Metagenomic Analysis of Gingival Sulcus Microbiota and Pathogenesis of Periodontitis Associated with Type 2 Diabetes Mellitus.

Biofilm of the gingival sulcus from 22 patients with type 2 diabetes mellitus and periodontitis, 30 patients with periodontitis not complicated by diabetes mellitus (reference group), and 22 healthy volunteers without signs of gingival disease (control group) was studied by quantitative PCR. Quantitative analysis for the content of P. gingivalis, T. forsythia, A. ctinomycetemcomitans, T. denticola, P. intermedia, F. nucleatum/periodonticum, and P. endodontalis in the dental plaque was performed with a Dentoscreen kit. The presence of other bacterial groups was verified by metagenomic sequencing of the 16S rRNA gene to evaluate some specific features of the etiological factor for periodontitis in type 2 diabetes mellitus. Specimens of the Porphiromonadaceae and Fusobacteriaceae families were characterized by an extremely high incidence in combined pathology. The amount of Sphingobacteriaceae bacteria in the biofilm was shown to decrease significantly during periodontitis. Metagenomic analysis confirmed the pathogenic role of microbiota in combined pathology, as well as the hypothesis on a possible influence of periodontitis on the course and development of type 2 diabetes mellitus.

[MOLECULAR MECHANISMS OF DRUG RESISTANCE NEISSERIA GONORRHOEAE HISTORY AND PROSPECTS].

Neisseria gonorrhoeae (gonococcus) is a strict human pathogen, which causes gonorrhea--an infectious disease, whose origin dates back to more than two thousand years. Due to the unique plasticity of the genetic material, these bacteria have acquired the capacity to adapt to the host immune system, cause repeated infections, as well as withstand antimicrobials. Since the introduction of antibiotics in 1930s, gonococcus has displayed its propensity to develop resistance to all clinically useful antibiotics. It is important to note that the known resistance determinants of N. gonorrhoeae were acquired through horizontal gene transfer, recombination and spontaneous mutagenesis, and may be located both in the chromosome and on the plasmid. After introduction of a new antimicrobial drug, gonococcus becomes resistant within two decades and replaces sensitive bacterial population. Currently Ceftriaxone is the last remaining antibiotic for first-line treatment of gonorrhea. However, the first gonococcus displaying high-level resistance to Ceftriaxone was isolated in Japan a few years ago. Therefore, in the near future, gonorrhea may become untreatable. In the present review, we discuss the chronology of the anti-gonorrhea drugs (antibiotics) replacement, the evolution of resistance mechanisms emergence and future perspectives of N. gonorrhoeae treatment.

[Variability in the relative quantity of human DNA resulted from metagenomic analysis of gut microbiota].

We conducted the comparative study of seven different methods of total DNA extraction from human feces. All these methods are recommended in protocols for metagenomic analysis of human gut microbiota. We studied the relative quantity of human DNA calculated from shotgun sequencing on a SOLiD 4 genetic analyzer of metagenomic samples. It was shown that either initial amount of feces or a method applied for total DNA extraction do not affect on final relative human DNA abundance, which is less than 1% in healthy people. Invariance of this parameter allows to consider increased abundance of human DNA in metagenomic samples as a potential marker of inflammatory bowel diseases.

[Analysis of genetic determinants of multidrug and extensively drug-resistant Mycobacterium tuberculosis using oligonucleotide microchip].

Steadily growing resistance of the tuberculosis causative agent towards a broad spectrum of anti-tuberculosis drugs calls for rapid and reliable methods for identifying the genetic determinants responsible for this resistance. In this study, we present a biochip-based method for simultaneous identification of mutations within rpoB gene associated with rifampin resistance, mutations in katG, inhA, ahpC genes responsible for isoniazid resistance, mutations within the regions of gyrA and gyrB genes leading to fluoroquinolones resistance, and mutations in the rrs gene and the eis promoter region associated with the resistance to kanamycin, capreomycin and amikacin. The oligonucleotide microchip, as the core element of this assay, provides simultaneous identification of 99 mutations in the format "one sample--one PCR--one microchip", and it makes it possible to complete analysis of multi-drug-resistant and extensively drug-resistant tuberculosis within a single day. The tests on 63 Mycobacterium tuberculosis clinical isolates with different resistance profiles using the developed approach allows us to reveal the spectrum of drug-resistance associated mutations, and to estimate the significance of the inclusion of extra genetic loci in the determination of M. tuberculosis drug resistance.

[Susceptibility of gramnegative carbapenemase-producing bacteria to various group antibiotics].

The study involved 25 isolates of gramnegative carbapenemase-producing bacteria. 17 isolates of Klebsiella pneumonia produced carbapenemase NDM-1 and were highly resistant to cephalosporins (MIC>128 mcg/ml), carbapenems (MIC>16 mcg/ml), aminoglycosides and fluoroquinoiones, while among them 4 isolates preserved susceptibility to azthreonam and all of them were susceptible to tigecycline and polymyxin. 2 isolates of Acinetobacter genomospecies 13 produced NDM-1 and were resistant to all the beta-lactams and amikacin, while preserved susceptibility to gentamicin, co-trimoxazole, tigecycline and polymyxin, the susceptibility to ciprofloxacin being lowered. Carbapenemase VIM-4 was produced by 2 isolates of Enterobacter cloacae, which were highly resistant to cephalosporins and azthreonam, significant synergism being observed between cefepim and clavulanate. The resistance of the isolates to carbapenems was low (MIC 0.5-4.0 mcg/ml), they also being resistant to aminoglycosides and ciprofioxacin and susceptible to tigecycline and polymyxin. Carbapenemases KPC-2 were detected in 2 isolates of K.pneumoniae and in 1 isolate of E.cloacae. The above isolates were resistant to all the beta-lactams, ciprofloxacin, aminoglycosides and co-trimoxazole. I isolate of E.cloacae showed resistance to tigecychine and I isolate of K.pneumoniae was resistant to polymyxin. Carbapenemase OXA-48 was detected in 1 isolate of K.pneumoniae. It was resistant to all the beta-lactams, ciprofloxacin and co-trimoxazole and susceptible to aminoglycosides, tigecycline and polymyxin.

[Microbiological and molecular genetic characteristics of coagulase-negative staphylococcal isolates from neonates in intensive care unit].

The problem of hospital-acquired infections due to coagulase-negative staphylococci (CoNS) in neonatal intensive care units is crucial over the last 20 years in the world. Neonates with very low or extremely low body weight belong to a special group of risks by the CoNS infection. However, in Russia CoNS up to now are frequently considered as contaminants and not as the main etiologic factors of pneumonia and sepsis in extremely premature infants. It was shown that hospital strains of CoNS causing fatal infections in extremely premature infants are always present in intensive care units.

[Strain differentiation of Staphylococcus aureus by means of direct MALDI TOF mass spectrometry profiling].

Staphylococcus aureus--one of the most interesting for clinical studies of microbial species with extensive strain diversity, primarily due to the variability of virulence factors and pathogenicity. The aim of this study was approbation of a method for the rapid strain differentiation of S. aureus on the basis of bacterial cell direct protein profiling approach by means of MALDI TOF MS. Beta-lactamase and alpha-hemolysin productions, cording by the blaZ and hla genes, respectively, were selected as markers for the strain differentiation. Mathematical analysis of MALDI mass spectra from 53 isolates allowed the construction of two independent classification models that can differentiate the strains on the presence/absence of blaZ or hla genes. A number of the most significant peaks (masses), which can be considered as markers of the strain differences in S. aureus, were identified using a statistical contribution of each mass peak in the models. These diagnostic models differ the sensitivity and the specificity, which were 97.5% and 82.5% for the classification of strains on the basis of beta-lactamase production, and 90.0% and 88.7% by the presence of alpha-hemolysin.

[Population pattern of pneumococci with lower susceptibility to penicillin and prospects of antipneumococcal vaccination to control antibiotic resistance distribution].

Large-scale antipneumococcal vaccination is followed by changes in the serotype composition and level of antibiotic resistance in pneumococci. The aim of the study was to evaluate the serotype composition and population pattern of pneumococci with lower susceptibility to penicillin before large-scale antipneumococcal vaccination. Among 260 Streptococcus pneumoniae strains isolated in the Russian Federation within 2003-2007, serotypes 23F (37.2%) and 19F (13.9%) were the most frequent ones. 19.3% of the isolates belonged to serogroup 6, 3.6% of the isolates each belonged to serotype 3 and serogroup 18, 4.9% of the isolates belonged to serotype 14 and 2.2% of the isolates belonged to serotype 19A. 66.8% of the isolates belonged to serotypes of the 7-valent conjugated pneumococcal vaccine, 67.3 and 82.1% of the isolates belonged to the 10- and 13-valent conjugated pneumococcal vaccines respectively. The isolates with lower susceptibility to penicillin were characterized by significant clonality and 56.9% of them belonged to 4 global clonal complexes (CC81, CC156, CC320 and CC315). Inclusion of the conjugated antipneumococcal vaccine to the National Vaccination Time-Table of the Russian Federation could promote lower levels of antibiotic resistance in pneumococci.

Nickel accumulation in rape shoots (Brassica napus L.) increased by putrescine.

Application of exogenous putrescine (Put) increases nickel accumulation in rape shoots (Brassica napus), improving potential for phytoremediation of contaminated soils. Plants were grown within a growth chamber in water culture for five weeks, then 250-500 microM NiCl2 was added to rooting media. Within 5 days of treatment, damaging effects of nickel manifested as a reduction of root system size and a decrease of Cu and especially Fe content in young leaves. Spraying leaves of adult plants with Put markedly reduced toxic effects of Ni on root growth, enhanced leaf supply with Fe, and increased Ni content in young leaves by 2.5 times. Plant growth in medium with elevated levels of Ni stimulated accumulation of endogenous spermidine (Spd), spermine (Spm), and especially Put (by 4 times as compared with the control). Results suggest that Ni-induced accumulation of endogenous polyamines in rape leaves is caused by activation of long-distance metal transport within the plant and reduction of its toxicity due to Put chelating action.

[Differentiation of α-hemolytic Streptococci by direct mass spectrometry profiling].

The modern phenotypic and genetic methods except for Multi Locus Sequence Typing do not allow the reliable differentiation within Mitis group of α-hemolytic streptococci. During this study the MALDI mass spectra were acquired for 28 clinical isolates initially identified as S. pneumoniae by routine bacteriological tests. Due to Multi Locus Sequence Typing these isolates were found to belong to two closely related species - S. pneumoniae (n = 22) and S. mitis (n = 6). Distribution of those isolates in accordance with cluster analysis of collected mass spectra matched to Multi Locus Sequence Typing data. The diagnostic model based on Genetic Algorithm classifier demonstrated the differentiation of α-hemolytic streptococci with 100% sensitivity and 94.6% accuracy. Statistical analysis of MS peak areas revealed 2 peaks which are different for S. mitis and S. pneumoniae groups.

Molecular typing of Mycobacterium tuberculosis circulated in Moscow, Russian Federation.

The present study investigates epidemiological diversity and multidrug resistance spreading among Mycobacterium tuberculosis strains circulating in Moscow, Russian Federation. Among 115 M. tuberculosis strains selected randomly from the sputum of epidemiologically unrelated tuberculosis (TB) patients, multidrug-resistant (MDR) strains predominated. Mutations in the RRDR of the rpoB gene were detected in 64 (83.1%) of 77 rifampicin (RIF)-resistant strains. The Ser531→Leu substitution was prevalent among them (76.5%). Aberrations in the Ser315 codon of katG and/or in the inhA promoter region were found in 79 (84.0%) of 94 isoniazid (INH)-resistant strains. Strains belonging to the Beijing family prevailed. Seventy-one different patterns were identified using the 24-VNTR loci typing scheme. Three main 24-loci VNTR clusters included 34 strains which belonged to the Beijing family. The spoligotyping and 24-loci VNTR typing combination demonstrated maximal discriminatory power. Among the Beijing strains, the MDR phenotype was revealed more frequently than among the others. High genetic heterogeneity of the studied population was shown by the assessment of VNTR loci variability in the analyzed group and in the strains from other parts of Russia. Comparison of the 24-VNTR locus typing and spoligotyping data with revealed resistance-associated mutation allows us to make a suggestion that the active transmission of MDR strains and the independent appearance of drug resistance during chemotherapy occurred in the studied population simultaneously.

[Investigation of molecular mechanisms of aminoglycoside resistance in Salmonella].

The spread of aminoglycoside resistance phenotype and respective genetic resistance determinants was evaluated in 243 Salmonella strains isolated within 1948-2010 and stored in the Culture Collection of the Russian State Research Institute for Control, Standardization and Certification of Veterinary Preparations (Moscow). The Salmonella strains showed resistance to streptomycin and gentamicin in 3.7% (n = 9) and 0.8% (n = 2) of the isolates respectively. Intermediate resistance to streptomycin was recorded in 9.9% (n = 24) of the isolates. To detect the genes responsible for the aminoglycoside resistance, primers for aadA1, aadA2, aadB, aphA1, aphA3, sat, strA, strB, aphA, aacC, rmtB, armA and rpsL genes amplification and sequencing were designed. The strains with lower susceptibility to streptomycin harbored aadA1, aadA2, strA, strB resistance genes encoding enzymes for aminoglicoside modification and rpsL mutant allele (K42N, G91D). Genetic mechanisms able to explain the gentamicin resistance development were not detected. Some strains carried genetic markers of streptomycine resistance but had no clinically sufficient resistance to it. In this regard, genetic testing is essential for prevention of drug resistance spreading due to horizontal transfer of genes in microbial population.

[A mass-spectrometric analysis of genetic markers of S. pneumoniae resistance to beta-lactam antibiotics].

Beta-lactam antibiotics remain the drugs of choice for treatment of S. pneumoniae infections in spite of growing level of resistance. The formation of S. pneumoniae resistance to these drugs is mediated by modifications of the penicillin-binding proteins (PBPs), the targets of the antibiotic action. A new approach to detection of mutations in PBP1A, 2B and 2X genes based on minisequencing reaction followed by MALDI-ToF (Matrix-Assisted Laser Desorption/Ionization Time of Flight) mass spectrometry was developed in this study. The evaluation of these mutations prevalence in clinical S. pneumoniae isolates (n = 194) with different susceptibility level to beta-lactam antibiotics was performed. Twenty-four different combinations of mutations in PBPs (genotypes) were detected. All isolates susceptible to penicillin (n = 49, MIC > or = 0.06 > or = gamma/ml) carried no mutations in all analyzed loci. For 145 S. pneumoniae isolates with reduced susceptibility to penicillin (MIC > 0.06 > or = gamma/ml) the mutations in PBPs were detected in 133 (91.7 %) cases that testify to high diagnostic sensitivity of such approach. The isolates with MIC > or = 4 > or = gamma/ml (n = 20) carried multiple mutations in all analyzed genes that confirms cumulative effects of penicillin resistance formation. However, it was not possible to associate observed mutations in PBPs genes with decrease of susceptibility to cefotaxime that allows suggesting the entire difference in molecular mechanisms of formation of resistance to penicillins and cephalosporins. The offered method of S. pneumoniae genotyping is suitable for susceptibility testing to penicillin of individual isolates and for molecular monitoring of the resistance determinants in population.

[Molecular characteristic of methicillin-resistant Staphylococcus aureus strains isolated in Moscow clinics].

UNLABELLED: OBJECTIVES; Methicillin-resistant Staphylococcus aureus (MRSA) is a common pathogen of nosocomial infection. The goal of this work was to evaluate the clonality of hospital-acquired MRSA (HA-MRSA) circulating in Russian Federation and to compare different multiplex PCR techniques with SNP-based approach for MRSA typing. METHODS: Epidemiologically unrelated MRSA isolates (n = 62) from Moscow hospitals were selected for typing. Genomic DNA from clinical isolates was purified using the DNA express kit (Lytech Ltd, Russia). Staphylococcus chromosomal cassette mec (SCCmec) typing was performed by PCR using the previously described methods. Seven loci from five housekeeping genes (arcC162, arcC210, aroE132, gmk123, tpi241, tpi243 and yqiL333) were used for SNP-typing. Detection of particular nucleotides in selected loci was carried out in the thermocyclic primer extension reaction, followed by mass spectrometry of the products. Standard MLST procedure was performed as reference method. RESULTS: The majority of the MRSA isolates (93.6%) belong to world-wide disseminated clonal complex (CC) 8. Three isolates (4.8%) belong to CC 1. All ST 239 isolates were found to carry SCCmec type III; ST 8 isolates, SCCmec type IV. CONCLUSION: Among Russian MRSA CC 8 isolates carrying SCCmec IV type are predominant. SNP-typing is powerful toll for studies of molecular epidemiology of MRSA.

[Detection of mutations in codon 306 of the embB gene for molecular genetic characterization of clinical Mycobacterium tuberculosis strains].

A total of 254 Mycobacterium tuberculosis strains were used in the study. Among them, there were 183 ethambutol (EMB)-resistant strains, 13 multidrug resistant ones, but EMB-sensitive, and 39 strains sensitive to rifampicin (RIF), isoniazid (INZ), and EMB. All the strains were analyzed for genetic changes in three loci: embB306, rpoB, and katG/inhA promoter, which were associated with the formation of resistance to EMB, RIF, and INZ, respectively. The Mycobacterium tuberculosis strains were obtained from pulmonary tuberculosis patients living in the Central Region of the Russian Federation. Resistance to RIF, INZ, and EMB was revealed by the absolute concentration test. The inhibitory concentration (IC) of EMB was determined for all the strains. Genetic changes in the above loci were estimated by mini-sequencing, followed by mass-spectrometry recording MALDI-TOF products. The relative low frequency of embB306 mutations was observed among the EMB-resistant strains (about 41.5%). Mutations in codon 306 were detected only in strains with EMB IC > or = 2 mg/L. A statistical significant association was found between the frequency of embB306 mutations and the multidrug resistant phenotype. A combination of these mutations with the traditional genetic markers of multidrug resistance may be used for the more effective detection of multidrug-resistant strains.

[Mass spectrometry of nucleic acids in molecular medicine].

A stable streamlining trend in the field of medical diagnostics by practical adoption of high-tech and knowledge-intensive analytical systems providing for molecular level studies has appeared during the last few decades. An illustrative example of such technologies is mass spectrometry methods for analyzing biomolecules. This review is intended to brief the potential of the state-of-the-art inventory of spectrometry equipment and illustrate the application of mass spectrometry of nucleic acids (DNA and RNA) for solving practical problems related to the analysis of human genomic DNA and clinically significant microorganisms of bacterial and viral natures.

[HCV genome variability in acute and chronic viral hepatitis C].

AIM: To evaluate HCV genome variability in acute and chronic phases of viral hepatitis C. MATERIAL AND METHODS: The study of heterogeneity of HCV in acute hepatitis C has detected genetic heterogeneity and variability of individual HCV population circulating in the blood. Significant genetic heterogeneity of HCV was observed in 1b, 2a and 3a genotypes. Variability of HCV did not depend on virus load. Genetic HCV structure changed significantly both in patients with manifest ALT deviations and in normal ALT, mean number of HCV genetic variants in these groups being the same. No significant correlations were found between virus concentration in the patient's blood, its variability and ALT values. Genetic heterogeneity of interferon-sensitive region of gene NS5A subtype 1b HCV was studied in blood of 16 patients with chronic hepatitis C resistant to interferon therapy. RESULTS: It is shown that genetic heterogeneity and variability of an individual HCV population circulating in blood serum can not be a prognostic criterion in assessment of variants of acute hepatitis C course. No mutations in ISDR region were found in 25% of 16 patients studied. 75% cases had 1-3 replacements of amino acid sequences, most frequent mutation was replacements in position 2218 (histidin/arginin). The above results are close to those obtained in Japanese and European populations. Results of ISDR sequence-analysis conducted before treatment may predict efficacy of interferon-alpha2 treatment in an individual patient in future. Large-scale trials are necessary for detection of mutations responsible for resistance to interferon-alpha2 in patients living in Russia.

A MALDI TOF MS-based minisequencing method for rapid detection of TEM-type extended-spectrum beta-lactamases in clinical strains of Enterobacteriaceae.

A minisequencing method based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI TOF MS) was developed for rapid identification of single nucleotide polymorphisms at bla(TEM) gene codons 104, 164 and 238 associated with extended-spectrum activity on TEM-type beta-lactamases. The method was validated by testing the Escherichia coli and Klebsiella pneumoniae strains possessing the known bla(TEM) gene sequences.