Comparative Genomics of Clostridium baratii Reveals Strain-Level Diversity in Toxin Abundance

Abstract

Clostridium baratii strains are rare opportunistic pathogens associated with botulism intoxication. They have been isolated from foods, soil and be carried asymptomatically or cause botulism outbreaks. Is not taxonomically related to Clostridium botulinum, but some strains are equipped with BoNT/F7 cluster. Despite their relationship with diseases, our knowledge regarding the genomic features and phylogenetic characteristics is limited. We analyzed the pangenome of C. baratii to understand the diversity and genomic features of this species. We compared existing genomes in public databases, metagenomes, and one newly sequenced strain isolated from an asymptomatic subject. The pangenome was open, indicating it comprises genetically diverse organisms. The core genome contained 28.49% of the total genes of the pangenome. Profiling virulence factors confirmed the presence of phospholipase C in some strains, a toxin capable of disrupting eukaryotic cell membranes. Furthermore, the genomic analysis indicated significant horizontal gene transfer (HGT) events as defined by the presence of prophage genomes. Seven strains were equipped with BoNT/F7 cluster. The active site was conserved in all strains, identifying a missing 7-aa region upstream of the active site in C. baratii genomes. This analysis could be important to advance our knowledge regarding opportunistic clostridia and better understand their contribution to disease.

Comparative Genomics Provides Insights Into Genetic Diversity of Clostridium tyrobutyricum and Potential Implications for Late Blowing Defects in Cheese

“…Furthermore, the fitted curve for the pangenome profile showed that the fitted exponent of the curve was positive, indicating that the pangenome of C. tyrobutyricum is open. This observation is in agreement with the few published reports on this topic on other members of the genus Clostridium cluster I ( Udaondo et al, 2017 ), such as Clostridium baratii ( Silva-Andrade et al, 2022 ), C. perfringens ( Kiu et al, 2017 ; Feng et al, 2020 ), C. beijerinckii ( Sedlar et al, 2021 ; Zou et al, 2021a ), and C. butyricum ( Zou et al, 2021b ). Open pangenomes may indicate the necessity of constant genomic adaptations and diversification to cope with heterogeneous environments ( Medini et al, 2005 ; Rouli et al, 2015 ).…”

“…The housekeeping COG categories included “amino acids transport and metabolism” (9.33%) “inorganic ion transport and metabolism” (6.14%), “energy production and conversion” (8.32%), and “coenzyme transport and metabolism” (5.46%). High abundance of these gene categories within the core genome indicates that the strains are metabolically similar, which is consistent with other clostridia, including C. butyricum , C. beijerinckii , C. sporogenes , and C. baratii , which have open pangenomes ( Wu et al, 2017 ; Sedlar et al, 2021 ; Zou et al, 2021b ; Silva-Andrade et al, 2022 ). Furthermore, genes from the category “translation, ribosomal structure and biogenesis” were also abundant in the core genome (1.59%).…”

Intra-species diversity of Clostridium perfringens: A diverse genetic repertoire reveals its pathogenic potential

“…Frontiers in Microbiology frontiersin.org relatedness among isolates and allowing a deeper understanding of transmission dynamics, emerging clones, key virulence loci, and the presence of AMR genes (Salipante et al, 2015;Quainoo et al, 2017;Pightling et al, 2018). The pangenome analysis of C. perfringens conducted in this study showed an accessory genome of 97.32%, an extremely high percentage in comparison with other closely related bacteria such as C. paraputrificum, species with an accessory genome of 67%, C. tertium with 37.6% of accessory genes (Muñoz et al, 2019), or C. baratii with an accessory genome of 24.43% (Silva-Andrade et al, 2022). This high level of genome plasticity is similar to the one found in Clostridioides difficile, which has an accessory genome of 87.2% (Knight et al, 2021).…”

Detection and Analysis of Clostridioides difficile Spores in a Hospital Environment

“…In addition to the detection of C. difficile in the direct environment of the patient, studies have also confirmed the presence of other pathogenic species, such as C. perfringens , C. sporogenes , C. innocuum and C. baratii . These are species which are also detected in other medical facilities and which may constitute a significant disease-causing problem related to HAI [ 35 , 36 , 37 , 38 , 39 , 40 , 41 ]. Analysis of the behaviour of hospital personnel was not a direct goal of this study, but it supplements the conducted research analyses.…”