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de Neeling AJ, Tagliani E, Ködmön C, van der Werf MJ, van Soolingen D, Cirillo DM, Anthony RM. Characteristic SNPs defining the major multidrug-resistant Mycobacterium tuberculosis clusters identified by EuSeqMyTB to support routine surveillance, EU/EEA, 2017 to 2019. Euro Surveill 2024; 29:2300583. [PMID: 38516788 PMCID: PMC11063679 DOI: 10.2807/1560-7917.es.2024.29.12.2300583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 03/01/2024] [Indexed: 03/23/2024] Open
Abstract
BackgroundThe EUSeqMyTB project, conducted in 2020, used whole genome sequencing (WGS) for surveillance of drug-resistant Mycobacterium tuberculosis in the European Union/European Economic Area (EU/EEA) and identified 56 internationally clustered multidrug-resistant (MDR) tuberculosis (TB) clones.AimWe aimed to define and establish a rapid and computationally simple screening method to identify probable members of the main cross-border MDR-TB clusters in WGS data to facilitate their identification and track their future spread.MethodsWe screened 34 of the larger cross-border clusters identified in the EuSeqMyTB pilot study (2017-19) for characteristic single nucleotide polymorphism (SNP) signatures that could identify and define members of each cluster. We also linked this analysis with published clusters identified in previous studies and identified more distant genetic relationships between some of the current clusters.ResultsA panel of 30 characteristic SNPs is presented that can be used as an initial (routine) screen for members of each cluster. For four of the clusters, no unique defining SNP could be identified; three of these are closely related (within approximately 20 SNPs) to one or more other clusters and likely represent a single established MDR-TB clade composed of multiple recent subclusters derived from the previously described ECDC0002 cluster.ConclusionThe identified SNP signatures can be integrated into routine pipelines and contribute to the more effective monitoring, rapid and widespread screening for TB. This SNP panel will also support accurate communication between laboratories about previously identified internationally transmitted MDR-TB genotypes.
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Affiliation(s)
- Albert J de Neeling
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Elisa Tagliani
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Csaba Ködmön
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | | | - Dick van Soolingen
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Richard M Anthony
- National Tuberculosis Reference Laboratory, Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
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Akhmetova A, Bismilda V, Chingissova L, Filipenko M, Akilzhanova A, Kozhamkulov U. Prevalence of Beijing Central Asian/Russian Cluster 94-32 among Multidrug-Resistant M. tuberculosis in Kazakhstan. Antibiotics (Basel) 2023; 13:9. [PMID: 38275319 PMCID: PMC10812519 DOI: 10.3390/antibiotics13010009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 01/27/2024] Open
Abstract
The Beijing genotype is the most distributed M. tuberculosis family in Kazakhstan. In this study, we identified dominant Beijing clusters in Kazakhstan and assessed their drug susceptibility profiles and association with the most widely spread mutation Ser531Leu of the rpoB gene and the mutation Ser315Thr of the katG gene associated with resistance to rifampicin and isoniazid, respectively. M. tuberculosis isolates (n = 540) from new TB cases were included in the study. MIRU-VNTR genotyping was performed for 540 clinical isolates to determine M. tuberculosis families using 24 loci. RD analysis was additionally performed for the Beijing isolates. The identification of mutations in the drug-resistance genes of M. tuberculosis was performed with allele-specific real-time PCR and Sanger sequencing. The Beijing genotype was identified in 60% (324/540) of the clinical isolates. Central Asian/Russian cluster 94-32 was the most distributed cluster among the Beijing isolates (50.3%; 163/324). Three other dominant Beijing clusters were identified as 94-33 (3.4%; 11/324), 100-32 (3.1%; 10/324) and 99-32 (3.1%; 10/324). The Beijing genotype was associated with drug-resistant TB (p < 0.0001), including multidrug-resistant TB (p < 0.0001), in our study. An association of the mutation Ser531Leu of the rpoB gene with the Beijing genotype was found (p < 0.0001; OR = 16.0000; 95%CI: 4.9161-52.0740). Among the Beijing isolates, cluster 94-32 showed an association with MDR-TB (p = 0.021). This is why the evaluation of the Beijing genotype and its clusters is needed to control MDR-TB in Kazakhstan.
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Affiliation(s)
- Ainur Akhmetova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
- Department of General Biology and Genomics, L.N. Gumilyov Eurasian National University, Astana 010000, Kazakhstan
| | - Venera Bismilda
- National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty 050000, Kazakhstan
| | - Lyailya Chingissova
- National Scientific Center of Phthisiopulmonology of the Republic of Kazakhstan, Almaty 050000, Kazakhstan
| | - Maxim Filipenko
- Laboratory of Pharmacogenomics, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630000, Russia
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Ainur Akilzhanova
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
| | - Ulan Kozhamkulov
- Laboratory of Genomic and Personalized Medicine, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana 010000, Kazakhstan
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Kharlamova N, Ogarkov O, Berdnikov I, Berdnikova N, Galeev R, Mokrousov I. Bioarchaeological and molecular evidence of tuberculosis in human skeletal remains from 18th-19th century orthodox cemeteries in Irkutsk, Eastern Siberia. Tuberculosis (Edinb) 2023; 143S:102368. [PMID: 38012918 DOI: 10.1016/j.tube.2023.102368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 06/20/2023] [Accepted: 06/25/2023] [Indexed: 11/29/2023]
Abstract
In this study, we tested the skeletal human remains from the 18th - early 19th century Orthodox cemeteries in Irkutsk, Eastern Siberia, for tuberculosis-associated morphological alterations and Mycobacterium tuberculosis DNA. The morphologically studied bone collection included 591 individuals of mainly Caucasian origin. The molecular methods (IS6110-PCR and spoligotyping) suggested that at least four individuals (out of 15 TB-suspected, DNA-tested) were positive for the presence of M. tuberculosis DNA. All of them were males (3 maturus, 1 maturus senilis). Two of them date back to the second and third quarters of the 18th century, another to the last quarter of the 18th century, and the last one to the second half of the 19th century. The combined molecular analysis cautiously suggested presence of different strains and at least some of them represented not the currently predominant in Siberia Beijing genotype (M. tuberculosis East-Asian lineage) but strains of European origin. In conclusion, this study presented bioarchaeological and molecular evidence of tuberculosis in human skeletal remains from 18th-19th century Orthodox cemeteries in Irkutsk, Eastern Siberia. The samples are not M. bovis and represent human M. tuberculosis sensu stricto. Their precise phylogenetic identity is elusive but evokes the European/Russian origin of at least some isolates.
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Affiliation(s)
- Natalia Kharlamova
- Center for Physical Anthropology, N.N. Mikloukho-Maklay Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, 119334, Russia.
| | - Oleg Ogarkov
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, 664003, Russia
| | - Ivan Berdnikov
- Scientific Research Center "Baikal Region", Irkutsk State University, Irkutsk, 664003, Russia
| | - Natalia Berdnikova
- Scientific Research Center "Baikal Region", Irkutsk State University, Irkutsk, 664003, Russia
| | - Ravil Galeev
- Laboratory of Facial Reconstruction, N.N. Mikloukho-Maklay Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, 119334, Russia
| | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, 197101, Russia.
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Zhdanova S, Jiao WW, Sinkov V, Khromova P, Solovieva N, Mushkin A, Mokrousov I, Belopolskaya O, Masharsky A, Vyazovaya A, Rychkova L, Kolesnikova L, Zhuravlev V, Shen AD, Ogarkov O. Insight into Population Structure and Drug Resistance of Pediatric Tuberculosis Strains from China and Russia Gained through Whole-Genome Sequencing. Int J Mol Sci 2023; 24:10302. [PMID: 37373451 DOI: 10.3390/ijms241210302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/07/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
This study aimed to determine phenotypic and genotypic drug resistance patterns of Mycobacterium tuberculosis strains from children with tuberculosis (TB) in China and Russia, two high-burden countries for multi/extensively-drug resistant (MDR/XDR) TB. Whole-genome sequencing data of M. tuberculosis isolates from China (n = 137) and Russia (n = 60) were analyzed for phylogenetic markers and drug-resistance mutations, followed by comparison with phenotypic susceptibility data. The Beijing genotype was detected in 126 Chinese and 50 Russian isolates. The Euro-American lineage was detected in 10 Russian and 11 Chinese isolates. In the Russian collection, the Beijing genotype and Beijing B0/W148-cluster were dominated by MDR strains (68% and 94%, respectively). Ninety percent of B0/W148 strains were phenotypically pre-XDR. In the Chinese collection, neither of the Beijing sublineages was associated with MDR/pre-XDR status. MDR was mostly caused by low fitness cost mutations (rpoB S450L, katG S315T, rpsL K43R). Chinese rifampicin-resistant strains demonstrated a higher diversity of resistance mutations than Russian isolates (p = 0.003). The rifampicin and isoniazid resistance compensatory mutations were detected in some MDR strains, but they were not widespread. The molecular mechanisms of M. tuberculosis adaptation to anti-TB treatment are not unique to the pediatric strains, but they reflect the general situation with TB in Russia and China.
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Affiliation(s)
- Svetlana Zhdanova
- Department of Epidemiology and Microbiology, Scientific Centre for Family Health and Human Reproduction Problems, 664003 Irkutsk, Russia
| | - Wei-Wei Jiao
- National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
| | - Viacheslav Sinkov
- Department of Epidemiology and Microbiology, Scientific Centre for Family Health and Human Reproduction Problems, 664003 Irkutsk, Russia
| | - Polina Khromova
- Department of Epidemiology and Microbiology, Scientific Centre for Family Health and Human Reproduction Problems, 664003 Irkutsk, Russia
| | - Natalia Solovieva
- St. Petersburg Research Institute of Phthisiopulmonology, 191036 St. Petersburg, Russia
| | - Alexander Mushkin
- St. Petersburg Research Institute of Phthisiopulmonology, 191036 St. Petersburg, Russia
| | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, 197101 St. Petersburg, Russia
- Henan International Joint Laboratory of Children's Infectious Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital Zhengzhou Children's Hospital, Zhengzhou 450012, China
| | - Olesya Belopolskaya
- The Bio-Bank Resource Center, Research Park, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Aleksey Masharsky
- The Bio-Bank Resource Center, Research Park, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anna Vyazovaya
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, 197101 St. Petersburg, Russia
| | - Lubov Rychkova
- Department of Epidemiology and Microbiology, Scientific Centre for Family Health and Human Reproduction Problems, 664003 Irkutsk, Russia
| | - Lubov Kolesnikova
- Department of Epidemiology and Microbiology, Scientific Centre for Family Health and Human Reproduction Problems, 664003 Irkutsk, Russia
| | - Viacheslav Zhuravlev
- St. Petersburg Research Institute of Phthisiopulmonology, 191036 St. Petersburg, Russia
| | - A-Dong Shen
- National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing 100045, China
- Henan International Joint Laboratory of Children's Infectious Diseases, Children's Hospital Affiliated to Zhengzhou University, Henan Children's Hospital Zhengzhou Children's Hospital, Zhengzhou 450012, China
| | - Oleg Ogarkov
- Department of Epidemiology and Microbiology, Scientific Centre for Family Health and Human Reproduction Problems, 664003 Irkutsk, Russia
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Saelens JW, Sweeney MI, Viswanathan G, Xet-Mull AM, Jurcic Smith KL, Sisk DM, Hu DD, Cronin RM, Hughes EJ, Brewer WJ, Coers J, Champion MM, Champion PA, Lowe CB, Smith CM, Lee S, Stout JE, Tobin DM. An ancestral mycobacterial effector promotes dissemination of infection. Cell 2022; 185:4507-4525.e18. [PMID: 36356582 PMCID: PMC9691622 DOI: 10.1016/j.cell.2022.10.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 08/27/2022] [Accepted: 10/16/2022] [Indexed: 11/11/2022]
Abstract
The human pathogen Mycobacterium tuberculosis typically causes lung disease but can also disseminate to other tissues. We identified a M. tuberculosis (Mtb) outbreak presenting with unusually high rates of extrapulmonary dissemination and bone disease. We found that the causal strain carried an ancestral full-length version of the type VII-secreted effector EsxM rather than the truncated version present in other modern Mtb lineages. The ancestral EsxM variant exacerbated dissemination through enhancement of macrophage motility, increased egress of macrophages from established granulomas, and alterations in macrophage actin dynamics. Reconstitution of the ancestral version of EsxM in an attenuated modern strain of Mtb altered the migratory mode of infected macrophages, enhancing their motility. In a zebrafish model, full-length EsxM promoted bone disease. The presence of a derived nonsense variant in EsxM throughout the major Mtb lineages 2, 3, and 4 is consistent with a role for EsxM in regulating the extent of dissemination.
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Affiliation(s)
- Joseph W Saelens
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Mollie I Sweeney
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Gopinath Viswanathan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ana María Xet-Mull
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kristen L Jurcic Smith
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Dana M Sisk
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Daniel D Hu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Rachel M Cronin
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Erika J Hughes
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - W Jared Brewer
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jörn Coers
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Matthew M Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Patricia A Champion
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA; Eck Institute for Global Health, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Craig B Lowe
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Clare M Smith
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Sunhee Lee
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA.
| | - Jason E Stout
- Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA; Division of Infectious Diseases and International Health, Duke University School of Medicine, Durham, NC 27710, USA.
| | - David M Tobin
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC 27710, USA; Department of Immunology, Duke University School of Medicine, Durham, NC 27710, USA.
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6
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Guo S, Chongsuvivatwong V, Lei S. Comparison on Major Gene Mutations Related to Rifampicin and Isoniazid Resistance between Beijing and Non-Beijing Strains of Mycobacterium tuberculosis: A Systematic Review and Bayesian Meta-Analysis. Genes (Basel) 2022; 13:genes13101849. [PMID: 36292734 PMCID: PMC9601453 DOI: 10.3390/genes13101849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 10/07/2022] [Accepted: 10/08/2022] [Indexed: 11/16/2022] Open
Abstract
Objective: The Beijing strain of Mycobacterium tuberculosis (MTB) is controversially presented as the predominant genotype and is more drug resistant to rifampicin and isoniazid compared to the non-Beijing strain. We aimed to compare the major gene mutations related to rifampicin and isoniazid drug resistance between Beijing and non-Beijing genotypes, and to extract the best evidence using the evidence-based methods for improving the service of TB control programs based on genetics of MTB. Method: Literature was searched in Google Scholar, PubMed and CNKI Database. Data analysis was conducted in R software. The conventional and Bayesian random-effects models were employed for meta-analysis, combining the examinations of publication bias and sensitivity. Results: Of the 8785 strains in the pooled studies, 5225 were identified as Beijing strains and 3560 as non-Beijing strains. The maximum and minimum strain sizes were 876 and 55, respectively. The mutations prevalence of rpoB, katG, inhA and oxyR-ahpC in Beijing strains was 52.40% (2738/5225), 57.88% (2781/4805), 12.75% (454/3562) and 6.26% (108/1724), respectively, and that in non-Beijing strains was 26.12% (930/3560), 28.65% (834/2911), 10.67% (157/1472) and 7.21% (33/458), separately. The pooled posterior value of OR for the mutations of rpoB was 2.72 ((95% confidence interval (CI): 1.90, 3.94) times higher in Beijing than in non-Beijing strains. That value for katG was 3.22 (95% CI: 2.12, 4.90) times. The estimate for inhA was 1.41 (95% CI: 0.97, 2.08) times higher in the non-Beijing than in Beijing strains. That for oxyR-ahpC was 1.46 (95% CI: 0.87, 2.48) times. The principal patterns of the variants for the mutations of the four genes were rpoB S531L, katG S315T, inhA-15C > T and oxyR-ahpC intergenic region. Conclusion: The mutations in rpoB and katG genes in Beijing are significantly more common than that in non-Beijing strains of MTB. We do not have sufficient evidence to support that the prevalence of mutations of inhA and oxyR-ahpC is higher in non-Beijing than in Beijing strains, which provides a reference basis for clinical medication selection.
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Affiliation(s)
- Shengqiong Guo
- Guizhou Provincial Center for Disease Prevention and Control, Guiyang 550004, China
- Department of Epidemiology, Faculty of Medicine, Prince of Songkla University, Hat Yai 90110, Thailand
- Correspondence:
| | | | - Shiguang Lei
- Guizhou Provincial Center for Disease Prevention and Control, Guiyang 550004, China
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Mokrousov I, Pasechnik O, Vyazovaya A, Yarusova I, Gerasimova A, Blokh A, Zhuravlev V. Impact of pathobiological diversity of Mycobacterium tuberculosis on clinical features and lethal outcome of tuberculosis. BMC Microbiol 2022; 22:50. [PMID: 35135478 PMCID: PMC8822639 DOI: 10.1186/s12866-022-02461-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 01/31/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycobacterium tuberculosis population in Russia is dominated by the notorious Beijing genotype whose major variants are characterized by contrasting resistance and virulence properties. Here we studied how these strain features could impact the progression of pulmonary tuberculosis (TB) concerning clinical manifestation and lethal outcome. RESULTS The study sample included 548 M. tuberculosis isolates from 548 patients with newly diagnosed pulmonary TB in Omsk, West Siberia, Russia. Strains were subjected to drug susceptibility testing and genotyping to detect lineages, sublineages, and subtypes (within Beijing genotype). The Beijing genotype was detected in 370 (67.5%) of the studied strains. The strongest association with multidrug resistance (MDR) was found for epidemic cluster Beijing B0/W148 (modern sublineage) and two recently discovered MDR clusters 1071-32 and 14717-15 of the ancient Beijing sublineage. The group of patients infected with hypervirulent and highly lethal (in a mouse model) Beijing 14717-15 showed the highest rate of lethal outcome (58.3%) compared to Beijing B0/W148 (31.4%; P = 0.06), Beijing Central Asian/Russian (29.7%, P = 0.037), and non-Beijing (15.2%, P = 0.001). The 14717-15 cluster mostly included isolates from patients with infiltrative but not with fibrous-cavernous and disseminated TB. In contrast, a group infected with low virulent 1071-32-cluster had the highest rate of fibrous-cavernous TB, possibly reflecting the capacity of these strains for prolonged survival and chronicity of the TB process. CONCLUSIONS The group of patients infected with hypervirulent and highly lethal in murine model 14717-15 cluster had the highest proportion of the lethal outcome (58.3%) compared to the groups infected with Beijing B0/W148 (31.4%) and non-Beijing (15.2%) isolates. This study carried out in the TB high-burden area highlights that not only drug resistance but also strain virulence should be considered in the implementation of personalized TB treatment.
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Affiliation(s)
- Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, 14 Mira street, St. Petersburg, 197101, Russia.
| | - Oksana Pasechnik
- Department of Public Health, Omsk State Medical University, Omsk, Russia
| | - Anna Vyazovaya
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, 14 Mira street, St. Petersburg, 197101, Russia
| | - Irina Yarusova
- Bacteriology Laboratory, Clinical Tuberculosis Dispensary, Omsk, Russia
| | - Alena Gerasimova
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, 14 Mira street, St. Petersburg, 197101, Russia
| | - Aleksey Blokh
- Department of Epidemiology, Omsk State Medical University, Omsk, Russia
| | - Viacheslav Zhuravlev
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
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8
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Ushtanit A, Mikhailova Y, Lyubimova A, Makarova M, Safonova S, Filippov A, Borisov S, Zimenkov D. Genetic Profile of Linezolid-Resistant M. tuberculosis Clinical Strains from Moscow. Antibiotics (Basel) 2021; 10:antibiotics10101243. [PMID: 34680823 PMCID: PMC8532644 DOI: 10.3390/antibiotics10101243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 10/06/2021] [Accepted: 10/11/2021] [Indexed: 01/04/2023] Open
Abstract
Background: Linezolid, bedaquiline, and newer fluoroquinolones are currently placed as priority Group A drugs for the treatment of drug-resistant tuberculosis. The number of reported linezolid-resistant clinical strains is still low, and the correlation of molecular determinants with phenotype is not perfect. Methods: We determined the linezolid MICs for clinical isolates from the Moscow region and identified mutations in rplC and rrl genes. Results: All 16 linezolid-resistant isolates had previously reported mutations in the rplC or rrl loci, and 13 of them bore a RplC C154R substitution. Detection of this substitution in a heteroresistant state was not successful, probably, due to the more stable DNA secondary structure of the mutated fragment, which precludes its amplification in mixes with the wild-type DNA. Strains with an rplC mutation had higher linezolid MIC compared to isolates with rrl mutations. Conclusions: Linezolid resistance mostly emerged during treatment with the latest regimen. Three primary cases with linezolid resistance question the possible transmission of totally drug-resistant tuberculosis in the Moscow region, which demands further investigation.
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Affiliation(s)
- Anastasia Ushtanit
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.U.); (A.L.)
| | - Yulia Mikhailova
- The Moscow Research and Clinical Center for Tuberculosis Control, Moscow Government Health Department, 107014 Moscow, Russia; (Y.M.); (M.M.); (S.S.); (A.F.); (S.B.)
| | - Alexandra Lyubimova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.U.); (A.L.)
| | - Marina Makarova
- The Moscow Research and Clinical Center for Tuberculosis Control, Moscow Government Health Department, 107014 Moscow, Russia; (Y.M.); (M.M.); (S.S.); (A.F.); (S.B.)
| | - Svetlana Safonova
- The Moscow Research and Clinical Center for Tuberculosis Control, Moscow Government Health Department, 107014 Moscow, Russia; (Y.M.); (M.M.); (S.S.); (A.F.); (S.B.)
| | - Alexey Filippov
- The Moscow Research and Clinical Center for Tuberculosis Control, Moscow Government Health Department, 107014 Moscow, Russia; (Y.M.); (M.M.); (S.S.); (A.F.); (S.B.)
| | - Sergey Borisov
- The Moscow Research and Clinical Center for Tuberculosis Control, Moscow Government Health Department, 107014 Moscow, Russia; (Y.M.); (M.M.); (S.S.); (A.F.); (S.B.)
| | - Danila Zimenkov
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (A.U.); (A.L.)
- Correspondence:
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9
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Genomic Variations in Drug Resistant Mycobacterium tuberculosis Strains Collected from Patients with Different Localization of Infection. Antibiotics (Basel) 2020; 10:antibiotics10010027. [PMID: 33396320 PMCID: PMC7824472 DOI: 10.3390/antibiotics10010027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/23/2020] [Accepted: 12/25/2020] [Indexed: 11/28/2022] Open
Abstract
Mycobacterium tuberculosis is a highly studied pathogen due to public health importance. Despite this, problems like early drug resistance, diagnostics and treatment success prediction are still not fully resolved. Here, we analyze the incidence of point mutations widely used for drug resistance detection in laboratory practice and conduct comparative analysis of whole-genome sequence (WGS) for clinical M. tuberculosis strains collected from patients with pulmonary tuberculosis (PTB) and extra-pulmonary tuberculosis (XPTB) localization. A total of 72 pulmonary and 73 extrapulmonary microbiologically characterized M. tuberculosis isolates were collected from patients from 2007 to 2014 in Russia. Genomic DNA was used for WGS and obtained data allowed identifying major mutations known to be associated with drug resistance to first-line and second-line antituberculous drugs. In some cases previously described mutations were not identified. Using genome-based phylogenetic analysis we identified M. tuberculosis substrains associated with distinctions in the occurrence in PTB vs. XPTB cases. Phylogenetic analyses did reveal M. tuberculosis genetic substrains associated with TB localization. XPTB was associated with Beijing sublineages Central Asia (Beijing CAO), Central Asia Clade A (Beijing A) and 4.8 groups, while PTB localization was associated with group LAM (4.3). Further, the XPTB strain in some cases showed elevated drug resistance patterns relative to PTB isolates. HIV was significantly associated with the development of XPTB in the Beijing B0/W148 group and among unclustered Beijing isolates.
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Vyazovaya A, Proshina E, Gerasimova A, Avadenii I, Solovieva N, Zhuravlev V, Narvskaya O, Mokrousov I. Increased transmissibility of Russian successful strain Beijing B0/W148 of Mycobacterium tuberculosis: Indirect clues from history and demographics. Tuberculosis (Edinb) 2020; 122:101937. [PMID: 32501261 DOI: 10.1016/j.tube.2020.101937] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/15/2020] [Accepted: 04/19/2020] [Indexed: 01/12/2023]
Abstract
The local situation with tuberculosis (TB) is shaped by the complex interplay of multiple factors related to both human host and Mycobacterium tuberculosis. We hypothesized that TB epidemiology in the rural regions in the Soviet Union was impacted by construction of the Gulag camps and significant incoming migration. This molecular M. tuberculosis study was conducted in 2017 in the Komi Republic in northern Russia, a region with high rate (26%) of primary multidrug-resistant (MDR) TB. MDR was detected in 30.8% (40/130) isolates; eight were extensively drug resistant. The Beijing genotype was predominant (56.2%). The main Beijing subtypes B0/W148 and 94-32 differed in the MDR rate, 83.3% and 27.2%, respectively. The non-Beijing isolates represented five genotypes (LAM, Ural, Haarlem, X, T). The proportion of Beijing B0/W148 in the "camp" cities (originated from Gulag camps) was twice as large as in other districts of the Komi Republic. To conclude, сirculation of the MDR-associated Beijing B0/W148 cluster critically influences the current situation with MDR-TB in this Russian region. The increased prevalence of B0/W148 in the urban setting on the whole, and in the "camp cities", in particular, indirectly points to the increased transmission capacity of this successful Russian strain of M. tuberculosis.
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Affiliation(s)
- Anna Vyazovaya
- St. Petersburg Pasteur Institute, St. Petersburg, Russia.
| | - Eugeniya Proshina
- Republican Anti-Tuberculosis Dispensary, Syktyvkar, Komi Republic, Russia
| | | | - Ion Avadenii
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Natalia Solovieva
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Viacheslav Zhuravlev
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Olga Narvskaya
- St. Petersburg Pasteur Institute, St. Petersburg, Russia; St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Igor Mokrousov
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
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Analysis of Clinical Factors, Bacterial Genotyping, and Drug Resistance for Spinal Tuberculosis in South-Central China. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9871390. [PMID: 32076625 PMCID: PMC6996694 DOI: 10.1155/2020/9871390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 08/04/2019] [Accepted: 08/12/2019] [Indexed: 11/17/2022]
Abstract
Spinal tuberculosis (STB), which is the most frequent and serious form of skeletal TB, is seriously harmful to a patient's life. However, very little research has been conducted on clinical isolates of STB. The purpose of this study was to genotype clinical isolates of Mycobacterium tuberculosis (MTB) from patients with STB, investigate their drug resistance profiles, and determine whether the genotypes and drug resistance patterns share any relationships with the demographic and clinical features of the patients. Preliminary species identification of the MTB strains was performed using a TCH/PNB culture method and multilocus polymerase chain reactions. Of the specimens collected from 85 hospital in-patients with STB at Xiangya Hospital, China, the 56 culture-positive MTB strains we identified were genotyped by spoligotyping. The strains were tested for resistance to anti-tuberculosis drugs (ATDs), and the demographic and clinical features of the patients were analyzed in combination with the genotyping and drug resistance results. Of the 56, cases, 53 involved M. tuberculosis and 3 involved M. bovis. Spoligotyping revealed 27 Beijing-type cases and 29 nonBeijing cases. When patients with STB were relapsing or experiencing systemic toxicity signs/symptoms (STS), the Beijing MTB-type strains predominated (p < 0.05), but when the patients were receiving initial treatment or lacked STS, the nonBeijing type MTB strains dominated. The Beijing and nonBeijing types differed in their resistance patterns to 8 ATDs, and the resistance rate of the Beijing type was higher than that of the nonBeijing type (p < 0.05). The bacteriological features of STB, including genotype and drug resistance, shared close relationships with the clinical features of patients with STB. Our data provide a reference for the diagnosis and treatment of STB.
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Mertaniasih NM. ACID-FAST BACILLI CONVERSION OF BEIJING AND NON-BEIJING STRAIN OF PULMONARY TUBERCULOSIS IN SOUTH SULAWESI. INDONESIAN JOURNAL OF TROPICAL AND INFECTIOUS DISEASE 2019. [DOI: 10.20473/ijtid.v7i5.9670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Beijing strains are a major part of the Mycobacterium tuberculosis Asian phylogenetic lineage. Beijing strains represent about 50% of all TB strains in East Asia and at least 13% of strains worldwide. Beijing strain of Mycobacterium tuberculosis is presumed as the factor of the increase in bacteria virulence and drug resistance, and the contributor in treatment failure. The aim of this study was to analyze the association between acid-fast bacilli conversion with strain genotipe Beijing and non-Beijing of pulmonary tuberculosis in South Sulawesi. The design of research was observational analytic with prospective approach. The sampling technique used consecutive sampling. Data were taken from active pulmonary tuberculosis patients’ medical record in Balai Besar Kesehatan Paru Masyarakat Makassar (Pulmonary Health Center of Makassar) and Community Health Center in Gowa Regency, South Sulawesi from March to June 2018. Collected sputum samples were screened for AFB and identified as Beijing strain and non Beijing strains using Multiplex PCR in Tropical Disease Institute of Universitas Airlangga. The results is showed that the characteristics of the respondents consisted of 12 respondents (33.3%) aged 56-65 years, 25 respondents (69.4%) men and 28 respondents (77.8%) had low category gradation of AFB smear. Univariate analysis showed 6 respondents (16.7%) with Beijing strains, 30 respondents (83.3%) with non-Beijing strains, 32 respondents (88.9%) conversion sputum AFB and 4 respondents (11.1%) non conversion sputum AFB. Bivariate analysis with Chi-Square statistical test shows that p value 0.022 < 0,05, that means there was association of Beijing strains with BTA conversion. Microscopic examination of BTA can be used to monitor and evaluate the treatment of new pulmonary TB patients undergoing treatment and the Beijing Mycobacterium tuberculosis strain has a significant correlation with the treatment failure of anti-tuberculosis drugs in South Sulawesi.
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Chernyaeva E, Rotkevich M, Krasheninnikova K, Yurchenko A, Vyazovaya A, Mokrousov I, Solovieva N, Zhuravlev V, Yablonsky P, O'Brien SJ. Whole-Genome Analysis of Mycobacterium tuberculosis from Patients with Tuberculous Spondylitis, Russia. Emerg Infect Dis 2019; 24:579-583. [PMID: 29460750 PMCID: PMC5823328 DOI: 10.3201/eid2403.170151] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Whole-genome analysis of Mycobacterium tuberculosis isolates collected in Russia (N = 71) from patients with tuberculous spondylitis supports a detailed characterization of pathogen strain distributions and drug resistance phenotype, plus distinguished occurrence and association of known resistance mutations. We identify known and novel genome determinants related to bacterial virulence, pathogenicity, and drug resistance.
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Sinkov V, Ogarkov O, Mokrousov I, Bukin Y, Zhdanova S, Heysell SK. New epidemic cluster of pre-extensively drug resistant isolates of Mycobacterium tuberculosis Ural family emerging in Eastern Europe. BMC Genomics 2018; 19:762. [PMID: 30348088 PMCID: PMC6198502 DOI: 10.1186/s12864-018-5162-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/11/2018] [Indexed: 01/08/2023] Open
Abstract
Background Ural genetic family is a part of the Euro-American lineage of Mycobacterium tuberculosis and is endemic in Northern Eurasia (former Soviet Union [FSU]). These strains were long described as drug susceptible and of low virulence, but recent studies reported an increasing circulation of the multidrug-resistant (MDR) and extensively drug-resistant (XDR) Ural strains. Here, we analyzed all publicly available whole genome sequence data of Ural genotype isolates, in order to elucidate their phylogenomic diversity with a special focus on MDR and potentially epidemic clones. Results A total of 149 M. tuberculosis genomes of Ural isolates from FSU countries were mined from the GMTV database and TB-ARC project. We identified 6002 variable amino acid positions that were assessed for functional significance and used to build ML, NJ trees and for Bayesian TMRCA estimation. Three robust monophyletic clades were identified: Clade A (31 isolates from Russia, Belarus, Moldova), Clade B (52 isolates from Russia), and Clade C (37 isolates from Moldova, 2 from Belarus). Clade C was significantly associated with XDR or pre-XDR status compared to the pooled Clades A and B (33/39 versus 5/83, P < 0.0001). Time of origin was estimated for Clade A at 77.7–137 years ago and for Clade B at 56.3–99.2 years ago compared to the significantly more recent origin for Clade C. in silico spoligotyping identified signatures specific of the Clade A (spoligotype SIT35), and Clades B and C (both SIT262). Conclusions A genetically compact and evolutionarily young Ural Clade C, likely originated after collapse of the Soviet Union, and reached epidemic proportions in Moldova in the last 20 years. This epidemic pre-XDR clone (mostly rifampin, isoniazid and kanamycin resistant) is characterized by a specific combination of mutations: KatG Ser315Thr, fabG1 -15C > T, RpoB Ser450Leu, RpsL Lys88Arg, eis -12G > A and EmbB Ser297Ala/T > G. Its further dissemination may occur towards both Russia and European Union and should be taken into consideration by health authorities. The identified spoligotyping signatures can serve for rapid preliminary detection and surveillance of the more hazardous pre-XDR associated strains of the Ural family, both in populations from countries of their endemic circulation and migrant communities. Electronic supplementary material The online version of this article (10.1186/s12864-018-5162-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Viacheslav Sinkov
- Department Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, 16 Timiriazeva street, Irkutsk, 664003, Russia
| | - Oleg Ogarkov
- Department Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, 16 Timiriazeva street, Irkutsk, 664003, Russia. .,Irkutsk State Medical Academy of Continuing Education, Irkutsk, 664049, Russia.
| | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, 14 Mira street, St. Petersburg, 197101, Russia.
| | - Yuri Bukin
- Limnological Institute SB RAS, Irkutsk, 664033, Russia.,Irkutsk National Research Technical University, Irkutsk, 664074, Russia
| | - Svetlana Zhdanova
- Department Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, 16 Timiriazeva street, Irkutsk, 664003, Russia
| | - Scott K Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Charlottesville, VA, 22908, USA
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Rapid Assay for Detection of the Epidemiologically Important Central Asian/Russian Strain of the Mycobacterium tuberculosis Beijing Genotype. J Clin Microbiol 2018; 56:JCM.01551-17. [PMID: 29142045 DOI: 10.1128/jcm.01551-17] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
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Genetic diversity of Mycobacterium tuberculosis and transmission associated with first-line drug resistance: a first analysis in Jalisco, Mexico. J Glob Antimicrob Resist 2017; 11:90-97. [DOI: 10.1016/j.jgar.2017.07.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/07/2017] [Accepted: 07/12/2017] [Indexed: 12/19/2022] Open
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17
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Ioannidis P, van Soolingen D, Mokrousov I, Papaventsis D, Karabela S, Konstantinidou E, Marinou I, Nikolaou S, Kanavaki S, Mantadakis E, Samonis G, Anthony R, Vogiatzakis E. Multidrug-resistant/extensively drug-resistant tuberculosis in Greece: predominance of Mycobacterium tuberculosis genotypes endemic in the Former Soviet Union countries. Clin Microbiol Infect 2017; 23:1002-1004. [DOI: 10.1016/j.cmi.2017.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 06/28/2017] [Accepted: 07/01/2017] [Indexed: 11/17/2022]
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Vyazovaya A, Levina K, Zhuravlev V, Viiklepp P, Kütt M, Mokrousov I. Emerging resistant clones of Mycobacterium tuberculosis in a spatiotemporal context. J Antimicrob Chemother 2017; 73:325-331. [DOI: 10.1093/jac/dkx372] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Accepted: 09/12/2017] [Indexed: 11/13/2022] Open
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Zhou Y, van den Hof S, Wang S, Pang Y, Zhao B, Xia H, Anthony R, Ou X, Li Q, Zheng Y, Song Y, Zhao Y, van Soolingen D. Association between genotype and drug resistance profiles of Mycobacterium tuberculosis strains circulating in China in a national drug resistance survey. PLoS One 2017; 12:e0174197. [PMID: 28333978 PMCID: PMC5363926 DOI: 10.1371/journal.pone.0174197] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 03/06/2017] [Indexed: 11/19/2022] Open
Abstract
We describe the population structure of a representative collection of 3,133 Mycobacterium tuberculosis isolates, collected within the framework of a national resistance survey from 2007 in China. Genotyping data indicate that the epidemic strains in China can be divided into seven major complexes, of which 92% belonged to the East Asian (mainly Beijing strains) or the Euro-American lineage. The epidemic Beijing strains in China are closely related to the Beijing B0/W148 strain earlier described in Russia and a large cluster of these strains has spread national wide. The density of Beijing strains is high in the whole of China (average 70%), but the highest prevalence was found North of the Yellow river. The Euro-American lineage consists of three sublineages (sublineage_1, 2, and 3) and is more prevalent in the South. Beijing lineage showed the highest cluster rate of 48% and a significantly higher level of resistance to rifampicin (14%, p<0.001), ethambutol (9%, p = 0.001), and ofloxacin (5%, p = 0.011). Within the Euro-American Lineage, sublineage_3 revealed the highest cluster rate (28%) and presented a significantly elevated level of resistance to streptomycin (44%, p<0.001). Our findings suggest that standardised treatment in this region may have contributed to the successful spread of certain strains: sublineage_3 in the Euro-American lineage may have thrived when streptomycin was used without rifampicin for treatment, while later under DOTS based treatment, in which rifampicin plays a key role, Beijing lineage appears to be spreading.
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Affiliation(s)
- Yang Zhou
- Chinese Centre for Disease Control and Prevention, Changping district, Beijing, China, P.R
| | - Susan van den Hof
- KNCV Tuberculosis Foundation, CC The Hague, The Netherlands
- Department of Global Health, Amsterdam Medical Center, Pietersbergweg 17, BM Amsterdam, The Netherlands
| | - Shengfen Wang
- Chinese Centre for Disease Control and Prevention, Changping district, Beijing, China, P.R
| | - Yu Pang
- Chinese Centre for Disease Control and Prevention, Changping district, Beijing, China, P.R
| | - Bing Zhao
- Chinese Centre for Disease Control and Prevention, Changping district, Beijing, China, P.R
| | - Hui Xia
- Chinese Centre for Disease Control and Prevention, Changping district, Beijing, China, P.R
| | - Richard Anthony
- National Institute for Public Health and the Environment, the Netherlands,BA Bilthoven, The Netherlands
| | - Xichao Ou
- Chinese Centre for Disease Control and Prevention, Changping district, Beijing, China, P.R
| | - Qiang Li
- Chinese Centre for Disease Control and Prevention, Changping district, Beijing, China, P.R
| | - Yang Zheng
- Chinese Centre for Disease Control and Prevention, Changping district, Beijing, China, P.R
| | - Yuanyuan Song
- Chinese Centre for Disease Control and Prevention, Changping district, Beijing, China, P.R
| | - Yanlin Zhao
- Chinese Centre for Disease Control and Prevention, Changping district, Beijing, China, P.R
- * E-mail: (DVS); (YLZ)
| | - Dick van Soolingen
- National Institute for Public Health and the Environment, the Netherlands,BA Bilthoven, The Netherlands
- * E-mail: (DVS); (YLZ)
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Vyazovaya AA, Vetrov VV, Lyalina LV, Mokrousov IV, Solovieva NS, Zhuravlev VY, Vishnevskiy BI, Narvskaya OV. CHARACTERIZATION OF MYCOBACTERIUM TUBERCULOSIS STRAINS (A 15-YEAR SURVEY IN LENINGRAD REGION, RUSSIA). ACTA ACUST UNITED AC 2017. [DOI: 10.15789/2220-7619-2017-1-34-40] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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21
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Evolutionary History and Ongoing Transmission of Phylogenetic Sublineages of Mycobacterium tuberculosis Beijing Genotype in China. Sci Rep 2016; 6:34353. [PMID: 27681182 PMCID: PMC5041183 DOI: 10.1038/srep34353] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 09/09/2016] [Indexed: 11/15/2022] Open
Abstract
Mycobacterium tuberculosis Beijing genotype originated in China and has undergone a dramatic population growth and global spread in the last century. Here, a collection of M. tuberculosis Beijing family isolates from different provinces across all China was genotyped by high-resolution (24-MIRU-VNTR) and low-resolution, high-rank (modern and ancient sublineages) markers. The molecular profiles and global and local phylogenies were compared to the strain phenotype and patient data. The phylogeographic patterns observed in the studied collection demonstrate that large-scale (but not middle/small-scale) distance remains one of the decisive factors of the genetic divergence of M. tuberculosis populations. Analysis of diversity and network topology of the local collections appears to corroborate a recent intriguing hypothesis about Beijing genotype originating in South China. Placing our results within the Eurasian context suggested that important Russian B0/W148 and Asian/Russian A0/94-32 epidemic clones of the Beijing genotype could trace their origins to the northeastern and northwestern regions of China, respectively. The higher clustering of the modern isolates in children and lack of increased MDR rate in any sublineage suggest that not association with drug resistance but other (e.g., speculatively, virulence-related) properties underlie an enhanced dissemination of the evolutionarily recent, modern sublineage of the Beijing genotype in China.
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Urgent Implementation in a Hospital Setting of a Strategy To Rule Out Secondary Cases Caused by Imported Extensively Drug-Resistant Mycobacterium tuberculosis Strains at Diagnosis. J Clin Microbiol 2016; 54:2969-2974. [PMID: 27682128 DOI: 10.1128/jcm.01718-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 09/14/2016] [Indexed: 11/20/2022] Open
Abstract
Current migratory movements require new strategies for rapidly tracking the transmission of high-risk imported Mycobacterium tuberculosis strains. Whole-genome sequencing (WGS) enables us to identify single-nucleotide polymorphisms (SNPs) and therefore design PCRs to track specific relevant strains. However, fast implementation of these strategies in the hospital setting is difficult because professionals working in diagnostics, molecular epidemiology, and genomics are generally at separate institutions. In this study, we describe the urgent implementation of a system that integrates genomics and molecular tools in a genuine high-risk epidemiological alert involving 2 independent importations of extensively drug resistant (XDR) and pre-XDR Beijing M. tuberculosis strains from Russia into Spain. Both cases involved commercial sex workers with long-standing tuberculosis (TB). The system was based on strain-specific PCRs tailored from WGS data that were transferred to the local node that was managing the epidemiological alert. The optimized tests were available for prospective implementation in the local node 33 working days after receiving the primary cultures of the XDR strains and were applied to all 42 new incident cases. An interpretable result was obtained in each case (directly from sputum for 27 stain-positive cases) and corresponded to the amplification profiles for strains other than the targeted pre-XDR and XDR strains, which made it possible to prospectively rule out transmission of these high-risk strains at diagnosis.
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Zimenkov DV, Kulagina EV, Antonova OV, Zhuravlev VY, Gryadunov DA. Simultaneous drug resistance detection and genotyping of Mycobacterium tuberculosis using a low-density hydrogel microarray. J Antimicrob Chemother 2016; 71:1520-31. [PMID: 26929267 DOI: 10.1093/jac/dkw015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/11/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Nucleic acid amplification tests are widely used in TB diagnostics. Priority tasks in their development consist of increasing the specificity and sensitivity of the detection of resistance to a wide spectrum of anti-TB drugs. METHODS We developed a multiplexed assay allowing the detection of 116 drug resistance-determining mutations in the rpoB, katG, inhA, ahpC, gyrA, gyrB, rrs, eis and embB genes in the Mycobacterium tuberculosis complex genome and six SNPs to identify the main lineages circulating in Russia. The assay is based on the amplification of 17 fragments of the genome using the universal primer adapter technique and heat pulses at the elongation step, followed by hybridization on a microarray. RESULTS The method was evaluated using 264 pairs of clinical samples and corresponding isolates. A significant proportion (25%) of smear-negative samples were correctly analysed by microarray analysis in addition to 96% of smear-positive samples. The sensitivity and specificity of the assay exceeded 90% for rifampicin, isoniazid, ofloxacin and second-line injection drugs. In agreement with previous studies, the specificity of ethambutol resistance was as low as 57%, while the sensitivity was 89.9%. Strong association of the Beijing lineage with a resistant phenotype was observed. Euro-American lineage strains, excluding Ural and LAM, were predominantly associated with the susceptible phenotype. CONCLUSIONS The developed test has a high sensitivity and specificity and can be directly applied to clinical samples. The combination of mutation-based drug resistance profiling and basic genotyping could be useful for clinical microbiology studies and epidemiological surveillance of the M. tuberculosis complex.
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Affiliation(s)
- Danila V Zimenkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Elena V Kulagina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Olga V Antonova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | | | - Dmitry A Gryadunov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
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Mokrousov I, Vyazovaya A, Solovieva N, Sunchalina T, Markelov Y, Chernyaeva E, Melnikova N, Dogonadze M, Starkova D, Vasilieva N, Gerasimova A, Kononenko Y, Zhuravlev V, Narvskaya O. Trends in molecular epidemiology of drug-resistant tuberculosis in Republic of Karelia, Russian Federation. BMC Microbiol 2015; 15:279. [PMID: 26679959 PMCID: PMC4683759 DOI: 10.1186/s12866-015-0613-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Accepted: 12/07/2015] [Indexed: 01/23/2023] Open
Abstract
Background Russian Republic of Karelia is located at the Russian-Finnish border. It contains most of the historical Karelia land inhabited with autochthonous Karels and more recently migrated Russians. Although tuberculosis (TB) incidence in Karelia is decreasing, it remains high (45.8/100 000 in 2014) with the rate of multi-drug resistance (MDR) among newly diagnosed TB patients reaching 46.5 %. The study aimed to genetically characterize Mycobacterium tuberculosis isolates obtained at different time points from TB patients from Karelia to gain insight into the phylogeographic specificity of the circulating genotypes and to assess trends in evolution of drug resistant subpopulations. Methods The sample included 150 M. tuberculosis isolates: 78 isolated in 2013–2014 (“new” collection) and 72 isolated in 2006 (“old” collection). Drug susceptibility testing was done by the method of absolute concentrations. Spoligotyping was used to test genotype-specific markers of a Latin-American-Mediterranean (LAM) family and its sublineages as well as a Beijing B0/W148-cluster. Results The largest spoligotypes were SIT1 (Beijing family, n = 42) and SIT40 (T family, n = 5). Beijing family was the largest (n = 43) followed by T (n = 11), Ural (n = 10) and LAM (n = 8). Successful Russian clone, Beijing В0/W148, was identified in 15 (34.9 %) of 43 Beijing isolates; all В0/W148 isolates were drug-resistant. Seven of 8 LAM isolates belonged to the RD115/LAM-RUS branch, 1 - to the LAM RD174/RD-Rio sublineage. MDR was found in Beijing (32/43), Ural (3/10), and LAM (3/8). In contrast, all T isolates were pansusceptible. Comparison of drug resistant subgroups of the new and old collections showed an increasing prevalence of the B0/W148 clonal cluster, from 18.0 % (mainly polyresistant) in 2006 to 32.6 % in 2014 (mainly MDR and pre-XDR). The West–east increasing gradient is observed for the Ural genotype that may be defined a ‘Russian’ strain. In contrast, the spoligotype SIT40 of the T family appears to be a historical Karelian strain. Conclusions Circulation of the MDR M. tuberculosis isolates of the Beijing genotype and its B0/W148 cluster continues to critically influence the current situation with the MDR-TB control in northwestern Russia including the Republic of Karelia. Revealed phylogeographic patterns of some genotypes reflect a complex demographic history of Karelia within the course of the 20th century.
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Affiliation(s)
- Igor Mokrousov
- Laboratory of Molecular Microbiology, St. Petersburg Pasteur Institute, 14 Mira street, St. Petersburg, 197101, Russia.
| | - Anna Vyazovaya
- Laboratory of Molecular Microbiology, St. Petersburg Pasteur Institute, 14 Mira street, St. Petersburg, 197101, Russia.
| | - Natalia Solovieva
- Laboratory of Etiological Diagnostics, Research Institute of Phthisiopulmonology, St. Petersburg, Russia.
| | - Tatiana Sunchalina
- Republican Tuberculosis Dispensary, Petrozavodsk, Republic of Karelia, Russia.
| | - Yuri Markelov
- Petrozavodsk State University, Petrozavodsk, Republic of Karelia, Russia.
| | - Ekaterina Chernyaeva
- Laboratory of Etiological Diagnostics, Research Institute of Phthisiopulmonology, St. Petersburg, Russia. .,Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University, St. Petersburg, Russia.
| | - Natalia Melnikova
- Laboratory of Etiological Diagnostics, Research Institute of Phthisiopulmonology, St. Petersburg, Russia.
| | - Marine Dogonadze
- Laboratory of Etiological Diagnostics, Research Institute of Phthisiopulmonology, St. Petersburg, Russia.
| | - Daria Starkova
- Laboratory of Molecular Microbiology, St. Petersburg Pasteur Institute, 14 Mira street, St. Petersburg, 197101, Russia.
| | - Neliya Vasilieva
- Laboratory of Etiological Diagnostics, Research Institute of Phthisiopulmonology, St. Petersburg, Russia.
| | - Alena Gerasimova
- Laboratory of Molecular Microbiology, St. Petersburg Pasteur Institute, 14 Mira street, St. Petersburg, 197101, Russia.
| | - Yulia Kononenko
- Republican Tuberculosis Dispensary, Petrozavodsk, Republic of Karelia, Russia.
| | - Viacheslav Zhuravlev
- Laboratory of Etiological Diagnostics, Research Institute of Phthisiopulmonology, St. Petersburg, Russia.
| | - Olga Narvskaya
- Laboratory of Molecular Microbiology, St. Petersburg Pasteur Institute, 14 Mira street, St. Petersburg, 197101, Russia. .,Laboratory of Etiological Diagnostics, Research Institute of Phthisiopulmonology, St. Petersburg, Russia.
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Singh PK, Jain A. Epidemiological perspective of drug resistant extrapulmonary tuberculosis. World J Clin Infect Dis 2015; 5:77-85. [DOI: 10.5495/wjcid.v5.i4.77] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 04/20/2015] [Accepted: 09/08/2015] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis (TB) remains one of the leading infectious diseases causing significant morbidity and mortality worldwide. Although, pulmonary TB is the most common presentation and is the main transmissible form of the disease, extrapulmonary TB also significantly contributes to the burden of disease and can cause severe complications and disabilities. At present, the most serious issue with TB control programme is emergence of multi and extensively drug resistant Mycobacterium tuberculosis strain world-wide. As the number of drug resistant pulmonary TB is increasing around the world, the number of drug resistant TB with extrapulmonary manifestations are also on rise. However, there is surprisingly scant information in medical literatures on prevalence and impact of extrapulmonary drug-resistant TB. Here, we appraise the recent epidemiological studies that underpin the status and impact of drug resistance in TB cases with extrapulmonary manifestations.
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