phylogeny.

Figure 1

Phylogenetic trees inferred from Mycoplasma capricolum subsp. capripneumoniae core genome SNPs analysis. a. This tree was constructed by analyzing a set of Mccp genomes retrieved from the NCBI website or Illumina reads from 34 Mccp strains. It is based on a total of 2880 SNPs with all nodes leading to the various phylogenetic groups being supported by 100 Shimodaira-Hasegawa test values. The two samples “11022”, obtained from Illumina reads, and “11022 genome”, obtained by creating pseudo-reads from a finished genome, positioned at the same tip of a branch. The effect of the in vitro passage of strain Gabes can be visualized by the positions of Gabes-22p and Gabes-102p on various branches whose length is proportional to the number of passages. Wild animal silhouettes correspond to: Pantholops hodgsonii, Capra aegagrus, Oryx dammah, Gazella marica and Oryx leucoryx. (from top to bottom). Phylogenteic groups A,B,C,D,E,F were inferred from Dupuy et al. (Dupuy et al., 2015), groups A’, G and H were created during this study. b. As the number of reads available for sample 19146 was much lower, this second tree was based only on 396 SNPs. Nevertheless, it allowed the reconstruction of a robust phylogenetic tree. The two samples from Niger, 95043 and 19146 are positioned on a branch supported by 87.9 Shimodaira-Hasegawa test value. The longer branch for 19146 materializes the genome evolution of two strains isolated at 24 years interval.

Figure 2

Geographic origins of the strains analyzed in this study. a. Strains are represented by symbols corresponding to their phylogenetic grouping. They are positioned at their sampling locations except for strains 87001 and F38 whose exact origins are unknown. Strain 19146 is the most western strain in Sub-Saharan Africa. b. All six Tanzanian Mccp strains isolated in 2013 had exactly the same genome sequence in spite of various geographical origins. c. Conversely, Mccp strains (16034) isolated from wildlife 31km apart from others were clearly distinguishable. This is in favor of separate contamination sources.