Genomic investigation of a sequence type 67 Clostridium difficile causing community-acquired fulminant colitis in Hong Kong

Exploring the modulatory effect of trehalose-derived galactooligosaccharides on key gut microbiota groups

Trehalose (α-d-glucopyranosyl-(1-1)-α-D-glucopyranoside) has found applications in diverse food products as a sweetener, stabilizer, and humectant. Recent attention has focused on trehalose due to its contradictory effects on the virulence of Clostridium difficile. In this study, we investigate the impact of novel trehalose-derived galactooligosaccharides (Treh-GOS) on the human gut microbiota using in vitro fecal fermentation models. Distinct Treh-GOS structures elicit varying taxonomic responses. For instance, β-Gal-(1-4)-trehalose [DP3(1-4)] leads to an increase of Bifidobacterium, comparable to results observed with commercial GOS. Conversely, β-Gal-(1-6)-trehalose [DP3(1-6)] prompts an increase in Lactobacillus. Notably, both of these trisaccharides yield the highest concentrations of butyric acid across all samples. On the other hand, Treh-GOS tetrasaccharide mixture (DP4), featuring a novel trehalose galactosylation in both glucose units, fosters the growth of Parabacteroides. Our findings underscore the capacity of novel Treh-GOS to modulate the human gut microbiota. Consequently, these innovative galactooligosaccharides emerge as promising candidates for novel prebiotic applications.

Genomic investigation of a Streptococcus pneumoniae serotype 24F strain causing meningoencephalitis in Hong Kong

Pneumococcal conjugate vaccines (PCVs) successfully decreased the incidence of invasive pneumococcal disease in children. However, many countries have reported serotype replacement and a rebound in diseases from non-vaccine serotypes. Here, we report the genomic investigation of a Streptococcus pneumoniae strain M215 that caused severe meningoencephalitis in an infant in 2019. The strain was assigned to serotype 24F using the bioinformatic pipeline SeroBA and pneumococcal type specific anti-sera. The strain was resistant to cotrimoxazole from mutations in both folA and folP genes. It was susceptible to penicillin and other non-β-lactam antibiotics. Phylogenetically, it belongs to Global Pneumococcal Sequence Cluster (GPSC) 6 and multi-locus sequence type 162. A total of 38 virulence genes were detected in the genome of M215. Upon comparison of the profile of virulence genes, GPSC6 but not non-GPSC6 strains of serotype 24F and related serotypes were found to possess the major virulence determinant, pilus islet-1, comprising genes encoding sortases (srtB, srtC, srtD), pilus proteins (rrgA, rrgB and rrgC) and one transcriptional regulator (rlrA), which was previously described to be characteristic feature of international clones in the pre-PCV era. In our locality, this represented the first detection of serotype 24F and GPSC6/ST162 causing serious pneumococcal disease. The emergence of the non-vaccine serotype 24F GPSC6/ST162 lineage with molecular feature of high virulence is concerning and emphasizes the need for full characterization of strains causing severe disease.

Enzymatic Synthesis and Structural Characterization of Novel Trehalose-Based Oligosaccharides

Trehalose, α-d-glucopyranosyl-(1↔1)-α-d-glucopyranoside, is a disaccharide with multiple effects on the human body. Synthesis of new trehalose derivatives was investigated through transgalactosylation reactions using β-galactosidase from four different species. β-galactosidases from Bacillus circulans (B. circulans) and Aspergillus oryzae (A. oryzae) were observed to be the best biocatalysts, using lactose as the donor and trehalose as the acceptor. Galactosyl derivatives of trehalose were characterized using nuclear magnetic resonance spectroscopy. Trisaccharides were the most abundant oligosaccharides obtained followed by the tetrasaccharide fraction (19.5% vs 8.2% carbohydrates). Interestingly, the pentasaccharide [β-Galp-(1→4)]³-trehalose was characterized for the first time. Greater oligosaccharide production was observed using β-galactosidase from B. circulans than that obtained from A. oryzae, where the main structures were based on galactose monomers linked by β-(1→6) and β-(1→4) bonds with trehalose in the ending. These results indicate the feasibility of commercially available β-galactosidases for the synthesis of trehalose-derived oligosaccharides, which might have functional properties, excluding the adverse effects of the single trehalose.

Complete genome sequence of the Clostridium difficile LCL126

Clostridium difficile (C. difficile) is a kind of obligate anaerobic gram-positive Bacillus related with intestinal diseases and antibiotic treatment. In present study, the C. difficile genome was studied employing met genomic technology. Genome sequencing identified C. difficile LCL126 has total size of 4,301,949 bp with a 27.97% of GC content. Specifically, 4119 predicted coding genes, 188 repeat sequences, 13 prophages and 8 gene islands were detected. Additionally, gene function analysis aspect of the function annotation, effector, and virulence were concluded that total of 3367 cluster of orthologous groups of proteins genes and classified into 24 categories, while the most outstanding class was metabolic process (1533) and catalytic activity (1498). The carbohydrate-active enzymes have been detected 127 genes, pathogenicity analysis revealed that 133 reduced and 22 increased virulence (hypervirulence) genes, while 54 unaffected and 10 loss of pathogenicity genes were found. Furthermore, perform the visualization and methylation expression were revealed that the dominant types comprised m4C, m5C, and m6C with the number of 6989, 36,666, and 3534, respectively. Overall, whole genome sequence information of C. difficile LCL126 was obtained and functional prediction was revealed its possible toxicological potential genes existence.

Microbiological features, epidemiology, and clinical presentation of Clostridioidesdifficile strains from MLST Clade 2: A narrative review

Clostridioides difficile is an emerging One Health pathogen and a common etiologic agent of diarrhea, both in healthcare settings and the community. This bacterial species is highly diverse, and its global population has been classified in eight clades by multilocus sequence typing (MLST). The C. difficile MLST Clade 2 includes the NAP1/RT027/ST01 strain, which is highly recognized due to its epidemicity and association with severe disease presentation and mortality. By contrast, the remaining 83 sequence types (STs) that compose this clade have received much less attention. In response to this shortcoming, we reviewed articles published in English between 1999 and 2020 and collected information for 27 Clade 2 STs, with an emphasis on STs 01, 67, 41 and 188/231/365. Our analysis provides evidence of large phenotypic differences that preclude support of the rather widespread notion that ST01 and Clade 2 strains are "hypervirulent". Moreover, it revealed a profound lack of (meta)data for nearly 70% of the Clade 2 STs that have been identified in surveillance efforts. Targeted studies aiming to relate wet-lab and bioinformatics results to patient and clinical parameters should be performed to gain a more in-depth insight into the biology of this intriguing group of C. difficile isolates.

In vivo animal models confirm an increased virulence potential and pathogenicity of the NAP1/RT027/ST01 genotype within the Clostridium difficile MLST Clade 2

Background

Based on MLST analyses the global population of C. difficile is distributed in eight clades, of which Clade 2 includes the “hypervirulent” NAP1/RT027/ST01 strain along with various unexplored sequence types (STs).

Methods

To clarify whether this clinically relevant phenotype is a widespread feature of C. difficile Clade 2, we used the murine ileal loop model to compare the in vivo pro-inflammatory (TNF-α, IL-1β, IL-6) and oxidative stress activities (MPO) of five Clade 2 clinical C. difficile isolates from sequence types (STs) 01, 41, 67, and 252. Besides, we infected Golden Syrian hamsters with spores from these strains to determine their lethality, and obtain a histological evaluation of tissue damage, WBC counts, and serum injury biomarkers (LDH, ALT, AST, albumin, BUN, creatinine, Na⁺, and Cl⁻). Genomic distances were calculated using Mash and FastANI to explore whether the responses were dictated by phylogeny.

Results

The ST01 isolate tested ranked first in all assays, as it induced the highest overall levels of pro-inflammatory cytokines, MPO activity, epithelial damage, biochemical markers, and mortality measured in both animal models. Statistically indistinguishable or rather similar outputs were obtained for a ST67 isolate in tests such as tissue damage, neutrophils count, and lethal activity. The results recorded for the two ST41 isolates tested were of intermediate magnitude and the ST252 isolate displayed the lowest pathogenic potential in all animal experiments. This ordering matched the genomic distance of the ST01 isolate to the non-ST01 isolates.

Conclusions

Despite their close phylogenic relatedness, our results demonstrate differences in pathogenicity and virulence levels in Clade 2 C. difficile strains, confirm the high severity of infections caused by the NAP1/RT027/ST01 strain, and highlight the importance of C. difficile typing.

Hypervirulent clade 2, ribotype 019/sequence type 67 Clostridioides difficile strain from Japan

Background

Clostridioides difficile ribotype (RT) 019/sequence type (ST) 67 strains belong to a hypervirulent lineage closely related to RT027/ST1; however, limited data are available for hypervirulent clade 2 lineages in Japan. Herein, we report the draft genome of a C. difficile strain B18-123 belonging to clade 2, RT019/ST67 for the first time in Japan.

Results

The pathogenicity locus carried by B18-123 (19.6 kb) showed higher homology (97.29% nucleotide identity) with strain R20291 (RT027/ST1) than the reference strain 630 (RT012/ST54), and B18-123 harbored 8-nucleotide substitutions in tcdC. However, it did not contain an 18-base pair (bp) deletion or a single-bp deletion at position 117 in tcdC, which was identified in the previous strain R20291. A cytotoxicity assay revealed similar cytotoxicity levels between strains B18-123 and ATCC BAA-1870 (RT027/ST1). The B18-123 strain was found to be susceptible to metronidazole and vancomycin.

Conclusion

Our findings contribute to the further understanding of the characteristics of hypervirulent clade 2 including RT019/ST67 lineages.