Molecular Typing of Ukrainian Bacillus anthracis Strains by Combining Whole-Genome Sequencing Techniques

Abstract

Anthrax is a recurrent zoonosis in the Ukraine with outbreaks occurring repeatedly in certain areas. For determining whether several Bacillus anthracis genotypes are circulating in this region, four strains from various sources isolated from different regions of the Ukraine were investigated. By combining long- and short-read next-generation sequencing techniques, highly accurate genomes were reconstructed, enabling detailed in silico genotyping. Thus, the strains could be assigned to the Tsiankovskii subgroup of the “TransEurAsia” clade, which is commonly found in this region. Their high genetic similarity suggests that the four strains are members of the endemic population whose progenitor was once introduced in the Ukraine and bordering regions. This study provides information on B. anthracis strains from a region where there is little knowledge of the local population, thereby adding to the picture of global B. anthracis genotype distribution. We also emphasize the importance of surveillance and prevention methods regarding anthrax outbreaks, as other studies predicted a higher number of cases in the future due to global warming.

Sequence-based detection and typing procedures for Burkholderia mallei: Assessment and prospects

“…Thereby, errors in the long nanopore-generated sequences can be corrected with highly accurate Illumina reads, while the long reads can span genomic regions which the short reads alone cannot disambiguate (49, 60). In that way, an in silico MLVA approach may become feasible, as was shown for Bacillus anthracis (58).…”

“…While this is commonly done for some pathogens, such as Brucella sp. ( 57 ), this approach has limitations for other bacteria such as Bacillus anthracis ( 58 ) and also B. mallei ( 59 ). Indeed, MLVA profiles obtained in silico from genomes of Pakistani B. mallei strains differed markedly from previously published profiles, disqualifying this in silico approach from sequencing data obtained by Illumina technology.…”

Comparison of Illumina and Oxford Nanopore Technology for genome analysis of Francisella tularensis, Bacillus anthracis, and Brucella suis

“…Databases and tools have been developed to detect genetic markers for virulence [ 18 ], resistance to antimicrobial and disinfection agents [ 19 , 20 ], and mobile genetic elements, such as plasmids [ 21 ]. Based on WGS data, researchers can reproduce (and partly replace) commonly used standard typing approaches, such as canonical Single-Nucleotide-Polymorphism (canSNP) typing [ 22 ], classical Multilocus Sequence Typing (MLST) using 7–9 genes [ 23 ], and Multi Locus Variable copy Numbers of Tandem Repeats (VNTR) Analysis (MLVA) [ 24 ]. Since information on (almost) the entire genome is available, WGS enables high-resolution genotyping using large amounts of genomic features.…”

“…These long reads simplify the assembly process and thus allow the reconstruction of complete and closed bacterial genomes [ 28 ]. Indeed, ONT data has recently been utilized for bacterial genotyping, both in combination with Illumina data [ 24 , 29 – 32 ], but also without Illumina data [ 33 , 34 ].…”

“…While single strains have been sequenced using nanopore technology for F. tularensis [ 39 ] and hybrid assemblies were used to support Ba. anthracis genotyping [ 24 ], to the authors’ knowledge no systematic comparison of Illumina and ONT sequencing for Ba. anthracis , Br.…”