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Voronina EN, Gordukova MA, Turina IE, Mishukova OV, Dymova MA, Galeeva EV, Korsunskiy AA, Filipenko ML. Molecular characterization of Mycoplasma pneumoniae infections in Moscow from 2015 to 2018. Eur J Clin Microbiol Infect Dis 2019; 39:257-263. [PMID: 31655931 DOI: 10.1007/s10096-019-03717-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 09/20/2019] [Indexed: 11/28/2022]
Abstract
The aim of this study was to assess which Mycoplasma pneumoniae genotypes were present in Moscow during the years 2015-2018 and whether the proportion between detected genotypes changed over time. We were also interested in the presence of macrolide resistance (MR)Mycoplasma pneumoniae. We performed multilocus variable-number tandem-repeat (VNTR) analysis (MLVA), SNP typing, and mutation typing in the 23S rRNA gene from 117 M. pneumoniae clinical isolates. Our analysis suggests two major MLVA types: 4572 and 3562. In 2017-2018, MLVA type 4572 gradually became predominant. In general, the SNP type range is the same as described earlier for European countries. The analysis of MR mutations showed that 7% of the isolates had an A2063G mutation in the 23S rRNA gene with no isolates carrying an A2064G mutation. In 2017-2018, MLVA type 4572 (SNP type 1) begins to spread in Moscow, which was widespread globally, especially in Asian countries. SNP typing of our sample showed higher discriminatory power than MLVA typing.
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Affiliation(s)
- Elena N Voronina
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Lavrentjeva, 8, Novosibirsk, Russia, 630090. .,Department of Molecular Biology, Novosibirsk State University, Pirogova, 2, Novosibirsk, Russia, 630090.
| | - Maria A Gordukova
- Moscow City Pediatric G. Speransky Clinical Hospital, No. 9, Shmitovsky Proezd 29, Moscow, Russia, 123317
| | - Irina E Turina
- The Federal State Autonomous Educational Institution of Higher Education "The I.M. Sechenov First Moscow State Medical University" of the Ministry of Health of the Russian Federation , Pogodinskaya St. 1, Moscow, Russia, 119991
| | - Olga V Mishukova
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Lavrentjeva, 8, Novosibirsk, Russia, 630090
| | - Maya A Dymova
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Lavrentjeva, 8, Novosibirsk, Russia, 630090
| | - Elena V Galeeva
- Moscow City Pediatric G. Speransky Clinical Hospital, No. 9, Shmitovsky Proezd 29, Moscow, Russia, 123317
| | - Anatoliy A Korsunskiy
- Moscow City Pediatric G. Speransky Clinical Hospital, No. 9, Shmitovsky Proezd 29, Moscow, Russia, 123317.,The Federal State Autonomous Educational Institution of Higher Education "The I.M. Sechenov First Moscow State Medical University" of the Ministry of Health of the Russian Federation , Pogodinskaya St. 1, Moscow, Russia, 119991
| | - Maxim L Filipenko
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Lavrentjeva, 8, Novosibirsk, Russia, 630090.,Department of Molecular Biology, Novosibirsk State University, Pirogova, 2, Novosibirsk, Russia, 630090
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Deripapa E, Balashov D, Rodina Y, Laberko A, Myakova N, Davydova NV, Gordukova MA, Abramov DS, Pay GV, Shelikhova L, Prodeus AP, Maschan MA, Maschan AA, Shcherbina A. Prospective Study of a Cohort of Russian Nijmegen Breakage Syndrome Patients Demonstrating Predictive Value of Low Kappa-Deleting Recombination Excision Circle (KREC) Numbers and Beneficial Effect of Hematopoietic Stem Cell Transplantation (HSCT). Front Immunol 2017; 8:807. [PMID: 28791007 PMCID: PMC5523727 DOI: 10.3389/fimmu.2017.00807] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/26/2017] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Nijmegen breakage syndrome (NBS) is a combined primary immunodeficiency with DNA repair defect, microcephaly, and other phenotypical features. It predominantly occurs in Slavic populations that have a high frequency of carriers with the causative NBN gene c.657_661del5 mutation. Due to the rarity of the disease in the rest of the world, studies of NBS patients are few. Here, we report a prospective study of a cohort of Russian NBS patients. METHODS 35 Russian NBS patients of ages 1-19 years, referred to our Center between years 2012 and 2016, were prospectively studied. RESULTS Despite the fact that in 80% of the patients microcephaly was diagnosed at birth or shortly thereafter, the average delay of NBS diagnosis was 6.5 years. Though 80% of the patients had laboratory signs of immunodeficiency, only 51% of the patients experienced significant infections. Autoimmune complications including interstitial lymphocytic lung disease and skin granulomas were noted in 34%, malignancies-in 57% of the patients. T-cell excision circle (TREC)/kappa-deleting recombination excision circle (KREC) levels were low in the majority of patients studied. Lower KREC levels correlated with autoimmune and oncological complications. Fifteen patients underwent hematopoietic stem cell transplantation (HSCT), 10 of them were alive and well, with good graft function. Three patients in the HSCT group and five non-transplanted patients died; tumor progression being the main cause of death. The probability of the overall survival since NBS diagnosis was 0.76 in the HSCT group and 0.3 in the non-transplanted group. CONCLUSION Based on our findings of low TRECs in most NBS patients, independent of their age, TREC detection can be potentially useful for detection of NBS patients during neonatal screening. KREC concentration can be used as a prognostic marker of disease severity. HSCT is a viable treatment option in NBS and should be especially considered in patients with low KREC numbers early on, before development of life-threatening complications.
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Affiliation(s)
- Elena Deripapa
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Dmitry Balashov
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Yulia Rodina
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Alexandra Laberko
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Natalya Myakova
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Nataliia V. Davydova
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russia
- Speransky Children’s Hospital, Moscow, Russia
| | | | - Dmitrii S. Abramov
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Galina V. Pay
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Larisa Shelikhova
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Andrey P. Prodeus
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russia
- Speransky Children’s Hospital, Moscow, Russia
| | - Mikhail A. Maschan
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Alexey A. Maschan
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russia
| | - Anna Shcherbina
- Dmitry Rogachev National Research and Clinical Center for Pediatric Hematology, Oncology and Immunology, Moscow, Russia
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Fantin YS, Neverov AD, Favorov AV, Alvarez-Figueroa MV, Braslavskaya SI, Gordukova MA, Karandashova IV, Kuleshov KV, Myznikova AI, Polishchuk MS, Reshetov DA, Voiciehovskaya YA, Mironov AA, Chulanov VP. Base-calling algorithm with vocabulary (BCV) method for analyzing population sequencing chromatograms. PLoS One 2013; 8:e54835. [PMID: 23382983 PMCID: PMC3557274 DOI: 10.1371/journal.pone.0054835] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2012] [Accepted: 12/19/2012] [Indexed: 02/01/2023] Open
Abstract
Sanger sequencing is a common method of reading DNA sequences. It is less expensive than high-throughput methods, and it is appropriate for numerous applications including molecular diagnostics. However, sequencing mixtures of similar DNA of pathogens with this method is challenging. This is important because most clinical samples contain such mixtures, rather than pure single strains. The traditional solution is to sequence selected clones of PCR products, a complicated, time-consuming, and expensive procedure. Here, we propose the base-calling with vocabulary (BCV) method that computationally deciphers Sanger chromatograms obtained from mixed DNA samples. The inputs to the BCV algorithm are a chromatogram and a dictionary of sequences that are similar to those we expect to obtain. We apply the base-calling function on a test dataset of chromatograms without ambiguous positions, as well as one with 3-14% sequence degeneracy. Furthermore, we use BCV to assemble a consensus sequence for an HIV genome fragment in a sample containing a mixture of viral DNA variants and to determine the positions of the indels. Finally, we detect drug-resistant Mycobacterium tuberculosis strains carrying frameshift mutations mixed with wild-type bacteria in the pncA gene, and roughly characterize bacterial communities in clinical samples by direct 16S rRNA sequencing.
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Affiliation(s)
- Yuri S. Fantin
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
| | - Alexey D. Neverov
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander V. Favorov
- Department of Oncology, Division of Biostatistics and Bioinformatics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- State Research Institute of Genetics and Selection of Industrial Microorganisms GosNIIGenetika, Moscow, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | | | | | - Maria A. Gordukova
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
| | - Inga V. Karandashova
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
| | - Konstantin V. Kuleshov
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
| | - Anna I. Myznikova
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
| | - Maya S. Polishchuk
- Engelhardt Institute of Molecular Biology Russian Academy of Sciences, Moscow, Russia
- Department of Statistics, University of California, Berkeley, California, United States of America
| | - Denis A. Reshetov
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
| | - Yana A. Voiciehovskaya
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
| | - Andrei A. Mironov
- Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- Institute for Information Transmission Problems (the Kharkevich Institute), Moscow, Russia
| | - Vladimir P. Chulanov
- Federal State Institution of Science Central Research Institute of Epidemiology, Moscow, Russia
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