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Effects of the movement of insertion sequences on the structure of VanA glycopeptide resistance elements in Enterococcus faecium.

A Tn1546-related element with IS1216V at position 8839 underwent a structural change after storage of the host strain of Enterococcus faecium at 4 degrees C. The element acquired IS1542 at position 3932, nucleotides 8732 to 8831 were deleted, and the first 3417 nucleotides were lost and replaced by an inverted copy of the IS1216V-vanY-vanZ-inverted-repeat block from the 3' end. Insertion sequence movement is likely to play a key role in the evolution of VanA resistance elements.

Anti-Bacterial Agents↗

Genome-wide expression profiling of the response to azole, polyene, echinocandin, and pyrimidine antifungal agents in Candida albicans.

Antifungal agents exert their activity through a variety of mechanisms, some of which are poorly understood. We examined changes in the gene expression profile of Candida albicans following exposure to representatives of the four currently available classes of antifungal agents used in the treatment of systemic fungal infections. Ketoconazole exposure increased expression of genes involved in lipid, fatty acid, and sterol metabolism, including NCP1, MCR1, CYB5, ERG2, ERG3, ERG10, ERG25, ERG251, and that encoding the azole target, ERG11. Ketoconazole also increased expression of several genes associated with azole resistance, including CDR1, CDR2, IFD4, DDR48, and RTA3. Amphotericin B produced changes in the expression of genes involved in small-molecule transport (ENA21), and in cell stress (YHB1, CTA1, AOX1, and SOD2). Also observed was decreased expression of genes involved in ergosterol biosynthesis, including ERG3 and ERG11. Caspofungin produced changes in expression of genes encoding cell wall maintenance proteins, including the beta-1,3-glucan synthase subunit GSL22, as well as PHR1, ECM21, ECM33, and FEN12. Flucytosine increased the expression of proteins involved in purine and pyrimidine biosynthesis, including YNK1, FUR1, and that encoding its target, CDC21. Real-time reverse transcription-PCR was used to confirm microarray results. Genes responding similarly to two or more drugs were also identified. These data shed new light on the effects of these classes of antifungal agents on C. albicans.

Amphotericin B↗

Overexpression of the D-alanine racemase gene confers resistance to D-cycloserine in Mycobacterium smegmatis.

D-Cycloserine is an effective second-line drug against Mycobacterium avium and Mycobacterium tuberculosis. To analyze the genetic determinants of D-cycloserine resistance in mycobacteria, a library of a resistant Mycobacterium smegmatis mutant was constructed. A resistant clone harboring a recombinant plasmid with a 3.1-kb insert that contained the glutamate decarboxylase (gadA) and D-alanine racemase (alrA) genes was identified. Subcloning experiments demonstrated that alrA was necessary and sufficient to confer a D-cycloserine resistance phenotype. The D-alanine racemase activities of wild-type and recombinant M. smegmatis strains were inhibited by D-cycloserine in a concentration-dependent manner. The D-cycloserine resistance phenotype in the recombinant clone was due to the overexpression of the wild-type alrA gene in a multicopy vector. Analysis of a spontaneous resistant mutant also demonstrated overproduction of wild-type AlrA enzyme. Nucleotide sequence analysis of the overproducing mutant revealed a single transversion (G-->T) at the alrA promoter, which resulted in elevated beta-galactosidase reporter gene expression. Furthermore, transformants of Mycobacterium intracellulare and Mycobacterium bovis BCG carrying the M. smegmatis wild-type alrA gene in a multicopy vector were resistant to D-cycloserine, suggesting that AlrA overproduction is a potential mechanism of D-cycloserine resistance in clinical isolates of M. tuberculosis and other pathogenic mycobacteria. In conclusion, these results show that one of the mechanisms of D-cycloserine resistance in M. smegmatis involves the overexpression of the alrA gene due to a promoter-up mutation.

Alanine Racemase↗

Isolation of verotoxin-producing Escherichia coli O-rough:K1:H7 from two patients with traveler's diarrhea.

Two Escherichia coli O-rough:K1:H7 strains producing verotoxin 1 that were isolated from stool samples of two travelers with diarrhea who consulted our clinic after trips to the Indian Subcontinent and Central America were characterized. Both strains were sorbitol negative, the same phenotype presented by E. coli O157:H7, but in contrast they were beta-glucuronidase positive. Low-frequency restriction analysis of chromosomal DNA and pulsed-field gel electrophoresis and repetitive extragenic palindrome-PCR showed that both strains were epidemiologically related. The illness was self-limited in both cases but involved long-duration, watery diarrhea (10 to 50 days) accompanied by abdominal cramps and flatulence. This serotype should be taken into account as a possible cause of traveler's diarrhea.

Adult↗

Type C retrovirus inactivation by human complement is determined by both the viral genome and the producer cell.

The inactivation of type C retroviruses by human serum may be a considerable impediment to the use of retroviral vectors in vivo for gene therapy. Here we show that virus inactivation is dependent both on the virus and on the cell line used to produce the virus. All viruses produced from murine NIH 3T3 or dog Cf2ThS+L- cells are sensitive to human serum. In contrast, those produced from mink Mv-1-Lu and human HOS or TE671 cells are at least partially resistant, with the exception of murine leukemia viruses. In particular, the feline endogenous virus RD114 is completely resistant to a panel of eight human sera when produced from Mv-1-Lu or HOS cells. This differential resistance is controlled by the viral envelope proteins. Virus inactivation can be correlated with the ability of the producer cells to be lysed by human serum. Inactivation of sensitive viruses requires the classical pathway of complement but does not require virion lysis.

3T3 Cells↗

Novelty, diversity, and genetic dark matter in enterococci of invertebrates.

Enterococci appear to have originated in the guts of early terrestrializing arthropods and invertebrates over 425 million years ago-hosts that are now highly diverse and widespread in nature today. Yet most knowledge of the genus comes from human infection-associated lineages with genomes swollen by the recent accretion of foreign DNA conveyed by mobile elements. Because invertebrates dominate terrestrial animal diversity and biomass, they would be predicted to constitute a major but little-explored reservoir of enterococcal diversity. We therefore systematically examined Enterococcus association and species diversification in invertebrate hosts of the comparatively natural, isolated, but well-characterized environment of the Azorean island of Terceira. Over 100 invertebrate specimens were examined for associated enterococci, which were taxonomically classified by whole-genome sequencing. Supporting the existence of a large pool of uncharacterized enterococci and Enterococcus-adapted genes, 40% (eight of 20) of the Enterococcus species identified were either undescribed, including four candidate new species described here, or very recently discovered. In contrast, control isolates from vertebrates were exclusively of known species typical of sampling elsewhere, discounting geographic isolation as a main driver of the novelty observed. Further, because of the abundance of E. casseliflavus and E. flavescens in this collection, we obtained the resolution necessary to quantify the divergence and decipher the drivers of speciation in the controversial division between these naturally vancomycin-resistant species. These findings provide robust support for the existence of a large pool of new species and unexplored adaptive traits in invertebrate-associated enterococci-diverse environmental survival traits optimized for expression in an enterococcal background, and well positioned for transmission into human-associated enterococcal strains.IMPORTANCEEnterococci are auxotrophic gut-associated bacteria that co-evolved with their terrestrial hosts over many eons. In the last 75 years-the "antibiotic era"-E. faecalis and E. faecium gained genes for antibiotic resistance and enhanced virulence, emerging as leading causes of multidrug-resistant infection. Little is known about the source of those genes or the pathway by which they entered human-associated strains. A recent global survey suggested a potentially large repository of uncharacterized genetic diversity in the enterococci of invertebrates. We directly tested this prospect by examining enterococci of invertebrate hosts in a largely natural and pastoral environment. Our findings provide clear evidence that invertebrates naturally harbor vast unexplored enterococcal diversity. Moreover, associations are likely driven by intrinsic host selection factors rather than geographic isolation. This expands our knowledge of Enterococcus biodiversity, including the identification of four novel species, identifying a vast reservoir of enterococcal genes available to species that colonize and infect humans.

Animals↗

The evolution of adaptive immunity.

Approximately 500 mya two types of recombinatorial adaptive immune systems appeared in vertebrates. Jawed vertebrates generate a diverse repertoire of B and T cell antigen receptors through the rearrangement of immunoglobulin V, D, and J gene fragments, whereas jawless fish assemble their variable lymphocyte receptors through recombinatorial usage of leucine-rich repeat (LRR) modular units. Invariant germ line-encoded, LRR-containing proteins are pivotal mediators of microbial recognition throughout the plant and animal kingdoms. Whereas the genomes of plants and deuterostome and chordate invertebrates harbor large arsenals of recognition receptors primarily encoding LRR-containing proteins, relatively few innate pattern recognition receptors suffice for survival of pathogen-infected nematodes, insects, and vertebrates. The appearance of a lymphocyte-based recombinatorial system of anticipatory immunity in the vertebrates may have been driven by a need to facilitate developmental and morphological plasticity in addition to the advantage conferred by the ability to recognize a larger portion of the antigenic world.

Adaptation, Physiological↗

SCMO: a deep learning model integrating the single-cell resolution TME ecosystem and multi-omics for survival prediction in CRC patients.

BACKGROUND: Colorectal cancer (CRC) remains a leading cause of global cancer mortality, highlighting the need for precise survival prediction to guide clinical decisions. Although tissue-level multi-omics is widely utilized for survival prediction, its limited resolution cannot capture tumor heterogeneity. Single-cell RNA sequencing (scRNA-seq) enables dissection of the tumor microenvironment (TME) at cellular resolution, supporting personalized prognostic assessment. METHODS: We collected 213 CRC scRNA-seq samples and established a CRC-specific TME atlas comprising 339,060 cells. Using this atlas as a reference, we deconvolved bulk RNA-seq data from TCGA-CRC cohort with the EcoTyper algorithm to reconstruct TME features. Clinical, genomic, and transcriptomic data were obtained from the Xena platform; microbial data were sourced from the BIC database. We integrated TME and multi-omics features through a self-normalizing neural network to construct a deep learning model (single-cell resolution TME ecosystem with multi-omics data [SCMO]) for survival prediction. To enhance interpretability, we utilized the Integrated Gradients algorithm and spatial transcriptomic data to analyze multi-omics and TME features. We performed anticancer drug screening with tumor necrosis factor receptor-associated protein 1 (TRAP1), a critical feature according to the Integrated Gradients algorithm, as a potential target. RESULTS: We identified 13 survival-related TME features from the CRC-specific atlas: 12 cell states and one multi-cellular ecosystem. SCMO, which combined TME and multi-omics features, improved survival prediction and outperformed existing methods, achieving a concordance index of 0.762. The SCMO demonstrated robust performance for long-term predictions, achieving areas under the curve (AUCs) of 0.752, 0.772, and 0.869 for 1-, 3-, and 5-year predictions in the training set, with corresponding test set AUCs of 0.639, 0.756, and 0.772. TME features from the SCMO model revealed that ecosystem density increased with CRC malignancy. Multi-omics features included TRAP1 as a potential drug target. Drug screening identified saikosaponin A as a novel TRAP1 inhibitor, and its anticancer activity was validated in vitro. We developed SCMO-Lite, a simplified model incorporating 12 high-attribution-weight multi-omics features, which demonstrated robust risk stratification. CONCLUSIONS: SCMO combines analytical precision with biological interpretability, offering novel insights for oncology survival prediction.

Humans↗

Identification of antimicrobial targets using a comprehensive genomic approach.

Regulated antisense RNA enables the construction of a defined set of conditional growth-defective/lethal strains. In this study, we expanded the regulated antisense RNA interference technology and developed a high-throughput screening strategy to identify the potential drug targets of novel antimicrobials. To prove this concept, the specific antisense sublibrary of different essential open reading frames were pooled in the presence of an inducer, and treated with or without sublethal levels of mupirocin, triclosan, or gentamicin. Antisense RNA-expressing strains that were sensitized for increased susceptibility to the antibiotics were selectively detected via DNA subtractive hybridization, microarray, and whole-cell analyses. No strain was identified as supersensitive to gentamicin because there was no target-specific antisense strain in this sublibrary. In contrast, strains expressing antisense to isoleucine tRNA synthetase (ileS) and enoyl-[acyl-carrier-protein] reductase (fabI) were specifically identified as having increased susceptibility to mupirocin and triclosan, respectively. These results demonstrated that ileS and fabI antisense strains showed significant increases of susceptibility only to their specific inhibitors. This data demonstrates that a regulated antisense RNA expression library provides an effective tool to assist in the identification of potential targets for novel antibacterial agents.

Anti-Bacterial Agents↗

Subgingival microbiota of chilean patients with chronic periodontitis.

BACKGROUND: An association between race/ethnicity and the composition of the subgingival microbiota has been found in chronic periodontitis. A study was undertaken to determine the characteristics of the subgingival microbiota of chronic periodontitis in Chileans residing in Santiago. METHODS: Twenty-six subjects (mean age 45 +/- 7 years) with chronic periodontitis, mean probing depth (PD) 2.63 +/- 0.5 mm, mean attachment level (AL) 3.70 +/- 0.77 mm, and without a history of periodontal therapy were selected. Measurements of PD, AL, bleeding on probing, and plaque accumulation were recorded at six sites per tooth. Subgingival plaque samples were taken from the mesial aspect of every tooth and evaluated for the presence, levels, and proportions of 40 bacterial taxa using whole genomic DNA probes and checkerboard DNA-DNA hybridization. The microbial data of the Chileans were compared with data from 115 chronic periodontitis patients from Boston, Massachusetts. Since several clinical and demographic parameters differed between the two populations, significance of differences for each species was determined using analysis of covariance, adjusting for age, plaque level, mean PD, gender, and smoking status. RESULTS: Each of the individual test species was present in at least 25 of the 26 subjects, and 12 subjects (46.1%) harbored all 40 test species. With the exception of Prevotella intermedia, all test species colonized more than 75% of sites, and 25 species colonized > or = 90% of sites including the co-colonizing species of advanced periodontal lesions, termed the red complex, composed of the three species Porphyromonas gingivalis, Tannerella forsythensis (formerly Bacteroides forsythus), and Treponema denticola as well as Fusobacterium nucleatum subspecies, Campylobacter rectus, Peptostreptococcus micros, and Treponerma socranskii. Sixteen of the 40 species differed significantly between Chilean and U.S. subjects. Red, yellow, and other complexes were significantly higher in the Chileans, while the Actinomyces were higher in the U.S. subjects. CONCLUSIONS: The composition of the subgingival plaque differs among different subject populations. Thus, care should be taken when extrapolating the findings of one study to different ethnic groups.

Adult↗

RNA and RNA-protein complexes as targets for therapeutic intervention.

Today, the majority of pharmaceuticals developed to treat cancers and viral/bacterial infections target cellular, bacterial or viral proteins known to be associated with a given pathology. Although proteins are the focus of most current drug discovery efforts, exciting new research has recently begun which aims to exploit ribonucleic acid (RNA) and RNP particles as novel targets for pharmaceutical development. These RNA-targeted research efforts have been fueled by an increased appreciation for the central role played by RNA and RNA-protein interactions in many biological processes and diseases, together with a better understanding of RNA structure and an improvement in biophysical/biochemical techniques available to study RNA. As for protein targets, genome sequencing is greatly accelerating the identification of human and microbial RNA transcripts for targeted drug discovery. With this explosion in the number of potential RNA and RNP targets, the effective development of specific small molecule RNA-based drugs requires robust and general approaches for detecting and quantifying RNA-ligand interactions, which can be used as high-throughput screens (HTS) and for obtaining rapid structural information to guide rational drug design. In this review, an overview of the potential for therapeutic intervention based on RNA and RNP targets is presented, together with recent efforts to develop generally useful nuclear magnetic resonance (NMR) and fluorescence binding assays for screening and optimizing drugs aimed at RNA and RNP targets.

Animals↗

[Development of fluoroquinolone (ciprofloxacin) resistance in Mycoplasma hominis in the presence of Hela cells].

The effect of cocultivation of eukaryotic HeLa cells and Mycoplasma hominis mycoplasma on the resistance of the latter to fluoroquinolones (ciprofloxacin) was examined. It was shown that cocultivation of the M. homonis and HeLa cells during 24 h with subsequent addition of ciprofloxacin resulted in an increase of the mircoplasma resistance to this antimicrobial agent. In the M. hominis cells cultivated in the presence of HeLa cells and the increasing concentration of ciprofloxacin mutations in the parC gene were observed only at low concentrations of the antimicrobial agent, while mutations in the gyrA gene were never detected. A gradual elevation of ciprofloxacin concentration up to 10 micrograms/ml resulted in the reversion of the parC mutations in mycoplasmas. Mycoplasma cells resistant to high flouroquinolone concentrations and isolated after cocultivation with the HeLa cells were characterized by the wild-type genotype in respect of the gyrA and parC genes. It was shown for the first time that infection of HeLa cells resulted in the appearance of genome rearrangements in M. hominis cells.

Anti-Infective Agents↗

[Present trends of drug-resistant tuberculosis and how to manage it by mycobacterial laboratories].

Global, domestic, and local trends of drug-resistant tuberculosis and how to manage increase in the resistance by mycobacterial laboratories were discussed based on literatures and our own data. At first, how to make drug-resistant tuberculosis was explained. Genetic drug-resistant bacteria were emerged spontaneously by mutation of the genome and were selected by inadequate treatment(mono-therapy or functional mono-therapy): acquired drug resistance(single, and then multi-drug resistance). In a mean time, some people were infected with the drug-resistant bacteria from the beginning and a part of them developed active disease: primary drug resistance (single or multi-drug resistance). Estonia, Latvia, Iran, and some part of Russia, China, and India were reported to be the most endemic region of drug resistant and multi-drug resistant tuberculosis in the world. The rate of primary resistance in Japan was as high as the median of the world, but the rate of acquired resistance was almost twice of the median. Since delays in reporting of the drug resistance from the laboratory seemed one of reasons for the inadequate treatment, drug susceptibility testing should be more rapid than usual, by using liquid media such as BACTEC MGIT 960 system, or gene analysis.

Drug Resistance, Multiple, Bacterial↗

Bacterial degradation of aromatic pollutants: a paradigm of metabolic versatility.

Although most organisms have detoxification abilities (i.e mineralization, transformation and/or immobilization of pollutants), microorganisms, particularly bacteria, play a crucial role in biogeochemical cycles and in sustainable development of the biosphere. Next to glucosyl residues, the benzene ring is the most widely distributed unit of chemical structure in nature, and many of the aromatic compounds are major environmental pollutants. Bacteria have developed strategies for obtaining energy from virtually every compound under oxic or anoxic conditions (using alternative final electron acceptors such as nitrate, sulfate, and ferric ions). Clusters of genes coding for the catabolism of aromatic compounds are usually found in mobile genetic elements, such as transposons and plasmids, which facilitate their horizontal gene transfer and, therefore, the rapid adaptation of microorganisms to new pollutants. A successful strategy for in situ bioremediation has been the combination, in a single bacterial strain or in a syntrophic bacterial consortium, of different degrading abilities with genetic traits that provide selective advantages in a given environment. The advent of high-throughput methods for DNA sequencing and analysis of gene expression (genomics) and function (proteomics), as well as advances in modelling microbial metabolism in silico, provide a global, rational approach to unravel the largely unexplored potentials of microorganisms in biotechnological processes thereby facilitating sustainable development.

Bacteria↗

[An important mission for microbiologists in the new century-cultivation of the unculturable microorganisms].

The present review summarizes the recent advances in cultivating the so-called recalcitrant microorganisms in various natural environments. Firstly, the use of new electron donors and acceptors reveals a list of unique and previously unrecognized physiotypes (Table 1), and the growth supporting reactions include oxidation of phosphite, arsenite, soil humic substances, benzene, Fe (II) and aryl-halides. The novel pure cultures obtained include: Desulfatogenum phosphitoxidans, lithochemotrophic arsenite oxidizing bacteria, Dechloromonas agitata, Dechalosoma suillum, and various Proteobacteria capable of decomposing soil humic substances anaerobically. Secondly, the adaption of nutrient-poor media (down to 1/100 of the traditional concentration), including sea water, soil extract and extension of natural habitats (insect hind-gut, submarine hot vent) are extremely rewarding. For example, cultivation of the ubiquitous SAR11 marine bacterioplankton clade reveals a phylum, small in cell size and genome, but dominating in ocean surface, thus constituting a huge biomass on earth. In addition, the nanosized hyperthermophilic Archaeon from a submarine hot vent, represents an unknown phylum, and because of its symbiotic living with Ignicocous cells, it is named Nanoarchaeum equitans. Its genome size is only 500kb, the smallest for prokaryote. Considering its hyperthermic living environment and small genome, N. equitans may possibly still a primitive form of microbial life and affords an advantageous culture for the study of life origin and evolution on earth. Thirdly, several novel isolation techniques have been developed such as gel microdrop encapsulation and diffusion chamber, both with the advantages of high-throughout operation and simulating to certain extent of the natural environment, thus allowing growth synergy based on cross-feeding to occur. Finally, it should be noted that the cultivation of unculturable microorganisms mentioned in this review does not require expensive and sophisticated equipments and most of the techniques can be adapted in our laboratory at home.

Bacteria↗

[Molecular typing by pulsed field gel electrophoresis of Enterobacter cloacae strains isolated from osteoarticular infections at the Nancy University Hospital 1990-1994].

Enterobacteriaceae represent more than 11% of bacteria involved in osteoarticular infections in adult and, among them, Enterobacter cloacae is found in 12% of the cases. The increased evolution of the antibiotic resistance rate of this species is worrying. However, all isolates responsible for this type of infection at the University Hospital of Nancy from 1990 to 1994 (24 strains isolated from 22 patients presented an identical antibiotype with especially a natural resistance phenotype to beta-lactam antibiotics except one cephalosporinase-over-producing strain. The DNA of these strains was studied by pulse-field gel electrophoresis after digestion by the restriction enzyme XbuI. The great genomic diversity obtained showed that the stability of the antibiotic susceptibility during the period studied was not due to the existence of unique clone but to that of multiple clones. The analysis of the restriction profiles has permitted to achieve a better differenciation of the strains than biotyping and antibiotyping, which confirms the high discrimination power of this genotypic method.

Adult↗

What can microbial genetics teach sociobiology?

Progress in our understanding of sociobiology has occurred with little knowledge of the genetic mechanisms that underlie social traits. However, several recent studies have described microbial genes that affect social traits, thereby bringing genetics to sociobiology. A key finding is that simple genetic changes can have marked social consequences, and mutations that affect cheating and recognition behaviors have been discovered. The study of these mutants confirms a central theoretical prediction of social evolution: that genetic relatedness promotes cooperation. Microbial genetics also provides an important new perspective: that the genome-to-phenome mapping of social organisms might be organized to constrain the evolution of social cheaters. This constraint can occur both through pleiotropic genes that link cheating to a personal cost and through the existence of phoenix genes, which rescue cooperative systems from selfish and destructive strategies. These new insights show the power of studying microorganisms to improve our understanding of the evolution of cooperation.

Animals↗

Suppressive subtractive hybridization as a tool for identifying genetic diversity in an environmental metagenome: the rumen as a model.

Molecular techniques previously used for genome comparisons of closely related bacterial species could prove extremely valuable for comparisons of complex microbial communities, or metagenomes. Our study aimed to determine the breadth and value of suppressive subtractive hybridization (SSH) in a pilot-scale analysis of metagenomic DNA from communities of microorganisms in the rumen. Suppressive subtractive hybridization was performed using total genomic DNA isolated from rumen fluid samples of two hay-fed steers, arbitrarily designated as tester or driver. Ninety-six subtraction DNA fragments from the tester metagenome were amplified, cloned and the DNA sequences were determined. Verification of the isolation of DNA fragments unique to the tester metagenome was accomplished through dot blot and Southern blot hybridizations. Tester-specific SSH fragments were found in 95 of 96 randomly selected clones. DNA sequences of subtraction fragments were analysed by computer assisted DNA and amino acid comparisons. Putative translations of 26 (32.1%) subtractive hybridization fragments exhibited significant similarity to Bacterial proteins, whereas 15 (18.5%) distinctive subtracted fragments had significant similarity to proteins from Archaea. The remainder of the subtractive hybridization fragments displayed no similarity to GenBank sequences. This metagenomic approach has exposed an unexpectedly large difference in Archaeal community structure between the rumen microbial populations of two steers fed identical diets and housed together. 16S rRNA dot blot hybridizations revealed similar proportions of Bacteria and Archaea in both rumen samples and suggest that the differences uncovered by SSH are the result of varying community structural composition. Our study demonstrates a novel approach to comparative analyses of environmental microbial communities through the use of SSH.

Animals↗