Core-, pan- and accessory genome analyses of Clostridium neonatale: insights into genetic diversity

Abstract

Clostridium neonatale is a potential opportunistic pathogen recovered from faecal samples in cases of necrotizing enterocolitis (NEC), a gastrointestinal disease affecting preterm neonates. Although the C. neonatale species description and name validation were published in 2018, comparative genomics are lacking. In the present study, we provide the closed genome assembly of the C. neonatale ATCC BAA-265T (=250.09) reference strain with a manually curated functional annotation of the coding sequences. Pan-, core- and accessory genome analyses were performed using the complete 250.09 genome (4.7 Mb), three new assemblies (4.6–5.6 Mb), and five publicly available draft genome assemblies (4.6–4.7 Mb). The C. neonatale pan-genome contains 6840 genes, while the core-genome has 3387 genes. Pan-genome analysis revealed an ‘open’ state and genomic diversity. The strain-specific gene families ranged from five to 742 genes. Multiple mobile genetic elements were predicted, including a total of 201 genomic islands, 13 insertion sequence families, one CRISPR-Cas type I-B system and 15 predicted intact prophage signatures. Primary virulence classes including offensive, defensive, regulation of virulence-associated genes and non-specific virulence factors were identified. The presence of a tet(W/N/W) gene encoding a tetracycline resistance ribosomal protection protein and a 23S rRNA methyltransferase ermQ gene were identified in two different strains. Together, our results revealed a genetic diversity and plasticity of C. neonatale genomes and provide a comprehensive view of this species genomic features, paving the way for the characterization of its biological capabilities.

Pan-Genome Analysis of Staphylococcus aureus Reveals Key Factors Influencing Genomic Plasticity

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Diagnosis and functional prediction of microbial markers in tumor tissues of sporadic colorectal cancer patients associated with the MLH1 protein phenotype

“…In contrast, the IM group showed enrichment in amino acid metabolism, xenobiotic biodegradation and metabolism, lipid metabolism, metabolism of other amino acids, terpenoids, and polyketides, and substance dependence. In the functional prediction analysis, it was found that the homologous genes of some prokaryotic microbiomes may be annotated to the metabolic pathway of eukaryotic organisms ( 39 – 41 ). In this case, we assume that the genes of these bacteria may be related to the two-component regulatory system, which will eventually reveal certain pathways that are not related to bacterial metabolism.…”

Clostridium neonatale antimicrobial susceptibility, genetic resistance determinants, and genotyping: a multicentre spatiotemporal retrospective analysis

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“…De novo assembly of the 35 genomes was performed as previously described. 22 Comparison of each housekeeping gene sequence was performed using the NCBI multisequence advanced BLAST software. 23 An allele number is assigned to each unique sequence.…”