Characteristics of Stenotrophomonas maltophilia isolates from cystic fibrosis patients in Russia.

Stenotrophomonas maltophilia is a common opportunistic microorganism and an important respiratory pathogen in cystic fibrosis (CF). The aim of this study was to determine antimicrobial resistance phenotypes, sequence-types (ST) and genetic determinants of antibiotic resistance in S. maltophilia strains recovered from CF patients in Russia. S. maltophilia isolates recovered from 170 CF patients were analyzed. Minimum inhibitory concentrations of antibacterial agents were determined using Sensititre Gram Negative GNX2F plates and the results were interpreted according to Clinical and Laboratory Standards Institute (CLSI) criteria. Whole-genome sequencing (WGS) was performed on MGISEQ-2000 platform. SPAdes software, Galaxy, ResFinder, Integrall and PubMLST were used for analysis of WGS data. S. maltophilia strains were identified from 24/170 (14%) CF patients. In total, 25 isolates were detected, two strains were isolated from the same patient. The isolates belonged to 17 different STs, including 5 new STs; ST4 was the most prevalent ST. Resistance to ceftazidime was observed in 60% of strains, to ticarcillin-clavulanate - in 32%, to levofloxacin - in 24%, to trimethoprim/sulfamethoxazole - in 12% of strains. All isolates were susceptible to minocycline. All ST4 isolates were resistant or intermediate to ceftazidime and ticarcillin-clavulanate. In two isolates, the sul1 gene was detected. In one isolate, sul1 was part of a class 1 integron. The detected integron also contained the blaGES-7 and aac(6')-Ib-cr genes. The ST4 sequence-type was the most prevalent ST among S. maltophilia strains recovered from CF patients in Russia. Antibiotic resistance genes, including sul1, blaGES-7, aac(6')-Ib-cr, were detected in single strains.

Genome features and antibiotic resistance of Pseudomonas aeruginosa strains isolated in patients with cystic fibrosis in the Russian Federation.

Cystic fibrosis (CF) is a common genetic disease, manifested by airway obstruction and chronic respiratory infection. The most prevalent infectious agent in airways of CF patients is Pseudomonas aeruginosa. This study aimed to determine sequence-types, antimicrobial resistance phenotypes and genes defining adaptive antibiotic resistance in P. aeruginosa isolates recovered from CF patients in Russia. In total, 84 P. aeruginosa strains from 64 CF patients were analyzed. Susceptibility to antibiotics was determined by disk diffusion test. Whole-genome sequencing (WGS) was performed on MGISEQ-2000 platform. SPAdes software, Galaxy, ResFinder, PubMLST were used for analysis of WGS data. Examined P. aeruginosa isolates belonged to 53 different sequence-types (STs), including 6 new STs. High-risk epidemic clone ST235 (10%) and clonal CF P. aeruginosa strains ST17, ST242, ST274 (7%) were detected. Non-susceptibility to ticarcillin-clavulanate, cefepime, imipenem was observed in 63%, 12% and 25% of isolates, respectively; to tobramycin - in 24%, to amikacin - in 35%; to ciprofloxacin, levofloxacin - in 35% and 57% of strains, respectively. Multidrug-resistant phenotype was detected in 18% of isolates. In examined strains, genes of beta-lactamases VIM-2 (5 ST235 strains), VEB-1 (two ST2592 strains), GES-1 (1 ST235 strain), PER-1 (1 ST235 strain) were found. Ciprofloxacin-modifying enzyme CrpP gene was detected in 67% of isolates, aminoglycoside-modifying enzymes AAD, ANT, AAC genes - in 7%, 4%, 12% of strains, respectively. P. aeruginosa isolates from CF patients in Russia demonstrate a high clonal diversity, which is similar to other P. aeruginosa infections. The isolates of high-risk clone and clonal CF P. aeruginosa strains are detected.

[Bacteria survival strategies in contact with antibiotics.]

Bacteria survival in the conditions of antimicrobial therapy is the global problem of health care. This review highlights the complexity and diversity of mechanisms used by bacteria to neutralize antibiotics. To analyze the problem, the search was made using PubMed database, Russian scientific electronic library eLIBRARY, search system of World Health Organization and European Society of Clinical Microbiology and Infectious Diseases (ESCMID). Based on the analysis of survival strategies in the conditions of antibiotics action we propose new classification of resistant bacteria. Classification criteria include the ability to divide under antibiotics action, the survival strategies application as a species trait, the presence of specialized genes determining the transition to the state with reduced/stopped metabolism. Two main groups are resistant bacteria and bacteria with reduced/stopped metabolism, which survive but do not divide in the presence of antibiotic. The first group includes two subgroups: bacteria with intrinsic and adaptive resistance. The second group includes (1) bacteria with specialized genes responsible for cell transformation to the state with reduced/stopped metabolism, (2) bacteria transforming to the state with reduced/stopped metabolism without involvement of special genes, and (3) cell forms with special morphology - spores, cysts and cyst-like cells. We described the usefulness of proposed classification including improved understanding of the correlation between bacteria survival in the presence of antibiotics and molecular mechanism of cell metabolism inhibition, presence or absence of targets for using molecular-genetic methods of bacteria resistant variant determination, the possibility for development of rational antimicrobial therapy methods.

[Integron diversity in blavim-2-carrying carbapenem-resistant clinical Pseudomonas aeruginosa isolates.]

The growing prevalence of metallo-ß-lactamase (MBL)-producing Pseudomonas aeruginosa in nosocomial pathogen populations has been attributed to their clonal spread, and/or horizontal transfer of MBL determinants in mobile genetic elements, including integrons. To characterize the genetic background of the beta-lactamase VIM-2 encoding gene in the population of carbapenemresistant (Carba-R) P. aeruginosa clinical isolates.The detection of class 1 integrons was performed by PCR. Typing of the class 1 integrons containing the blaVIM gene cassette was performed by the PCR-restriction fragment length polymorphism (RFLP) approach followed by sequencing of variable regions of class 1 integrons. Five types of the blaVIM-2-carrying integrons were identified: ST654-isolates accounting for more than 50% of the Carba-R population harbored In56; ST235-isolates contained In559 (26% Carba-R isolates); ST111-isolates (19% Carba-R isolates) were characterized by carrying In59-like integron; two ST235-isolates harbored In59 and In249 each. Except In56, carrying the only blaVIM-2-gene cassette, all other identified integron types harbored the genes of resistance to trimethoprim and/or aminoglycosides. No new types of integrons were identified in the P. aeruginosa clinical isolates. The observed correlation of the integron type with specific STs indicates a clonal dissemination of significant resistance determinant producers - ST111, ST654 and ST235 epidemic lines. The features of the integron variable regions can be used for the epidemiological characterization of clinical P. aeruginosa isolates.

[The mass-spectrometric evaluation of сarbapenemase activity of Pseudomonas aeruginosa.]

The Pseudomonas aeruginosa is among number of leading opportunistic pathogens. The evaluation of sensitivity of hospital isolates of P. aeruginosa to antibiotics is an important stage in the struggle with Pseudomonas sepsis pathology. The purpose of study is to confirm diagnostic efficiency of mass spectrometry approach in evaluation of сarbapenemase activity in clinical isolates of P. aeruginosa. The study was targeted to detection of сarbapenemases in 50 clinical isolates of P. aeruginosa, non-sensitive to сarbapenemas (control group - 9 isolates of P. aeruginosa sensitive to сarbapenemas). The comparative analysis was implemented concerning the results obtained using laser desorption ionization time-of-flight mass spectrometry and using such common techniques as phenotype detection of presence of metallo-beta-lactamase using E-tests and detection of presence of genes of carbapenemases (VIM, IMP, NDM) using polymerase chain reaction in real-time. The metallo-beta-lactamase activity was established in 14 (28%) out of 50 non-sensitive to сarbapenemas strains. All of them had genes of carbapenemases VIM-type. No IMP and NDM genes were detected in any strain. The VIM genes were detected only in metallo-beta-lactamase positive strains and metallo-beta-lactamase activity was registered only in carriers of VIM genes. According data of MALDI-TOF, all metallo-beta-lactamase and VIM positive strains demonstrated increased capacity of hydrolyzing meropenem. The percentage of hydrolysis under testing of the given strains made up to from 7.6 to 59.3. The absence of carbapenemase activity was demonstrated by 36 (72%) out of 50 strains non-sensitive to сarbapenemases with percentage of hydrolysis from 0 to 4. None of 9 control isolates sensitive to сarbapenemases had metallo-beta-lactamase activity, carried analyzed genes of сarbapenemas and hydrolyzed meropenem. The MALDI-TOF mass spectrometry is a perspective technique to be applied in practice of clinical microbiology for detect isolates of P. aeruginosa, producing сarbapenemases.

[The comparison of methods for determination of colistin susceptibility in carbapenem-resistant Klebsiella pneumoniae.]

In recent years, because of carbapenemase spreading in Klebsiella pneumoniae strains, the antibiotic of reserve group, colistin, is increasingly prescribed. In vitro testing of colistin susceptibility in everyday practice has a number of difficulties due to the cationic properties of molecule and weak diffusion into agar. Therefore it is recommended to use the reference Broth Microdilution Method (BMD) for determination of the Minimum Inhibitory Concentration (MIC) for colistin. The purpose of the study was to determine susceptibility to colistin in 119 carbapenem-resistant K. pneumoniae (CRKp) which were isolated from the patients at three hospitals in Moscow in 2012-2016 by the broth microdilution method (BMD) and to compare these data with the ones obtained by epsilometer test (E-test) and VITEK 2 Compact. The proportion of resistant isolates (MIC>2 mg/L) was 52%, 39%, 35% respectively. Both commercial methods demonstrated a high level of the very major error (VME) that was 26% for the E-test method and 34% for the VITEK 2 Compact. The values of categorical agreement and essential agreement (CA, EA) were less than 90%. A single major error (ME) was detected for the VITEK 2 Compact. In conclusion, results of both commercial tests for determination of MIC for colistin showed differences with the results of the reference BMD. It is necessary for clinical laboratories to be aware about this discrepancy and to use E-tests and VITEK 2 Compact with caution to determine colistin susceptibility.

[SPECTRUM OF ANTIBIOTIC RESISTANCE AND PREVALENCE OF OXA-CARBAPENEMASES AMONG ACINETOBACTER BAUMANNII STRAINS, ISOLATED FROM PATIENTS OF SURGICAL AND REANIMATION DEPARTMENTS IN MOSCOW].

AIM: Characterize spectrum of antibiotics resistance of Acinetobacter baumannii strains, isolated from patients of 8 surgical and reanimation departments of 3 medical institution of Moscow, and determine molecular-genetic mechanisms of stability of their carbapenem-resistant forms. MATERIALS AND METHODS: 95 strains of A. baumannii, isolated from patients of reanimation and surgical departments of Moscow in 2012-2014, were studied. Sensitivity of strains to antibiotics was tested phenotypically according to recommendations of EUCAST. The presence of VIM, IMP, OXA-23, OXA-40, OXA-48, OXA-58 and NDM genes in the studied strains was determined by polymerase chain reaction in real time. RESULTS: 86.3% of strains turnedout to be non-sensitive to carbapenems, sensitive--13.7%. 80.0% of strains were non-sensitive to gentamicin, 80.0% of strains--to netilmicin, 94.7% of strains--to ciprofloxacin 2.1%--to colistin. 91.6% of isolates have shown non-sensitivity to members of 2 and more classes of antibiotics, 78.9% of strains--to members of 3 classes. 2 strains were panresistant, 4.2% (4/95) of the isolates were sensitive to all the classes of antibiotics. Metallo-ß-lactamases were not detected. Genes of carbapenemases (OXA-23 and/or OXA-40) were detected in 85.3% (81/95) of strains, characterized phenotypically as non-sensitive to carbapenems. CONCLUSION: The results obtained shown an increase of resistance to carbapenems and multiple resistance in clinically significant strains of A. baumannii. Resistance to carbapenems is associated with OXA-23 and OXA-40 genes. The conclusions allow to justify perspectives of introduction of technologies of molecular-genetic testing of antibiotics resistance.

[Antibiotic Resistance and Its Molecular Mechanisms in Carbapenem-Nonsusceptible Klebsiellapneumoniae Isolated in Pediatric ICUs in Moscow.]

Klebsiellapneumoniae is a significant pathogen associated with hospital infections. Its was isolated in intensive care units (ICU) at two pediatric hospitals in Moscow in 2012-2014 from 41% (387/935) of the patients. The rate of carbapenem-nonsusceptibility (Carba-NS) amounted to 25% for imipenem and 27% for meropenem. For further analyses, 67 isolates were selected, including 57 Carba-NS and 10 Carba-susceptible (Carba-S). Among the isolates, 100% was nonsusceptible to the III-IV generation cephalosporins, 50-84% was resistant to aminoglycosides. The rate of nonsusceptibility to ciprofloxacin and phosphomycin exceeded 90%. All the tested Carba-S Kpneumoniae isolates were susceptible to tigecycline, whereas 25% of the Carba-NS isolates was tigecycline-NS. The prevalence of the colistin-NS isolates was the same in Carba-S (20%) and Carba-NS (26%) bacteria. The blamrx_ gene was carried by 100% of the Carba-S isolates, combining with the blaTEM gene in 60% of the isolates. In 89% of the Carba-NS isolates the OXA-48 carbapenemase was detected, which was combined with CTX-M and/or TEM in all but 1 isolate. Thus, over the last decade, the rate of Carba-NS among nosocomial Kpneuynoniae increased and the OXA-48 carbapenemase was shown to be dominating in the mechanism of Carba-NS in the pediatric ICUs in Moscow.

[The possibilities, problems and perspectives of mass-spectrometry in medical microbiology: publications review].

The publications review deals with analysis of possibilities, shortcomings and perspectives of mass-spectrometry - important applied technology that is headlong introduced in medical microbiology. The main achievement of mass-spectrometry is fast and valid identification of most species of microbes actual for medicine both in pure growths and biologic samples. There are only single taxonomic which representatives are identified unreliably in case of using of mass-spectrometry. The examples are given concerning methods of intraspecific identification of clinically/epidemiologically significant strains and evaluation of their characteristics, including virulence and resistance. The perspectives of mass-spectrometry are related to implementation into microbiological practice the modes of evaluation of virulence, resistance and identification of microorganisms in mixed cultures (including biological samples) and absence of standard criteria in evaluation of antibiotic resistance of microbes.

[BIOFILM FORMATION BY STREPTOCOCCUS PNEUMONIAE].

The biofilm process in Streptococcus pneumoniae (pneumococcus) is described. Virtually all wild-type pneumococci are capable of the biofilm formation. The pneumococcal capsule may reduce the biofilm production, and the propensity to form biofilms has a reverse correlation with the amount of the capsule material. Invasive pneumococcal isolates and noninvasive strains that persist in the nasopharynx have different biofilm potential. A number of issues related to effector and regulatory factors in the pneumococcal biofilms are discussed in this review. In the summary, a biofilm may be essential only for the persistent pneumococcal infection.

Scanning electron microscopy of biofilms adherent to the inner catheter surface.

The inner surface of the drainage catheter used in surgical interventions for biliary system pathologies was examined by scanning electron microscopy. Microflora in the catheter lumen reflects etiological characteristics of the pathological process and helps to predict possible complications. The developed scanning electron microscopy imaging technique of visualization of the fi ne spatial structure of microbial biofilm formed on the catheter surface allows describing the cell pool and structure of the biofilm.

[Acinetobacter: microbiological, pathogenetic and resistant properties].

Species of the genus Acinetobacter represent opportunistic bacteria with a growing clinical significance. In this literature review, we focus on the current role of Acinetobacter in infectious pathology and describe physiology, taxonomy, ecology, pathogenicity, and antibiotic resistance of these bacteria. Molecular pathogenesis and regulation of virulence factors in Acinetobacter spp. are described in detail. The majority of acinetobacterial infections are associated with A. baumannii and occur predominantly in an immunocompromised host. Usually, acinetobacterial infections are characterized by local purulent inflammation; in severe cases, meningitis and sepsis may develop. Antibiotic resistance ofAcinetobacter is a major clinical problem; therefore we give special attention to laboratory testing of resistance as well as identification of Acinetobacter. In addition, treatment and prophylaxis of acinetobacterial infections are discussed.

[Neutrophils and bacterial biofilms: dialectics of relationship].

The review is dedicated to the problem of interaction of human neutrophils with bacterial biofilms that complicate the course of infectious process. Neutrophils being the most important effectors of innate immunity may attack bacterial biofilms causing their rejections and damage of biofilm microbes. Mechanisms of neutrophil-dependent destruction of biofilms are analyzed in the review. Variants of defense of biofilm bacteria from phagocytosis that are used by them for evading neutrophils and consolidation of biofilm structures are discussed.

Application of Dimethicone to Prevent Culture Media from Drying in Microbiological Diagnostics.

The search for novel modifications of culture media aimed at culture prolongation is a prerequisite for microbiological diagnostic progress. The aim of the study was to assess the possibilities of applying dimethicone (polymethylsiloxane) as a barrier between the agar surface and atmosphere to prevent drying of solid and semisolid culture medium providing the retention of its useful properties. Materials and Methods: We studied the dynamics of water (volume) loss of culture media used in microbiology, and the effect of dimethicone on the process. Dimethicone was arranged in layers on culture medium surface. The effect of dimethicone on growth and generation of fast-growing (Staphylococcus aureus, Escherichia coli, Salmonella enterica Serovar Typhimurium, Burkholderia cenocepacia) and slow-growing (Mycobacterium avium) bacteria was studied, as well as on bacterial mobility (Pseudomonas aeruginosa and Escherichia coli) in semisolid agars. Results: The dynamics of water loss in culture media showed the weight loss in all media without dimethicone (control) in 24 h to be statistically significant (p<0.05); 7-8 days later, they lost 50% of weight, and 14 days later they lost approximately 70%. The weight of media under dimethicone underwent no significant changes during the observation period. Growth index of fast-growing bacteria (S. aureus, E. coli, S. Typhimurium, B. cenocepacia) on control culture media without applying any substance, and on culture media under dimethicone had no significant differences. Visible M. avium growth on chocolate agar in controls was recorded on day 19, under dimethicone - on days 18-19. The number of colonies on culture day 19 under dimethicone tenfold exceeded the control values. The mobility indices of P. aeruginosa and E. coli on semisolid agar under dimethicone 24 h later were significantly higher than under control conditions (p<0.05 in both cases). Conclusion: The study confirmed marked deterioration of culture media properties under prolonged cultivation. The suggested protection technology of culture media growth properties using dimethicone showed beneficial effects.

[Pseudomonas aeruginosa: characteristics of biofilm process].

Definition of the biofilm process as one of the types of intercellular bacterial communications is presented. The modern data concerning the structure of the Pseudomonas aeruginosa biofilm matrix and genetic mechanisms necessary for its production are described. Active and passive rejections of biofilm bacteria, which are the basis of bacterial spreading to new surfaces, are discussed. The complexity and chain type of the reactions associated with biofilm formation are emphasized.

[Mechanisms of antibiofilm immunity].

The formation of microbial biomembranes complicates clinical course of infectious diseases. The review deals with the problem of interaction between immune system and specific components of microbial biofilms. The immune mechanisms which may destroy biomembranes and damage biomembrane-associated microorganisms are analyzed. The vulnerable spots of immune defense against microbal biomembranes are described. This review also issues future prospects of immune-based control of microbal biomembrane processes.

[Neutrophil dependent breakdown of biofilms formed by Staphylococcus aureus].

AIM: Study of effects during interaction of neutrophils with Staphylococcus aureus biofilms in vitro. MATERIALS AND METHODS: 2 day biofilms (BF) based on Staphylococcus aureus (strain 5983) were used as a model. Destruction of BF was evaluated at 5, 15, 30, 45 and 60 minutes of incubation with neutrophils. Quantitative evaluation of staphylococci was performed by using microfilming (Shangrao Optical Instruments) and a computer program described by I.V.Chebotaret al., 2010. Measurement of thickness of BF during reaction with neutrophils was evaluated by using laser scanning microscope LSM 510 Meta (Zeiss). RESULTS: Human neutrophils can influence the breakdown effect on BF formed by S. auerus. A pronounced breakdown was observed at 15 minutes of the reaction, by 45 minutes staphylococci content in the BF remained only around 2%. Breakdown of BF was accompanied by an increase of quantity of viable staphylococci in the supernatant. Around 80% of neutrophils perished at 30 minutes of interaction with BE Neutrophil lysate at 30 minutes caused 30% destruction of staphylococci BF. CONCLUSION: Adhesive staphylococci are more resistant to the effect of neutrophils than BE Neutrophil dependent destruction of staphylococci BF could be the result ofbreakdown of intracellular matrix by phagocyte secretion products and direct phagocytosis.

[Interspecies interaction of bacteria and the formation of mixed (polymicrobial) biofilm].

Natural biofilms rarely exist as monocultures. Usually they are formed from various microorganism species that interact with each other, have shared metabolites, strengthen the attachment of each other to the support substrate, provide expression of "foreign" genes etc. Material on factors and mechanisms that determine the formation of mixed (polymicrobial) biofilms is analyzed in the review. The significance of interspecies interaction between bacteria based on QS system signal autoinductors is underlined. Examples of humoral and contact communications between bacteria and eukaryotes including host cells are provided. Study of polymicrobial processes and their interaction with innate and adaptive immune response seems important for further development of medical microbiology (especially regarding chronic infectious diseases).

[Staphylococcal biofilms: structure, regulation, rejection].

Staphylococci are able to cause chronic (persistent) infections, which develop in native tissues as well as on invasive materials artificially introduced into an organism. Such infections are associated with formation of biofilms. The review determines the definition of biofilms, describes factors, which contribute to their formation, characterizes adaptive stability of staphylococcal biofilms, which provides their long-term persistence in host organism. Genetic organization and regulation of polysaccharide and protein biofilms of staphylococci are described. Strategy for prevention and treatment of staphylococcal biofilm diseases is discussed.

Computer Program for Detection and Analyzing the Porin-Mediated Antibiotic Resistance of Bacteria.

The aim of this work was to develop a new software tool for identifying gene mutations that determine the porin-mediated resistance to antibiotics in gram-negative bacteria and to demonstrate the functionality of this program by detecting porin-mediated resistance to carbapenems in clinical isolates of Pseudomonas aeruginosa. Materials and Methods: The proposed algorithm is based on searching for a correspondence between the reference and the studied genes. When the sought nucleotide sequence is found in the analyzed genome, it is compared with the reference one and analyzed. The genomic analysis is then verified by comparing between the amino acid sequences encoded by the reference and studied genes. The genes of the susceptible P. aeruginosa ATCC 27853 strain were used as the reference nucleotide sequences encoding for porins (OprD, OpdD, and OpdP) involved in the transport of carbapenems into the bacterial cell. The complete genomes of clinical P. aeruginosa isolates from the PATRIC database 3.6.9 and our own collection were used to test the functionality of the proposed program. The analyzed isolates were phenotypically characterized according to the CLSI standard. The search for carbapenemase genes in the studied genomes of P. aeruginosa was carried out using the ResFinder 4.1. Results: The developed program for detecting the genetic determinants of non-plasmid antibiotic resistance made it possible to identify mutations of various types and significance in the porin genes of P. aeruginosa clinical isolates. These mutations led to modifications of the peptide structure of porin proteins. Single amino acid substitutions prevailed in the OpdD and OpdP porins of carbapenem-susceptible and carbapenem-resistant isolates. In the carbapenem-resistant strains, the gene encoding for OprD porin was found heavily modified, including insertions and/or deletions, which led to premature termination of porin synthesis. In several isolates resistant to meropenem, no mutations were detected in the gene encoding for OprD, which might be associated with alternative mechanisms of resistance to carbapenems. Conclusion: The proposed software product can become an effective tool for deciphering the molecular genetic mechanisms of bacterial chromosomal resistance to antibiotics. Testing the program revealed differences between the occurrences of mutations significant for carbapenem resistance in the oprD, opdD, and opdP genes.