In silico approach to identify microsatellite candidate biomarkers to differentiate the biovar of Corynebacterium pseudotuberculosis genomes

Kenny da Costa Pinheiro; Bruna Verônica Azevedo Gois; Wylerson Guimarães Nogueira; Fabrício Almeida Araújo; Ana Lídia Cavalcante Queiroz; Oscar Cardenas-Alegria; Artur Luiz da Costa da Silva; Antônio Márcio Gomes Martins Júnior; Rommel Thiago Jucá Ramos

doi:10.3389/fbinf.2022.931583

In silico approach to identify microsatellite candidate biomarkers to differentiate the biovar of Corynebacterium pseudotuberculosis genomes

Front Bioinform. 2022 Sep 16:2:931583. doi: 10.3389/fbinf.2022.931583. eCollection 2022.

Authors

Kenny da Costa Pinheiro¹, Bruna Verônica Azevedo Gois¹, Wylerson Guimarães Nogueira², Fabrício Almeida Araújo¹, Ana Lídia Cavalcante Queiroz¹, Oscar Cardenas-Alegria¹, Artur Luiz da Costa da Silva³, Antônio Márcio Gomes Martins Júnior⁴, Rommel Thiago Jucá Ramos¹

Affiliations

¹ Institute of Biological Sciences, Federal University of Pará, Belém, Pará, Brazil.
² Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
³ Laboratory of Genomic and Bioinformatics, Center of Genomics and System Biology, Federal University of Pará, Belém, Pará, Brazil.
⁴ Laboratory of Genetics, Evolution and Bioinformatics, Federal Institute of Pará, Tucuruí, Pará, Brazil.

Abstract

Corynebacterium pseudotuberculosis is the causative bacterial agent of the zoonotic disease known as caseous lymphadenitis, and it presents several mechanisms of response to host defenses, including the presence of virulence factors (VFs). The genomes of these bacteria have several polymorphic markers known as microsatellites, or simple sequence repeats (SSRs), that can be used to characterize the genome, to study possible polymorphisms existing among strains, and to verify the effects of such polymorphic markers in coding regions and regions associated with VFs. In this study, several SSRs were identified within coding regions throughout the 54 genomes of this species, revealing possible polymorphisms associated with coding regions that could be used as strain-specific or serotype-specific identifiers of C. pseudotuberculosis. The similarities associated with SSRs amongst the different serum variants of C. pseudotuberculosis, biovars equi and ovis, were also evaluated, and it was possible to identify SSRs located in coding regions responsible for a VF enrolled in pathogenesis known to mediate bacterial adherence (SpaH-type pili virulence factor). Phylogenetic analyses revealed that strains sharing SSR patterns, including the possible polymorphisms identified in the same position of gene-coding regions, were displayed by strains with a common ancestor, corroborating with the Genome Tree Report of the NCBI. Statistical analysis showed that the microsatellite groups belonging to equi and ovis biovars have a significance of 0.006 (p-value) in similarity, thus indicating them as good biomarker candidates for C. pseudotuberculosis.

Keywords: Corynebacterium pseudotuberculosis; biomarkers; caseous lymphadenitis; microsatellites; simple sequence repeats (SSRs); virulence factors (VFs).