The identification of novel single nucleotide polymorphisms to assist in mapping the spread of Bacillus anthracis across the Southern Caucasus

Mitat Sahin,Adam Kotorashvili,Fatih Buyuk,Roman Wölfel,Alexandra Rehn,Markus Antwerpen,Les Baillie,Gregor Grass

doi:10.1038/s41598-018-29738-3

Abstract

Anthrax is common as a zoonotic disease in the southern Caucasus area including parts of Turkey and Georgia. In this region, population genetics of the etiological agent Bacillus anthracis comprises, where known, the major canonical single nucleotide polymorphism (canSNP) groups A.Br.Aust94 and A.Br.008/009 of the pathogen’s global phylogeny, respectively. Previously, isolates of B. anthracis from Turkey have been genotyped predominantly by multi locus variable number of tandem repeat analysis (MLVA) or canSNP typing. While whole genome sequencing is the future gold standard, it is currently still costly. For that reason we were interested in identifying novel SNPs which could assist in further distinguishing closely related isolates using low cost assay platforms. In this study we sequenced the genomes of seven B. anthracis strains collected from the Kars province of Eastern Anatolia in Turkey and discovered new SNPs which allowed us to assign these and other geographically related strains to three novel branches of the major A-branch canSNP-group (A.Br.) Aust94. These new branches were named Kafkas-Geo 1–3 and comprised isolates from the Kars region and the neighboring republic of Georgia suggesting a common ancestry. The novel SNPs identified in this study connect the population genetics of B. anthracis in the South Caucasus and Turkey and will likely assist efforts to map the spread of the pathogen across this region.

Highlights

In many parts of the world the zoonotic disease anthrax remains endemic as evidenced by a significant number of human infections
For Georgia there is a quite detailed map of the genetic diversity of the pathogen present in the country[10] and for Turkey similar efforts are ongoing[6]. These efforts have been facilitated by applying the original canSNP scheme that has been used to establish a global genetic population structure of B. anthracis[12]. In both countries we find B. anthracis strains belonging to the canonical SNP groups A.Br.Aust[948,10] and A.Br.008/00910,13, respectively
The authors included the analysis of several strains of Turkish origin in their study and the results confirmed the close relationship of Georgian and Eastern Anatolian strains within several sublineages of A.Br.Aust9410

Summary

Introduction

In many parts of the world the zoonotic disease anthrax remains endemic as evidenced by a significant number of human infections. From 2009 to 2017 there were an additional 89 human infections[14] and between 2012 and 2017 a total of 129 animal cases in 73 outbreaks in Kars province reported (Kars Directorate of Provincial Food Agriculture And Livestock, Turkey: https://kars.tarim.gov.tr/; 2017) In their recent study Khmaladze et al.[8] applied 25-(multi)-locus variable-number tandem repeat analysis (MLVA-25) and canSNP-typing in order to genotypically characterize a collection of 30 Turkish and 30 Georgian B. anthracis isolates. In order to obtain a clearer picture on the phylogenetic population structure of Eastern Anatolian B. anthracis, we have analyzed several representative strains from a recent study on isolates from Georgia and the northeastern part of Turkey on a genomic level This information was used to design and test new SNP-based assays which could be used to further characterize the transboundary spread of the bacterium across the region

Methods

Results

Conclusion