Rapidly evolving changes and gene loss associated with host switching in Corynebacterium pseudotuberculosis

Viana, Marcus Vinícius Canário; Sahm, Arne; Góes-Neto, Aristóteles; Figueiredo, Henrique César Pereira; Wattam, Alice R.; Azevedo, Vasco

doi:10.1371/journal.pone.0207304

Cited by 7 publications

(5 citation statements)

References 100 publications

(141 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The main differences among the analyzed genomes were recorded between the biovars equi and ovis. As in other studies, pan-genome analysis proved the absence of these CDS coding for genes connected to nitrate reduction in all genomes of the C. pseudotuberculosis biovar ovis strains as well as the absence of the CRISPR-Cas system [46,47]. Therefore, based on ANI values and the absence of CDS coding for genes connected to nitrate reduction, the strains sequenced in this study belong to the biovar ovis, which also corresponds to their isolation from sheep or goat lesions.…”

Section: Pan-genomic Analysissupporting

confidence: 80%

Ovine and Caprine Strains of Corynebacterium pseudotuberculosis on Czech Farms—A Comparative Study

Markova,

Langova,

Babak

et al. 2024

Microorganisms

View full text Add to dashboard Cite

Caseous lymphadenitis (CLA) is a worldwide disease of small ruminants caused by Corynebacterium pseudotuberculosis, a facultative intracellular pathogen that is able to survive and multiply in certain white blood cells of the host. In this study, 33 strains of C. pseudotuberculosis were isolated from sheep and goats suffering from CLA on nine farms in the Czech Republic. All these strains were tested for their antibiotic susceptibility, ability to form a biofilm and resistance to the effects of commonly used disinfectant agents. To better understand the virulence of C. pseudotuberculosis, the genomes of strains were sequenced and comparative genomic analysis was performed with another 123 genomes of the same species, including ovis and equi biovars, downloaded from the NCBI. The genetic determinants for the virulence factors responsible for adherence and virulence factors specialized for iron uptake and exotoxin phospholipase D were revealed in every analyzed genome. Carbohydrate-Active Enzymes were compared, revealing the presence of genetic determinants encoding exo-α-sialidase (GH33) and the CP40 protein in most of the analyzed genomes. Thirty-three Czech strains of C. pseudotuberculosis were identified as the biovar ovis on the basis of comparative genome analysis. All the compared genomes of the biovar ovis strains were highly similar regardless of their country of origin or host, reflecting their clonal behavior.

show abstract

Section: Pan-genomic Analysissupporting

confidence: 80%

Ovine and Caprine Strains of Corynebacterium pseudotuberculosis on Czech Farms—A Comparative Study

Markova,

Langova,

Babak

et al. 2024

Microorganisms

View full text Add to dashboard Cite

show abstract

“…Positive selection was also found to be an important driving force for adaptive evolution of Acidiphilium. Genes can be changed by positive selection for fixation of beneficial variants in a population/species over time if they increase survival fitness, which might help fine-tune gene expression in adaption to changing environmental conditions (27)(28)(29)(30). Those genes under positive selection in Acidiphilium were prone to play key multifunctional roles, of which even small adaptive changes in their coding sequences might influence multiple pathways, bringing considerable benefits for survival of microbes during evolution in response to changing global conditions and shifting of niches.…”

Section: Discussionmentioning

confidence: 99%

“…Horizontal gene transfer refers to the acquisition of genetic elements from distant lineages for genetic and phenotypic innovations, a process contributing significantly to evolution within challenging environments and during global geologic and/or climatic events (25,26). Positive selection, on the other hand, mediating survival fitness by adaptive mutations, has also been an indispensable driving force in microbial evolution, and recent investigations have shifted from testing selection on individual genes to the entire genomes (27)(28)(29)(30).…”

mentioning

confidence: 99%

Insights into the Metabolism and Evolution of the Genus Acidiphilium , a Typical Acidophile in Acid Mine Drainage

Liu

Zhang

et al. 2020

mSystems

View full text Add to dashboard Cite

Here, we report three new Acidiphilium genomes, reclassified existing Acidiphilium species, and performed the first comparative genomic analysis on Acidiphilium in an attempt to address the metabolic potential, ecological functions, and evolutionary history of the genus Acidiphilium. In the genomes of Acidiphilium, we found an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic expansion, including genes conferring photosynthesis (puf, puh), CO2 assimilation (rbc), capacity for methane metabolism (mmo, mdh, frm), nitrogen source utilization (nar, cyn, hmp), sulfur compound utilization (sox, psr, sqr), and multiple metal and osmotic stress resistance capacities (czc, cop, ect). Additionally, the predicted donors of horizontal gene transfer were present in a cooccurrence network of Acidiphilium. Genome-scale positive selection analysis revealed that 15 genes contained adaptive mutations, most of which were multifunctional and played critical roles in the survival of extreme conditions. We proposed that Acidiphilium originated in mild conditions and adapted to extreme environments such as acidic mineral sites after the acquisition of many essential functions. IMPORTANCE Extremophiles, organisms that thrive in extreme environments, are key models for research on biological adaption. They can provide hints for the origin and evolution of life, as well as improve the understanding of biogeochemical cycling of elements. Extremely acidophilic bacteria such as Acidiphilium are widespread in acid mine drainage (AMD) systems, but the metabolic potential, ecological functions, and evolutionary history of this genus are still ambiguous. Here, we sequenced the genomes of three new Acidiphilium strains and performed comparative genomic analysis on this extremely acidophilic bacterial genus. We found in the genomes of Acidiphilium an abundant repertoire of horizontally transferred genes (HTGs) contributing to environmental adaption and metabolic ability expansion, as indicated by phylogenetic reconstruction and gene context comparison. This study has advanced our understanding of microbial evolution and biogeochemical cycling in extreme niches.

show abstract

“…Exploring the complete genome sequences for dozens of CP strains, another study attempted to find additional molecular markers for the Ovis and Equi biovars. Despite the high genomic conservation reported for CP, the authors identified 27 genes undergoing distinct adaptative changes in Ovis and Equi . However, CP biovar classification had not been assured using the genome information, and the present study effectively distinguished the CP biovars based on whole genome analysis.…”

Section: Resultsmentioning

confidence: 99%

“…Despite the high genomic conservation reported for CP, the authors identified 27 genes undergoing distinct adaptative changes in Ovis and Equi. 37 However, CP biovar classification had not been assured using the genome information, and the present study effectively distinguished the CP biovars based on whole genome analysis. Concatenation of the ANI blast and TNA results generated genomic signatures that allowed accurate grouping of the Ovis and Equi biovars (Figure 2).…”

Section: ■ Introductionmentioning

confidence: 99%

Exploring the MALDI Biotyper for the Identification of Corynebacterium pseudotuberculosis biovar Ovis and Equi

Santos

Seyffert

Dorneles

et al. 2022

J. Am. Soc. Mass Spectrom.

Self Cite

View full text Add to dashboard Cite

Biochemical, serological, and molecular methods have been developed for the laboratory diagnosis of diseases caused by C. pseudotuberculosis (CP), but the identification of the pathogen and biovars differentiation may be time-consuming, expensive, and confusing compared with other bacteria. This study aimed to evaluate MALDI Biotyper and Overall Genome Relatedness Index (OGRI) analysis to optimize the identification and differentiation of biovars of C. pseudotuberculosis. Out of 230 strains isolated from several hosts and countries, 202 (87.8%) were precisely classified using MALDI Biotyper and the BioNumerics platform. The classification accuracies for the Ovis and Equi biovars were 80 (88.75%) and 82 (92.68%), respectively. When analyzing a sampling of these strains by Average Nucleotide Identity based on BLAST and TETRA analyses using genomic sequence data, it was possible to differentiate 100% of the strains in Equi and Ovis. Our data show that MALDI Biotyper and OGRI analysis help identify C. pseudotuberculosis at the species and biovar levels.

show abstract

Rapidly evolving changes and gene loss associated with host switching in Corynebacterium pseudotuberculosis

Cited by 7 publications

References 100 publications

Ovine and Caprine Strains of Corynebacterium pseudotuberculosis on Czech Farms—A Comparative Study

Ovine and Caprine Strains of Corynebacterium pseudotuberculosis on Czech Farms—A Comparative Study

Insights into the Metabolism and Evolution of the Genus Acidiphilium , a Typical Acidophile in Acid Mine Drainage

Exploring the MALDI Biotyper for the Identification of Corynebacterium pseudotuberculosis biovar Ovis and Equi

Contact Info

Product

Resources

About