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

Etienne Loire,Abdoulkarim Issa Ibrahim,Lucía Manso-Silván,Louis Lignereux,François Thiaucourt

doi:10.1016/j.heliyon.2020.e05146

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.

Highlights

During the early days of bacterial genome sequencing, one mycoplasma was chosen as an example, the agent of contagious bovine pleuropneumonia (CBPP) Mycoplasma mycoides subsp. mycoides (Mmm)
Whole genome sequencing (WGS) offers a unique opportunity to expand our knowledge on the epidemiology of contagious caprine pleuropneumonia (CCPP)
It included strains originating from the various regions where CCPP is known to be present and, notably, five strains isolated from wildlife (wild goat from Qatar (Capra aegagrus) (Arif et al, 2007), and Arabian sand gazelle (Gazella marica) (Lignereux et al, 2018), Arabian oryx (Oryx leucoryx) (Chaber et al, 2014) and scimitar-horned oryx (Oryx dammah) from the United Arab Emirates

Summary

Introduction

During the early days of bacterial genome sequencing, one mycoplasma was chosen as an example, the agent of contagious bovine pleuropneumonia (CBPP) Mycoplasma mycoides subsp. mycoides (Mmm). The reasons for this choice: because mycoplasmas are the simplest selfreplicating organisms possessing very small genomes (Westberg et al, 2004) These scientists picked the wrong species as Mmm genome is riddled with repetitive elements such as insertion sequences (Frey et al, 1995; Vilei et al, 1999). The situation has dramatically changed today that it is viable to sequence dozens of bacterial genomes simultaneously It is even easier with bacterial genomes that do not possess mobile genetic elements and are not prone to horizontal gene transfer (Sirand-Pugnet et al, 2007). This is the case with the agent of contagious caprine pleuropneumonia (CCPP), Mycoplasma capricolum subsp. Whole genome sequencing (WGS) offers a unique opportunity to expand our knowledge on the epidemiology of CCPP

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Results