Here, we report the extensive bioinformatic and functional analyses of the unusual pLOCK 0919, a plasmid originating from the probiotic Lactobacillus casei LOCK 0919 strain. This plasmid is atypical because it harbors the spaCBA-srtC gene cluster encoding SpaCBA pili. We show that all other spaCBA-srtC sequences of the Lactobacillus genus that have been previously described and deposited in GenBank are present in the chromosomal DNA. Another important observation for pLOCK 0919 is that the spaCBA-srtC gene cluster and its surrounding genes are highly similar to the respective DNA region that is present in the most well-known and active SpaCBA pili producer, the probiotic Lactobacillus rhamnosus GG strain. Our results demonstrate that the spaCBA-srtC clusters of pLOCK 0919 and L. rhamnosus GG are genealogically similar, located in DNA regions that are rich in transposase genes and are poorly conserved among the publicly available sequences of Lactobacillus sp. In contrast to chromosomally localized pilus gene clusters from L. casei and Lactobacillus paracasei, the plasmidic spaC of L. casei LOCK 0919 is expressed and undergoes a slight glucose-induced repression. Moreover, results of series of in vitro tests demonstrate that L. casei LOCK 0919 has an adhesion potential, which is largely determined by the presence of the pLOCK 0919 plasmid. In particular, the plasmid occurrence positively influenced the hydrophobicity and aggregation abilities of L. casei LOCK 0919. Moreover, in vivo studies indicate that among the three Lactobacillus strains used to colonize the gastrointestinal tract of germ-free mice, already after 2 days of colonization, L. casei LOCK 0919 became the dominant strain and persisted there for at least 48 days.

• MeSH
• aminoacyltransferasy genetika   MeSH
• bakteriální fimbrie genetika   MeSH
• bakteriální proteiny genetika   MeSH
• cysteinové endopeptidasy genetika   MeSH
• genom bakteriální * MeSH
• Lactobacillus casei genetika   MeSH
• membránové proteiny genetika   MeSH
• molekulární sekvence - údaje MeSH
• multigenová rodina * MeSH
• plazmidy genetika   MeSH
• sekvence aminokyselin MeSH
• transposasy genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

One hundred twenty-four patients-53 with neuroborreliosis, 48 with erythema migrans, and 23 with Lyme arthritis-were tested in a prospective study for the presence of the DNA of Borrelia burgdorferi sensu lato in plasma, cerebrospinal fluid (CSF), urine, and synovial fluid by nested polymerase chain reaction (PCR). Specific DNA was detected using five amplification systems simultaneously: three targeted chromosomal genes encoding 16S rDNA, flagellin, and p66; and two plasmid sequences of OspA and OspC. Patients were examined clinically and by PCR before and after treatment and again after 3 and 6 months. Before treatment, the specific DNA was detected in 78 patients (62.9 %). Forty-one neuroborreliosis patients were DNA-positive (77.4 %), with CSF positivity in 26 patients, urine in 25, and plasma in 16. Twenty-six erythema migrans patients were DNA-positive (54.2 %), with plasma positivity in 18 cases and urine in 14. Eleven Lyme arthritis cases (47.8 %) were DNA positive (six in urine, five in plasma, and four in synovial fluid). The frequency of PCR positives was comparable in CSF and urine, and it was lower by approximately 50 % in plasma. Specific DNA was also found in a significant number of patients in later testing periods: 48 patients after treatment, 29 patients after 3 months, and 6 patients after 6 months. The prolonged PCR positivity was not explainable by persistent infection according to the clinical manifestations of the disease. Possible explanations of the problem are discussed.

• MeSH
• Borrelia burgdorferi komplex genetika   MeSH
• časové faktory MeSH
• DNA bakterií izolace a purifikace   MeSH
• lidé MeSH
• lymeská nemoc farmakoterapie   mikrobiologie   MeSH
• polymerázová řetězová reakce MeSH
• tělesné tekutiny mikrobiologie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

BACKGROUND: Conjugative plasmids play a major role in the dissemination of antibiotic resistance genes. Knowledge of the plasmid characteristics and behaviour can allow development of control strategies. Here we focus on the IncX group of plasmids carrying genes conferring quinolone resistance (PMQR), reporting their transfer and persistence within host bacteria of various genotypes under distinct conditions and levels of induced stress in form of temperature change and various concentrations of ciprofloxacin supplementation. METHODS: Complete nucleotide sequences were determined for eight qnr-carrying IncX-type plasmids, of IncX1 (3), IncX2 (3) and a hybrid IncX1-2 (2) types, recovered from Escherichia coli of various origins. This data was compared with further complete sequences of IncX1 and IncX2 plasmids carrying qnr genes (n = 41) retrieved from GenBank and phylogenetic tree was constructed. Representatives of IncX1 (pHP2) and IncX2 (p194) and their qnrS knockout mutants, were studied for influence of induced stress and genetic background on conjugative transfer and maintenance. RESULTS: A high level of IncX core-genome similarity was found in plasmids of animal, environmental and clinical origin. Significant differences were found between the individual IncX plasmids, with IncX1 subgroup plasmids showing higher conjugative transfer rates than IncX2 plasmids. Knockout of qnr modified transfer frequency of both plasmids. Two stresses applied simultaneously were needed to affect transfer rate of wildtype plasmids, whereas a single stress was sufficient to affect the IncX ΔqnrS plasmids. The conjugative transfer was shown to be biased towards the host phylogenetic proximity. A long-term cultivation experiment pointed out the persistence of IncX plasmids in the antibiotic-free environment. CONCLUSIONS: The study indicated the stimulating effect of ciprofloxacin supplementation on the plasmid transfer that can be nullified by the carriage of a single PMQR gene. The findings present the significant properties and behaviour of IncX plasmids carrying antibiotic resistance genes that are likely to play a role in their dissemination and stability in bacterial populations.

• MeSH
• antibakteriální látky farmakologie   MeSH
• bakteriální léková rezistence genetika   MeSH
• ciprofloxacin farmakologie   MeSH
• Escherichia coli * genetika   MeSH
• fylogeneze MeSH
• genomika MeSH
• konjugace genetická MeSH
• plazmidy genetika   MeSH
• proteiny z Escherichia coli * genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Toxin-antitoxin systems (TAS) emerged more than 25 years ago and developed as an important field in molecular microbiology. TAS are autoregulated operons coding a stable toxin and an unstable antitoxin found in plasmids and chromosomes of Bacteria and Archaea. The conditional activation of their toxins interferes with cell growth/viability and, depending on the context, can influence plasmid maintenance, stress management, bacterial persistence, cell differentiation and, likely, bacterial virulence. This review summarizes recent results on the parD system of plasmid R1 and on the chromosomal relBE systems found in Escherichia coli and in Streptococcus pneumoniae with a focus on the RNase activity of their toxins, their regulation and their biomedical applications and implications.

• MeSH
• antitoxiny genetika   imunologie   metabolismus   MeSH
• bakteriální toxiny genetika   imunologie   metabolismus   MeSH
• biotechnologie metody   trendy   MeSH
• buňky - růstové procesy genetika   imunologie   MeSH
• financování organizované MeSH
• inhibitory syntézy proteinů imunologie   metabolismus   MeSH
• lidé MeSH
• mikrobiologie trendy   MeSH
• molekulární biologie metody   trendy   MeSH
• plazmidy genetika   MeSH
• ribonukleasy genetika   imunologie   toxicita   MeSH
• ribozomy genetika   imunologie   MeSH
• RNA genetika   imunologie   toxicita   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• přehledy MeSH

BACKGROUND: Conversely to common coated iron oxide nanoparticles, novel naked surface active maghemite nanoparticles (SAMNs) can covalently bind DNA. Plasmid (pDNA) harboring the coding gene for GFP was directly chemisorbed onto SAMNs, leading to a novel DNA nanovector (SAMN@pDNA). The spontaneous internalization of SAMN@pDNA into cells was compared with an extensively studied fluorescent SAMN derivative (SAMN@RITC). Moreover, the transfection efficiency of SAMN@pDNA was evaluated and explained by computational model. METHODS: SAMN@pDNA was prepared and characterized by spectroscopic and computational methods, and molecular dynamic simulation. The size and hydrodynamic properties of SAMN@pDNA and SAMN@RITC were studied by electron transmission microscopy, light scattering and zeta-potential. The two nanomaterials were tested by confocal scanning microscopy on equine peripheral blood-derived mesenchymal stem cells (ePB-MSCs) and GFP expression by SAMN@pDNA was determined. RESULTS: Nanomaterials characterized by similar hydrodynamic properties were successfully internalized and stored into mesenchymal stem cells. Transfection by SAMN@pDNA occurred and GFP expression was higher than lipofectamine procedure, even in the absence of an external magnetic field. A computational model clarified that transfection efficiency can be ascribed to DNA availability inside cells. CONCLUSIONS: Direct covalent binding of DNA on naked magnetic nanoparticles led to an extremely robust gene delivery tool. Hydrodynamic and chemical-physical properties of SAMN@pDNA were responsible of the successful uptake by cells and of the efficiency of GFP gene transfection. GENERAL SIGNIFICANCE: SAMNs are characterized by colloidal stability, excellent cell uptake, persistence in the host cells, low toxicity and are proposed as novel intelligent DNA nanovectors for efficient cell transfection.

• MeSH
• biofyzikální jevy MeSH
• DNA chemie   genetika   MeSH
• genetické vektory MeSH
• koloidy chemie   MeSH
• lidé MeSH
• nanočástice chemie   ultrastruktura   MeSH
• plazmidy chemie   genetika   MeSH
• technika přenosu genů * MeSH
• transfekce metody   MeSH
• transmisní elektronová mikroskopie MeSH
• velikost částic MeSH
• železité sloučeniny chemie   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Borrelia burgdorferi, the etiological agent of Lyme disease, persists in nature through an enzootic cycle consisting of a vertebrate host and an Ixodes tick vector. The sequence motifs modified by two well-characterized restriction/modification (R/M) loci of B. burgdorferi type strain B31 were recently described, but the methylation profiles of other Lyme disease Borrelia bacteria have not been characterized. Here, the methylomes of B. burgdorferi type strain B31 and 7 clonal derivatives, along with B. burgdorferi N40, B. burgdorferi 297, B. burgdorferi CA-11, B. afzelii PKo, B. afzelii BO23, and B. garinii PBr, were defined through PacBio single-molecule real-time (SMRT) sequencing. This analysis revealed 9 novel sequence motifs methylated by the plasmid-encoded restriction/modification enzymes of these Borrelia strains. Furthermore, while a previous analysis of B. burgdorferi B31 revealed an epigenetic impact of methylation on the global transcriptome, the current data contradict those findings; our analyses of wild-type B. burgdorferi B31 revealed no consistent differences in gene expression among isogenic derivatives lacking one or more restriction/modification enzymes. IMPORTANCE The principal causative agent of Lyme disease in humans in the United States is Borrelia burgdorferi, while B. burgdorferi, B. afzelii, and B. garinii, collectively members of the Borrelia burgdorferi sensu lato species complex, cause Lyme disease in Europe and Asia. Two plasmid-encoded restriction/modification systems have been shown to limit the genetic transformation of B. burgdorferi type strain B31 with foreign DNA, but little is known about the restriction/modification systems of other Lyme disease Borrelia bacteria. This paper describes the methylation motifs present on genomic DNAs of multiple B. burgdorferi, B. afzelii, and B. garinii strains. Contrary to a previous report, we did not find evidence for an epigenetic impact on gene expression by methylation. Knowledge of the motifs recognized and methylated by the restriction/modification enzymes of Lyme disease Borrelia will facilitate molecular genetic investigations of these important human pathogens. Additionally, the similar motifs methylated by orthologous restriction/modification systems of Lyme disease Borrelia bacteria and the presence of these motifs within recombinogenic loci suggest a biological role for these ubiquitous restriction/modification systems in horizontal gene transfer.

• MeSH
• Borrelia burgdorferi klasifikace   genetika   MeSH
• DNA bakterií genetika   MeSH
• epigenomika * MeSH
• lidé MeSH
• lymeská nemoc mikrobiologie   MeSH
• metylace MeSH
• nukleotidové motivy * MeSH
• plazmidy genetika   metabolismus   MeSH
• sekvenční analýza DNA * MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Research Support, N.I.H., Intramural MeSH

We evaluated the prevalence and epidemiology of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli isolates in pigs during production cycle on a Czech farm with the history of previous use of ceftiofur. ESBL-producing E. coli isolates were obtained from rectal swabs from pigs of different age groups (suckling piglets, weaned piglets, growers and sows). Collected samples were directly cultivated on MacConkey agar with cefotaxime (2 mg l-1 ), whereas intestinal swabs of slaughtered pigs and surface swabs from pig carcasses were also pre-enriched in buffered peptone water without antimicrobials before the cultivation. Clonal relationship of selected isolates was determined by XbaI pulse-field gel electrophoresis and multi-locus sequence typing. The transferability of plasmids carrying blaCTX-M genes was tested by conjugation experiments. From all examined samples, 141 (43·7%, n = 323) were positive for ESBL-producing E. coli. All ESBL-producing isolates showed resistance to multiple antimicrobials and were positive for blaCTX-M genes. The blaCTX-M-1 was carried by conjugative IncN/ST1 plasmids (c. 40-45 kb) while the blaCTX-M-15 was located on conjugative F plasmids with F:18:A5:B1 formula (c. 165 kb). This study demonstrated the persistence of CTX-M-positive E. coli isolates 2 months after banner of ceftiofur usage and indicated possible risk of transmission of these isolates to humans via the food chain.

• MeSH
• beta-laktamasy genetika   metabolismus   MeSH
• Escherichia coli enzymologie   genetika   izolace a purifikace   MeSH
• farmy MeSH
• infekce vyvolané Escherichia coli mikrobiologie   patofyziologie   veterinární   MeSH
• lidé MeSH
• multilokusová sekvenční typizace MeSH
• nemoci prasat mikrobiologie   patofyziologie   MeSH
• plazmidy genetika   metabolismus   MeSH
• prasata růst a vývoj   mikrobiologie   MeSH
• proteiny z Escherichia coli genetika   metabolismus   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Česká republika MeSH

Antibiotika se v dnešní době běžně používají při léčbě infekčních nemocí. Nelze si však nevšimnout pozvolna rostoucího trendu v počtu přežívajících bakterií, které i přes aplikaci antibiotik nadále perzistují v těle pacientů a ohrožují jejich zdraví. Důvodem může být nevhodný výběr používaného antibiotika. Častější příčinou je však zvýšená odolnost mikroorganismů vůči těmto antimikrobiálním látkám, zprostředkovaná různými mechanismy vzniku a přenosu rezistence, jako jsou změny cílových míst antibiotik, genové mutace, horizontální genový transfer genů rezistence, specifické enzymy degradující antibiotika či efluxní systém. K snazšímu a rychlejšímu šíření rezistencí přispívá i schopnost některých mikroorganismů tvořit biofilm, útvar o vysoké stabilitě, který může být i rezervoárem genů nesoucích rezistenci k antibiotikům.

Antibiotics are commonly used for the treatment of infectious diseases. It is evident that the number of bacteria resistant to antibiotic remarkably increased and pathogenic strains persists in the body of patients and endangering their health. The reason may be the inappropriate use of antibiotics. However, the more common cause is increased resistance of microorganisms mediated by various mechanisms of resistance, such as changes in the target sites of antibiotics, gene mutations, horizontal gene transfer of resistance genes, specific enzymes degrading the antibiotic, or efflux system. The ability of some microorganisms to form a biofilm (a structure of high stability, which can form a reservoir of genes carrying resistance to antibiotics) also contributes to easier and more rapid spread of bacterial resistance to antibiotics.

• Klíčová slova
• mechanismy rezistence,
• MeSH
• antibakteriální látky * farmakologie   chemie   klasifikace   MeSH
• Bacteria genetika   patogenita   účinky léků   MeSH
• bakteriální léková rezistence * genetika   účinky léků   MeSH
• lidé MeSH
• mutace MeSH
• plazmidy genetika   MeSH
• přenos genů horizontální MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• práce podpořená grantem MeSH
• přehledy MeSH

Individual groups of retroviruses and retroviral vectors differ in their integration site preference and interaction with the host genome. Hence, immediately after infection genome-wide distribution of integrated proviruses is non-random. During long-term in vitro or persistent in vivo infection, the genomic position and chromatin environment of the provirus affects its transcriptional activity. Thus, a selection of long-term stably expressed proviruses and elimination of proviruses, which have been gradually silenced by epigenetic mechanisms, helps in the identification of genomic compartments permissive for proviral transcription. We compare here the extent and time course of provirus silencing in single cell clones of the K562 human myeloid lymphoblastoma cell line that have been infected with retroviral reporter vectors derived from avian sarcoma/leukosis virus (ASLV), human immunodeficiency virus type 1 (HIV) and murine leukaemia virus (MLV). While MLV proviruses remain transcriptionally active, ASLV proviruses are prone to rapid silencing. The HIV provirus displays gradual silencing only after an extended time period in culture. The analysis of integration sites of long-term stably expressed proviruses shows a strong bias for some genomic features-especially integration close to the transcription start sites of active transcription units. Furthermore, complex analysis of histone modifications enriched at the site of integration points to the accumulation of proviruses of all three groups in gene regulatory segments, particularly close to the enhancer loci. We conclude that the proximity to active regulatory chromatin segments correlates with stable provirus expression in various retroviral species.

• MeSH
• aktivace transkripce * MeSH
• Alpharetrovirus genetika   MeSH
• buněčné linie MeSH
• chromatin genetika   MeSH
• epigeneze genetická MeSH
• genetické vektory genetika   MeSH
• genový targeting MeSH
• HIV-1 genetika   MeSH
• integrace viru MeSH
• lidé MeSH
• myši MeSH
• plazmidy genetika   MeSH
• počátek transkripce MeSH
• proviry genetika   MeSH
• regulace exprese virových genů MeSH
• regulační oblasti nukleových kyselin * MeSH
• stabilita RNA MeSH
• umlčování genů MeSH
• virus myší leukemie genetika   MeSH
• zesilovače transkripce MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Bacillus anthracis, the causative agent of anthrax is a Gram-positive, non-motile, spore forming bacterium. Its spores can persist in soil and water for years and can also be aerosolized. A rapid, sensitive and specific method to detect B. anthracis is important for clinical management and preventing spread of anthrax. Loop-mediated isothermal amplification (LAMP) assay is a rapid technique that amplifies target DNA in isothermal conditions with high sensitivity and specificity. In this study, a LAMP assay set targeting a chromosomal and two plasmid markers was developed. The individual assays of the LAMP set targeting pXO1 plasmid (lef), pXO2 plasmid (capB), and chromosome (BA5345) sequences could detect 10, 250, and 100 fg of genomic DNA and 10, 100, and 50 copies of the DNA targets harboured in recombinant plasmids, respectively. The lef and capB LAMP assays could detect ≥ 1 × 103 CFU per mL of bacteria in spiked human blood samples, while BA5345 LAMP assay could detect ≥ 1 × 104 CFU of bacteria per mL of spiked blood. The amplification was monitored in real-time by turbidimeter, and visual detection was also accomplished under normal and UV light after adding SYBR Green 1 dye on completion of the reaction. The assay set was found to be highly sensitive and did not cross-react with the closely related Bacillus spp. and other bacterial strains used in the study.

• MeSH
• antrax * mikrobiologie   prevence a kontrola   MeSH
• Bacillus anthracis * genetika   MeSH
• diagnostické techniky molekulární * normy   MeSH
• DNA bakterií genetika   MeSH
• senzitivita a specificita MeSH
• techniky amplifikace nukleových kyselin * normy   MeSH
• Publikační typ
• časopisecké články MeSH