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PLoS Neglected Tropical Diseases May 2024
Topics: Leishmania tropica; Animals; Phlebotomus; Salivary Proteins and Peptides; Plasmids; Insect Proteins; Mice; Humans; Leishmaniasis, Cutaneous; Female
PubMed: 38814961
DOI: 10.1371/journal.pntd.0012218 -
Microbial Genomics May 2024is an emerging human enteric pathogen. However, the genomic features and virulence genes of strains from human gastroenteritis and other sources have not been fully...
Analysis of global genomes revealed that strains carrying T6SS are more common in human gastroenteritis than in environmental sources and are often phylogenetically related.
is an emerging human enteric pathogen. However, the genomic features and virulence genes of strains from human gastroenteritis and other sources have not been fully elucidated. Here, we conducted a genomic analysis of 565 global strains isolated from different sources, including 261 strains isolated from faecal samples of gastroenteritis patients, of which 18 genomes were sequenced in this study. The presence of bacterial virulence genes and secretion systems in strains from different sources was compared, and the phylogenetic relationship of strains was assessed based on the core genome. The complete genome of strain A20-9 isolated from a gastroenteritis patient was obtained in this study, from which 300 putative virulence factors and a T4SS-encoding plasmid, pAC, were identified. Genes encoding T4SS were also identified in a novel genomic island, ACI-1, from other T4SS-positive strains. The prevalence of T4SS was significantly lower in strains from gastroenteritis patients than in environmental strains (3 %, <0.0001 vs 14 %, <0.01). Conversely, the prevalence of T6SS was significantly higher in strains isolated from gastroenteritis patients than in environmental strains (25 %, <0.05 vs 13 %, <0.01). Four phylogenetic clusters were formed based on the core genome of 565 . strains, and strains carrying T6SS often showed close phylogenetic relationships. T3SS, aerolysin and thermostable cytotonic enterotoxin were absent in all 565 . strains. Our findings provide novel information on the genomic features of and suggest that T6SS may play a role in -induced human gastroenteritis.
Topics: Gastroenteritis; Humans; Phylogeny; Genome, Bacterial; Aeromonas caviae; Virulence Factors; Type VI Secretion Systems; Feces; Gram-Negative Bacterial Infections; Genomic Islands; Plasmids
PubMed: 38814176
DOI: 10.1099/mgen.0.001258 -
Infection and Drug Resistance 2024is a common causative bacteria in nosocomial infections. This study aims to describe the structure and evolutionary characteristics of mobile genetic elements (MGEs)...
PURPOSE
is a common causative bacteria in nosocomial infections. This study aims to describe the structure and evolutionary characteristics of mobile genetic elements (MGEs) carrying antibiotic resistance genes (ARGs) from and to conduct bioinformatics and comparative genomic analysis to provide a deeper understanding of the genetic characteristics and diversity of MGEs in .
METHODS
Fifteen clinical isolates of from China were collected and sequenced in this study, and 15 novel MGEs were identified. Together with four MGEs from GenBank, a total of 19 MGEs were used to perform detailed modular structure dissection and sequence comparison. Then, the biological experiments were carried out to verify the biological characteristics of these isolates and MEGs.
RESULTS
The novel MGEs identified in this study displayed diversification in modular structures, which showed complex mosaic natures. The seven types of 19 MGEs included in this study were divided into three groups: i) novel MGEs (firstly identified in this study): four Inc plasmids and three Tn-related integrative and mobilizable elements (IMEs); ii) newly defined MGEs (firstly designated in this study, but with previously determined sequences): four Tn-related IMEs; iii) novel transposons with reference prototypes identified in this study: two Tn-related integrative and conjugative elements (ICEs), two IS-based transposition units, two Tn-related unit transposons, two Tn-related unit transposons. At least 36 ARGs involved in resistance to 11 different classes of antimicrobials and heavy metals were identified. Additionally, three novel variants were identified. Antimicrobial susceptibility testing showed that these variants were resistant to some β-lactamase antibiotics and was additionally resistant to cephalosporins.
CONCLUSION
The continuous evolution of ARG-carrying MGEs during transmission, leading to the emergence of novel MGEs or ARGs, which facilitates the spread of antibiotic resistance in and enhances the diversity of transmission modes of bacterial resistance.
PubMed: 38813527
DOI: 10.2147/IDR.S462670 -
Frontiers in Bioengineering and... 2024Methanotrophic bacteria are promising hosts for methane bioconversion to biochemicals or bioproducts. However, due to limitations associated with long genetic...
Methanotrophic bacteria are promising hosts for methane bioconversion to biochemicals or bioproducts. However, due to limitations associated with long genetic manipulation timelines and, lack of choice in genetic tools required for strain engineering, methanotrophs are currently not employed for bioconversion technologies. In this study, a rapid and reproducible electroporation protocol is developed for type 1 methanotroph, using common laboratory solutions, analyzing optimal electroshock voltages and post-shock cell recovery time. Successful reproducibility of the developed method was achieved when different replicative plasmids were assessed on lab adapted vs. wild-type strains (DASS vs. DSM19304). Overall, a ∼ 3-fold decrease in time is reported with use of electroporation protocol developed here, compared to conjugation, which is the traditionally employed approach. Additionally, an inducible (3-methyl benzoate) and a constitutive (sucrose phosphate synthase) promoter is characterized for their strength in driving gene expression.
PubMed: 38812915
DOI: 10.3389/fbioe.2024.1412410 -
Frontiers in Microbiology 2024The predominant hybrid pathogenic , enterohemorrhagic (EHEC), combines characteristics of Shiga toxin-producing (STEC) and enteropathogenic (EPEC), contributing to...
INTRODUCTION
The predominant hybrid pathogenic , enterohemorrhagic (EHEC), combines characteristics of Shiga toxin-producing (STEC) and enteropathogenic (EPEC), contributing to global outbreaks with severe symptoms including fatal consequences. Since EHEC infection was designated as a notifiable disease in 2000 in South Korea, around 2000 cases have been reported, averaging approximately 90 cases annually.
AIM
In this work, genome-based characteristic analysis and cell-based assay of hybrid STEC/aEPEC strains isolated from livestock feces, animal source foods, and water in South Korea was performed.
METHODS
To identify the virulence and antimicrobial resistance genes, determining the phylogenetic position of hybrid STEC/aEPEC strains isolated in South Korea, a combination of real-time PCR and whole-genome sequencing (WGS) was used. Additionally, to assess the virulence of the hybrid strains and compare them with genomic characterization, we performed a cell cytotoxicity and invasion assays.
RESULTS
The hybrid STEC/aEPEC strains harbored and genes, encoding Shiga toxins and attachment/effacement related protein of STEC and EPEC, respectively. Furthermore, all hybrid strains harbored plasmid-carried enterohemolysin(), a key virulence factor in prevalent pathogenic infections, such as diarrheal disease and hemolytic-uremic syndrome (HUS). Genome-wide phylogenetic analysis revealed a close association between all hybrid strains and specific EPEC strains, suggesting the potential acquisition of Stx phages during STEC/aEPEC hybrid formation. Some hybrid strains showed cytotoxic activity against HeLa cells and invasive properties against epithelial cells. Notably, all STEC/aEPEC hybrids with sequence type (ST) 1,034 ( = 11) exhibited higher invasiveness than those with E2348/69. This highlights the importance of investigating potential correlations between STs and virulence characteristics of hybrid strains.
CONCLUSION
Through genome-based characterization, we confirmed that the hybrid STEC/aEPEC strains are likely EPEC strains that have acquired STEC virulence genes via phage. Furthermore, our results emphasize the potential increased danger to humans posed by hybrid STEC/aEPEC strains isolated in South Korea, containing both and , compared to STEC or EPEC alone.
PubMed: 38812694
DOI: 10.3389/fmicb.2024.1398262 -
Nature Communications May 2024Bacterial pathogens carrying multidrug resistance (MDR) plasmids are a major threat to human health. The acquisition of antibiotic resistance genes (ARGs) in plasmids is...
Bacterial pathogens carrying multidrug resistance (MDR) plasmids are a major threat to human health. The acquisition of antibiotic resistance genes (ARGs) in plasmids is often facilitated by mobile genetic elements that copy or translocate ARGs between DNA molecules. The agglomeration of mobile elements in plasmids generates resistance islands comprising multiple ARGs. However, whether the emergence of resistance islands is restricted to specific MDR plasmid lineages remains understudied. Here we show that the agglomeration of ARGs in resistance islands is biased towards specific large plasmid lineages. Analyzing 6784 plasmids in 2441 Escherichia, Salmonella, and Klebsiella isolates, we quantify that 84% of the ARGs in MDR plasmids are found in resistance islands. We furthermore observe rapid evolution of ARG combinations in resistance islands. Most regions identified as resistance islands are shared among closely related plasmids but rarely among distantly related plasmids. Our results suggest the presence of barriers for the dissemination of ARGs between plasmid lineages, which are related to plasmid genetic properties, host range and the plasmid evolutionary history. The agglomeration of ARGs in plasmids is attributed to the workings of mobile genetic elements that operate within the framework of existing plasmid lineages.
Topics: Plasmids; Evolution, Molecular; Salmonella; Anti-Bacterial Agents; Humans; Drug Resistance, Multiple, Bacterial; Klebsiella; Genomic Islands; Escherichia coli; Interspersed Repetitive Sequences
PubMed: 38811529
DOI: 10.1038/s41467-024-48352-8 -
Microbes and Environments 2024The extremely halophilic archaeon Haloarcula japonica accumulates the C carotenoid, bacterioruberin (BR). To reveal the BR biosynthetic pathway, unidentified phytoene...
Two Distinct Enzymes Have Both Phytoene Desaturase and 3,4-Desaturase Activities Involved in Carotenoid Biosynthesis by the Extremely Halophilic Archaeon Haloarcula japonica.
The extremely halophilic archaeon Haloarcula japonica accumulates the C carotenoid, bacterioruberin (BR). To reveal the BR biosynthetic pathway, unidentified phytoene desaturase candidates were functionally characterized in the present study. Two genes encoding the potential phytoene desaturases, c0507 and d1086, were found from the Ha. japonica genome sequence by a homology search using the Basic Local Align Search Tool. Disruption mutants of c0507 and d1086 and their complemented strains transformed with expression plasmids for c0507 and d1086 were subsequently constructed. High-performance liquid chromatography (HPLC) ana-lyses of carotenoids produced by these strains revealed that C0507 and D1086 were both bifunctional enzymes with the same activities as both phytoene desaturase (CrtI) and 3,4-desaturase (CrtD). C0507 and D1086 complemented each other during BR biosynthesis in Ha. japonica. This is the first study to identify two distinct enzymes with both CrtI and CrtD activities in an extremely halophilic archaeon.
Topics: Carotenoids; Haloarcula; Oxidoreductases; Biosynthetic Pathways; Archaeal Proteins; Genetic Complementation Test; Phylogeny
PubMed: 38811235
DOI: 10.1264/jsme2.ME24004 -
Chemical & Pharmaceutical Bulletin 2024Cell-penetrating peptides (CPPs) serve as potent vehicles for delivering membrane-impermeable compounds, including nucleic acids, into cells. In a previous study, we...
Cell-penetrating peptides (CPPs) serve as potent vehicles for delivering membrane-impermeable compounds, including nucleic acids, into cells. In a previous study, we reported the successful intracellular delivery of small interfering RNAs (siRNAs) with negligible cytotoxicity using a peptide containing an unnatural amino acid (dipropylglycine). In the present study, we employed the same seven peptides as the previous study to evaluate their efficacy in delivering plasmid DNA (pDNA) intracellularly. Although pDNA and siRNA are nucleic acids, they differ in size and biological function, which may influence the optimal peptide sequences for their delivery. Herein, three peptides demonstrated effective pDNA transfection abilities. Notably, only one of the three peptides previously exhibited efficient gene-silencing effect with siRNA. These findings validate our hypothesis and offer insights for the personalized design of CPPs for the delivery of pDNA and siRNA.
Topics: Cell-Penetrating Peptides; Plasmids; Humans; DNA; RNA, Small Interfering; Glycine; Transfection; HeLa Cells; Cell Survival
PubMed: 38811213
DOI: 10.1248/cpb.c24-00221 -
Life Science Alliance Aug 2024A major pathway for horizontal gene transfer is the transmission of DNA from donor to recipient cells via plasmid-encoded type IV secretion systems (T4SSs). Many...
A major pathway for horizontal gene transfer is the transmission of DNA from donor to recipient cells via plasmid-encoded type IV secretion systems (T4SSs). Many conjugative plasmids encode for a single-stranded DNA-binding protein (SSB) together with their T4SS. Some of these SSBs have been suggested to aid in establishing the plasmid in the recipient cell, but for many, their function remains unclear. Here, we characterize PrgE, a proposed SSB from the plasmid pCF10. We show that PrgE is not essential for conjugation. Structurally, it has the characteristic OB-fold of SSBs, but it has very unusual DNA-binding properties. Our DNA-bound structure shows that PrgE binds ssDNA like beads on a string supported by its N-terminal tail. In vitro studies highlight the plasticity of PrgE oligomerization and confirm the importance of the N-terminus. Unlike other SSBs, PrgE binds both double- and single-stranded DNA equally well. This shows that PrgE has a quaternary assembly and DNA-binding properties that are very different from the prototypical bacterial SSB, but also different from eukaryotic SSBs.
Topics: Plasmids; DNA-Binding Proteins; Bacterial Proteins; Enterococcus faecalis; DNA, Single-Stranded; Protein Binding; Conjugation, Genetic; Type IV Secretion Systems; Models, Molecular; Gene Transfer, Horizontal; DNA, Bacterial
PubMed: 38811160
DOI: 10.26508/lsa.202402693 -
Protective efficacy of Eimeria maxima EmLPL and EmTregIM-1 against homologous challenge in chickens.Poultry Science May 2024Chicken coccidiosis has inflicted significant economic losses upon the poultry industry. The primary strategies for preventing and controlling chicken coccidiosis...
Chicken coccidiosis has inflicted significant economic losses upon the poultry industry. The primary strategies for preventing and controlling chicken coccidiosis include anticoccidial drugs and vaccination. However, these approaches face limitations, such as drug residues and resistance associated with anticoccidial drugs, and safety concerns related to live vaccines. Consequently, the urgent development of innovative vaccines, such as subunit vaccines, is imperative. In previous study, we screened 2 candidate antigens: Eimeria maxima lysophospholipase (EmLPL) and E. maxima regulatory T cell inducing molecule 1 (EmTregIM-1). To investigate the immune protective effect of the 2 candidate antigens against Eimeria maxima (E. maxima) infection, we constructed recombinant plasmids, namely pET-28a-EmLPL and pET-28a-EmTregIM-1, proceeded to induce the expression of recombinant proteins of EmLPL (rEmLPL) and EmTregIM-1 (rEmTregIM-1). The immunogenic properties of these proteins were confirmed through western blot analysis. Targeting EmLPL and EmTregIM-1, we developed subunit vaccines and encapsulated them in PLGA nanoparticles, resulting in nano-vaccines: PLGA-rEmLPL and PLGA-rEmTregIM-1. The efficacy of these vaccines was assessed through animal protection experiments. The results demonstrated that rEmLPL and rEmTregIM-1 were successfully recognized by anti-E. maxima chicken sera and His-conjugated mouse monoclonal antibodies. Immunization with both subunit and nano-vaccines containing EmLPL and EmTregIM-1 markedly mitigated weight loss and reduced oocyst shedding in chickens infected with E. maxima. Furthermore, the anticoccidial indexes (ACI) for both rEmLPL and PLGA-rEmLPL exceeded 160, whereas those for rEmTregIM-1 and PLGA-rEmTregIM-1 were above 120 but did not reach 160, indicating superior protective efficacy of the rEmLPL and PLGA-rEmLPL formulations. By contrast, the protection afforded by rEmTregIM-1 and PLGA-rEmTregIM-1 was comparatively lower. Thus, EmLPL is identified as a promising candidate antigen for vaccine development against E. maxima infection.
PubMed: 38810564
DOI: 10.1016/j.psj.2024.103865