Jinhu Huang

Streptococcus suis and extraintestinal pathogenic Escherichia coli (ExPEC) cause severe swine infections and major economic losses worldwide. Antimicrobial resistance (AMR) and polymicrobial interactions complicate disease control. Existing vaccine strategies are insufficient to provide broad cross‐serotype protection against S. suis strains while simultaneously combating ExPEC infections. We developed a bivalent vaccine platform that integrates bacterial ghost (BG) technology with surface antigen display. By utilizing the porcine ExPEC strain PU‐1 as a carrier, which could cause acute sepsis in mouse infection model. Using an Lpp’‐OmpA surface display system, we constructed recombinant BGs derived from E. coli that express a multi‐epitope antigen against S. suis (MEAS 1), while retaining native E. coli antigenic components as the immunogen against ExPEC. Administration of this vaccine induced robust cellular and humoral immune responses specific to both S. suis and E. coli . The vaccine demonstrated dual protection: 70%–90% survival against S. suis (serotypes 2/9) and 70% against ExPEC challenge in mouse model. Porcine trials demonstrated a significant reduction in bacteremia and provided effective protection against pathogenic challenges. This platform offers a potential solution for preventing infections caused by S. suis and ExPEC.

Phages and integrative and conjugative elements (ICEs) drive bacterial evolution, but how their interplay shapes bacterial adaptation and antimicrobial resistance (AMR) dissemination remains unclear. Here, we characterize phage-ICE tandems formed by site-specific accretion of phages and ICEs into cotransferable units. In Streptococcus , phage-encoded integrases (IntIE _Phage ) drive stress-inducible excision and circularization, after which ICE machinery mediates conduction of the tandem. When excision is impaired, phage and phage-ICE fragments disseminate by transformation and integrate via RecA-dependent homologous recombination (HR), providing a fail-safe route. This pathway enables cotransfer of flanking chromosomal DNA, generating length-variable integrations that remodel transcriptional programs and increase oxidative stress tolerance. A global screen identified 612 phage-ICE tandems across seven phyla and 135 species, including multidrug-resistant pathogens, with lineage-specific repertoires of AMR, virulence, and metabolic genes. Rather than a hybrid element, these structures represent functional interplay where prophages exploit ICE conjugation while facilitating mobilization of the composite region. By coupling excision, transfer, and recombination, phage-ICEs shape adaptation and accelerate AMR spread.

Background and objectives: Mobile genetic elements drive antimicrobial-resistance dissemination in Gram-positive pathogens. In Streptococcus suis we previously identified a genomic island, GISsuJHJ17_rpsI, integrated at the conserved rpsI locus and carrying erm(B) and aadE. Here we investigated the genetic features and helper functions associated with mobilization of this island, including its transfer from S. suis to E. faecalis. Methods: Genetic annotation established that GISsuJHJ17_rpsI lacks a self-encoded conjugation apparatus but harbours an origin of transfer (oriT) sharing ∼85% nucleotide identity with the co-resident integrative and conjugative element (ICE). We performed filter-mating assays to test ICE-mediated mobilization in trans, constructed precise deletions of oriTGISsuJHJ17 and of the ICE relaxase, carried out complementation, and assessed fitness by growth and head-to-head competition of transconjugants. Results: Filter-mating assays showed that mobilization of GISsuJHJ17_rpsI in the S. suis recipient model required the helper-ICE relaxase and the candidate GI oriT region. Deletion of either determinant yielded no verified transconjugants under the assay conditions, whereas relaxase complementation and chromosomal oriT repair restored detectable transfer. These findings support a model in which the helper ICE provides the DNA-processing function required for GI mobilization, using the co-resident ICE transfer apparatus, as inferred from the ICE gene content. Fitness assays revealed no measurable growth defect or competitive disadvantage associated with acquisition of GISsuJHJ17_rpsI, indicating a minimal short-term fitness cost. Conclusions: These findings show that GISsuJHJ17_rpsI can transfer from S. suis to E. faecalis and integrate at an rpsI-associated site. In the S. suis recipient model, mobilization required the helper-ICE relaxase and the GISsuJHJ17_rpsI oriT region, supporting a helper-ICE-dependent mechanism for genomic-island mobilization.

Peptide therapeutics offer great promise in drug discovery, yet the accurate identification of peptide toxicity remains essential for both safety assessment and biodefense. We developed ToxMamba, a toxic peptide prediction framework that integrates Implicit Structure Model (ISM)-derived pretrained embeddings, state space models, multi-scale feature learning, and ensemble inference. Built upon the Mamba architecture, ToxMamba enables efficient sequence modeling and captures contextual patterns across multiple receptive fields from parallel branches. On the independent test set, ToxMamba consistently surpasses existing methods, improving the F1 score and Matthews Correlation Coefficient by 3.9–18.3 and 7.5–46.9 percentage points, respectively. Ablation analyses further showed that Mamba-based models generally achieved stronger overall performance than Transformer-, Convolutional Neural Network-Long Short-Term Memory-Attention-, and Kolmogorov–Arnold Network-based variants. Feature visualization showed that ISM embeddings yielded clearer separation between toxic and non-toxic peptides in the latent space. Intermediate-layer feature analysis highlighted residue-level regions associated with toxicity-related sequence motifs, supporting the biological interpretability of ToxMamba. Overall, this study provides an efficient and interpretable computational framework for high-throughput toxic peptide screening.

Mobile genetic elements (MGEs) drive genome plasticity, horizontal gene transfer, and antimicrobial resistance (AMR) dissemination in Streptococcus , yet genus-wide comparisons across major MGE classes remain limited. Here, we analyzed 1961 complete chromosomes from 60 Streptococcus species together with 225 plasmids, and compared integrative and conjugative elements (ICEs), integrative and mobilizable elements (IMEs), prophages, and plasmids with respect to host distribution, boundary-supported integration-site preference, mobility-associated modules, representative backbones, and AMR cargo. We identified 1172 ICEs, 2362 IMEs, 3397 prophages, and 225 plasmids, and found that the streptococcal mobilome was strongly partitioned by host lineage, with ICEs and IMEs enriched in Streptococcus dysgalactiae , prophages in Streptococcus pyogenes , and plasmids in Streptococcus suis . Integrated MGEs also displayed class-specific hotspot hierarchies after boundary inspection: ICEs were highly concentrated at rplL , with secondary hotspots at rlmD and rpmH ; IMEs were dominated by tRNA-associated sites together with rpsI and rpmG , whereas prophages occupied a broader hotspot spectrum centered on tRNA, rpmE , rpsD , hlpA , and mutL . Mobility analyses further distinguished the classes, showing that ICEs retained a narrow repertoire of conjugative backbones dominated by typeFATA, IMEs displayed the broadest relaxase diversity, and plasmids were mainly non-mobile or mobilizable. Representative family analyses resolved recurrent backbone types within each class, whereas AMR cargo was concentrated in ICEs and plasmids and was further stratified by host species. Together, these findings reveal a previously underappreciated class- and host-dependent organization of the streptococcal mobilome and its AMR cargo.

This review focuses on the research progress on natural products as β-lactam antibiotic adjuvants, aiming to address the escalating challenge of antibiotic resistance, particularly the inactivation of antibiotics caused by β-lactamases. The article provides an in-depth analysis of the mechanisms by which plant-derived (e.g., flavonoids, tannins, phenolics, terpenoids, and alkaloids) and microbial-derived (e.g., clavulanic acid, fungal metabolites, bacteriophages) natural products enhance antimicrobial efficacy. Key potentiation strategies discussed include efflux pump inhibition, membrane permeability alteration, biofilm disruption, PBP2a inhibition, and direct β-lactamase inhibition. Additionally, the review outlines in vitro methods (e.g., dilution and checkerboard assays) and in vivo models (e.g., mouse infection models) used to assess synergistic effects. It also addresses major challenges in identifying active compounds, elucidating mechanisms of action, and pharmacokinetic characterization. Looking forward, the article highlights the potential of multi-omics approaches, artificial intelligence, and nanotechnology to overcome existing bottlenecks, providing novel strategies for the development of effective and safe antibiotic adjuvants. These advances are expected to provide both theoretical insights and practical guidance for combating antibiotic-resistant bacterial infections.

The global spread of multidrug-resistant (MDR) bacteria prompts the exploration of innovative antimicrobial strategies. Phage lysins—peptidoglycan hydrolases known for species-specific activity and low resistance potential—offer promising alternatives to conventional antibiotics. However, their typically narrow spectrum limits broad therapeutic application. To overcome this limitation, we leveraged the wide distribution of streptococcal mobilizable prophage (SMphage) families across Streptococcus species as a strategy to discover lysins with inherent broad-spectrum potential. Within these conserved prophages, we expressed PlyNJ3, an SMphage-derived endolysin homolog identified in S. suis, and evaluated its therapeutic efficacy in infection models. PlyNJ3 exhibited potent lytic activity against a broad panel of streptococci, including diverse S. suis clinical isolates (15 serotypes), 83.3% of S. uberis, and key strains of S. agalactiae, S. dysgalactiae, and S. pyogenes. Optimal bacteriolytic activity occurred at physiological temperature (37 °C) with dose-dependent efficacy. Electron microscopy revealed PlyNJ3-mediated cell wall perforation, cytoplasmic content release, and structural disintegration. In a murine invasive S. suis infection model, high-dose intraperitoneal PlyNJ3 (0.9 mg/head) conferred 87.5% survival, while synergism with ampicillin prolonged survival. Intramuscular administration in a murine thigh infection model enhanced bacterial clearance compared to intraperitoneal delivery. Phylogenetic and structural analysis confirmed conservation across SMphage-derived lysins, underpinning their broad streptococcal target potential. Our findings establish SMphage-derived lysins as a conserved, therapeutically valuable class of antimicrobials with inherent broad-spectrum potential across diverse streptococcal pathogens. Building on the previously demonstrated in vivo efficacy of PlySK1249 against S. dysgalactiae and S. agalactiae, we show that its structural homolog, PlyNJ3, exhibits robust therapeutic activity against S. suis infections. Together, these results validate the SMphage lysin platform for generating precision-targeted agents against specific streptococcal infections.

Mobile genetic elements (MGEs) drive horizontal gene transfer and microbial evolution, spreading adaptive genes across microbial communities. While extensively studied in other ecosystems, the role of MGEs in shaping ruminant gastrointestinal microbiomes—especially their impact on diversity, adaptation, and dietary responsiveness—remains largely unexplored. This study systematically profiles MGE distribution and functionality across gastrointestinal regions in multiple ruminant species to advance our understanding of microbial adaptation. Across 2458 metagenomic samples from eight ruminant species, we identified 4,764,110 MGEs—a ~ 216-fold increase over existing MGE databases. These elements included integrative and conjugative elements, integrons, insertion sequences, phages, and plasmids, with mobilization patterns largely confined to closely related microbial lineages. The distribution of MGEs varied by GIT regions, often reflecting nutritional gradients. In a validation cohort, GH1-carrying plasmids enriched in carbohydrate-active enzymes were found to predominate in the stomach, showing notable responsiveness to forage-based diets. All annotated MGEs have been compiled into a publicly accessible database, rumMGE ( https://rummge.liulab-njau.com ), to support further research. This study substantially expands the catalog of known MGEs in ruminants, revealing their diverse roles in microbial evolution and functional adaptation to dietary changes. The findings provide a valuable resource for advancing research on microbial functionality and offer insights with potential applications for enhancing ruminant health and productivity, through strategies aimed at modulating the microbiome in agricultural contexts.