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  • 1
    Online Resource
    Online Resource
    Development of accelerated genodiagnosis method of pertussis and pertussis-like diseases on the basis of mPCR-RT
    EKOlab ; 2020
    In:  Russian Clinical Laboratory Diagnostics Vol. 65, No. 9 ( 2020-09-16), p. 567-573
    Details
    In: Russian Clinical Laboratory Diagnostics, EKOlab, Vol. 65, No. 9 ( 2020-09-16), p. 567-573
    Abstract: The aim of the work was to develop an accelerated genodiagnosis method based on mPCR-RT for the detection DNA of B. pertussis, B. parapertussis, B. holmesii. Materials and methods. The study used 104 strains of microorganisms, of which: 50 strains of B. pertussis, 37 - B. parapertussis, 17 - heterologous species of microorganisms. Assessment of analytical specificity was carried out using DNA strains of various microorganisms with a concentration at least 109 GE / ml. To check the analytical sensitivity we studied a series of serial dilutions of bacterial cultures of the control strains B. pertussis № 143, B. parapertussis № 38b, B. holmesii DSM 13416 with a concentration of 5x109 - 5 μm/ml. Results. Insertion sequences were chosen as diagnostic targets: for B. parapertussis - a specific fragment IS1001, for B. holmesii - a specific fragment hlIS1001, for B.pertussis - a fragment IS481. To develop a genodiagnosis method specific primers were designed and combined into a single multi-primer mixture, the composition of the reaction mixture and the amplification conditions were selected. The analytical sensitivity of the developed method for detecting pertussis and pertussis-like pathogens was 5×101 GE / ml. Verification of the developed methodology of gene diagnostics showed 100% analytical specificity. Conclusion. An accelerated genodiagnosis method based on mPCR-RT has been developed, it allows you to identify DNA of B. pertussis, B. parapertussis, B. holmesii, which expands the possibilities of examining patients with suspected pertussis and pertussis-like diseases in order to increase laboratory confirmation of the diagnosis.
    Type of Medium: Online Resource
    ISSN: 2412-1320 , 0869-2084
    URL: Issue
    URL: Journal
    URL: Article
    DOI: 10.18821/0869-2084-2020-65-9
    DOI: 10.18821/0869-2084
    DOI: 10.18821/0869-2084-2020-65-9-567-573
    Language: Unknown
    Publisher: EKOlab
    Publication Date: 2020
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  • 2
    Online Resource
    Online Resource
    OPTIMIZATION OF A METHOD OF ISOTHERMAL AMPLIFICATION (LAMP) FOR DIAGNOSIS OF WHOOPING COUGH
    Central Research Institute for Epidemiology ; 2018
    In:  Journal of microbiology, epidemiology and immunobiology Vol. 95, No. 5 ( 2018-10-28), p. 37-46
    Details
    In: Journal of microbiology, epidemiology and immunobiology, Central Research Institute for Epidemiology, Vol. 95, No. 5 ( 2018-10-28), p. 37-46
    Abstract: Aim. Optimization of the accelerated whooping cough method of isothermal amplification for DNA Bordetela pertussis. Materials and methods. The research was conducted on 35 standard collection strains and 169 strains of Bordetella allocated in bacteriological laboratories of territorial subjects of the Russian Federation. The research included 329 clinical samples received from patients with whooping cough and the persons, contact with them, hospitalized in IDCH No. 1 DZM. Chromosomal DNA was extracted with a standard method of boiling from strains, from clinical samples by means of commercial sets. Identification of causative agents of whooping cough were performed with use of the АмплиСенс® Bordetella multi-FL. Results. We performed optimization method of a diagnostics of whooping cough by LAMP with detection by means of an electrophoresis and with naked-eye inspection under normal light is developed. The developed method allows to detect a DNA of B.pertussis within 4 - 5 hours in clinical material. The analytical sensitivity was 102 GE/ml. Assessment of validity showed that the developed method possesses 99,6% sensitivity and 98,7% specificity; predictive value positiveness and negative result was 99,6% and 98,7%, respectively; the index of accuracy (diagnostic efficiency) - 99,4%; the likelihood ratio of positive and negative result - 76,6 and 0,004, respectively. Assessment of analytical reliability in 100% of cases showed convergence and reproducibility of a technique. Conclusion. Diagnostic test on DNA of B.pertussis identification by LAMP method will allow to increase efficiency of laboratory diagnosis of whooping cough.
    Type of Medium: Online Resource
    ISSN: 2686-7613 , 0372-9311
    URL: Issue
    URL: Article
    DOI: 10.36233/0372-9311-2018-5
    DOI: 10.36233/0372-9311-2018-5-37-46
    Language: Unknown
    Publisher: Central Research Institute for Epidemiology
    Publication Date: 2018
    SSG: 12
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  • 3
    Online Resource
    Online Resource
    MICROBIOCENOSIS OF SKIN IN BROMHIDROSIS PATIENTS
    Central Research Institute for Epidemiology ; 2017
    In:  Journal of microbiology, epidemiology and immunobiology Vol. 94, No. 5 ( 2017-10-28), p. 53-58
    Details
    In: Journal of microbiology, epidemiology and immunobiology, Central Research Institute for Epidemiology, Vol. 94, No. 5 ( 2017-10-28), p. 53-58
    Abstract: Aim. Evaluate the composition of microorganisms of skin microbiocenosis of axilla in brom-hidrosis patients. Materials and methods. 23 patients were examined (11 - 17 years) under the observation at Pirogov CCDC of the National Medical-Surgery Centre. Identification was carried out using biochemical test-systems BioMerieux VITEK MS MALDI-TOF («bioMerieux», France) and 16SrRNA genesequencing with consequent juxtaposition with EMBL/NCBI. Medium and high degree of skin seeding with microbiota was present in most of the patients with bromhidrosis (52.2 and 43.5%). 137 strains belonging to 5 genera of microorganisms were identified - Corynebacterium, Staphylococcus, Moraxella, Micrococcus, Candida and Bacillus spp. Coiynehacte-rium genus strains (8 species) and Staphylococcus genus (5 species) prevailed in microbiocenosis (89.1%). C. tuberculostearicum strains dominated among Corynebacterium, and S. hominis - Staphylococcus. Conclusion. In most of the cases (82.6%) in patients microbiocenosis of skin of axilla was presented by consortiums of microorganisms with prevalence of Corynebacterium and Staphylococcus microorganisms.
    Type of Medium: Online Resource
    ISSN: 2686-7613 , 0372-9311
    URL: Issue
    URL: Article
    DOI: 10.36233/0372-9311-2017-5
    DOI: 10.36233/0372-9311-2017-5-53-58
    Language: Unknown
    Publisher: Central Research Institute for Epidemiology
    Publication Date: 2017
    SSG: 12
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  • 4
    Online Resource
    Online Resource
    PCR-based diagnosis of whooping cough in the Russian Federation
    EKOlab ; 2021
    In:  Russian Clinical Laboratory Diagnostics Vol. 66, No. 1 ( 2021-02-10), p. 52-58
    Details
    In: Russian Clinical Laboratory Diagnostics, EKOlab, Vol. 66, No. 1 ( 2021-02-10), p. 52-58
    Abstract: The aim was to determine how often the PCR method is used in different laboratories in Russia. In 2018, we conducted a questionnaire survey in diagnostic laboratories of medical organizations and the Centers of Hygiene and Epidemiology that performed PCR studies to identify microorganisms of the genus Bordetella in all 85 Russian regions. We found that in 2013 the PCR was used in 33 (38.8%) regions, but in 2017 the number of regions increased to 64 (75.3%). During 2013-2017 the study has not been applied in 21 regions. The number of PCR tests performed in the laboratories of medical organizations was significantly different. There has been an increase in the number of tests for the diagnosis of pertussis among people with clinical signs of infection and among contact persons in foci of infection. Compared to the Centers of Hygiene and Epidemiology, in medical organizations the rate of introduction of the PCR was higher. Between 2013 and 2017 the proportion of samples containing DNA B.pertussis decreased, but the proportion of samples containing DNA of other representatives of the genus Bordetella increased. Moreover, in the case of isolation DNA Bordetella spp. clinicians diagnose «Whooping cough, other unspecified organism», since there is no information on the species of the pathogen. Thus, in order to improve the diagnosis of pertussis, it is necessary to optimize PCR tests by including target genes that allow to identify of currently relevant DNAs of different representatives of the genus Bordetella.
    Type of Medium: Online Resource
    ISSN: 2412-1320 , 0869-2084
    URL: Issue
    URL: Journal
    URL: Article
    DOI: 10.18821/0869-2084-2021-66-1
    DOI: 10.18821/0869-2084
    DOI: 10.18821/0869-2084-2021-66-1-52-58
    Language: Unknown
    Publisher: EKOlab
    Publication Date: 2021
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  • 5
    Online Resource
    Online Resource
    EFFECTIVENESS OF MOLECULAR-GENETIC DIAGNOSTICS DURING PERTUSSIS INFECTION FOCI EXAMINATION
    SPb RAACI ; 2017
    In:  Russian Journal of Infection and Immunity Vol. 7, No. 2 ( 2017-06-19), p. 162-170
    Details
    In: Russian Journal of Infection and Immunity, SPb RAACI, Vol. 7, No. 2 ( 2017-06-19), p. 162-170
    Abstract: Purpose: whooping cough diagnostics by molecular-genetic methods.Materials and methods. Under observation there were 4930 people during the period from 2012 to 2015. All samples were received in 8 schools of Moscow and the Moscow region: in 3 schools had been found children with whooping cough, in other 5 schools – only children with prolonged cough. Whooping cough diagnosis had been given earlier by bacteriological and serological methods. 430 clinical samples were studied by 2 methods: PCR with fluorescent hybridized detection of amplified products and isothermal amplification.Results. In three of eight schools whooping cough cases at 7 children at the age of 7, 9, 11 and 15 years were revealed earlier. The diagnosis of whooping cough at them was confirmed by means of bacteriological and serological methods. 33 positive DNA samples (7.7%) are revealed. DNA-positive samples are allocated from 18 pupils and 15 employees of schools. In two schools where earlier infection sources were established, 15 DNA-positive samples from which in three cases clinical manifestations were observed are revealed. In those schools where it wasn’t earlier established a source of an infection and examinations conducted it is long the coughing children, 18 DNA-positive samples are revealed, and in two cases clinical manifestations in the form of cough were observed.Conclusion. Performed research confirmed high efectiveness of molecular-genetic methods during pertussis infection foci examination in schools for infection source identification also amongst long coughing children. 
    Type of Medium: Online Resource
    ISSN: 2313-7398 , 2220-7619
    URL: Issue
    URL: Article
    DOI: 10.15789/2220-7619-2017-2
    DOI: 10.15789/2220-7619-2017-2-162-170
    Language: Unknown
    Publisher: SPb RAACI
    Publication Date: 2017
    detail.hit.zdb_id: 3046274-5
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  • 6
    Online Resource
    Online Resource
    Effect of different types of dry swabs and their storage conditions on the inoculation of Corynebacterium diphtheriae
    EKOlab ; 2022
    In:  Russian Clinical Laboratory Diagnostics Vol. 67, No. 5 ( 2022-05-21), p. 296-300
    Details
    In: Russian Clinical Laboratory Diagnostics, EKOlab, Vol. 67, No. 5 ( 2022-05-21), p. 296-300
    Abstract: The results of evaluating the effectiveness of C. diphtheriae inoculation using different types of dry swabs in studies simulating various conditions of its storage at the preanalytical stage of a laboratory study for diphtheria are presented. A typical toxigenic strain of C. diphtheriae biovar gravis No. 665 was used. A commercial dry, sterile cotton swab probe (Ningbo Greetmed Medical Instruments Co., LTD, China), a commercial dry, sterile swab probe (plastic and viscose) (COPAN, Italy), tufters with a fluffy probe-tampon on a polystyrene applicator, standard (DELTALAB, SL, Spain). The tampons were pooled with a 24-hour bacterial culture of C. diphtheriae, then immediately seeded on Tellurite-containing blood agar and Corynebacagar. Storage conditions were simulated for 3 hours: at room conditions +(20-25)°C, in the refrigerator +(4-8)°C, in a thermostat +(37±1)°C. Optimal storage of C. diphtheriae on all three types of dry swabs at + (4-8) ° C; at +(20-25)° C - growth is observed when seeding from a cotton swab; in a swab with a fleecy probe-tampon, a decrease in the inoculation of C. diphtheriae was noted; when using a viscose swab - a significant loss of C. diphtheriae. At +(37±1)°C, a significant decrease in the inoculation of C. diphtheriae on all three types of tampons was noted, up to the absence of growth when using a viscose tampon. To exclude the loss of C. diphtheriae, it is necessary to observe the conditions for taking and storing biological material at the preanalytical stage of a laboratory study, which will improve the quality of laboratory microbiological studies for diphtheria infection.
    Type of Medium: Online Resource
    ISSN: 2412-1320 , 0869-2084
    URL: Issue
    URL: Article
    DOI: 10.51620/0869-2084-2022-67-5
    DOI: 10.51620/0869-2084-2022-67-5-296-300
    Language: Unknown
    Publisher: EKOlab
    Publication Date: 2022
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  • 7
    Online Resource
    Online Resource
    Comparative tests of quality of bacteriological investigation with Corynebacterium diphtheriae isolation
    EKOlab ; 2021
    In:  Russian Clinical Laboratory Diagnostics Vol. 66, No. 8 ( 2021-08-13), p. 509-512
    Details
    In: Russian Clinical Laboratory Diagnostics, EKOlab, Vol. 66, No. 8 ( 2021-08-13), p. 509-512
    Abstract: The results of comparative experimental studies of identification of nontoxigenic C. diphtheriae strain by three different commercial laboratories are presented. A typical nontoxigenic strain of C. diphtheriae biovar mitis was used. For the studies, three lines of ten-fold dilutions of bacterial culture were prepared, followed by control planting on the medium and counting CFU/ml. In the experiment, tampons were pooled with a 24-hour bacterial culture of a nontoxigenic C. diphtheriae strain. Tampons were provided from three different laboratories - ∑-Transwab® with Ames liquid medium (from the first and second laboratories) and a viscose tampon with coal medium (from the third laboratory). After pooled, tampons were delivered to commercial laboratories. And as a result of the experiment, Corynebacterium spp. was identified in first laboratory (103 CFU/tamp), S. epidermidis (102 CFU/ml) - in second laboratory and nontoxigenic C. diphtheriae biovar gravis - in third laboratory. The study indicates that there is a need to the supervision of bacteriological investigations conducted in various laboratories. This will improve the quality of investigations on diphtheria infection and identify of diphtheria carrier, which is a reservoir of the causative agent of diphtheria, and will contribute to the maintenance of sanitary and epidemiological well-being in our country.
    Type of Medium: Online Resource
    ISSN: 2412-1320 , 0869-2084
    URL: Issue
    URL: Article
    DOI: 10.51620/0869-2084-2021-66-8
    DOI: 10.51620/0869-2084-2021-66-8-509-512
    Language: Unknown
    Publisher: EKOlab
    Publication Date: 2021
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  • 8
    Online Resource
    Online Resource
    AN ACCELERATED METHOD OF DIPHTHERIA GENE DIAGNOSTICS BASED ON ISOTHERMAL AMPLIFICATION TO DETECT DNA OF THE CAUSATIVE AGENT
    Central Research Institute for Epidemiology ; 2017
    In:  Journal of microbiology, epidemiology and immunobiology Vol. 94, No. 5 ( 2017-10-28), p. 24-32
    Details
    In: Journal of microbiology, epidemiology and immunobiology, Central Research Institute for Epidemiology, Vol. 94, No. 5 ( 2017-10-28), p. 24-32
    Abstract: Aim. Development of an accelerated method of gene diagnostics of diphtheria based on isothermal amplification for detection of DNA of the causative agent. Materials and methods. The study was carried out in typical collection strains from GKPM-Obolensk, as well as in 135 strains of C. diphtheriae isolated from bacteriological laboratories of the regions of Russian Federation and sent to the Gabrichevsky Moscow Research Institute of Epidemiology and Microbiology Strain isolation was carried out in accordance with Ml 4.2.698-98 and 4.2.3065-13. Chromosomal DNA was isolated by standard heating method, as well as using 3 commercial kits. Detection of the amplification results was carried out in horizontal electrophoresis in 1.5% agarose gel. Results. The developed method of gene diagnostics was established to allow detection of DNA of toxigenic C. diphtheriae strains of 2 biovars, as well as DNA of non-toxigenic tox-gene bearing strains (NTTB) of C. diphtheriae mitis biovar with mechanisms of lack of expression of diphtheria toxin gene due to the presence of deletion or mobile genetic IS element in the tox gene. Non-toxigenic tox-gene bearing C. diphtheriae strain with the mechanism of lack of diphtheria toxin gene expression due to the presence of transposon in the tox gene are identified as non-toxigenic. Evaluation of the analytical sensitivity in comparative studies using 3 commercial kits for FNA isolation has shown that sensitivity reached 4.5x 101 GE/ml using Ribo-prep kit. H igh specificity of the developed method is shown, it was evaluated in 18 strains of 16 other members of the Corynebacterium genus and 20 typical strains of microorganisms isolated from oropharynx or causing infections of the respiratory tract. Approbation of the developed method was carried out in model experiments in imitators of clinical samples by infection of single-use sterile dry tampons by consecutive dilutions of the bacterial cultures (with parallel seeding into dense nutrient media) and was 103 GE/ml. Conclusion. The developed method of accelerated gene diagnostics of the diphtheria infection has a high diagnostic effectiveness, specificity and sensitivity, allows to detect 103 - 4.5x10 GE/ml C. diphtheriae in clinical material with simultaneous verification of toxigenic and non-toxigenic strains.
    Type of Medium: Online Resource
    ISSN: 2686-7613 , 0372-9311
    URL: Issue
    URL: Article
    DOI: 10.36233/0372-9311-2017-5
    DOI: 10.36233/0372-9311-2017-5-24-32
    Language: Unknown
    Publisher: Central Research Institute for Epidemiology
    Publication Date: 2017
    SSG: 12
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  • 9
    Online Resource
    Online Resource
    Status and problems of bacteriological diagnosis of diphtheria infection in the Russian Federation
    EKOlab ; 2020
    In:  Russian Clinical Laboratory Diagnostics Vol. 65, No. 11 ( 2020-12-04), p. 717-723
    Details
    In: Russian Clinical Laboratory Diagnostics, EKOlab, Vol. 65, No. 11 ( 2020-12-04), p. 717-723
    Abstract: The purpose of the work was to assess the state of bacteriological diagnosis of diphtheria infection in Russia in order to establish possible reasons for the decrease in the release of C. diphtheriae. The Reference Center for Monitoring the Pathogens of Measles, Rubella, Mumps, Pertussis and Diphtheria in 2018 in 85 subjects of Russia conducted a questionnaire of laboratories of medical organizations and the Centers for Hygiene and Epidemiology of Rospotrebnadzor, carrying out bacteriological studies for diphtheria infection. It was found that the number of studies conducted over the five-year period decreased by 1.2 times. The tendency to decrease the number of bacteriological studies for diphtheria is observed in the territories of almost all federal districts. In 99% and 29% of cases, the institutions of the FBUZ Centers for Hygiene and Epidemiology and medical organizations (MO) and use in their work documents regulating bacteriological studies for diphtheria infection. In a number of territories, the list of documents used includes documents that are invalid or do not define such studies. Most organizations use dry tampons when examining for diphtheria, however, 13.1% and 53.4% of FBUZ Centers for Hygiene and Epidemiology and medical organizations (respectively) use commercial transport environments, which does not comply with regulatory documentation. Analysis of the quality of work of bacteriological laboratories showed shortcomings at the stage of preparation of media (use of donor blood, or absence of addition of blood and potassium tellurite), Elek tests (addition of horse serum or absence of serum to the medium), setting of incomplete biochemical series (absence of tests for urease and nitrate reductase), absence of standard control strains, incomplete volume of internal laboratory quality control. Given the continuing circulation of the pathogen in various countries of the world and in our country, as well as the possibility of imported cases of infection from endemic regions, the analysis was aimed at drawing the attention of specialists to the problem of improving the quality of laboratory diagnosis of diphtheria in Russia.
    Type of Medium: Online Resource
    ISSN: 2412-1320 , 0869-2084
    URL: Issue
    URL: Journal
    URL: Article
    DOI: 10.18821/0869-2084-2020-65-11
    DOI: 10.18821/0869-2084
    DOI: 10.18821/0869-2084-2020-65-11-717-723
    Language: Unknown
    Publisher: EKOlab
    Publication Date: 2020
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  • 10
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    Online Resource
    The structure of the oropharyngeal genus Candida fungi community in HIVinfected patients
    SPb RAACI ; 2020
    In:  Russian Journal of Infection and Immunity Vol. 11, No. 4 ( 2020-10-08), p. 737-745
    Details
    In: Russian Journal of Infection and Immunity, SPb RAACI, Vol. 11, No. 4 ( 2020-10-08), p. 737-745
    Abstract: At the present time virtually no data are available about the structure of the genus Candida fungus able to target HIV-infected patients and serve as an etiological factor of candidiasis. The aforementioned shaped the aim of the study: to examine structure of the Candida genus community colonizing the oropharynx in HIV-infected patients with clinical manifestations of oropharyngeal candidiasis. There was conducted a microbiological study of the oropharynx in 31 HIV-infected patients (51.6% males and 48.4% females) with clinical manifestations of oropharyngeal candidiasis treated at Moscow Infectious Clinic No. 2 inpatient department in the years 2015–2017. We confirmed the diversity of the oropharyngeal Candida spp. community found in HIV-infected patients. Total 52 isolates of the genus Candida were isolated. C. albicans dominated in 57.7% cases, whereas C. glabrata prevailed (21.1%) among non-albicans species. Minor components were represented by C. tropicalis (11.5%) and C. krusei (9.6%). C. albicans and C. glabrata were sensitive to polyenes, whereas minor community components — to itroconazole and clotrimazole. The vast majority of fungal strains were resistant to fluconazole. The genus Candida community reveals a unique architecture so that any member may exist in the oropharyngeal biotope of HIV-infected patients as a monoculture or in association: homogeneous, consisting of a single species strains, or heterogeneous, formed by several species. Candida fungi in 18 patients (58.1%) were isolated as a monoculture, whereas in 13 (41.9%) subjects — in association consisting of 34 isolates (65.4% of total number), of which 16 (30.8%) and 18 (34.6%) were isolated from homogeneous and heterogeneous associations, respectively. There were identified 9 two-component associations (69.2%), and 4 (30.8%) consisting of three or more components. It turned out that pattern of the examined community was mainly determined by species composition that agrees with previous data. Most common associations were presented by C. krusei (100%) and C. albicans (73.3%). Upon that, most often C. albicans (72.7%) formed a homogeneous type of associations. Sensitivity of Candida fungi to antimycotic drugs also depended on the architecture of related community. C. albicans isolates in heterogeneous associations revealed a wide range of resistance acquired by contact with non-albicans species.
    Type of Medium: Online Resource
    ISSN: 2313-7398 , 2220-7619
    URL: Article
    DOI: 10.15789/2220-7619-TSO-1450
    Language: Unknown
    Publisher: SPb RAACI
    Publication Date: 2020
    detail.hit.zdb_id: 3046274-5
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