Preterm Infant-Associated Clostridium tertium, Clostridium cadaveris, and Clostridium paraputrificum Strains: Genomic and Evolutionary Insights

Abstract

Clostridium species (particularly Clostridium difficile, Clostridium botulinum, Clostridium tetani and Clostridium perfringens) are associated with a range of human and animal diseases. Several other species including Clostridium tertium, Clostridium cadaveris, and Clostridium paraputrificum have also been linked with sporadic human infections, however there is very limited, or in some cases, no genomic information publicly available. Thus, we isolated one C. tertium strain, one C. cadaveris strain and three C. paraputrificum strains from preterm infants residing within neonatal intensive care units and performed Whole Genome Sequencing (WGS) using Illumina HiSeq. In this report, we announce the open availability of the draft genomes: C. tertium LH009, C. cadaveris LH052, C. paraputrificum LH025, C. paraputrificum LH058, and C. paraputrificum LH141. These genomes were checked for contamination in silico to ensure purity, and we confirmed species identity and phylogeny using both 16S rRNA gene sequences (from PCR and in silico) and WGS-based approaches. Average Nucleotide Identity (ANI) was used to differentiate genomes from their closest relatives to further confirm speciation boundaries. We also analysed the genomes for virulence-related factors and antimicrobial resistance genes, and detected presence of tetracycline and methicillin resistance, and potentially harmful enzymes, including multiple phospholipases and toxins. The availability of genomic data in open databases, in tandem with our initial insights into the genomic content and virulence traits of these pathogenic Clostridium species, should enable the scientific community to further investigate the disease-causing mechanisms of these bacteria with a view to enhancing clinical diagnosis and treatment.

Effects of regulating gut microbiota on the serotonin metabolism in the chronic unpredictable mild stress rat model

“…Clostridium spp. are Gram‐positive spore‐forming anaerobes, which are found all over the place in the atmosphere and the abdominal tract of humans plus animals . Furthermore, we found there was a noteworthy positive association of the ratio of Firmicutes in total gut microbiota versus colonic 5‐HT through Pearson correlation analysis (Pearson r = 0.923; Figure ).…”

“…16 Clostridium is categorized as a genus under the phylum Firmicutes and class Clostridia, plus includes 221 types till date (September 2017). 47 Clostridium spp. are Gram-positive spore-forming anaerobes, which are found all over the place in the atmosphere and the abdominal tract of humans plus animals.…”

Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors

“…DNA was extracted using a phenol– chloroform method fully described previously [17] from overnight cultures of strains, and sequenced using the 96-plex Illumina HiSeq 2500 platform to generate 125 bp paired-end reads [18]. Raw data provided by the sequencing centre were checked using fastqc v0.11.4 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/); no adapter trimming was required, and reads had an average Phred score >25.…”

Genomic analysis on broiler-associated Clostridium perfringens strains and caecal microbiome profiling reveals key factors linked to poultry Necrotic Enteritis

“…Single black colonies were re-streaked on brain heart infusion agar (Oxoid, UK) and incubated anaerobically at 37°C overnight. Several colonies were collected and subjected to identification of the plc gene by PCR, followed by 16S rRNA full-length amplicon sequencing as described previously for species verification [58, 59].…”

“…We isolated 22 novel C. perfringens strains from broilers and environmental samples from farms in Oxford, UK. Genomic DNA of these bacterial isolates was extracted using phenol-chloroform method as described previously [59]. Details of these isolates are given in Additional file 1: Table S1.…”