Transposon Insertion Sequencing Elucidates Novel Gene Involvement in Susceptibility and Resistance to Phages T4 and T7 in Escherichia coli O157

Uncovering potential biomarkers and metabolic pathways in systemic lupus erythematosus and lupus nephritis through integrated microbiome and metabolome analysis

OBJECTIVE

This study aims to explore the relationship between gut microbiota and fecal metabolomic profiles in patients with systemic lupus erythematosus (SLE), with and without lupus nephritis (LN), in order to identify potentially relevant biomarkers and better understand their association with disease progression.

METHODS

Fecal samples from 15 healthy controls (HC) and 36 SLE patients (18 SLE-nonLN and 18 SLE-LN) were analyzed using 16S rRNA gene sequencing and untargeted metabolomics. Differential microbial taxa and metabolites were identified using Linear Discriminant Analysis Effect Size (LEfSe) and Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA). Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and Receiver Operating Characteristic (ROC) curve analyses were used to assess the potential clinical relevance of selected metabolites.

RESULTS

Beta diversity analysis demonstrated distinct microbial clustering between groups (p < 0.05). SLE-LN samples showed an increased relative abundance of Proteobacteria and decreased Firmicutes compared to SLE-nonLN. Metabolomic profiling identified multiple differentially abundant metabolites, with notable enrichment in primary bile acid biosynthesis pathways (e.g., Glycocholic acid, AUC = 0.951). In the SLE-nonLN group, increased Glycoursodeoxycholic acid levels (AUC = 0.922) were observed in pathways related to taurine and hypotaurine metabolism. Correlation analysis indicated a negative association between Escherichia-Shigella and bile acid levels (p < 0.01).

CONCLUSION

This integrative analysis suggests that patients with SLE and LN harbor distinct gut microbiota and metabolomic profiles. The identified microbial taxa and metabolites may have potential as non-invasive biomarkers and could contribute to a better understanding of SLE pathogenesis and progression.

Exploring the therapeutic potential of Thymus vulgaris ethanol extract: a computational screening for antimicrobial compounds against COVID-19 induced mucormycosis

COVID-19-associated mucormycosis (CAM) has emerged as a concerning complication during the COVID-19 pandemic. In this study, we explored the potential of phytochemicals and flavonoids identified through High-Performance Liquid Chromatography (HPLC) analysis of Thymus vulgaris plant extract against key proteins of CAM, namely heat shock protein A5 (GPR78) and epidermal growth factor receptor (EGFR). HPLC analysis revealed the presence of bioactive compounds, including chlorogenic acid, cinamic acid, quercetin, coumaric acid, gallic acid, and syringic acid. To assess their efficacy against CAM, computational analyses were performed, including molecular docking analysis, pharmacophore characterization, ADME and molecular dynamics simulations. The results demonstrated that chlorogenic acid exhibited strong binding affinity against EGFR with a docking score of -7.6 kcal/mol, while quercetin showed favorable binding affinity against HSP A5 (GPR78) with a docking score of -10.1 kcal/mol. Both chlorogenic acid and quercetin displayed promising ADME properties, indicating their potential as drug candidates. Nevertheless, it was observed that chlorogenic acid did not adhere to Lipinski's rule, and its gastrointestinal (GI) absorption was relatively low when compared to quercetin. Unlike chlorogenic acid, quercetin does conform to Lipinski's rule and showed high GI absorption. Moreover, pharmacophore characterization of both drug candidates revealed a substantial number of binding sites, suggesting the likelihood of stable bond formation. Normal mode analysis revealed higher eigenvalues for the quercetin-HSPA5 complex compared to the chlorogenic acid-EGFR complex, indicating greater structural rigidity and stability. Overall, our findings highlight the potential of chlorogenic acid and quercetin as promising drug candidates against CAM. Furthermore, in-vitro and in-vivo studies are needed to validate their efficacy and safety for clinical use in treating mucormycosis associated with COVID-19. These findings may offer valuable insights into the development of novel therapeutic options to combat this challenging co-infectious disease.

Plant development influences dynamic shifts in the root compartment microbiomes of wild and domesticated finger millet cultivars

BACKGROUND

Plant-microbe interactions in the rhizosphere and endosphere are crucial for maintaining plant health and ecosystem dynamics. These interactions are shaped by several factors, including the plant's developmental stage, domestication, and specific root compartments. Different plant cultivars influence unique microbial communities by secreting root exudates that either support beneficial symbionts or inhibit pathogens. This study examined the microbial community structures in the endosphere and rhizosphere of wild-type finger millet and five domesticated cultivars at two developmental stages.

RESULTS

Our results revealed that the plant developmental stage, root compartment, and domestication significantly influence the root-associated microbiomes. Interestingly, only about 8% of the core microbiota was consistently shared between the soil and plants, indicating that 92% shifted dynamically depending on plant type and developmental stage. Pseudomonadota, Actinomycedota, and Bacteroidota were the dominant bacterial phyla, while Ascomycota and Basidiomycota were the primary fungal phyla across all samples, displaying distinct abundance patterns. Notably, an increase in Actinomycedota in the endosphere correlated with a reduction in Pseudomonadota. The most significant shifts in microbial community composition occurred in the rhizosphere during the flowering stage, primarily driven by the genus Pseudomonas. These findings demonstrate that plant developmental stages and domestication influence the recruitment of specific microbial taxa to meet the plant's needs, particularly in various root compartments. This selective recruitment highlights the active role of plants in shaping their microbiomes, providing insights into the potential for manipulating these communities to enhance crop productivity sustainably.

CONCLUSION

Our results indicate that both the host developmental stage and domestication significantly influence the assembly and structure of the plant microbiome. Plant root compartments can selectively recruit specific taxa from associated core microbial communities to meet their needs, depending on the plant's developmental stage and the particular root compartment involved. These findings demonstrate that the deterministic selection pressures exerted by plants during their growth and development greatly affect their microbial communities. This has important implications for developing sustainable farming practices, reducing reliance on chemical fertilizers and pesticides, and enhancing future crop productivity.

Targeting immunogenic proteins of Zika virus for the prediction of immunoinformatics-driven circular mRNA vaccine model

Zika virus (ZIKV) is an arbovirus with single-stranded RNA that has become a major health concern worldwide, particularly in tropical and subtropical areas where it is transmitted by Aedes aegypti mosquitoes. Infection can leads to severe neurological complications, including microcephaly in infants and Guillain-Barré syndrome in adults. Due to the absence of a licensed vaccine, the current study was conceived to design a novel circular mRNA vaccine, capable of inducing an effective immune response by targeting the ZIKV proteins. Total 26 top-ranked epitopes (IC50 ≤ 100 nM) were prioritized from the conserved regions of ZIKV proteins. A multi-epitope construct was designed by incorporation of prioritized epitopes and β-defensin III adjuvant sequences to enhance immune activation. Molecular docking analysis revealed significant molecular interactions between the designed vaccine molecule and Toll-like receptors (TLRs), predicting an effective immune capability of the model vaccine. Molecular dynamics simulation validated the molecular and structural stability of the vaccine structure under physiological conditions. Immune simulations analysis predicted that the vaccine molecule could boost antibody production and is capable of achieving a global population coverage of 93.22%. Additionally, the circular mRNA vaccine design exhibited stability, with a minimum free energy (MFE) of - 1515.60 kcal/mol and a secondary centroid structure of - 1181.42 kcal/mol, speculating a resilient vaccine framework for potential ZIKV immunity.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-025-00362-0.

Evaluating HIV drug resistance in the middle East and North Africa and its associated factors: a systematic review

OBJECTIVE

One of the obstacles to achieving successful treatment of HIV infections is the development and spread of mutations linked to resistance. Thus, it is important to monitor the prevalence and occurrence of drug resistance in HIV consistently. This study aimed to investigate how drug resistance affects the effectiveness of ART.

METHODS

This systematic review focused on surveying ART resistance in both treatment-naïve and treatment-experienced PWH from 2004 to 2024.

RESULTS

Out of 101 potential publications, 41 studies were included in this review. ART-experienced PWH in MENA countries commonly receive a regimen consisting of two NRTI drugs in combination with one NNRTI drug. The most frequent mutations were found in NRTIs (M184V, D67N, V75M, M41L, and T69N), NNRTIs (K103N, K101E, V106A, and G190S), and PIs (M36I and H69K). The ART-experienced groups in Israel and Iran presented the highest rates of resistance, reaching 52.78% and 43.03%, respectively, whereas the ART-naïve group in Turkey presented a resistance rate of 53.57%. The most prevalent HIV-1 subtypes in the region were B, CRF35-AD, CRF01-AE, A1, CR02-AG, C, and D. A high frequency of drug resistance mutations, such as M184V and K103N/S, was observed in the CRF35-AD, A, and C subtypes.

CONCLUSION

This is the first report to provide deep insight into ART resistance patterns in the MENA region among both ART-naïve and ART-experienced PWH. The results revealed a significant occurrence of drug resistance to RTIs, PIs, and INSTIs among both groups. This finding highlights the importance of prescribing the INTIs in native and PWH with resistance to RTIs and/or PIs to increase the chance of response to ART as well as regular monitoring of resistance to ART in MENA countries. This also involves identifying the key factors contributing to drug resistance, including inadequate adherence to ART and a lack of adequate monitoring systems to prevent treatment failure. Since the MENA region is significant as an economic challenge, PWH with poor adherence to ART medication and insufficient monitoring systems may hinder successful infection control; therefore, HIV control strategies may prevent viruses from spreading in other countries.

CLINICAL TRIAL NUMBER

Not applicable.

Legacy of Repeated Cultivation Drives Cyclical Microbial Community Development in a Tropical Oxisol Soil

Agricultural practices and the crop being actively cultivated are some of the most important contributors to soil microbial community assembly processes in agroecosystems. However, it is not well-understood how the cultivation of diverse crop species can directionally shift complex soil microbial communities, especially under continuous monoculture systems. Here, we conducted a field experiment to assess how three crop species (Lactuca sativa, Brassica juncea, and Zea mays) may shift soil microbial (bacteria/archaea and fungi) communities when planted in a monoculture and repeatedly grown for three cycles in a tropical Oxisol soil. We found that while plant species made limited contributions to microbial community differentiation, repeated cultivation was a strong driver of community development over time. The bacterial/archaeal communities exhibited a cyclical community development pattern, initially with strong differentiation that attenuated to a steady state at the end of the three cycles. In contrast, fungal communities generally developed more linearly and may have only started to stabilize after three cropping cycles. These developments may speak to the stronger legacy effects on fungal communities. Together, these results highlight the differences between how bacteria/archaea and fungal communities develop, especially in tropical, underdeveloped, intensively degraded, or marginal soils.

Profiling the nasopharyngeal Microbiome in patients with community-acquired pneumonia caused by Streptococcus pneumoniae: diagnostic challenges and ecological insights

Community-acquired pneumonia (CAP) is a significant health threat for adults. Although conjugate vaccines have reduced pneumococcal CAP incidence in children, Streptococcus pneumoniae-related CAP remains prevalent among older adults. The nasopharynx acts as a reservoir for S. pneumoniae, yet the interplay between this pathogen and the nasopharyngeal microbiome during and after pneumonia remains poorly understood. This study included 61 adult patients diagnosed with pneumococcal CAP and 61 matched healthy controls. An S. pneumoniae-specific PCR, urine antigen tests and bacterial cultures were performed. Nasopharyngeal swabs collected at admission and three months post-infection were analyzed for microbiome dynamics through 16 S rRNA gene amplicon sequencing. 16 S rRNA gene amplicon sequencing revealed Streptococcus spp. in the majority of all nasopharyngeal samples during infection compared to the other diagnostic test performed. While overall bacterial biomass did not differ between groups, patients exhibited higher alpha diversity (p = 0.012) and lower microbiome stability post-infection. Beta diversity analysis distinguished infection from healthy status (p = 0.002). Taxonomic analysis showed similar core microbiota across groups, but Streptococcus spp. was significantly more abundant during infection, particularly in those patients with viral co-infections. Notably, unique significant bacterial interactions were identified both during and after infection, as well as in healthy states. A negative correlation was observed between Corynebacterium and Streptococcus spp. in infected patients, suggesting a potential antagonistic interaction between these taxa. The nasopharyngeal microbiome in patients with pneumococcal CAP demonstrates persistent disruption post-infection, characterized by lower resilience three months after acute illness. Additionally, we identified specific bacterial interplays during and after infection that differed from those in healthy donors. These bacterial dynamics might play critical roles in pathogen colonization resistance and infection prevention. Thus, our findings highlight the need for further investigation into microbial interactions and potential microbiome-based therapies for respiratory infections, particularly in vulnerable populations.

Microbiome and biofilm insights from normal vs tumor tissues in Thai colorectal cancer patients

Colorectal cancer (CRC) is a prevalent global malignancy with complex etiologies, including microbiota alterations. This study investigates gut microbiota and biofilm-producing bacteria in 35 Thai CRC patients, analyzing paired normal and tumor biopsy samples. Bacterial DNA from the V3-V4 region of 16S rRNA was sequenced, and biofilms were visualized via scanning electron microscopy and fluorescence in situ hybridization (FISH). Results revealed Firmicutes as the dominant phylum, followed by Bacteroidota, Proteobacteria, and Fusobacteriota, with Fusobacteriota and Bacteroidota notably enriched in left-sided CRC. Key biofilm producers-Bacteroides fragilis, Fusobacterium nucleatum, and Pasteurella stomatis-showed significantly higher gene expression in tumor tissues. Dense biofilms and higher Fusobacterium abundance, localized within the crypts of Lieberkuhn, were observed in CRC tissues. These findings highlight CRC-associated microbiota alterations and pathogenic biofilm production, emphasizing a spatial relationship between tumor location and microbial distribution, with potential implications for understanding CRC pathogenesis and therapeutic targeting.

Decoding Microbial Plastic Colonisation: Multi-Omic Insights Into the Fast-Evolving Dynamics of Early-Stage Biofilms

Marine plastispheres represent dynamic microhabitats where microorganisms colonise plastic debris and interact. Metaproteomics has provided novel insights into the metabolic processes within these communities; however, the early metabolic interactions driving the plastisphere formation remain unclear. This study utilised metaproteomic and metagenomic approaches to explore early plastisphere formation on low-density polyethylene (LDPE) over 3 (D3) and 7 (D7) days, focusing on microbial diversity, activity and biofilm development. In total, 2948 proteins were analysed, revealing dominant proteomes from Pseudomonas and Marinomonas, with near-complete metagenome-assembled genomes (MAGs). Pseudomonas dominated at D3, whilst at D7, Marinomonas, along with Acinetobacter, Vibrio and other genera became more prevalent. Pseudomonas and Marinomonas showed high expression of reactive oxygen species (ROS) suppression proteins, associated with oxidative stress regulation, whilst granule formation, and alternative carbon utilisation enzymes, also indicated nutrient limitations. Interestingly, 13 alkanes and other xenobiotic degradation enzymes were expressed by five genera. The expression of toxins, several type VI secretion system (TVISS) proteins, and biofilm formation proteins by Pseudomonas indicated their competitive advantage against other taxa. Upregulated metabolic pathways relating to substrate transport also suggested enhanced nutrient cross-feeding within the more diverse biofilm community. These insights enhance our understanding of plastisphere ecology and its potential for biotechnological applications.

Manipulating subcellular protein localization to enhance target protein accumulation in minicells

BACKGROUND

Minicells are chromosome-free derivatives of bacteria formed through irregular cell division. Unlike simplified structures, minicells retain all cellular components of the parent cell except for the chromosome. This feature reduces immunogenic responses, making them advantageous for various biotechnological applications, including chemical production and drug delivery. To effectively utilize minicells, it is essential to ensure the accumulation of target proteins within them, enhancing their efficiency as delivery vehicles.

RESULTS

In this study, we engineered Escherichia coli by deleting the minCD genes, generating minicell-producing strains, and investigated strategies to enhance protein accumulation within the minicells. Comparative proteomic analysis revealed that minicells retain most parent-cell proteins but exhibit an asymmetric proteome distribution, leading to selective protein enrichment. We demonstrated that heterologous proteins, such as GFP and RFP, accumulate more abundantly in minicells than in parent cells, regardless of expression levels. To further enhance this accumulation, we manipulated protein localization by fusing target proteins to polar localization signals. While proteins fused with PtsI and Tsr exhibited 2.6-fold and 2.8-fold increases in accumulation, respectively, fusion with the heterologous PopZ protein resulted in a remarkable 15-fold increase in protein concentration under low induction conditions.

CONCLUSIONS

These findings highlight the critical role of spatial protein organization in enhancing the cargo-loading capabilities of minicells. By leveraging polar localization signals, this work provides a robust framework for optimizing minicells as efficient carriers for diverse applications, from therapeutic delivery to industrial biomanufacturing.

Co-occurrence of mcr-9 and blaNDM-5 in Multidrug-Resistant Enterobacter hormaechei Strain Isolated from a Patient with Bloodstream Infection

Enterobacter hormaechei (E. hormaechei), a member of the Enterobacter cloacae complex, has emerged as an important pathogen in healthcare-associated infections. In this study, a multidrug-resistant E. hormaechei EH001 co-carrying mcr-9 and blaNDM-5 was isolated from a patient with bloodstream infection in China. To investigate the genomic characteristics of a multidrug-resistant E. hormaechei EH001 co-carrying mcr-9 and blaNDM-5, whole-genome sequencing was employed and conjugation experiment was performed by using the recipient E. coli EC600. The antimicrobial susceptibility profiles of E. hormaechei EH001 revealed resistance to the most commonly used antimicrobial agents, with the exception of polymyxin B, polymyxin E, and minocycline. E. hormaechei EH001 was classified as sequence type 78 (ST78) and harbored multiple resistance genes, especially co-carried mcr-9 and blaNDM-5 located on an IncHI2 plasmid (pMCR9_EH001) and an IncX3 plasmid (pNDM5_EH001), respectively. Both plasmids were successfully co-transferred to E. coli EC600 by conjugation. Analysis of the genetic environment of mcr-9 and blaNDM-5 revealed the multiple mobile genetic elements, such as insertion sequences (IS) and transposon (Tn). ∆Tn3-IS3000-∆ISAba125-5'-IS5-∆ISAba125-3' were situated upstream of blaNDM-5, while bleMBL-trpF-dsbD-CutA-IS26 were situated downstream of it. In addition, rcnR, rcnA, pcoE, pcoS, and IS5 family transposase (IS903B) were situated upstream of mcr-9, while IS3000 was situated downstream of it, followed by blaCTX-M-3 and IS26. The majority of the plasmid-mediated resistance genes reside within or adjacent to diverse mobile genetic elements, which may potentially promote the horizontal transfer of antibiotic resistance determinants. This study represents the initial investigation providing the detailed genomic characteristics associated with co-occurrence of mcr-9 and blaNDM-5 in E. hormaechei. The findings advocate for heightened clinical vigilance toward such strains, particularly to prevent nosocomial transmission.

The Effect of the Combination of Probiotics and Heavy Metals From Various Aspects in Humans: A Systematic Review of Clinical Trial Studies

Background and Aims

Probiotics usually have beneficial effects on the absorption of trace elements and detoxification of toxic metals in human. Hence, the aim of the systematic review was to evaluate various aspects of the effect of the combination of probiotics and heavy metals in human clinical trial studies.

Methods

Nine databases were searched for clinical trials up to June 2024 investigating probiotics for heavy metal exposure in humans. Two reviewers independently screened records and extracted data on study characteristics, interventions, outcomes, and results. Risk of bias was assessed.

Results

The analysis included 31 clinical trials with a total of 4,611 participants, focusing on the effects of probiotics, prebiotics, and synbiotics. Among the trials, 23 investigated probiotics, five looked at prebiotics, and three explored synbiotics, with probiotic doses ranging from 107 to 2.5 × 1010 CFU/day. Results indicated that probiotics combined with zinc significantly reduced the time to resolution of vomiting and diarrhea compared to zinc alone, improved the treatment efficacy of antibiotic-associated diarrhea linked to pneumonia, and shortened hospital stays relative to probiotics alone. Probiotics did not show significant effects on blood parameters compared to placebo; however, prebiotic galactooligosaccharides enhanced iron absorption in women and children. The addition of probiotics to bismuth quadruple therapy did not improve Helicobacter pylori eradication rates but reduced side effects like diarrhea and vomiting. One trial reported a decrease in toxic metal levels in pregnant women due to probiotics, but no similar effects were observed in children.

Conclusions

Probiotics are one of the new methods employed to improve or eliminate the adverse effects of heavy metals in the body. Although many studies have investigated the effects of probiotics on heavy metals, there is still a need for more in-depth and extensive studies.

The occurrence and bioactivity of tetrahydronaphthoquinoline-diones (THNQ-dione)

Natural products have been important in the discovery of new drugs, but their use is limited due to issues with accessibility and synthesis. Tetrahydronaphthoquinoline-dione (THNQ-dione) is a key structural feature found in several natural and synthetic compounds that exhibit notable biological properties. The unique properties of THNQ-diones can be attributed to the fusion of tetrahydroquinoline and anthraquinone moieties. These alkaloids are synthesised through various biosynthetic pathways, leading to diverse structures and bioactivities. Despite their significance, THNQ-diones have not been extensively covered in the review literature, highlighting the importance of this article in discussing their natural occurrence and biological activities. This article explores the distribution of THNQ-dione alkaloids in different organisms and their potential as a source of novel bioactive natural products.

Systematic review and meta-analysis of colistin heteroresistance in Klebsiella pneumoniae isolates

BACKGROUND

Antibiotic heteroresistance is a common phenotype observed in a variety of pathogenic bacteria such as K. pneumonia: A subpopulation of cells with a higher MIC than the dominant population is defined as heteroresistance. Several studies have demonstrated colistin heteroresistance in K. pneumonia leading to treatment failures. Therefore, we performed a systematic meta-analysis to summarize the current evidence on the prevalence of colistin heteroresistance in K. pneumonia isolates.

METHODS

Multiple databases were searched to find relevant literature from 2008 to 2024, including PubMed, Scopus, Embase, and Web of Science.

RESULTS

The meta-analysis included eighteen articles. According to the random effects model, the pooled proportion of heteroresistant K. pneumoniae was 0.315 (95% CI: 0.179-0.492). The heterogeneity was substantial, with Q [17] = 335.020, I² = 94.93%, and p < 0.001, suggesting that heteroresistance rates varied widely across the 18 included studies.

CONCLUSION

In conclusion, our findings revealed that a prevalence of colistin heteroresistant detected in approximately 31.5%, of K. pneumonia. These findings are obtained and highlighted in this meta-analysis as a new guidance document for diagnosing and treating K. pneumonia infections is needed to raise the awareness of infectious disease specialists, gastroenterologists, and microbiologists to the heteroresistance to colistin in patients with a K. pneumonia infection.

Wolbachia enhances the survival of Drosophila infected with fungal pathogens

BACKGROUND

Wolbachia bacteria of arthropods are at the forefront of basic and translational research on multipartite host-symbiont-pathogen interactions. These vertically transmitted microbes are the most widespread endosymbionts on the planet due to factors including host reproductive manipulation and fitness benefits. Importantly, some strains of Wolbachia can inhibit viral pathogenesis within and between arthropod hosts. Mosquitoes carrying the wMel Wolbachia strain of Drosophila melanogaster have a greatly reduced capacity to spread viruses like dengue and Zika to humans. While significant research efforts have focused on viruses, relatively little attention has been given to Wolbachia-fungal interactions despite the ubiquity of fungal entomopathogens in nature.

RESULTS

Here, we demonstrate that Wolbachia increase the longevity of their Drosophila melanogaster hosts when challenged with a spectrum of yeast and filamentous fungal pathogens. We find that this pattern can vary based on host genotype, sex, and fungal species. Further, Wolbachia correlates with higher fertility and reduced pathogen titers during initial fungal infection, indicating a significant fitness benefit. Finally, RNA sequencing results show altered expression of many immune and stress response genes in the context of Wolbachia and fungal infection, suggesting host immunity may be involved in the mechanism.

CONCLUSIONS

This study demonstrates Wolbachia's protective role in diverse fungal pathogen interactions and determines that the phenotype is broad, but with several variables that influence both the presence and strength of the phenotype. It also is a critical step forward to understanding how symbionts can protect their hosts from a variety of pathogens.

Ceftazidime-avibactam tolerance and persistence among difficult-to-treat KPC-producing Klebsiella pneumoniae clinical isolates from bloodstream infections

PURPOSE

Tolerance and persistence occur "silently" in bacteria categorized as susceptible by antimicrobial susceptibility testing in clinical microbiology laboratories. They are different from resistance phenomena, not well-studied, and often remain unnoticeable. We aimed to investigate and characterize ceftazidime-avibactam (CZA) tolerance/persistence in 80 Klebsiella pneumoniae isolates from bloodstream infections.

METHODS

We used the Tolerance Disk Test (TDtest) to detect CZA tolerance/persistence and investigate the avibactam (AVI) influence on them, and time-kill assays with minimal duration for killing (MDK) determination to characterize/differentiate CZA tolerance from persistence, for selected isolates. Whole genome sequencing was performed for 49/80 selected isolates to investigate genes related to beta-lactam tolerance/persistence and resistance as well as phylogeny studies.

RESULTS

Tolerance/persistence to CZA was detected in 48/80 (60%) isolates, all extensively drug-resistant (XDR) or multidrug-resistant, carbapenem-resistant K. pneumoniae (CRKp), KPC producers, and previously categorized as susceptible (not resistant) to CZA. No heteroresistance was detected. CZA tolerance/persistence occurred due to ceftazidime tolerance/persistence and was not related to AVI in the CZA combination. 5/11 isolates were characterized as CZA-tolerant and 5/11 as CZA-persistent. The single (1/11) XDR and CRKp non-KPC producer was truly susceptible. All the CZA-tolerant/persistent isolates (ST11, ST258, ST340, ST437, ST16, ST17, and ST307) harbored the carbapenemase-encoding gene blaKPC-2. Mutation in only two genes (rpoS and degQ) related to beta-lactam tolerance/persistence was found in only 7/49 CZA-tolerant/persistent isolates, suggesting the presence of yet unknown beta-lactam tolerance/persistence genes.

CONCLUSION

Among the K. pneumoniae bloodstream isolates studied, 60%, previously categorized as susceptible to CZA, were, actually, tolerant/persistent to this antibiotic, all these KPC producers.

Diet links gut chemistry with cancer risk in C57Bl/6 mice and human colorectal cancer patients

Background & Aims

Western-style diets, characterized by higher fat and protein, and low micronutrient levels, promote the development of colorectal cancer (CRC). Here, we investigate the role of a Western diet on microbiome composition, sulfide production, and intestinal epithelial damage in pre-CRC mice, and validate taxonomic changes in a meta-analysis of human CRC patients.

Methods

NWD1 is a purified Western-style diet that produces sporadic intestinal and colon tumors in wild-type C57BL/6 mice in the absence of genetic or carcinogen exposure. To determine how this diet influences cancer risk by shaping microbial composition and sulfide chemistry, mice were fed NWD1 or a purified control diet for 24 weeks. Microbiome composition, sulfide production, and intestinal stem cell mRNA expression were assessed. Observed microbiome changes were validated in a human CRC meta-analysis.

Results

Fecal sulfide levels were tripled in NWD1-fed mice ( P< 0.00001 ), concurrent with increased abundance of the sulfidogenic Erysipelotrichaceae family. NWD1-fed mice had increased expression of mitochondrial sulfide oxidation genes in Lgr5 hi intestinal stem cells, demonstrating an adaptive response to elevated sulfide. In a meta-analysis of human CRC studies, we observed that Erysipelotrichaceae were associated with CRC, validating both canonical CRC microbes such as Solobacterium moorei and highlighting the potential contribution of previously unrecognized, disease-associated microbes.

Conclusions

Our analyses connect the risk factors of Western diet, sulfide, and epithelial damage in a pre-cancer mouse model to microbiome changes observed in human CRC patients and suggest that microbial signatures of CRC and gut ecosystem alteration may manifest long before disease development.

Disulfide bonds are required for cell division, cell envelope biogenesis and antibiotic resistance proteins in mycobacteria

Mycobacteria, including Mycobacterium tuberculosis-the etiological agent of tuberculosis-have a unique cell envelope critical for their survival and resistance. The cell envelope's assembly and maintenance influence permeability, making it a key target against multidrug-resistant strains. Disulfide bond (DSB) formation is crucial for the folding of cell envelope proteins. The DSB pathway in mycobacteria includes two enzymes, DsbA and VKOR, required for survival. Using bioinformatics and cysteine profiling proteomics, we identified cell envelope proteins dependent on DSBs. We validated via in vivo alkylation that key proteins like LamA (MmpS3), PstP, LpqW, and EmbB rely on DSBs for stability. Furthermore, chemical inhibition of VKOR results in phenotypes similar to those of Δvkor. Thus, targeting DsbA-VKOR systems could compromise both cell division and mycomembrane integrity. These findings emphasize the potential of DSB inhibition as a novel strategy to combat mycobacterial infections.

Decoupling microbial iron reduction from anoxic microsite formation in oxic sediments: a microscale investigation through microfluidic models

Iron (Fe) reduction is one of the oldest microbial processes on Earth. After the atmosphere and ocean became oxygenated, this anaerobic process was relegated to niche anoxic environments. However, evidence of Fe reduction in oxic, partially saturated subsurface systems, such as soils and vadose zones, has been reported, with the common explanation being the formation of anoxic microsites that remain undetected by bulk measurements. To explore how microscale oxygen concentrations regulate microbial Fe reduction, we cultivated a facultative Fe-reducing bacterium using a microfluidic setup integrated with transparent planar oxygen sensors. Contrary to expectations, Fe reduction occurred under fully oxic conditions, without the formation of anoxic microsites. Our results suggest that microbially mediated Fe-reduction could be more widespread in oxic subsurface environments than previously assumed. Moreover, our mathematical modeling of oxygen dynamics around biomass-rich layers revealed that the onset of anoxia is mainly controlled by biomass spatial organization rather than the conventionally used water saturation index. This opens a new perspective on the proxies needed to predict anoxic microsite formation and Fe(III) reduction occurrence.

Partial loss of FITM2 function causes hereditary spastic paraplegia

FITM2 encodes fat-storage inducing transmembrane protein 2 (FIT2), a lipid diphosphatase in the ER that cleaves acyl-CoAs and is crucial for ER homeostasis. In humans, homozygous null mutations in FITM2 are associated with a syndrome characterized by deafness and dystonia. Here, we report two families with hereditary spastic paraplegia (HSP) in whom exome sequencing revealed compound heterozygosity for FITM2 mutations. In each family, the affected probands carry one putative null allele and one G100R missense allele. Functional analyses demonstrated that the G100R allele is hypomorphic, with FIT2 protein levels reduced to 20% of wild type, leading to proportionately decreased enzyme activity. The occurrence of similar HSP disease phenotypes and the same hypomorphic mutation in these families suggests that the G100R mutation and its associated reduced enzyme activity represent a newly recognized clinical manifestation of FITM2 mutations, expanding the spectrum of conditions associated with this gene.

Whole-genome evaluation and prophages characterization associated with genome of carbapenem-resistant Acinetobacter baumannii UOL-KIMZ-24-2

Carbapenem-resistant Acinetobacter baumannii (CRAB) is an emerging threat to healthcare settings in many countries, principally in South Asia. The current study was aimed to identify, evaluate whole-genome and characterize the prophages in genome of CRAB strain, recovered from patients of Lahore General Hospital, Lahore. More than 200 samples were collected and identified by morphological and biochemical tests. These strains were also subjected to a comprehensive antimicrobial susceptibility evaluation using Kirby-Bauer method and further confirmed as CRAB strains by exploring blaOXA-51. In addition, the whole-genome evaluation of a Acinetobacter baumannii UOL-KIMZ-24-2 was carried out using various Bioinformatics tools. A total of 150 strains of A. baumannii were recovered and identified in the current study. Among them, 49% strains were found resistant to carbapenem. The blaOXA-51 was found prevalent in the genome of A. baumannii recovered from medical ICU (38%). In addition, the UOL-KIMZ-24-2 genome analysis based on multilocus sequence typing (MLST) highlighted that UOL-KIMZ-24-2 belonged to ST2 (Pasteur scheme) sequence type. A total of 29 antimicrobial resistance (AMR) genes were present, importantly, blaOXA-66, blaOXA-23 and blaOXA-25. The mobile genetic elements (MGEs) were identified as transposases and belonged to four classes e.g. IS15d1, ISAba24, ISEc29, and ISEc35. A total of 14 virulence factors encoded by 58 different genes were detected in UOL-KIMZ-24-2. In addition, the phage sequences were identified in genome of UOL-KIMZ-24-2, divided into 3 regions. In conclusion, UOL-KIMZ-24-2 contained a mixture of AMR genes, MGEs. prophages sequences and virulence genes.

Genetic profiling of extended-spectrum β-Lactamase and carbapenemase-producing Escherichia coli O157:H7 from clinical samples among diarrheal patients in Shashemene, Ethiopia

BACKGROUND

Escherichia coli (E. coli) O157:H7, associated with diarrhea, poses a global health risk. In Ethiopia, where diarrhea is common, there is limited knowledge about these resistant strains and a lack of data on Extended-Spectrum β-Lactamase (ESBL) and carbapenemase production. Understanding the prevalence of antimicrobial resistance genes associated with ESBL and carbapenems is crucial for addressing diarrheal disease. This study aimed to investigate the genetic profile of ESBL and carbapenemase coding gene carriage in E. coli O157:H7 from clinical stool samples and evaluate antimicrobial susceptibility patterns.

METHODS

A total of twenty-nine bacterial isolates obtained from diarrheal patients were subjected to conventional culture and phenotypic (Kirby Bauer disc diffusion method) testing for antimicrobial resistance. Additionally, screening for the production of ESBL (combined disk method) and carbapenemase (modified carbapenem inactivation method) was conducted. Isolates that tested positive for ESBL and carbapenemase production were further analyzed, targeting five genes (blaNDM, blaKPC, blaCTX-M, blaTEM, and blaSHV) associated with ESBL and carbapenemase production. Data analysis was performed using SPSS version 27.0, employing logistic regression and descriptive statistics.

RESULTS

We analyzed a total of 27 isolates that were ESBL-positive and 12 isolates that were found to produce carbapenemase phenotypically. These isolates were obtained from clinical stool samples and (9/27) 33.3% of the isolates were from under five years children, predominantly from urban areas, and those that have contact with domestic animals. Genes coding ESBL were found in (19/27) 70.4% of the isolates, the most predominant being blaCTX-M and blaTEM. Eight isolates carried blaKPC, but none had blaNDM, while five isolates carried both blaCTX-M and blaTEM genes. blaSHV-carrying isolates showed phenotypic resistance to ampicillin and cephalosporins, while blaKPC-carrying isolates exhibited resistance to ampicillin, carbapenems, and tetracycline.

CONCLUSION

This study identifies a significant prevalence of multidrug resistance in E. coli O157:H7, which can be attributed to the presence of resistance genes coding for ESBL and carbapenem production. Key factors contributing to this resistance, such as urban environments, children under the age of five, and domestic animal ownership, have been emphasized. Additionally, this research underscores the urgent need for enhanced surveillance and targeted interventions to address this pressing public health concern.

Genetic determinants of silver nanoparticle resistance and the impact of gamma irradiation on nanoparticle stability

BACKGROUND

One of the main issues facing public health with microbial infections is antibiotic resistance. Nanoparticles (NPs) are among the best alternatives to overcome this issue. Silver nanoparticle (AgNPs) preparations are widely applied to treat multidrug-resistant pathogens. Therefore, there is an urgent need for greater knowledge regarding the effects of improper and excessive use of these medications. The current study describes the consequences of long-term exposure to sub-lethal concentrations of AgNPs on the bacterial sensitivity to NPs and the reflection of this change on the bacterial genome.

RESULTS

Chemical methods have been used to prepare AgNPs and gamma irradiation has been utilized to produce more stable AgNPs. Different techniques were used to characterize and identify the prepared AgNPs including UV-visible spectrophotometer, Fourier Transform Infrared (FT-IR), Dynamic light scattering (DLS), and zeta potential. Transmission electron microscope (TEM) and Scanning electron microscope (SEM) showed 50-100 nm spherical-shaped AgNPs. Eleven gram-negative and gram-positive bacterial isolates were collected from different wound infections. The minimum inhibitory concentrations (MICs) of AgNPs against the tested isolates were evaluated using the agar dilution method. This was followed by the induction of bacterial resistance to AgNPs using increasing concentrations of AgNPs. All isolates changed their susceptibility level to become resistant to high concentrations of AgNPs upon recultivation at increasing concentrations of AgNPs. Whole genome sequencing (WGS) was performed on selected susceptible isolates of gram-positive Staphylococcus lentus (St.L.1), gram-negative Klebsiella pneumonia (KP.1), and their resistant isolates St.L_R.Ag and KP_R.Ag to detect the genomic changes and mutations.

CONCLUSIONS

For the detection of single-nucleotide polymorphisms (SNPs) and the identification of all variants (SNPs, insertions, and deletions) in our isolates, the Variation Analysis Service tool available in the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) was used. Compared to the susceptible isolates, the AgNPs-resistant isolates St.L_R.Ag and KP_R.Ag had unique mutations in specific efflux pump systems, stress response, outer membrane proteins, and permeases. These findings might help to explain how single-nucleotide variants contribute to AgNPs resistance. Consequently, strict regulations and rules regarding the use and disposal of nano waste worldwide, strict knowledge of microbe-nanoparticle interaction, and the regulated disposal of NPs are required to prevent pathogens from developing nanoparticle resistance.

Genomic characteristics and phylogenetic relationships of Cutibacterium acnes breast milk isolates

BACKGROUND

Cutibacterium acnes is one of the most commonly found microbes in breast milk. However, little is known about the genomic characteristics of C. acnes isolated from breast milk. In this study, the sequencing and assembly results of 10 C. acnes isolates from breast milk were compared with the genomic data of 454 strains downloaded from NCBI, and the characteristics of breast milk isolates from various perspectives, including phylogeny, genomic characteristics, virulence genes, drug resistance genes, and carbohydrate utilization, were elucidated.

RESULTS

The findings of this study revealed no differences between the breast milk isolates and other isolates in terms of genomic features, phylogenetic relationships, virulence, and resistance-related genes. However, breast milk-derived isolates exhibited significantly lower copies of the carbohydrate metabolic enzyme genes GT5 and GT51 (P < 0.05) and a higher copy number of the GH31 gene (P < 0.05) than others. C. acnes primarily consists of three genetic branches (A, B, and C), which correspond to the three subspecies of C. acnes (C. acnes subsp. elongatum, C. acnes subsp. defendens, C. acnes subsp. acnes). The genetic differences between branches B and C were smaller than that between branch A. Branches A and B carry a higher number of copies of carbohydrate enzymes, including CE1, CE10, GH3, and CBM32 than branch C. Branches B and C possess the carbohydrate enzymes PL8 and GH23, which are absent in branch A. Core genes, core intergenic regions, and concatenated sequences of core genes and core intergenic regions were compared to construct a phylogenetic tree, and it was found that core intergenic regions could be used to describe phylogenetic relationships.

CONCLUSIONS

It is therefore speculated that the C. acnes in breast milk originates from the nipple or breast surface. This study provides a novel genetic basis for genetic differentiation of C. acnes isolates from breast milk.

Next-generation vaccines for influenza B virus: advancements and challenges

To battle seasonal outbreaks of influenza B virus infection, which continue to pose a major threat to world health, new and improved vaccines are urgently needed. In this article, we discuss the current state of next-generation influenza B vaccine development, including both advancements and challenges. This review covers the shortcomings of existing influenza vaccines and stresses the need for more-effective and broadly protective vaccines and more-easily scalable manufacturing processes. New possibilities for vaccine development have emerged due to recent technical developments such as virus-like particle (VLP) platforms, recombinant DNA technologies, and reverse genetics. By using these methods, vaccines can be developed that elicit stronger and longer-lasting immune responses against various strains of influenza B virus. Vaccines may be more effective and immunogenic when adjuvants and new delivery mechanisms are used. Progress has been made in the development of influenza B vaccine mRNA vaccines, nanoparticle-based vaccines, and vector-based vaccines. However, there are still several obstacles to overcome before next-generation influenza B vaccines can be widely used, including the challenge of antigenic drift, the extinction of the B/Yamagata lineage, and difficulties in strain selection. There are also other challenges related to public acceptance, vaccine distribution, manufacturing complexity, and regulations. To overcome these challenges, scientists, politicians, and pharmaceutical firms must work together to expedite the development and licensing of vaccines and the establishment of immunization programs. The need for constant monitoring and quick adaptation of vaccines to match the currently circulating strains is further highlighted by the appearance of novel influenza B virus variants. To be ready for future pandemics and influenza B outbreaks, we need better vaccines and better monitoring systems.

The contributions of T cell-mediated immunity to protection from vaccine-preventable diseases: A primer

In the face of the ever-present burden of emerging and reemerging infectious diseases, there is a growing need to comprehensively assess individual- and population-level immunity to vaccine-preventable diseases (VPDs). Many of these efforts, however, focus exclusively on antibody-mediated immunity, ignoring the role of T cells. Aimed at clinicians, public health practioners, and others who play central roles in human vaccine research but do not have formal training in immunology, we review how vaccines against infectious diseases elicit T cell responses, what types of vaccines elicit T cell responses, and how T cell responses are measured. We then use examples to demonstrate six ways that T cells contribute to protection from VPD, including directly mediating protection, enabling antibody responses, reducing disease severity, increasing cross-reactivity, improving durability, and protecting special populations. We conclude with a discussion of challenges and solutions to more widespread consideration of T cell responses in clinical vaccinology.

The ability of clostridium novyi-NT spores to induce apoptosis via the mitochondrial pathway in mice with HPV-positive cervical cancer tumors derived from the TC-1 cell line

BACKGROUND

A precise observation is that the cervix's solid tumors possess hypoxic regions where the oxygen concentration drops below 1.5%. Hypoxia negatively impacts the host's immune system and significantly diminishes the effectiveness of several treatments, including radiotherapy and chemotherapy. Utilizing oncolytic spores of Clostridium novyi-NT to target the hypoxic regions of solid tumors has emerged as a noteworthy treatment strategy.

METHODS

The transplantation procedure involved injecting TC-1 cells, capable of expressing HPV-16 E6/7 oncoproteins, into the subcutaneous layer of 6-8-week-old female C57/BL6 mice. The TC-1 cell line, was subcutaneously transplanted into 6-8-week-old female C57/BL6 mice. The tumor-bearing mice were randomly divided into 4 groups, and after selecting the control group, they were treated with different methods. Group 1- control without treatment (0.1 ml sterile PBS intratumor) Group 2- received cisplatin intraperitoneally (10 mg/kg) Group 3- received 107Clostridium novyi-NT spores systemically through the tail vein Group 4-tumor mice received 107Clostridium novyi-NT spores intratumorally. 20 days after the start of treatment, the mice were sacrificed and tumor tissues were isolated. In order to clarify the mechanism of the therapeutic effect with spores, the amount of ROS and ceramide was measured by ELISA technique, and the expression level of cytochrome c, cleaved caspase- 3, Bax, Bcl-2, HIF-1α, and VEGF proteins was measured by western blotting.

RESULTS

Our results clearly showed that the injection of Clostridium novyi-NT spores (either intratumorally or intravenously) causes the regression of mouse cervical tumors. Spore germination induces internal apoptosis in cancer cells by inducing ROS production and increasing total cell ceramide, releasing cytochrome c and damaging mitochondria. Additionally, the results provided clear evidence of a significant decrease in the expression of HIF-1 alpha and VEGF proteins among the tumor groups that received spores, when compared to both the cisplatin-treated group and the control group.

CONCLUSIONS

The study's outcomes demonstrated that the introduction of Clostridium novyi-NT spores triggered apoptosis in cervical cancer cells (derived from the TC-1 cell line) via the mitochondrial pathway, subsequently resulting in tumor regression in a mouse model.

Early detection of bacterial pneumonia by characteristic induced odor signatures

INTRODUCTION

The ability to detect pathogenic bacteria before the onsets of severe respiratory symptoms and to differentiate bacterial infection allows to improve patient-tailored treatment leading to a significant reduction in illness severity, comorbidity as well as antibiotic resistance. As such, this study refines the application of the non-invasive Secondary Electrospray Ionization-High Resolution Mass Spectrometry (SESI-HRMS) methodology for real-time and early detection of human respiratory bacterial pathogens in the respiratory tract of a mouse infection model.

METHODS

A real-time analysis of changes in volatile metabolites excreted by mice undergoing a lung infection by Staphylococcus aureus or Streptococcus pneumoniae were evaluated using a SESI-HRMS instrument. The infection status was confirmed using classical CFU enumeration and tissue histology. The detected VOCs were analyzed using a pre- and post-processing algorithm along with ANOVA and RASCA statistical evaluation methods.

RESULTS

Characteristic changes in the VOCs emitted from the mice were detected as early as 4-6 h post-inoculation. Additionally, by using each mouse as its own baseline, we mimicked the inherent variation within biological organism and reported significant variations in 25 volatile organic compounds (VOCs) during the course of a lung bacterial infection.

CONCLUSION

the non-invasive SESI-HRMS enables real-time detection of infection specific VOCs. However, further refinement of this technology is necessary to improve clinical patient management, treatment, and facilitate decisions regarding antibiotic use due to early infection detection.

Yield increment and transcriptome response caused by blue light treatment in Hericium coralloides

BACKGROUND

Hericium coralloides is a traditional edible and medicinal mushroom. Light is a key factor in forming fruiting bodies of fungi; however, the effects of different light on the yield and morphogenesis of H. coralloides are still unknown. Therefore, the morphology, yield, and transcriptome of H. coralloides under blue, red, and white light conditions were investigated.

RESULT

Fruiting bodies under blue light exhibited superior morphological traits, such as milky white color, larger size, elongated stalks, and higher spine count, leading to higher yields. Different light treatments led to dramatic transcriptome changes ranging from 10,827 differentially expressed genes (DEGs) induced by blue light in Blue-4d to 11,375 DEGs induced by red light in Red-4d and accounted for 64.56% to 67.81% of all expressed genes. This massive amount of light-responsive genes has never been reported in fungi. Gene Ontology analysis showed that light affected nearly all aspects of life in H. coralloides; suggesting that the influence of light on fungi may have been underestimated. Blue light-induced yield increment may be achieved by specifically upregulating the growth-related processes such as DNA replication, chromosomes, and cell division.

CONCLUSIONS

This study offers preliminary insights into the potential role of blue light in modulating gene expression and yield stimulation in H. coralloides, potentially improving cultivation practice.

Shaping the environment - Drosophila suzukii larvae construct their own niche

In holometabolous insects, the choice of oviposition substrate by the adult needs to be coordinated with the developmental needs of the larva. Drosophila suzukii female flies possess an enlarged serrated ovipositor, which has enabled them to conquer the ripening fruit as an oviposition niche. They insert their eggs through the skin of priced small fruits. However, this specialization seems to clash with the nutritional needs for larval development since ripening fruits have a low protein content and are high in sugars. In this work, we studied how D. suzukii larvae develop in and interact with the blueberry. We show that despite its hardness and composition, D. suzukii's first instar larvae are able to use the ripening fruit by engaging in niche construction. They display unique physical and behavioral characteristics that allow them to process the hard-ripening fruit and provoke an improvement in its composition that better suits larval nutritional needs.

Inhibitory effects of nafcillin and diosmin on biofilm formation by Salmonella Typhimurium

OBJECTIVE

The foodborne pathogen Salmonella enterica serovar Typhimurium causes self-limiting gastroenteritis in humans and is difficult to eliminate due to its ability to adhere to surfaces and form biofilms that exhibit high resistance to antimicrobial agents. To explore alternative strategies for biofilm treatment, it is essential to investigate novel agents that inhibit Salmonella biofilms.

METHOD

In this study, we investigated the minimum biofilm inhibitory concentrations (MBICs) and minimum biofilm eradication concentrations (MBECs) of nafcillin and diosmin, both previously identified as Lon protease inhibitors, against biofilms formed by S. Typhimurium. Furthermore, we examined the expression of genes associated with the type II toxin-antitoxin system to enhance our understanding of the impact of these inhibitors.

RESULTS

The findings indicated a strong antibiofilm effect of nafcillin, with MBIC and MBEC values of 8 µg/mL and 32 µg/mL, respectively. These results were confirmed by field emission scanning electron microscopy (FE-SEM), which showed that biofilm formation was reduced in the presence of nafcillin. Additionally, it revealed morphological changes in the bacteria within the nafcillin-treated biofilms. Furthermore, gene expression analyses demonstrated a significant reduction in the expression of type II TA system genes following treatment with nafcillin and diosmin.

CONCLUSION

This study highlights the effectiveness of nafcillin in disrupting the biofilms of S. Typhimurium. These results suggest promising avenues for the development of novel therapeutic strategies targeting biofilms associated with S. Typhimurium.

mRNA cancer vaccines from bench to bedside: a new era in cancer immunotherapy

Harnessing the power of the immune system to target cancer cells is one of the most appealing approaches for cancer therapy. Among these immunotherapies, messenger ribonucleic acid (mRNA) cancer vaccines are worthy of consideration, as they have demonstrated promising results in clinical trials. These vaccines have proven to be safe and well-tolerated. They can be easily mass-produced in a relatively short time and induce a systemic immune response effective against both the primary tumor and metastases. Transcripts encoding immunomodulatory molecules can also be incorporated into the mRNA, enhancing its efficacy. On the other hand, there are some challenges associated with their application, including mRNA instability, insufficient uptake by immune cells, and intrinsic immunogenicity, which can block mRNA translation. Many innovations have been suggested to overcome these obstacles, including structural modification (such as 5' cap modification), optimizing delivery vehicles (especially dendritic cells (DCs) and nanoparticles), and using antigens that can enhance immunogenicity by circumventing tolerance mechanisms. A popular approach is to combine mRNA cancer vaccines with traditional and novel cancer treatments like chemotherapy, radiotherapy, and immune checkpoint blockade (ICB). They are most efficacious when combined with other therapies like ICBs. There is still a long way to go before these vaccines enter the standard of care for cancer patients, but with the incredible pace of development in this field, their clinical application will soon be witnessed. This review highlights the recent advances and challenges of mRNA cancer vaccines. Finally, some of the most prominent clinical applications of these vaccines will be reviewed.

Combined transcriptome and metabolome analysis revealed the antimicrobial mechanism of Griseorhodin C against Methicillin-resistant Staphylococcus aureus

The global rise of multidrug-resistant pathogens, particularly Methicillin-resistant Staphylococcus aureus (MRSA), has become a critical public health concern, necessitating the urgent discovery of new antimicrobial agents. Griseorhodin C, a hydroxyquinone compound isolated from Streptomyces, has demonstrated significant inhibitory effects against MRSA. In this study, we employed a comprehensive approach combining transcriptome and metabolome analyses to investigate the underlying antimicrobial mechanism of Griseorhodin C. Our findings reveal that Griseorhodin C interferes with multiple bacterial metabolic pathways, including those essential for the biosynthesis and metabolism of amino acids, purine metabolism and energy metabolism, ultimately leading to bacterial growth inhibition and cell death. Notably, Griseorhodin C showed superior inhibitory effects compared to the clinical standard, vancomycin, both in vivo and vitro. These results highlight the potential of Griseorhodin C as a promising candidate for the development of new therapeutic strategies aimed at combating MRSA infections. The study underscores the importance of exploring natural products as sources of novel antibiotics in the ongoing fight against antimicrobial resistance.

Genome Editing in Apicomplexan Parasites: Current Status, Challenges, and Future Possibilities

Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas) technology has revolutionized genome editing across various biological systems, including the Apicomplexa phylum. This review describes the status, challenges, and applications of CRISPR-Cas9 editing technology in apicomplexan parasites, such as Plasmodium, Toxoplasma, Theileria, Babesia, and Cryptosporidium. The discussion encompasses successfully implemented CRISPR-Cas9-based techniques in these parasites, highlighting the achieved milestones, from precise gene modifications to genome-wide screening. In addition, the review addresses the challenges hampering efficient genome editing, including the parasites' complex life cycles, multiple intracellular stages, and the lack of robust genetic tools. It further explores the ethical and policy considerations surrounding genome editing and the future perspectives of CRISPR-Cas applications in apicomplexan parasites.

Tracking SARS-CoV-2 variants in wastewater in San Pedro de la Paz, Chile

Studies have shown the presence of SARS-CoV-2 in the stool of both symptomatic and asymptomatic COVID-19 patients, enabling wastewater-based surveillance (WBS) to complement clinical monitoring. The emergence of variants can enhance viral transmissibility, highlighting the need for ongoing surveillance to detect and control infectious diseases. This study aimed to detect SARS-CoV-2 variants in wastewater from a treatment plant in San Pedro de la Paz, Chile, between January and November 2021. Wastewater samples were concentrated using the polyethylene glycol method, and RT-qPCR assays were performed to analyze SARS-CoV-2 and its variants (Alpha, Beta, Gamma, Lambda, and Delta), with results compared to Illumina amplicon sequencing. The concentration method achieved about 11% viral recovery. The detection of viruses and variants in wastewater proved sensitive and consistent with clinical data, providing additional surveillance insights. Notably, Lambda and Delta variants were the most frequently detected during the second and third infection waves, with some variants identified in wastewater before the first confirmed clinical cases. However, Illumina sequencing lacked sufficient genome coverage, suggesting the need for better sequencing methods for this matrix. This study demonstrates that WBS is a rapid, cost-effective tool for detecting SARS-CoV-2 and its mutations, particularly useful during overwhelming clinical situations or when cost is prohibitively high.

Exogenous NADH promotes the bactericidal effect of aminoglycoside antibiotics against Edwardsiella tarda

The global surge in multidrug-resistant bacteria owing to antibiotic misuse and overuse poses considerable risks to human and animal health. With existing antibiotics losing their effectiveness and the protracted process of developing new antibiotics, urgent alternatives are imperative to curb disease spread. Notably, improving the bactericidal effect of antibiotics by using non-antibiotic substances has emerged as a viable strategy. Although reduced nicotinamide adenine dinucleotide (NADH) may play a crucial role in regulating bacterial resistance, studies examining how the change of metabolic profile and bacterial resistance following by exogenous administration are scarce. Therefore, this study aimed to elucidate the metabolic changes that occur in Edwardsiella tarda (E. tarda), which exhibits resistance to various antibiotics, following the exogenous addition of NADH using metabolomics. The effects of these alterations on the bactericidal activity of neomycin were investigated. NADH enhanced the effectiveness of aminoglycoside antibiotics against E. tarda ATCC15947, achieving bacterial eradication at low doses. Metabolomic analysis revealed that NADH reprogrammed the ATCC15947 metabolic profile by promoting purine metabolism and energy metabolism, yielding increased adenosine triphosphate (ATP) levels. Increased ATP levels played a crucial role in enhancing the bactericidal effects of neomycin. Moreover, exogenous NADH promoted the bactericidal efficacy of tetracyclines and chloramphenicols. NADH in combination with neomycin was effective against other clinically resistant bacteria, including Aeromonas hydrophila, Vibrio parahaemolyticus, methicillin-resistant Staphylococcus aureus, and Listeria monocytogenes. These results may facilitate the development of effective approaches for preventing and managing E. tarda-induced infections and multidrug resistance in aquaculture and clinical settings.

Pathogenicity and virulence of O'nyong-nyong virus: A less studied Togaviridae with pandemic potential

O'nyong-nyong virus (ONNV) is a neglected mosquito-borne alphavirus belonging to the Togaviridae family. ONNV is known to be responsible for sporadic outbreaks of acute febrile disease and polyarthralgia in Africa. As climate change increases the geographical range of known and potential new vectors, recent data indicate a possibility for ONNV to spread outside of the African continent and grow into a greater public health concern. In this review, we summarise the current knowledge on ONNV epidemiology, host-pathogen interactions, vector-virus responses, and insights into possible avenues to control risk of further epidemics. In this review, the limited ONNV literature is compared and correlated to other findings on mainly Old World alphaviruses. We highlight and discuss studies that investigate viral and host factors that determine viral-vector specificity, along with important mechanisms that determine severity and disease outcome of ONNV infection.

Epstein-Barr Virus and gastric carcinoma pathogenesis with emphasis on underlying epigenetic mechanisms

Gastric cancer (GC) remains one of the top causes of cancer-related mortality around the world. The pathogenesis of GC is attributed to lifestyle, family history, genetic mutations, epigenetic alterations, as well as infectious agents such as Epstein-Barr Virus (EBV). EBV, a ubiquitous human gamma herpes virus, with latent asymptomatic infection in more than 95% of the world's population, is able to infect through the oral epithelium. EBV is described as the first virus found in human neoplastic, when it was detected in Burkitt lymphoma tumor biopsy. Nowadays this virus is considered to be involved in various human malignancies such as GC. Despite comprehensive efforts and immense studies, the main underlying mechanism is not well described as there are crucial contradictions regarding the presence of this virus and the prognosis of the disease. Immunological alterations, genetic mutations, and epigenetic modifications are among the most important criteria presented in EBV- associated gastric cancer (EBVaGC), leading to its consideration as a separate subtype with unique clinical, histological, biochemical, and genetic characteristics. The current study aimed to review the association between EBV and GC with an emphasis on the role of epigenetic modifications in the suppression or progression of carcinogenesis. To put all findings in a nutshell, several genes and chromatin mutations, promoter hypermethylation and subsequent silencing of related genes, and histone modifications and aberrant micro RNAs (miRNAs) expression were considered as the major altered mechanisms in the pathogenesis of EBVaGC, most of which able to be suggested as therapeutic targets. However, the current knowledge appeared to be imperfect, hence further studies are encouraged.

Phage cocktail amikacin combination as a potential therapy for bacteremia associated with carbapenemase producing colistin resistant Klebsiella pneumoniae

The increasing occurrence of hospital-associated infections, particularly bacteremia, caused by extensively drug-resistant (XDR) carbapenemase-producing colistin-resistant Klebsiella pneumoniae highlights a critical requirement to discover new therapeutic alternatives. Bacteriophages having host-specific bacteriolytic effects are promising alternatives for combating these pathogens. Among 12 phages isolated from public wastewater in Thailand, two phages-vB_kpnM_05 (myovirus) and vB_kpnP_08 (podovirus) showed broad-host range, producing bacteriolytic activities against 81.3% (n = 26) and 78.1% (n = 25) of 32 XDR carbapenemase-producing colistin-resistant K. pneumoniae, with capsular types-K15, K17, K50, K51, K52/wzi-50 and K2/wzi-2. Both phages showed short replication times, large burst sizes with rapid adsorptions. They exhibited significant stability under various environmental conditions. Genomic analysis revealed that both phages are genetically distinct phages from Myoviridae and Podoviridae family, with the lack of toxin, virulence, lysogeny and antibiotic resistance genes. These characteristics highlighted their promising potential for utilizing in phage therapy for combating XDR K. pneumoniae. Although phage cocktail combining vB_kpnM_05 and vB_kpnP_08 provided significant bacteriolysis for longer duration (8 h) than its monophage (6 h), bacterial regrowth was observed which suggested an evitable development of phage resistance under phages' selection pressures. Future study will be undertaken to elucidate the precise mechanisms by which these XDR K. pneumoniae developed phage resistance and their associated fitness cost. Remarkably, combining phage cocktail with amikacin at their sub-inhibitory concentrations produced potent synergy by completely suppressing bacterial regrowth in vitro. Our study demonstrated the significant therapeutic and prophylactic effectiveness of a phage cocktail-amikacin combination as a promising alternative strategy for overcoming bacteremia associated with XDR K. pneumoniae having carbapenemase and colistin resistance in vivo.

The antimicrobial and antibiofilm effects of gentamicin, imipenem, and fucoidan combinations against dual-species biofilms of Staphylococcus aureus and Acinetobacter baumannii isolated from diabetic foot ulcers

INTRODUCTION

Diabetes mellitus is a chronic metabolic disorder characterized by persistent hyperglycemia due to impaired insulin production or utilization, leading to severe health complications. Diabetic foot ulcers (DFUs) represent a major complication, often exacerbated by polymicrobial infections involving Staphylococcus aureus and Acinetobacter baumannii. These pathogens, notorious for their resistance to antibiotics, complicate treatment efforts, especially due to biofilm formation, which enhances bacterial survival and resistance. This study explores the synergistic effects of combining gentamicin, imipenem, and fucoidan, a sulfated polysaccharide with antimicrobial properties, against both planktonic and biofilm forms of S. aureus and A. baumannii.

METHODS

Isolates of S. aureus and A. baumannii were collected from DFUs and genetically confirmed. Methicillin resistance in S. aureus was identified through disk diffusion and PCR. Biofilm formation, including dual-species biofilms, was analyzed using the microtiter plate method. The antimicrobial efficacy of gentamicin, imipenem, and fucoidan was assessed by determining the minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), minimum biofilm inhibitory concentration (MBIC), and minimum biofilm eradication concentration (MBEC). Synergistic interactions were evaluated using the fractional inhibitory concentration index (FICi) and fractional bactericidal concentration index (FBCi). The expression of biofilm-associated genes (icaA in S. aureus and bap in A. baumannii) was analyzed, and the cytotoxicity of fucoidan was assessed.

RESULTS

The study revealed that 77.4% of S. aureus and all A. baumannii isolates showed multidrug resistance. Among 837 tested conditions for dual-species biofilm formation, 72 resulted in strong biofilm formation and 67 in moderate biofilm formation. The geometric mean MIC values for gentamicin were 12.2 µg/mL for S. aureus, 22.62 µg/mL for A. baumannii, and 5.87 µg/mL for their co-culture; for imipenem, they were 19.84, 9.18, and 3.70 µg/mL, respectively, and for fucoidan, 48.50, 31.20, and 19.65 µg/mL, respectively. The MBC values for gentamicin were 119.42, 128, and 11.75 µg/mL; for imipenem, they were 48.50, 14.92, and 8 µg/mL; and for fucoidan, they were 88.37, 62.62, and 42.48 µg/mL. The MBIC values were 55.71, 119.42, and 18.66 µg/mL for gentamicin; 68.59, 48.50, and 25.39 µg/mL for imipenem; and 153.89, 101.49, and 53.53 µg/mL for fucoidan. The MBEC values were 315.17, 362.03, and 59.25 µg/mL for gentamicin; 207.93, 157.58, and 74.65 µg/mL for imipenem; and 353.55, 189.46, and 99.19 µg/mL for fucoidan. When cultured in planktonic form, the geometric mean FICi and FBCi values indicated additive effects, while co-culture showed FICi values of ≤ 0.5, suggesting a synergistic interaction. Treatment with gentamicin and fucoidan led to significant downregulation of the icaA and bap genes in both single-species and dual-species biofilms of S. aureus and A. baumannii. The reductions in gene expression were more pronounced in dual-species biofilms compared to single-species biofilms. Additionally, treatment with imipenem and fucoidan also resulted in significant downregulation of these genes in both biofilm types. Cytotoxicity assessments indicated that higher concentrations of fucoidan were toxic, yet no harmful effects were noted at the optimal synergistic concentrations used with antibiotics.

CONCLUSION

In our investigation, we found that combining gentamicin, imipenem, and fucoidan had a synergistic effect on dual-species biofilms of S. aureus and A. baumannii, suggesting potential benefits for treating such infections effectively. This underscores the importance of understanding microbial interactions, antibiotic susceptibility, and biofilm formation in DFUs.

Genome-wide analysis of quorum sensing regulon in marine fish pathogen Vibrio scophthalmi

Opportunistic fish pathogen Vibrio scophthalmi frequently infects olive flounder and turbot, which are primary marine species cultured for seafood production in Far East Asia. These infections cause substantial yield reductions and significant economic losses. Although quorum sensing (QS) genes were previously reported in V. scophthalmi, the impacts of QS on genome-wide gene expression and consequent behaviors and physiological traits have remained largely unexplored. In this study, we conducted genomic and transcriptomic analyses to uncover the global regulatory network governed by LuxRVs, a QS master regulator in V. scophthalmi. By comparing the wild-type strain and a luxRVs deletion mutant strain, we found that LuxRVs positively regulates biosynthetic genes for poly-hydroxyalkanoate (PHA) while negatively controlling genes for biofilm formation. Quantification of intracellular PHAs and biofilm biomass on borosilicate tubes confirmed these results. Gene set enrichment analyses further demonstrated that LuxRVs also governs genes related to osmoprotection and defense against reactive oxygen species. Overall, these findings indicate that LuxRVs acts as a global transcriptional regulator, controlling a wide range of physiological processes in V. scophthalmi. Targeting LuxRVs could therefore be a promising strategy for improving seafood production by disrupting diverse physiological and pathogenic traits in this fish pathogen.

Profiling the bacterial microbiome diversity and assessing the potential to detect antimicrobial resistance bacteria in wastewater in Kimberley, South Africa

Wastewater treatment plants (WWTPs) are hotspots for pathogens, and can facilitate horizontal gene transfer, potentially releasing harmful genetic material and antimicrobial resistance genes into the environment. Little information exists on the composition and behavior of microbes in WWTPs, especially in developing countries. This study used environmental DNA (eDNA) techniques to examine the microbiome load of wastewater from WWTPs. The DNA was isolated from wastewater samples collected from the treatment trains of three WWTPs in Kimberley, South Africa, and the microbial diversity and composition was compared through 16 S rRNA gene sequencing. The microbes detected were of the Kingdom Bacteria, and of these, 48.27% were successfully identified to genus level. The majority of reads from the combined bacterial data fall within the class Gammaproteobacteria, which is known to adversely impact ecological and human health. Arcobacteraceae constituted 19% of the bacterial reads, which is expected as this family is widespread in aquatic environments. Interestingly, the most abundant bacterial group was Bacteroides, which contain a variety of antibiotic-resistant members. Overall, various antibiotic-resistant taxa were detected in the wastewater, indicating a concerning level of antibiotic resistance within the bacterial community. Therefore, eDNA analysis can be a valuable tool in monitoring and assessing the bacterial microbiome in wastewater, thus providing important information for the optimization and improvement of wastewater treatment systems and mitigate public health risks.

Proton motive force and antibiotic tolerance in bacteria

Bacterial antibiotic tolerance is a decades-old phenomenon in which a bacterial sub-population, commonly known as persisters, does not respond to antibiotics and remains viable upon prolonged antimicrobial treatment. Persisters are detectable in populations of bacterial strains that are not antibiotic-resistant and are known to be responsible for treatment failure and the occurrence of chronic and recurrent infection. The clinical significance of antibiotic tolerance is increasingly being recognized and comparable to antibiotic resistance. To eradicate persisters, it is necessary to understand the cellular mechanisms underlying tolerance development. Previous works showed that bacterial antibiotic tolerance was attributed to the reduction in metabolic activities and activation of the stringent response, SOS response and the toxin-antitoxin system which down-regulates transcription functions. The latest research findings, however, showed that decreased metabolic activities alone do not confer a long-lasting tolerance phenotype in persisters, and that active defence mechanisms such as efflux and DNA repair are required for the long-term maintenance of phenotypic tolerance. As such active tolerance-maintenance mechanisms are energy-demanding, persisters need to generate and maintain the transmembrane proton motive force (PMF) for oxidative phosphorylation. This minireview summarizes the current understanding of cellular mechanisms essential for prolonged expression of phenotypic antibiotic tolerance in bacteria, with an emphasis on the importance of generation and maintenance of PMF in enabling proper functioning of the active tolerance mechanisms in persisters. How such mechanisms can be utilized as targets for the development of anti-persister strategies will be discussed.

Synergy Effects of HPV E6-E7 Encoding mRNA and Nucleic Acid Immunostimulators Improve Therapeutic Potential in TC-1 Graft Tumor

Cervical cancer is the second most common cancer among women globally and the most prevalent cancer in developing countries, which was caused by human papillomavirus (HPV) infection. Messenger RNA (mRNA) vaccines have opened up new avenues for vaccine development and pandemic preparedness with potent scalability, which may possess the potential antitumor effects of an mRNA-HPV therapeutic vaccine containing nononcogenic E6 and E7 proteins. Here, we reported a lipid nanoparticle (LNP) plus nucleic acid immunostimulators (CPG 1018 and Poly I:C) mRNA vaccine platform. The LNP-CPG 1018 capsulated HPV E6-E7 mRNA significantly promoted the maturation of bone marrow-derived dendritic cells (BMDC) in vitro and were capable of efficiently migrating to lymph nodes (LN) in vivo. In TC-1 tumor-bearing mice, the subcutaneous immunization of LNP-CPG 1018 capsulated HPV E6-E7 mRNA elicited robust tumor-specific T-cell immunity, reshaped the tumor microenvironment, and inhibited tumor growth. In conclusion, the LNP-CPG 1018 system is a promising delivery platform for facilitating the development of HPV E6-E7 mRNA cancer vaccines.

Global landscape of vancomycin-resistant enterococci in hematopoietic stem-cell transplantation patients: a systematic review and meta-analysis

BACKGROUND

One of the main risks of infection after hematopoietic stem cell transplantation (HSCT) is infection by gram-positive bacteria, including vancomycin-resistant enterococci (VRE). Based on the format of a global review and meta-analysis study, this study aims to investigate the incidence of VRE bloodstream infection (BSI) after HSCT in colonized individuals.

METHODS

The keywords of the systematic search included vancomycin-resistant enterococci and HSCT. These words were searched in Google Scholar, PubMed/Medline, Scopus, and Web of Science databases from January 1, 2000, to March 1, 2024. Studies that reported the prevalence of vancomycin-resistant enterococci in patients undergoing HSCT were included. The random effects model was used for the meta-analyses. Investigations were conducted according to PRISMA guidelines, and the protocol was registered in PROSPERO: CRD42024543491.

RESULTS

Out of 1100 screened papers, 28 were eligible. The random effects model was established to analyze the incidence of VRE BSI after HSCT. The pooled prevalence of co-infection for Allo-HSCT recipients was 3.023 (95% CI, Z-value = -3.5, p-value < 0.0001), and this value for Auto-HSCT recipients was 11.89 (95% CI, Z-value = -2.923, p-value < 0.001). These results showed that the rate of BSI due to vancomycin-resistant enterococcus in Auto-HSCT recipients is higher than Allo-HSCT.

CONCLUSIONS

The prevalence of vancomycin-resistant enterococci in Auto-HSCT recipients is higher than that of Allo-HSCT, possibly due to colonization of the intestines of these people with vancomycin-resistant enterococci before transplantation. VRE Colonization before transplantation increases the likelihood of post-transplant VRE BSI and other bacterial infections, including Gram-negative. The strains should be analyzed by sequencing before and after HSCT for a more detailed investigation.

Biofilm matrix: a multifaceted layer of biomolecules and a defensive barrier against antimicrobials

Bacterial cells often exist in the form of sessile aggregates known as biofilms, which are polymicrobial in nature and can produce slimy Extracellular Polymeric Substances (EPS). EPS is often referred to as a biofilm matrix and is a heterogeneous mixture of various biomolecules such as polysaccharides, proteins, and extracellular DNA/RNA (eDNA/RNA). In addition, bacteriophage (phage) was also found to be an integral component of the matrix and can serve as a protective barrier. In recent years, the roles of proteins, polysaccharides, and phages in the virulence of biofilms have been well studied. However, a mechanistic understanding of the release of such biomolecules and their interactions with antimicrobials requires a thorough review. Therefore, this article critically reviews the various mechanisms of release of matrix polymers. In addition, this article also provides a contemporary understanding of interactions between various biomolecules to protect biofilms against antimicrobials. In summary, this article will provide a thorough understanding of the functions of various biofilm matrix molecules.

MERS-CoV-nsp5 expression in human epithelial BEAS 2b cells attenuates type I interferon production by inhibiting IRF3 nuclear translocation

Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is an enveloped, positive-sense RNA virus that emerged in 2012, causing sporadic cases and localized outbreaks of severe respiratory illness with high fatality rates. A characteristic feature of the immune response to MERS-CoV infection is low type I IFN induction, despite its importance in viral clearance. The non-structural proteins (nsps) of other coronaviruses have been shown to block IFN production. However, the role of nsp5 from MERS-CoV in IFN induction of human respiratory cells is unclear. In this study, we elucidated the role of MERS-CoV-nsp5, the viral main protease, in modulating the host's antiviral responses in human bronchial epithelial BEAS 2b cells. We found that overexpression of MERS-CoV-nsp5 had a dose-dependent inhibitory effect on IFN-β promoter activation and cytokine production induced by HMW-poly(I:C). It also suppressed IFN-β promoter activation triggered by overexpression of key components in the RIG-I-like receptor (RLR) pathway, including RIG-I, MAVS, IKK-ε and IRF3. Moreover, the overexpression of MERS-CoV-nsp5 did not impair expression or phosphorylation of IRF3, but suppressed the nuclear translocation of IRF3. Further investigation revealed that MERS-CoV-nsp5 specifically interacted with IRF3. Using docking and molecular dynamic (MD) simulations, we also found that amino acids on MERS-CoV-nsp5, IRF3, and KPNA4 may participate in protein-protein interactions. Additionally, we uncovered protein conformations that mask the nuclear localization signal (NLS) regions of IRF3 and KPNA4 when interacting with MERS-CoV-nsp5, suggesting a mechanism by which this viral protein blocks IRF3 nuclear translocation. Of note, the IFN-β expression was restored after administration of protease inhibitors targeting nsp5, indicating this suppression of IFN-β production was dependent on the enzyme activity of nsp5. Collectively, our findings elucidate a mechanism by which MERS-CoV-nsp5 disrupts the host's innate antiviral immunity and thus provides insights into viral pathogenesis.

Time to define One Health approaches to tackling antimicrobial resistance

Antimicrobial resistance is a One Health problem that impacts humans, animals, and the environment. In this Comment, the authors discuss evidence for antimicrobial resistance transmission to humans, highlighting contrasting pictures between high- and low/middle-income settings.

A decade of dinoflagellate genomics illuminating an enigmatic eukaryote cell

Dinoflagellates are a remarkable group of protists, not only for their association with harmful algal blooms and coral reefs but also for their numerous characteristics deviating from the rules of eukaryotic biology. Genome research on dinoflagellates has lagged due to their immense genome sizes in most species (~ 1-250 Gbp). Nevertheless, the last decade marked a fruitful era of dinoflagellate genomics, with 27 genomes sequenced and many insights attained. This review aims to synthesize information from these genomes, along with other omic data, to reflect on where we are now in understanding dinoflagellates and where we are heading in the future. The most notable insights from the decade-long genomics work include: (1) dinoflagellate genomes have been expanded in multiple times independently, probably by a combination of rampant retroposition, accumulation of repetitive DNA, and genome duplication; (2) Symbiodiniacean genomes are highly divergent, but share about 3,445 core unigenes concentrated in 219 KEGG pathways; (3) Most dinoflagellate genes are encoded unidirectionally and are not intron-poor; (4) The dinoflagellate nucleus has undergone extreme evolutionary changes, including complete or nearly complete loss of nucleosome and histone H1, and acquisition of dinoflagellate viral nuclear protein (DVNP); (5) Major basic nuclear protein (MBNP), histone-like protein (HLP), and bacterial HU-like protein (HCc) belong to the same protein family, and MBNP can be the unifying name; (6) Dinoflagellate gene expression is regulated by poorly understood mechanisms, but microRNA and other epigenetic mechanisms are likely important; (7) Over 50% of dinoflagellate genes are "dark" and their functions remain to be deciphered using functional genetics; (8) Initial insights into the genomic basis of parasitism and mutualism have emerged. The review then highlights functionally unique and interesting genes. Future research needs to obtain a finished genome, tackle large genomes, characterize the unknown genes, and develop a quantitative molecular ecological model for addressing ecological questions.

Iron homeostasis as a cell detoxification mechanism in Mesorhizobium qingshengii J19 under yttrium exposure

Yttrium (Y), an important rare earth element (REE), is increasingly prevalent in the environment due to industrial activities, raising concerns about its toxicity. Understanding the effects of Y on microorganisms is essential for bioremediation and biorecovery processes. This study investigates how Mesorhizobium qingshengii J19, a strain with notable resistance to Y, manages iron homeostasis as a detoxifying mechanism under Y stress. Using comparative genomic and transcriptomic analyses, we explored the gene expression profile of strain J19 to identify the mechanisms underlying its high Y resistance and effective Y removal from the medium. Genome-wide transcriptional profiling revealed 127 significantly differentially expressed genes out of 6,343 under Y stress, with 36.2 % up-regulated and 63.8 % down-regulated. Notably, Y exposure significantly affects cellular iron homeostasis and activates arsenic detoxifying mechanisms. A key finding was the 7.6-fold up-regulation of a TonB transporter gene, indicating its crucial role in Y detoxification. Real-time PCR (RT-PCR) analysis of the selected gene confirmed the accuracy of RNA sequencing results. Further validation showed that iron supplementation mitigates Y-induced growth inhibition, leading to reduced ROS production in strain J19. This study elucidates the molecular mechanisms by which strain M. qingshengii J19 adapts to Y stress, emphasizing the importance of iron in controlling ROS and protecting against Y toxicity. It also highlights critical pathways and adaptive responses involved in the strain's resilience to metal stress.