151
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Ates LS. New insights into the mycobacterial PE and PPE proteins provide a framework for future research. Mol Microbiol 2020; 113:4-21. [PMID: 31661176 PMCID: PMC7028111 DOI: 10.1111/mmi.14409] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/25/2019] [Indexed: 12/30/2022]
Abstract
The PE and PPE proteins of Mycobacterium tuberculosis have been studied with great interest since their discovery. Named after the conserved proline (P) and glutamic acid (E) residues in their N-terminal domains, these proteins are postulated to perform wide-ranging roles in virulence and immune modulation. However, technical challenges in studying these proteins and their encoding genes have hampered the elucidation of molecular mechanisms and leave many open questions regarding the biological functions mediated by these proteins. Here, I review the shared and unique characteristics of PE and PPE proteins from a molecular perspective linking this information to their functions in mycobacterial virulence. I discuss how the different subgroups (PE_PGRS, PPE-PPW, PPE-SVP and PPE-MPTR) are defined and why this classification of paramount importance to understand the PE and PPE proteins as individuals and or groups. The goal of this MicroReview is to summarize and structure the existing information on this gene family into a simplified framework of thinking about PE and PPE proteins and genes. Thereby, I hope to provide helpful starting points in studying these genes and proteins for researchers with different backgrounds. This has particular implications for the design and monitoring of novel vaccine candidates and in understanding the evolution of the M. tuberculosis complex.
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Affiliation(s)
- Louis S. Ates
- Department of Experimental ImmunologyAmsterdam Infection & Immunity InstituteAmsterdam UMCUniversity of AmsterdamMeibergdreef 9Amsterdamthe Netherlands
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152
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Mourik BC, de Steenwinkel JEM, de Knegt GJ, Huizinga R, Verbon A, Ottenhoff THM, van Soolingen D, Leenen PJM. Mycobacterium tuberculosis clinical isolates of the Beijing and East-African Indian lineage induce fundamentally different host responses in mice compared to H37Rv. Sci Rep 2019; 9:19922. [PMID: 31882653 PMCID: PMC6934500 DOI: 10.1038/s41598-019-56300-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 11/14/2019] [Indexed: 11/15/2022] Open
Abstract
Substantial differences exist in virulence among Mycobacterium tuberculosis strains in preclinical TB models. In this study we show how virulence affects host responses in mice during the first four weeks of infection with a mycobacterial strain belonging to the Beijing, East-African-Indian or Euro-American lineage. BALB/c mice were infected with clinical isolates of the Beijing-1585 strain or the East-African Indian (EAI)-1627 strain and host responses were compared to mice infected with the non-clinical H37Rv strain of the Euro-American lineage. We found that H37Rv induced a ‘classical’ T-cell influx with high IFN-γ levels, while Beijing-1585 and EAI-1627 induced an influx of B-cells into the lungs together with elevated pulmonary IL-4 protein levels. Myeloid cells in the lungs appeared functionally impaired upon infection with Beijing-1585 and EAI-1627 with reduced iNOS and IL-12 expression levels compared to H37Rv infection. This impairment might be related to significantly reduced expression in the bone marrow of IFN-γ, TNF-α and IFN-β in mice infected with Beijing-1585 and EAI-1627, which could be detected from the third day post infection onwards. Our findings suggest that increased virulence of two clinical isolates compared to H37Rv is associated with a fundamentally different systemic immune response, which already can be detected early during infection.
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Affiliation(s)
- Bas C Mourik
- Department Medical Microbiology & Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jurriaan E M de Steenwinkel
- Department Medical Microbiology & Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Gerjo J de Knegt
- Department Medical Microbiology & Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ruth Huizinga
- Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Annelies Verbon
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Tom H M Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Dick van Soolingen
- National Tuberculosis Reference Laboratory, National Institute of Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Pieter J M Leenen
- Department of Immunology, Erasmus University Medical Center, Rotterdam, The Netherlands.
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153
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Levillain F, Kim H, Woong Kwon K, Clark S, Cia F, Malaga W, Lanni F, Brodin P, Gicquel B, Guilhot C, Bancroft GJ, Williams A, Jae Shin S, Poquet Y, Neyrolles O. Preclinical assessment of a new live attenuated Mycobacterium tuberculosis Beijing-based vaccine for tuberculosis. Vaccine 2019; 38:1416-1423. [PMID: 31862194 DOI: 10.1016/j.vaccine.2019.11.085] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 11/14/2019] [Accepted: 11/29/2019] [Indexed: 01/16/2023]
Abstract
Tuberculosis still claims more lives than any other pathogen, and a vaccine better than BCG is urgently needed. One of the challenges for novel TB vaccines is to protect against all Mycobacterium tuberculosis lineages, including the most virulent ones, such as the Beijing lineage. Here we developed a live attenuated M. tuberculosis mutant derived from GC1237, a Beijing strain responsible for tuberculosis outbreaks in the Canary Islands. The mutant strain is inactivated both in the Rv1503c gene, responsible for surface glycolipid synthesis, and in the two-component global regulator PhoPR. This double mutant is as safe as BCG in immunodeficient SCID mice. In immune-competent mice and guinea pigs, the mutant is as protective as BCG against M. tuberculosis strains of common lineage 4 (Euro-American). By contrast, in mice the vaccine is protective against a M. tuberculosis strain of lineage 2 (East-Asian, Beijing), while BCG is not. These results highlight differences in protection efficacy of live attenuated M. tuberculosis-derived vaccine candidates depending on their genetic background, and provide insights for the development of novel live vaccines against TB, especially in East-Asian countries where M. tuberculosis strains of the Beijing family are highly dominant.
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Affiliation(s)
- Florence Levillain
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Hongmin Kim
- Department of Microbiology, Institute for Immunology and Immunological Disease, Yonsei University College of Medicine, Seoul, South Korea
| | - Kee Woong Kwon
- Department of Microbiology, Institute for Immunology and Immunological Disease, Yonsei University College of Medicine, Seoul, South Korea
| | - Simon Clark
- Public Health England, Salisbury, United Kingdom
| | - Felipe Cia
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Wladimir Malaga
- Department of Microbiology, Institute for Immunology and Immunological Disease, Yonsei University College of Medicine, Seoul, South Korea
| | - Faye Lanni
- Public Health England, Salisbury, United Kingdom
| | - Priscille Brodin
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Brigitte Gicquel
- Unité de Génétique Mycobactérienne, Institut Pasteur, Paris, France; Department of Tuberculosis Control and Prevention, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Christophe Guilhot
- Department of Microbiology, Institute for Immunology and Immunological Disease, Yonsei University College of Medicine, Seoul, South Korea
| | | | - Ann Williams
- Public Health England, Salisbury, United Kingdom
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Disease, Yonsei University College of Medicine, Seoul, South Korea
| | - Yannick Poquet
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Olivier Neyrolles
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.
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154
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Bespyatykh J, Shitikov E, Guliaev A, Smolyakov A, Klimina K, Veselovsky V, Malakhova M, Arapidi G, Dogonadze M, Manicheva O, Bespiatykh D, Mokrousov I, Zhuravlev V, Ilina E, Govorun V. System OMICs analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster. Sci Rep 2019; 9:19255. [PMID: 31848428 PMCID: PMC6917788 DOI: 10.1038/s41598-019-55896-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 12/04/2019] [Indexed: 11/30/2022] Open
Abstract
Mycobacterium tuberculosis Beijing B0/W148 is one of the most widely distributed clusters in the Russian Federation and in some countries of the former Soviet Union. Recent studies have improved our understanding of the reasons for the "success" of the cluster but this area remains incompletely studied. Here, we focused on the system omics analysis of the RUS_B0 strain belonging to the Beijing B0/W148 cluster. Completed genome sequence of RUS_B0 (CP020093.1) and a collection of WGS for 394 cluster strains were used to describe the main genetic features of the population. In turn, proteome and transcriptome studies allowed to confirm the genomic data and to identify a number of finds that have not previously been described. Our results demonstrated that expression of the whiB6 which contains cluster-specific polymorphism (a151c) increased almost 40 times in RUS_B0. Additionally, the level of ethA transcripts in RUS_B0 was increased by more than 7 times compared to the H37Rv. Start sites for 10 genes were corrected based on the combination of proteomic and transcriptomic data. Additionally, based on the omics approach, we identified 5 new genes. In summary, our analysis allowed us to summarize the available results and also to obtain fundamentally new data.
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Affiliation(s)
- Julia Bespyatykh
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation.
| | - Egor Shitikov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Andrei Guliaev
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Alexander Smolyakov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russian Federation
| | - Ksenia Klimina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Vladimir Veselovsky
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Maya Malakhova
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Georgij Arapidi
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russian Federation
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Russian Federation
| | - Marine Dogonadze
- Research Institute of Phtisiopulmonology, St. Petersburg, Russian Federation
| | - Olga Manicheva
- Research Institute of Phtisiopulmonology, St. Petersburg, Russian Federation
| | - Dmitry Bespiatykh
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Igor Mokrousov
- St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation
| | | | - Elena Ilina
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Vadim Govorun
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
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155
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Jandrasits C, Kröger S, Haas W, Renard BY. Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters. PLoS Comput Biol 2019; 15:e1007527. [PMID: 31815935 PMCID: PMC6922483 DOI: 10.1371/journal.pcbi.1007527] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 12/19/2019] [Accepted: 11/03/2019] [Indexed: 12/30/2022] Open
Abstract
Next-generation sequencing based base-by-base distance measures have become an integral complement to epidemiological investigation of infectious disease outbreaks. This study introduces PANPASCO, a computational pan-genome mapping based, pairwise distance method that is highly sensitive to differences between cases, even when located in regions of lineage specific reference genomes. We show that our approach is superior to previously published methods in several datasets and across different Mycobacterium tuberculosis lineages, as its characteristics allow the comparison of a high number of diverse samples in one analysis—a scenario that becomes more and more likely with the increased usage of whole-genome sequencing in transmission surveillance. Tuberculosis still is a threat to global health. It is essential to detect and interrupt transmissions to stop the spread of this infectious disease. With the rising use of next-generation sequencing methods, its application in the surveillance of Mycobacterium tuberculosis has become increasingly important in the last years. The main goal of molecular surveillance is the identification of patient-patient transmission and cluster detection. The mutation rate of M. tuberculosis is very low and stable. Therefore, many existing methods for comparative analysis of isolates provide inadequate results since their resolution is too limited. There is a need for a method that takes every detectable difference into account. We developed PANPASCO, a novel approach for comparing pairs of isolates using all genomic information available for each pair. We combine improved SNP-distance calculation with the use of a pan-genome incorporating more than 100 M. tuberculosis reference genomes representing lineages 1-4 for read mapping prior to variant detection. We thereby enable the collective analysis and comparison of similar and diverse isolates associated with different M. tuberculosis strains.
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Affiliation(s)
| | - Stefan Kröger
- Respiratory Infections Unit, Robert Koch Institute, Berlin, Germany
| | - Walter Haas
- Respiratory Infections Unit, Robert Koch Institute, Berlin, Germany
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156
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Klotoe BJ, Kurepina N, Zholdibayeva E, Panaiotov S, Kreiswirth BN, Anthony R, Sola C, Refrégier G. NTF-RINT, a new method for the epidemiological surveillance of MDR Mycobacterium tuberculosis L2/Beijing strains. Tuberculosis (Edinb) 2019; 120:101894. [PMID: 32090855 DOI: 10.1016/j.tube.2019.101894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/29/2019] [Accepted: 12/08/2019] [Indexed: 11/24/2022]
Abstract
The most widely discussed antibiotic-resistant tuberculosis strains ("W" and "B0/W148", "CAO") belong to L2/Beijing Lineage and are characterized by IS6110 insertion sequences at the NTF locus. We present a high-throughput, microbead-based method, called NTF-RINT for detection of IS in NTF and Rifampicin and Isoniazid Typing. This method provides tuberculosis diagnostic confirmation, screens for the so-called modern L2/Beijing sublineage and detects mutations involved in resistance to Rifampicin (RIF) and Isoniazid (INH).
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Affiliation(s)
- Bernice J Klotoe
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Natalia Kurepina
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | | | - S Panaiotov
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - Barry N Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | | | - Christophe Sola
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Guislaine Refrégier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
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157
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Mora-Pinargote C, Garzon-Chavez D, Franco-Sotomayor G, Leon-Benitez M, Granda-Pardo JC, Trueba G, de Waard JH, Garcia-Bereguiain MA. Country-wide rapid screening for the Mycobacterium tuberculosis Beijing sublineage in Ecuador using a single-nucleotide polymorphism-polymerase chain reaction method. Int J Mycobacteriol 2019; 8:366-370. [PMID: 31793507 DOI: 10.4103/ijmy.ijmy_132_19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Background Strains of the Beijing sublineage of Mycobacterium tuberculosis have caused large outbreaks of tuberculosis, often involving multidrug resistance strains and this genetically highly conserved family of strains predominates in some geographic areas. For most of the countries of Latin America, no country-wide studies about the prevalence of the Beijing lineage are available. Methods In this study, we determine the prevalence of the Beijing sublineage in Ecuador, using a large nation-wide sample of 991 isolates from the years 2014-2016 and with the strains, in case-related-proportional representation, emerging from most of the provinces of the country. The isolates were genotyped with asinglenucleotidespecific polymorphism (SNP) polymerase chain reaction for the Beijing sublineage. SNPpositive strains were confirmed as belonging to this lineage with 24 mycobacterial interspersed repetitive unitvariable number of tandem repeat and DNA sequencing. Results We identified only four Beijing isolates in this collection of 991 strains and calculated a prevalence rate of 0.43%. Conclusions Our study shows a limited dissemination of the Beijing strains in the Ecuadorian population. This in contrast with the neighbor countries of Peru and Colombia were locally a prevalence of up to 16% has been reported.
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Affiliation(s)
- Carlos Mora-Pinargote
- Laboratorio Para Investigaciones Biomedicas, Facultad de Ciencias de la Vida, Escuela Superior Politecnica del Litoral, Guayaquil, Ecuador
| | | | - Greta Franco-Sotomayor
- Instituto Nacional de Salud Publica e Investigacion "Leopoldo Izquieta Perez", Guayaquil, Ecuador; Facultad de Ciencias de la Salud, Universidad Catolica Santiago de Guayaquil, Guayaquil, Venezuela
| | - Margarita Leon-Benitez
- Instituto Nacional de Salud Publica e Investigacion "Leopoldo Izquieta Perez", Guayaquil, Ecuador
| | - Juan Carlos Granda-Pardo
- Instituto Nacional de Salud Publica e Investigacion "Leopoldo Izquieta Perez", Guayaquil, Ecuador
| | - Gabriel Trueba
- Instituto de Microbiologia, Universidad San Francisco de Quito, Quito, Ecuador
| | - Jacobus Henri de Waard
- One Health Research Group, Universidad de las Americas, Quito; Laboratorio de Tuberculosis, Instituto de Biomedicina Dr. Jacinto Convit, Universidad Central de Venezuela, Caracas, Venezuela
| | - Miguel Angel Garcia-Bereguiain
- Laboratorio Para Investigaciones Biomedicas, Facultad de Ciencias de la Vida, Escuela Superior Politecnica del Litoral, Guayaquil, Ecuador; One Health Research Group, Universidad de las Americas, Quito, Venezuela
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158
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Cerezo-Cortés MI, Rodríguez-Castillo JG, Hernández-Pando R, Murcia MI. Circulation of M. tuberculosis Beijing genotype in Latin America and the Caribbean. Pathog Glob Health 2019; 113:336-351. [PMID: 31903874 PMCID: PMC7006823 DOI: 10.1080/20477724.2019.1710066] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Lineage 2 (East Asian), which includes the Beijing genotype, is one of the most prevalent lineages of Mycobacterium tuberculosis (Mtb) throughout the world. The Beijing family is associated to hypervirulence and drug-resistant tuberculosis. The study of this genotype's circulation in Latin America is crucial for achieving total control of TB, the goal established by the World Health Organization, for the American sub-continent, before 2035. In this sense, the present work presents an overview of the status of the Beijing genotype for this region, with a bibliographical review, and data analysis of MIRU-VNTRs for available Beijing isolates. Certain countries present a prevalent trend of <5%, suggesting low transmissibility for the region, with the exception of Cuba (17.2%), Perú (16%) and Colombia (5%). Minimum Spanning Tree analysis, obtained from MIRU-VNTR data, shows distribution of specific clonal complex strains in each country. From this data, in most countries, we found that molecular epidemiology has not been a tool used for the control of TB, suggesting that the Beijing genotype may be underestimated in Latin America. It is recommended that countries with the highest incidence of the Beijing genotype use effective control strategies and increased care, as a requirement for public health systems.
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Affiliation(s)
- MI Cerezo-Cortés
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - JG Rodríguez-Castillo
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - R Hernández-Pando
- Experimental Pathology Section, Department of Pathology, National Institute of Medical Sciences and Nutrition, México D.F., Mexico
| | - MI Murcia
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
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159
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Pole I, Trofimova J, Norvaisa I, Supply P, Skenders G, Nodieva A, Ozere I, Riekstina V, Igumnova V, Storozenko J, Jansone I, Viksna L, Ranka R. Analysis of Mycobacterium tuberculosis genetic lineages circulating in Riga and Riga region, Latvia, isolated between 2008 and 2012. INFECTION GENETICS AND EVOLUTION 2019; 78:104126. [PMID: 31783188 DOI: 10.1016/j.meegid.2019.104126] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 11/21/2019] [Accepted: 11/24/2019] [Indexed: 11/17/2022]
Abstract
Although the number of new tuberculosis (TB) cases registered per year has decreased by 3-fold between 2001 and 2017 in Latvia, the TB incidence and rates of multidrug resistant TB in this Baltic country remain substantially higher than in most other European countries. Molecular typing methods of Mycobacterium tuberculosis (MTB) play an important role both in clinical studies of the disease and the epidemiological investigations, allowing to describe and characterize the pathogen's population structure and spread of particular genotypes. Aim of this study was to examine the prevalence of MTB lineages in Riga and Riga region of Latvia within a five-year period (2008-2012), and to evaluate the discriminatory power (DP) of spoligotyping, standard 24-locus MIRU-VNTR and IS6110-RFLP methods in this setting. The results showed that the main MTB spoligotype families were Beijing (25.3%) and LAM (24.3%), followed by T (22.1%), Ural (11.2%), Haarlem (6.6%) and X superfamily (3.4%). This distribution remained stable over the five consecutive years. 67.6% of MTB isolates were pan-susceptible, and 32.4% were resistant to any drug; multi-drug resistance was found in 5.8% of MTB strains, and 7.6% of MTB isolates were extensively drug-resistant. Drug resistance was associated with SIT1, SIT283 and SIT42 genotypes, while SIT1 and SIT42 were overrepresented among multi drug-resistant MTB strains. Overall, DP of spoligotyping method alone was 0.8953, while DP of both 24-locus MIRU-VNTR analysis and IS6110 RFLP was higher (DP = 0.9846 and 0.9927, respectively), mainly due to the improvement of the resolution for the Beijing strains. In conclusion, this work represents the first comprehensive molecular epidemiological description of TB in Latvia, highlighting the high genetic diversity of MTB strains circulating in Riga and Riga region. In combination with detailed epidemiological data this approach was helpful for the in-depth understanding of epidemiological processes in settings where the Next-Gen sequencing is not available as a routine method.
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MESH Headings
- Adolescent
- Adult
- Aged
- Aged, 80 and over
- Antitubercular Agents/pharmacology
- Child
- Child, Preschool
- Drug Resistance, Multiple, Bacterial/drug effects
- Drug Resistance, Multiple, Bacterial/genetics
- Female
- Genetic Variation
- Genotyping Techniques
- Humans
- Infant
- Infant, Newborn
- Latvia/epidemiology
- Male
- Microbial Sensitivity Tests
- Middle Aged
- Minisatellite Repeats
- Molecular Epidemiology
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/isolation & purification
- Polymorphism, Restriction Fragment Length
- Prevalence
- Tuberculosis/epidemiology
- Tuberculosis/microbiology
- Tuberculosis, Multidrug-Resistant/epidemiology
- Tuberculosis, Multidrug-Resistant/microbiology
- Young Adult
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Affiliation(s)
- Ilva Pole
- Riga East University Hospital, Centre of Tuberculosis and Lung Diseases, Latvia; Latvian Biomedical Research and Study Centre, Latvia
| | - Julija Trofimova
- Riga East University Hospital, Centre of Tuberculosis and Lung Diseases, Latvia
| | - Inga Norvaisa
- Riga East University Hospital, Centre of Tuberculosis and Lung Diseases, Latvia
| | - Philip Supply
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, CIIL - Center for Infection and Immunity of Lille, U1019 - UMR 8204, Lille F-59000, France
| | - Girts Skenders
- Riga East University Hospital, Centre of Tuberculosis and Lung Diseases, Latvia
| | | | - Iveta Ozere
- Riga East University Hospital, Centre of Tuberculosis and Lung Diseases, Latvia; Riga Stradiņš University, Latvia
| | - Vija Riekstina
- Riga East University Hospital, Centre of Tuberculosis and Lung Diseases, Latvia
| | - Viktorija Igumnova
- Latvian Biomedical Research and Study Centre, Latvia; Riga Stradiņš University, Latvia
| | - Jelena Storozenko
- Riga Stradiņš University, Latvia; Riga East University Hospital, Latvian Centre of Infectious Diseases, Latvia
| | - Inta Jansone
- Latvian Biomedical Research and Study Centre, Latvia
| | - Ludmila Viksna
- Riga Stradiņš University, Latvia; Riga East University Hospital, Latvian Centre of Infectious Diseases, Latvia
| | - Renate Ranka
- Latvian Biomedical Research and Study Centre, Latvia; Riga Stradiņš University, Latvia.
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160
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Engström A, Antonenka U, Kadyrov A, Kalmambetova G, Kranzer K, Merker M, Kabirov O, Parpieva N, Rajabov A, Sahalchyk E, Sayfudtinov Z, Niemann S, Hoffmann H. Population structure of drug-resistant Mycobacterium tuberculosis in Central Asia. BMC Infect Dis 2019; 19:908. [PMID: 31664926 PMCID: PMC6819405 DOI: 10.1186/s12879-019-4480-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Accepted: 09/13/2019] [Indexed: 05/13/2023] Open
Abstract
Background Drug-resistant tuberculosis (TB) is a major public health concern threathing the success of TB control efforts, and this is particularily problematic in Central Asia. Here, we present the first analysis of the population structure of Mycobacterium tuberculosis complex isolates in the Central Asian republics Uzbekistan, Tajikistan, and Kyrgyzstan. Methods The study set consisted of 607 isolates with 235 from Uzbekistan, 206 from Tajikistan, and 166 from Kyrgyzstan. 24-loci MIRU-VNTR (Mycobacterial Interspersed Repetitive Units - Variable Number of Tandem Repeats) typing and spoligotyping were combined for genotyping. In addition, phenotypic drug suceptibility was performed. Results The population structure mainly comprises strains of the Beijing lineage (411/607). 349 of the 411 Beijing isolates formed clusters, compared to only 33 of the 196 isolates from other clades. Beijing 94–32 (n = 145) and 100–32 (n = 70) formed the largest clusters. Beijing isolates were more frequently multidrug-resistant, pre-extensively resistant (pre-XDR)- or XDR-TB than other genotypes. Conclusions Beijing clusters 94–32 and 100–32 are the dominant MTB genotypes in Central Asia. The relative size of 100–32 compared to previous studies in Kazakhstan and its unequal geographic distribution support the hypothesis of its more recent emergence in Central Asia. The data also demonstrate that clonal spread of resistant TB strains, particularly of the Beijing lineage, is a root of the so far uncontroled MDR-TB epidemic in Central Asia.
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Affiliation(s)
- Anna Engström
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany. .,Department of Medical Biochemistry and Microbiology, Uppsala University, IMBIM, Box 582, 751 23, Uppsala, Uppsala, Sweden. .,Present address: Clinical Genomics, Science for Life Laboratory, Tomtebodavägen 23 A, 17165, Solna, Sweden. .,Present address: School of Engineering Sciences in Chemistry, Biotechnology and Health, Division of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden. .,Postal address: Science for Life Laboratory, Tomtebodavägen 23 A, 17165, Solna, Sweden.
| | - Uladzimir Antonenka
- WHO Supranational Reference Laboratory of Tuberculosis, IML red GmbH, Institute of Microbiology and Laboratory Medicine, Robert Koch-Allee 2, D-82131, Gauting, Germany
| | - Abdylat Kadyrov
- National Tuberculosis Institute, 90a Ahuunbaen Street, 720075, Bishkek, Kyrgyzstan
| | - Gulmira Kalmambetova
- National Reference Laboratory of Tuberculosis, 90a Ahuunbaen Street, 720075, Bishkek, Kyrgyzstan
| | - Katharina Kranzer
- Clinical Research Department, London School of Hygiene and Tropical Medicine, London, UK
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany
| | - Olim Kabirov
- National Reference Laboratory of Tuberculosis, Vakhdat District, Dushanbe, Tajikistan
| | - Nargiza Parpieva
- Republican Specialized Scientific and Practical Medical Center of Tuberculosis and Pulmonology, Alimov Str.1, Tashkent, Uzbekistan, 100086
| | - Asliddin Rajabov
- National TB Center, National Tuberculosis Program, Dushanbe, Tajikistan
| | - Evgeni Sahalchyk
- WHO Supranational Reference Laboratory of Tuberculosis, IML red GmbH, Institute of Microbiology and Laboratory Medicine, Robert Koch-Allee 2, D-82131, Gauting, Germany
| | - Zayniddin Sayfudtinov
- National Reference Laboratory of Tuberculosis, Alimov Str.1, Tashkent, Uzbekistan, 100086
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Parkallee 1, 23845, Borstel, Germany
| | - Harald Hoffmann
- WHO Supranational Reference Laboratory of Tuberculosis, IML red GmbH, Institute of Microbiology and Laboratory Medicine, Robert Koch-Allee 2, D-82131, Gauting, Germany.,SYNLAB Gauting, SYNLAB Human Genetics Munich, Robert Koch-Allee 2, 82131, Gauting, Germany.,Kuratorium Tuberculosis in the World e.V, Robert Koch-Allee 2, 82131, Gauting, Germany
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161
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Kwon KW, Lee A, Larsen SE, Baldwin SL, Coler RN, Reed SG, Cho SN, Ha SJ, Shin SJ. Long-term protective efficacy with a BCG-prime ID93/GLA-SE boost regimen against the hyper-virulent Mycobacterium tuberculosis strain K in a mouse model. Sci Rep 2019; 9:15560. [PMID: 31664157 PMCID: PMC6820558 DOI: 10.1038/s41598-019-52146-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 10/04/2019] [Indexed: 02/07/2023] Open
Abstract
Since ID93/GLA-SE was developed as a targeted BCG-prime booster vaccine, in the present study, we evaluated the protective efficacy of ID93/GLA-SE as a boost to a BCG-prime against the hypervirulent Mycobacterium tuberculosis (Mtb) K challenge to provide further information on the development and application of this vaccine candidate. Boosting BCG with the ID93/GLA-SE vaccine significantly reduced bacterial burden at 16 weeks post-challenge while the BCG vaccine alone did not confer significant protection against Mtb K. The pathological analysis of the lung from the challenged mice also showed the remarkably protective boosting effect of ID93/GLA-SE on BCG-immunised animals. Moreover, qualitative and quantitative analysis of the immune responses following ID93/GLA-SE-immunisation demonstrated that ID93/GLA-SE was able to elicit robust and sustained Th1-biased antigen-specific multifunctional CD4+ T-cell responses up to 16 weeks post-challenge as well as a high magnitude of an antigen-specific IgG response. Our findings demonstrate that the ID93/GLA-SE vaccine candidate given as a BCG-prime boost regimen confers a high level of long-term protection against the hypervirulent Mtb Beijing infection. These findings will provide further and more feasible validation for the potential utility of this vaccine candidate particularly in East-Asian countries, with the predominance of the Beijing genotype, after BCG vaccination.
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Affiliation(s)
- Kee Woong Kwon
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Ara Lee
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul, 03722, South Korea
| | - Sasha E Larsen
- Infectious Disease Research Institute, 1616 Eastlake Ave E, Suite 400, Seattle, WA, 98102, USA
| | - Susan L Baldwin
- Infectious Disease Research Institute, 1616 Eastlake Ave E, Suite 400, Seattle, WA, 98102, USA
| | - Rhea N Coler
- Infectious Disease Research Institute, 1616 Eastlake Ave E, Suite 400, Seattle, WA, 98102, USA.,Department of Global Health, University of Washington, Seattle, USA.,PAI Life Sciences Inc., Seattle, USA
| | - Steven G Reed
- Infectious Disease Research Institute, 1616 Eastlake Ave E, Suite 400, Seattle, WA, 98102, USA
| | - Sang-Nae Cho
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea
| | - Sang-Jun Ha
- Department of Biochemistry, College of Life Science & Biotechnology, Yonsei University, Seoul, 03722, South Korea
| | - Sung Jae Shin
- Department of Microbiology, Institute for Immunology and Immunological Disease, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, South Korea.
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162
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Guthrie JL, Kong C, Roth D, Jorgensen D, Rodrigues M, Hoang L, Tang P, Cook V, Johnston J, Gardy JL. Molecular Epidemiology of Tuberculosis in British Columbia, Canada: A 10-Year Retrospective Study. Clin Infect Dis 2019; 66:849-856. [PMID: 29069284 PMCID: PMC5850024 DOI: 10.1093/cid/cix906] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 10/17/2017] [Indexed: 11/14/2022] Open
Abstract
Background Understanding regional molecular epidemiology allows for the development of more efficient tuberculosis prevention strategies in low-incidence settings. Methods We analyzed 24-locus mycobacterial interspersed repetitive-unit–variable-number tandem repeat (MIRU-VNTR) genotyping for 2290 Mycobacterium tuberculosis clinical isolates collected in the province of British Columbia (BC), Canada, in 2005–2014. Laboratory data for each isolate were linked to case-level clinical and demographic data. These data were used to describe the molecular epidemiology of tuberculosis across the province. Results We detected >1500 distinct genotypes across the 4 major M. tuberculosis lineages, reflecting BC’s diverse population. Disease site and clustering rates varied across lineages, and MIRU-VNTR was used to group the 2290 isolates into 189 clusters (2–70 isolates per cluster), with an overall clustering rate of 42.4% and an estimated local transmission rate of 34.1%. Risk factors for clustering varied between Canadian-born and foreign-born individuals; the former had increased odds (odds ratio, 7.8; 95% confidence interval [CI], 6.2–9.6) of belonging to a genotypic cluster, although nearly one-quarter of clusters included both Canadian- and foreign-born persons. Large clusters (≥10 cases) occurred more frequently within the M. tuberculosis Euro-American lineage, and individual-level risk factors associated with belonging to a large cluster included being Canadian born (adjusted odds ratio, 3.3; 95% CI, 2.3–4.8), residing in a rural area (2.3; 1.2–4.5), and illicit drug use (2.0; 1.2–3.4). Conclusions Although tuberculosis in BC largely arises through reactivation of latent tuberculosis in foreign-born persons, locally transmitted infections occur in discrete populations with distinct disease and risk factor profiles, representing groups for targeted interventions.
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Affiliation(s)
| | - Clare Kong
- British Columbia Centre for Disease Control Public Health Laboratory
| | - David Roth
- British Columbia Centre for Disease Control
| | | | - Mabel Rodrigues
- British Columbia Centre for Disease Control Public Health Laboratory
| | - Linda Hoang
- British Columbia Centre for Disease Control Public Health Laboratory.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Patrick Tang
- Department of Pathology, Sidra Medical and Research Center, Doha, Qatar
| | - Victoria Cook
- British Columbia Centre for Disease Control.,Respiratory Medicine, University of British Columbia, Vancouver, Canada
| | - James Johnston
- British Columbia Centre for Disease Control.,Respiratory Medicine, University of British Columbia, Vancouver, Canada
| | - Jennifer L Gardy
- School of Population and Public Health, University of British Columbia.,British Columbia Centre for Disease Control
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163
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Sinkov VV, Ogarkov OB, Plotnikov AO, Gogoleva NE, Zhdanova SN, Pervanchuk VL, Belkova NL, Koshcheev ME, Thomas TA, Liu J, Zorkaltseva EY, Heysell SK. Metagenomic analysis of mycobacterial transrenal DNA in patients with HIV and tuberculosis coinfection. INFECTION GENETICS AND EVOLUTION 2019; 77:104057. [PMID: 31629083 DOI: 10.1016/j.meegid.2019.104057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 09/23/2019] [Accepted: 09/29/2019] [Indexed: 10/25/2022]
Abstract
The existence of "transrenal" DNA (tr-DNA), i.e. cell-free DNA that has distributed through the renal barrier to the urine, was first shown from a pathogen in 2000 (Botezatu et al., 2000). However, a targeted search for tr-DNA from Mycobacterium tuberculosis (MBT) started relatively recently (Cannas et al., 2008; Green et al., 2009). While other MBT cellular components found in the urine, e.g. lipoarabinomannan, have been used as an enhanced diagnostic tool, tr-DNA has the potential for strain specific identification or a more persistent biomarker during treatment of active disease. We therefore sought to identify by high-throughput next generation sequencing (NGS) MBT genome fragments in the urine of people with human immunodeficiency virus and tuberculosis (HIV-TB) co-infection living in a co-epidemic setting, and to evaluate whether these DNA targets are suitable for the development a quantitative TaqMan polymerase chain reaction with real-time detection (rt-PCR). Selection and mapping to the reference MBT genome of strain H37Rv (NC_000962) revealed 158 fragments of mycobacterial DNA with length from 19 to 44 base pairs (bp) repeated in different DNA samples. Five targets were chosen for design of rt-PCR primers and probes. Comparative analysis of the newly developed tests that were based on the results of NGS did not reveal a significant increase in sensitivity and specificity relative to the previous empirically designed targets. Howver, highly reproducible NGS reads of mycobacterial tr-DNA were obtained. rt-PCR test development suitable for more practical clinical use was likely limited by the small size of the secreted DNA fragments. It is necessary to develop further molecular approaches for the detection of mycobacterial tr-DNA or rely on NGS techniques with inherent bioinformatics requirements.
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Affiliation(s)
- Viacheslav V Sinkov
- Department of Epidemiology and Microbiology, "Scientific Centre for Family Health and Human Reproduction Problems", Irkutsk, Russia
| | - Oleg B Ogarkov
- Department of Epidemiology and Microbiology, "Scientific Centre for Family Health and Human Reproduction Problems", Irkutsk, Russia; Irkutsk State Medical Academy of Continuing Education, Irkutsk, Russia.
| | - Andrey O Plotnikov
- Center of Shared Scientific Equipment "Persistence of microorganisms", Institute for Cellular and Intracellular Symbiosis, Ural Branch of Russian Academy of Sciences, Orenburg, Russia
| | - Natalya E Gogoleva
- Center of Shared Scientific Equipment "Persistence of microorganisms", Institute for Cellular and Intracellular Symbiosis, Ural Branch of Russian Academy of Sciences, Orenburg, Russia; Kazan Institute of Biochemistry and Biophysics, Russian Academy of Sciences, Kazan, Russia
| | - Svetlana N Zhdanova
- Department of Epidemiology and Microbiology, "Scientific Centre for Family Health and Human Reproduction Problems", Irkutsk, Russia
| | | | - Natalia L Belkova
- Limnological Institute Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | | | - Tania A Thomas
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
| | - Jie Liu
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
| | | | - Scott K Heysell
- Division of Infectious Diseases and International Health, University of Virginia, Virginia, USA
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164
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Ajawatanawong P, Yanai H, Smittipat N, Disratthakit A, Yamada N, Miyahara R, Nedsuwan S, Imasanguan W, Kantipong P, Chaiyasirinroje B, Wongyai J, Plitphonganphim S, Tantivitayakul P, Phelan J, Parkhill J, Clark TG, Hibberd ML, Ruangchai W, Palittapongarnpim P, Juthayothin T, Thawornwattana Y, Viratyosin W, Tongsima S, Mahasirimongkol S, Tokunaga K, Palittapongarnpim P. A novel Ancestral Beijing sublineage of Mycobacterium tuberculosis suggests the transition site to Modern Beijing sublineages. Sci Rep 2019; 9:13718. [PMID: 31548561 PMCID: PMC6757101 DOI: 10.1038/s41598-019-50078-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 08/27/2019] [Indexed: 11/08/2022] Open
Abstract
Global Mycobacterium tuberculosis population comprises 7 major lineages. The Beijing strains, particularly the ones classified as Modern groups, have been found worldwide, frequently associated with drug resistance, younger ages, outbreaks and appear to be expanding. Here, we report analysis of whole genome sequences of 1170 M. tuberculosis isolates together with their patient profiles. Our samples belonged to Lineage 1-4 (L1-L4) with those of L1 and L2 being equally dominant. Phylogenetic analysis revealed several new or rare sublineages. Differential associations between sublineages of M. tuberculosis and patient profiles, including ages, ethnicity, HIV (human immunodeficiency virus) infection and drug resistance were demonstrated. The Ancestral Beijing strains and some sublineages of L4 were associated with ethnic minorities while L1 was more common in Thais. L2.2.1.Ancestral 4 surprisingly had a mutation that is typical of the Modern Beijing sublineages and was common in Akha and Lahu tribes who have migrated from Southern China in the last century. This may indicate that the evolutionary transition from the Ancestral to Modern Beijing sublineages might be gradual and occur in Southern China, where the presence of multiple ethnic groups might have allowed for the circulations of various co-evolving sublineages which ultimately lead to the emergence of the Modern Beijing strains.
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Affiliation(s)
- Pravech Ajawatanawong
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand
| | - Hideki Yanai
- Fukujuji Hospital, Japan Anti-Tuberculosis Association (JATA), Kiyose, Japan
| | - Nat Smittipat
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | - Areeya Disratthakit
- Department of Medical Sciences, Ministry of Public Health, Tiwanon Road, Nonthaburi, Thailand
| | - Norio Yamada
- Research Institute of Tuberculosis, JATA, Kiyose, Japan
| | - Reiko Miyahara
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Supalert Nedsuwan
- Chiangrai Prachanukroh Hospital, Ministry of Public Health, Chiangrai, Thailand
| | - Worarat Imasanguan
- Chiangrai Prachanukroh Hospital, Ministry of Public Health, Chiangrai, Thailand
| | - Pacharee Kantipong
- Chiangrai Prachanukroh Hospital, Ministry of Public Health, Chiangrai, Thailand
| | | | | | - Supada Plitphonganphim
- Department of Biostatistics, Faculty of Public Health, Mahidol University, Bangkok, Thailand
| | - Pornpen Tantivitayakul
- Department of Oral Microbiology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
| | - Jody Phelan
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Taane G Clark
- London School of Hygiene and Tropical Medicine, London, UK
| | | | - Wuthiwat Ruangchai
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand
| | | | - Tada Juthayothin
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | - Yuttapong Thawornwattana
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand
| | - Wasna Viratyosin
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand
| | | | - Katsushi Tokunaga
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo, Japan
| | - Prasit Palittapongarnpim
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand.
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Phahonyothin Road, Pathumthani, Thailand.
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165
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Günther G, van Leth F, Alexandru S, Altet N, Avsar K, Bang D, Barbuta R, Bothamley G, Ciobanu A, Crudu V, Danilovits M, Dedicoat M, Duarte R, Gualano G, Kunst H, de Lange W, Leimane V, McLaughlin AM, Magis-Escurra C, Muylle I, Polcová V, Popa C, Rumetshofer R, Skrahina A, Solodovnikova V, Spinu V, Tiberi S, Viiklepp P, Lange C. Clinical Management of Multidrug-Resistant Tuberculosis in 16 European Countries. Am J Respir Crit Care Med 2019; 198:379-386. [PMID: 29509468 DOI: 10.1164/rccm.201710-2141oc] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
RATIONALE Multidrug-resistant tuberculosis (MDR-TB) is a major burden to public health in Europe. Reported treatment success rates are around 50% or less, and cure rates are even lower. OBJECTIVES To document the management and treatment outcome in patients with MDR-TB in Europe. METHODS We performed a prospective cohort study, analyzing management and treatment outcomes stratified by incidence of patients with MDR-TB in Europe. Treatment outcomes were compared by World Health Organization and alternative simplified definitions by the Tuberculosis Network European Trialsgroup (TBNET). MEASUREMENTS AND MAIN RESULTS A total of 380 patients with MDR-TB were recruited and followed up between 2010 and 2014 in 16 European countries. Patients in high-incidence countries compared with low-incidence countries were treated more frequently with standardized regimen (83.2% vs. 9.9%), had delayed treatment initiation (median, 111 vs. 28 d), developed more additional drug resistance (23% vs. 5.8%), and had increased mortality (9.4% vs. 1.9%). Only 20.1% of patients using pyrazinamide had proven susceptibility to the drug. Applying World Health Organization outcome definitions, frequency of cure (38.7% vs. 9.7%) was higher in high-incidence countries. Simplified outcome definitions that include 1 year of follow-up after the end of treatment showed similar frequency of relapse-free cure in low- (58.3%), intermediate- (55.8%), and high-incidence (57.1%) countries, but highest frequency of failure in high-incidence countries (24.1% vs. 14.6%). CONCLUSIONS Conventional standard MDR-TB treatment regimens resulted in a higher frequency of failure compared with individualized treatments. Overall, cure from MDR-TB is substantially more frequent than previously anticipated, and poorly reflected by World Health Organization outcome definitions.
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Affiliation(s)
- Gunar Günther
- 1 Research Center Borstel, Clinical Infectious Diseases, German Center for Infection Research, Borstel, Germany.,2 Department of Medicine, University of Namibia School of Medicine, Windhoek, Namibia
| | - Frank van Leth
- 3 Department of Global Health, Academic Medical Center, University of Amsterdam, Amsterdam, the Netherlands.,4 Amsterdam Institute for Global Health and Development, Amsterdam, the Netherlands
| | - Sofia Alexandru
- 5 Institute of Phthisiopneumology, Chisinau, Republic of Moldova
| | - Neus Altet
- 6 Hospital Universitari Vall d'Hebron, Research Institute-IDIAP Jordi Gol, Barcelona, Spain
| | | | - Didi Bang
- 8 Statens Serum Institut, Copenhagen, Denmark
| | - Raisa Barbuta
- 9 Balti Municipal Hospital, Balti, Republic of Moldova
| | | | - Ana Ciobanu
- 5 Institute of Phthisiopneumology, Chisinau, Republic of Moldova
| | - Valeriu Crudu
- 5 Institute of Phthisiopneumology, Chisinau, Republic of Moldova.,11 National Tuberculosis Reference Laboratory, Chisinau, Republic of Moldova
| | | | - Martin Dedicoat
- 13 Heart of England Foundation Trust, Birmingham, United Kingdom.,14 University of Warwick, Coventry, United Kingdom
| | - Raquel Duarte
- 15 EpiUnit, Institute of Public Health, Porto University, Porto, Portugal.,16 Department of Clinical Epidemiology, Predictive Medicine and Public Health, University of Porto Medical School, Porto, Portugal
| | - Gina Gualano
- 17 National Institute for Infectious Diseases "L, Spallanzani," Rome, Italy
| | - Heinke Kunst
- 18 Queen Mary University, London, United Kingdom
| | - Wiel de Lange
- 19 University of Groningen, University Medical Center Groningen, Tuberculosis Centre Beatrixoord, Haren, the Netherlands
| | - Vaira Leimane
- 20 Riga East University Hospital, Tuberculosis and Lung Diseases Centre, Riga, Latvia
| | | | - Cecile Magis-Escurra
- 22 Radboud University Medical Centre-TB Expert Centre UCCZ Dekkerswald, Nijmegen-Groesbeek, the Netherlands
| | - Inge Muylle
- 23 University Medical Center St. Pieter, Brussels, Belgium
| | | | | | | | - Alena Skrahina
- 27 Republican Research and Practical Centre for Pulmonology and Tuberculosis, Minsk, Belarus
| | - Varvara Solodovnikova
- 27 Republican Research and Practical Centre for Pulmonology and Tuberculosis, Minsk, Belarus
| | | | - Simon Tiberi
- 28 Ospedale Eugenio Morelli Reference Hospital for MDR and HIV-TB, Sondalo, Italy.,29 Barts Health NHS Trust, London, United Kingdom
| | - Piret Viiklepp
- 30 National Institute for Health Development, Tallinn, Estonia
| | - Christoph Lange
- 1 Research Center Borstel, Clinical Infectious Diseases, German Center for Infection Research, Borstel, Germany.,31 International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany.,32 Department of Medicine, Karolinska Institute, Stockholm, Sweden; and.,33 German Center for Infection Research, Borstel, Germany
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166
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Acosta-Herrera M, Strauss M, Casares-Marfil D, Martín J. Genomic medicine in Chagas disease. Acta Trop 2019; 197:105062. [PMID: 31201776 DOI: 10.1016/j.actatropica.2019.105062] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 06/11/2019] [Indexed: 02/07/2023]
Abstract
Genetic approaches have been proposed for improving the understanding of the causes of differential susceptibility to Trypanosoma cruzi infection and Chagas disease outcome. Polymorphisms in genes involved in the immune/inflammatory response are being studied in order to clarify their possible role in the occurrence or severity of the cardiac and/or gastrointestinal complications. However still today, the number of significant associated genes is limited and the pathophysiological mechanisms underlying this condition are unknown. This article review the information currently available from the published scientific literature regarding the genetic variants of molecules of the immune system and other variants that can contribute to the clinical presentation of the disease. Genomic medicine will improve our knowledge about the molecular basis of Chagas disease, will open new avenues for developing biomarkers of disease progression, new therapeutic strategies to suit the requirements of individual patients, and will contribute to the control of one of the infections with the greatest socio-economic impact in the Americas.
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167
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Menardo F, Duchêne S, Brites D, Gagneux S. The molecular clock of Mycobacterium tuberculosis. PLoS Pathog 2019; 15:e1008067. [PMID: 31513651 PMCID: PMC6759198 DOI: 10.1371/journal.ppat.1008067] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 09/24/2019] [Accepted: 09/03/2019] [Indexed: 12/20/2022] Open
Abstract
The molecular clock and its phylogenetic applications to genomic data have changed how we study and understand one of the major human pathogens, Mycobacterium tuberculosis (MTB), the etiologic agent of tuberculosis. Genome sequences of MTB strains sampled at different times are increasingly used to infer when a particular outbreak begun, when a drug-resistant clone appeared and expanded, or when a strain was introduced into a specific region. Despite the growing importance of the molecular clock in tuberculosis research, there is a lack of consensus as to whether MTB displays a clocklike behavior and about its rate of evolution. Here we performed a systematic study of the molecular clock of MTB on a large genomic data set (6,285 strains), covering different epidemiological settings and most of the known global diversity. We found that sampling times below 15-20 years were often insufficient to calibrate the clock of MTB. For data sets where such calibration was possible, we obtained a clock rate between 1x10-8 and 5x10-7 nucleotide changes per-site-per-year (0.04-2.2 SNPs per-genome-per-year), with substantial differences between clades. These estimates were not strongly dependent on the time of the calibration points as they changed only marginally when we used epidemiological isolates (sampled in the last 40 years) or three ancient DNA samples (about 1,000 years old) to calibrate the tree. Additionally, the uncertainty and the discrepancies in the results of different methods were sometimes large, highlighting the importance of using different methods, and of considering carefully their assumptions and limitations.
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Affiliation(s)
- Fabrizio Menardo
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastian Duchêne
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Daniela Brites
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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168
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Immunological mechanisms of human resistance to persistent Mycobacterium tuberculosis infection. Nat Rev Immunol 2019; 18:575-589. [PMID: 29895826 DOI: 10.1038/s41577-018-0025-3] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Mycobacterium tuberculosis is a leading cause of mortality worldwide and establishes a long-lived latent infection in a substantial proportion of the human population. Multiple lines of evidence suggest that some individuals are resistant to latent M. tuberculosis infection despite long-term and intense exposure, and we term these individuals 'resisters'. In this Review, we discuss the epidemiological and genetic data that support the existence of resisters and propose criteria to optimally define and characterize the resister phenotype. We review recent insights into the immune mechanisms of M. tuberculosis clearance, including responses mediated by macrophages, T cells and B cells. Understanding the cellular mechanisms that underlie resistance to M. tuberculosis infection may reveal immune correlates of protection that could be utilized for improved diagnostics, vaccine development and novel host-directed therapeutic strategies.
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169
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El Achkar S, Demanche C, Osman M, Rafei R, Ismail MB, Yaacoub H, Pinçon C, Duthoy S, De Matos F, Gaudin C, Trovato A, Cirillo DM, Hamze M, Supply P. Drug-Resistant Tuberculosis, Lebanon, 2016 - 2017. Emerg Infect Dis 2019; 25:564-568. [PMID: 30789124 PMCID: PMC6390733 DOI: 10.3201/eid2503.181375] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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
In a 12-month nationwide study on the prevalence of drug-resistant tuberculosis (TB) in Lebanon, we identified 3 multidrug-resistant cases and 3 extensively drug-resistant TB cases in refugees, migrants, and 1 Lebanon resident. Enhanced diagnostics, particularly in major destinations for refugees, asylum seekers, and migrant workers, can inform treatment decisions and may help prevent the spread of drug-resistant TB.
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Arandjelović I, Merker M, Richter E, Kohl TA, Savić B, Soldatović I, Wirth T, Vuković D, Niemann S. Longitudinal Outbreak of Multidrug-Resistant Tuberculosis in a Hospital Setting, Serbia. Emerg Infect Dis 2019; 25:555-558. [PMID: 30789133 PMCID: PMC6390760 DOI: 10.3201/eid2503.181220] [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: 12/01/2022] Open
Abstract
A retrospective population-based molecular epidemiologic study of multidrug-resistant Mycobacterium tuberculosis complex strains in Serbia (2008–2014) revealed an outbreak of TUR genotype strains in a psychiatric hospital starting around 1990. Drug unavailability, poor infection control, and schizophrenia likely fueled acquisition of additional resistance and bacterial fitness–related mutations over 2 decades.
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Genestet C, Tatai C, Berland JL, Claude JB, Westeel E, Hodille E, Fredenucci I, Rasigade JP, Ponsoda M, Jacomo V, Vachée A, Gaudart A, Gaillard JL, Roux AL, Ader F, Tararbit K, Terpant G, Bryant JE, Lina G, Dumitrescu O. Prospective Whole-Genome Sequencing in Tuberculosis Outbreak Investigation, France, 2017-2018. Emerg Infect Dis 2019; 25:589-592. [PMID: 30789329 PMCID: PMC6390740 DOI: 10.3201/eid2503.181124] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
During June 2017–April 2018, active tuberculosis with Beijing SIT1 isolates was diagnosed in 14 persons living in 4 distant cities in France. Whole-genome sequencing indicated that these patients belonged to a single transmission chain. Whole-genome sequencing–based laboratory investigations enabled prompt tracing of linked cases to improve tuberculosis control.
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Bainomugisa A, Pandey S, Donnan E, Simpson G, Foster J, Lavu E, Hiasihri S, McBryde ES, Moke R, Vincent S, Sintchenko V, Marais BJ, Coin LJM, Coulter C. Cross-Border Movement of Highly Drug-Resistant Mycobacterium tuberculosis from Papua New Guinea to Australia through Torres Strait Protected Zone, 2010-2015. Emerg Infect Dis 2019; 25:406-415. [PMID: 30789135 DOI: 10.3201/eid2503.181003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In this retrospective study, we used whole-genome sequencing (WGS) to delineate transmission dynamics, characterize drug-resistance markers, and identify risk factors of transmission among Papua New Guinea residents of the Torres Strait Protected Zone (TSPZ) who had tuberculosis diagnoses during 2010-2015. Of 117 isolates collected, we could acquire WGS data for 100; 79 were Beijing sublineage 2.2.1.1, which was associated with active transmission (odds ratio 6.190, 95% CI 2.221-18.077). Strains were distributed widely throughout the TSPZ. Clustering occurred more often within than between villages (p = 0.0013). Including 4 multidrug-resistant tuberculosis isolates from Australia citizens epidemiologically linked to the TSPZ into the transmission network analysis revealed 2 probable cross-border transmission events. All multidrug-resistant isolates (33/104) belonged to Beijing sublineage 2.2.1.1 and had high-level isoniazid and ethionamide co-resistance; 2 isolates were extensively drug resistant. Including WGS in regional surveillance could improve tuberculosis transmission tracking and control strategies within the TSPZ.
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173
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Chiner-Oms Á, Comas I. Large genomics datasets shed light on the evolution of the Mycobacterium tuberculosis complex. INFECTION GENETICS AND EVOLUTION 2019; 72:10-15. [DOI: 10.1016/j.meegid.2019.02.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/21/2019] [Accepted: 02/25/2019] [Indexed: 01/21/2023]
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Thain N, Le C, Crossa A, Ahuja SD, Meissner JS, Mathema B, Kreiswirth B, Kurepina N, Cohen T, Chindelevitch L. Towards better prediction of Mycobacterium tuberculosis lineages from MIRU-VNTR data. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2019; 72:59-66. [PMID: 29960078 PMCID: PMC6708508 DOI: 10.1016/j.meegid.2018.06.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 06/20/2018] [Accepted: 06/22/2018] [Indexed: 11/30/2022]
Abstract
The determination of lineages from strain-based molecular genotyping information is an important problem in tuberculosis. Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing is a commonly used molecular genotyping approach that uses counts of the number of times pre-specified loci repeat in a strain. There are three main approaches for determining lineage based on MIRU-VNTR data - one based on a direct comparison to the strains in a curated database, and two others, on machine learning algorithms trained on a large collection of labeled data. All existing methods have limitations. The direct approach imposes an arbitrary threshold on how much a database strain can differ from a given one to be informative. On the other hand, the machine learning-based approaches require a substantial amount of labeled data. Notably, all three methods exhibit suboptimal classification accuracy without additional data. We explore several computational approaches to address these limitations. First, we show that eliminating the arbitrary threshold improves the performance of the direct approach. Second, we introduce RuleTB, an alternative direct method that proposes a concise set of rules for determining lineages. Lastly, we propose StackTB, a machine learning approach that requires only a fraction of the training data to outperform the accuracy of both existing machine learning methods. Our approaches demonstrate superior performance on a training dataset collected in New York City over 10 years, and the improvement in performance translates to a held-out testing set. We conclude that our methods provide opportunities for improving the determination of pathogenic lineages based on MIRU-VNTR data.
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Affiliation(s)
- Nithum Thain
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
| | - Christopher Le
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
| | - Aldo Crossa
- New York City Department of Health and Mental Hygiene, Queens, NY, USA
| | - Shama Desai Ahuja
- New York City Department of Health and Mental Hygiene, Queens, NY, USA
| | | | - Barun Mathema
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Barry Kreiswirth
- Public Health Research Institute TB Center, Rutgers University, Newark, NJ, USA
| | - Natalia Kurepina
- Public Health Research Institute TB Center, Rutgers University, Newark, NJ, USA
| | - Ted Cohen
- Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
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175
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Wheeler N. We are falling behind on TB elimination targets: can whole-genome sequencing guide our efforts? Thorax 2019; 74:833-834. [PMID: 31331948 PMCID: PMC6824606 DOI: 10.1136/thoraxjnl-2019-213098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/05/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Nicole Wheeler
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Cambridge, UK
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176
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Liu Q, Wang D, Martinez L, Lu P, Zhu L, Lu W, Wang J. Mycobacterium tuberculosis Beijing genotype strains and unfavourable treatment outcomes: a systematic review and meta-analysis. Clin Microbiol Infect 2019; 26:180-188. [PMID: 31336202 DOI: 10.1016/j.cmi.2019.07.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/09/2019] [Accepted: 07/13/2019] [Indexed: 01/29/2023]
Abstract
OBJECTIVES The Mycobacterium tuberculosis Beijing genotype was first described in 1995 and is now the predominant strain among patients with tuberculosis in many Asian countries. The rapid global spread of the Beijing genotype is receiving increasing attention because it can cause a higher risk of treatment failures. Our objective was to assess the association between the Beijing genotype and unfavourable treatment outcomes of tuberculosis. METHODS We searched for eligible studies through PubMed, Web of Science, Chinese National Knowledge Infrastructure and Wanfang Data. We included cohort studies that evaluated treatment outcomes and Beijing genotype strains. Participants were individuals with active pulmonary tuberculosis. The association between Beijing genotype and the risk of unfavourable treatment outcomes was assessed using the pooled odds ratios (ORs) with corresponding confidence intervals (CIs). RESULTS In total, 7489 tuberculosis patients were involved in the analysis. Patients infected with the Beijing genotype were more likely to have unfavourable treatment outcomes, with the OR of 2.04 (95% CI 1.52-2.75). The pooled OR was 2.33 (95% CI 1.71-3.16) for recurrence, 2.36 (95% CI 1.69-3.30) for relapse and 2.62 (95% CI 1.90-3.61) for treatment failure, respectively. Subgroup analysis revealed that Beijing genotype was a significant risk factor for unfavourable treatment outcomes in Asians (OR 2.28, 95% CI 1.82-2.86) or in drug-susceptible TB patients (OR 2.11, 95% CI 1.31-3.39). No significant association was observed among non-Asian populations (OR 1.17, 95% CI 0.73-1.86) or patients with multidrug-resistant (MDR) tuberculosis (OR 0.97, 95% CI 0.48-1.94). CONCLUSIONS Our results suggest that Mycobacterium tuberculosis Beijing genotype is associated with an increased risk of unfavourable treatment outcomes, including treatment failure and relapse.
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Affiliation(s)
- Q Liu
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China; Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, PR China
| | - D Wang
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing, PR China
| | - L Martinez
- Division of Infectious Diseases and Geographic Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - P Lu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, PR China
| | - L Zhu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, PR China
| | - W Lu
- Department of Chronic Communicable Disease, Center for Disease Control and Prevention of Jiangsu Province, Nanjing, PR China
| | - J Wang
- Department of Epidemiology, Center for Global Health, School of Public Health, Nanjing Medical University, Nanjing, PR China.
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177
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Personalized Approach as a Basis for the Future Diagnosis of Tuberculosis (Literature Review). ACTA BIOMEDICA SCIENTIFICA 2019. [DOI: 10.29413/abs.2019-4.3.17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The global spread of tuberculosis remains one of actual problems of public health despite of introduction of public health safety programs. Early, rapid and accurate identification of M. tuberculosis and determination of drug susceptibility are essential for treatment and management of this disease. Delay in delivering results prolongs potentially inappropriate antituberculosis therapy, contributing to emergence of drug resistance, reducing treatment options and increasing treatment duration and associated costs, resulting in increased mortality and morbidity. Faster, more comprehensive diagnostics will enable earlier use of the most appropriate drug regimen, thus improving patient outcomes and reducing overall healthcare costs. The treatment of infection based on the using of massive antimicrobial therapy with analysis of bacterial strains resistance to first line drugs (FLD) isoniazid (INH), rifampin (RIF), pyrazinamide (PZA), ethambutol (EMB) and streptomycin (SM). However, the public health practitioners pay no attention to functional activity of human immune system genes. The interaction of bacterial genomes and immune system genes plays the major role in infection progress. There is growing evidence that, together with human and environmental factors, Mycobacterium tuberculosis complex strain diversity contributes to the variable outcome of infection and disease in human TB. We suppose that the future of diagnosis and treatment of tuberculosis lies in the field of personal medicine with comprehensive analysis of host and pathogen genes.
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178
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Pradipta IS, van’t Boveneind-Vrubleuskaya N, Akkerman OW, Alffenaar JWC, Hak E. Treatment outcomes of drug-resistant tuberculosis in the Netherlands, 2005-2015. Antimicrob Resist Infect Control 2019; 8:115. [PMID: 31338162 PMCID: PMC6626402 DOI: 10.1186/s13756-019-0561-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 06/14/2019] [Indexed: 11/10/2022] Open
Abstract
Background Since in low incidence TB countries population migration and complex treatment of drug-resistant tuberculosis (DR-TB) patients are major issues, we aimed to analyse patient risk factors associated with the incidence of poor outcome of TB treatment among DR-TB patients in the Netherlands. Methods This retrospective cohort study included adult patients with confirmed DR-TB treated from 2005 to 2015. We obtained data from a nationwide exhaustive registry of tuberculosis patients in the Netherlands. Predictors for unsuccessful TB treatment (defaulted and failed treatment) and TB-associated mortality were analysed using multivariate logistic regression. Results Among 10,303 registered TB patients, 545 patients with DR-TB were analysed. Six types of DR-TB were identified from the included patients, i.e. isoniazid mono- or poly-resistance (68%); rifampicin mono- or poly-resistance (3.1%); pyrazinamide mono-resistance (8.3%); ethambutol mono-resistance (0.1%); multidrug-resistance (18.9%); and extensively drug-resistance (0.7%). The majority of patients were foreign-born (86%) and newly diagnosed TB (89%) patients. The cumulative incidence of unsuccessful treatment and mortality were 5 and 1%, respectively. Among all DR-TB cases, patients with Multi Drug-Resistant Tuberculosis (MDR-TB) (OR 4.43; 95%CI 1.70-11.60) were more likely to have unsuccessful treatment, while miliary and central nervous system TB (OR 15.60; 95%CI 2.18-111.52) may also be predictors for TB mortality. Additionally, patients with substance abuse and homelessness tend to have unsuccessful treatment. Conclusions In recent years, we identified a low incidence of DR-TB as well as the poor outcome of DR-TB treatment. The majority of cases were primary drug-resistant and foreign-born. To further improve treatment outcome, special attention should be given to the high-risk DR-TB patients.
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Affiliation(s)
- Ivan S. Pradipta
- Groningen Research Institute of Pharmacy, Unit of Pharmaco-Therapy, - Epidemiology & - Economics (PTE2), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, the Netherlands
- Department of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, Universitas Padjadjaran, Jawa Barat, Indonesia
- Center of Excellence in Higher Education for Pharmaceutical Care Innovation, Universitas Padjadjaran, Jawa Barat, Indonesia
| | - Natasha van’t Boveneind-Vrubleuskaya
- Department of Clinical Pharmacy and Pharmacology, University Medical Centrum Groningen, Groningen, the Netherlands
- Department of Public Health Tuberculosis Control, Metropolitan Public Health Services , the Hague, the Netherlands
| | - Onno W. Akkerman
- Department of Pulmonary Diseases and Tuberculosis, University Medical Centre Groningen, University of Groningen, Groningen, the Netherlands
- Tuberculosis Centre Beatrixoord, University Medical Centre Groningen, University of Groningen, Haren, the Netherlands
| | - Jan-Willem C. Alffenaar
- Department of Clinical Pharmacy and Pharmacology, University Medical Centrum Groningen, Groningen, the Netherlands
- Faculty of Medicine and Health, School of Pharmacy, University of Sydney, Sydney, Australia
- Westmead Hospital, Sydney, Australia
| | - Eelko Hak
- Groningen Research Institute of Pharmacy, Unit of Pharmaco-Therapy, - Epidemiology & - Economics (PTE2), University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, the Netherlands
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179
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Mendis C, Thevanesam V, Kumara A, Wickramasinghe S, Madegedara D, Gamage C, Gordon SV, Suzuki Y, Ratnatunga C, Nakajima C. Insight into genetic diversity of Mycobacterium tuberculosis in Kandy, Sri Lanka reveals predominance of the Euro-American lineage. Int J Infect Dis 2019; 87:84-91. [PMID: 31299365 DOI: 10.1016/j.ijid.2019.07.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/24/2019] [Accepted: 07/01/2019] [Indexed: 12/12/2022] Open
Abstract
OBJECTIVE Sri Lanka is a country where the molecular epidemiology of Mycobacterium tuberculosis (MTB) is poorly explored. Therefore, this study was performed to identify circulating lineages/sub-lineages of MTB and their transmission patterns. METHODS DNA was extracted from 89 isolates of MTB collected during 2012 and 2013 from new pulmonary tuberculosis patients in Kandy, Sri Lanka and analyzed by spoligotyping, large sequence polymorphism (LSP), mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) typing, and drug resistance-associated gene sequencing. RESULTS The predominant lineage was lineage 4 (Euro-American, 45.9%), followed by lineage 1 (Indo-Oceanic, 29.4%), lineage 2 (East-Asian, 23.5%), and lineage 3 (Central-Asian, 1.2%). Among 26 spoligotype patterns, eight were undesignated or new types and seven of these belonged to lineage 4. Undesignated lineage 4/SIT124 (n=2/8) and SIT3234 (n=8/8) clustered together based on 24-locus MIRU-VNTR typing. The dominant sub-lineage was Beijing/SIT1 (n=19), with the isoniazid resistance katG G944C mutation (Ser315Thr) detected in two of them. CONCLUSIONS The population structure of MTB in Kandy, Sri Lanka was different from that in the South Asian region. The clonal expansion of locally evolved lineage 4/SIT3234 and detection of the pre-multidrug resistant Beijing isolates from new tuberculosis patients is alarming and will require continuous monitoring.
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Affiliation(s)
- Charitha Mendis
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Department of Medical Laboratory Science, Faculty of Allied Health Sciences, University of Peradeniya, Sri Lanka
| | - Vasanthi Thevanesam
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Sri Lanka
| | - Athula Kumara
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Sri Lanka
| | - Susiji Wickramasinghe
- Department of Parasitology, Faculty of Medicine, University of Peradeniya, Sri Lanka
| | | | - Chandika Gamage
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Sri Lanka
| | - Stephen V Gordon
- School of Veterinary Medicine, University College Dublin, Belfield, Dublin, Ireland; Global Station for Zoonosis Control, Hokkaido University Global Institute for Collaborative Research and Education, Sapporo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Global Station for Zoonosis Control, Hokkaido University Global Institute for Collaborative Research and Education, Sapporo, Japan
| | - Champa Ratnatunga
- Department of Microbiology, Faculty of Medicine, University of Peradeniya, Sri Lanka.
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan; Global Station for Zoonosis Control, Hokkaido University Global Institute for Collaborative Research and Education, Sapporo, Japan.
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180
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Stimson J, Gardy J, Mathema B, Crudu V, Cohen T, Colijn C. Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions. Mol Biol Evol 2019; 36:587-603. [PMID: 30690464 DOI: 10.1093/molbev/msy242] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Whole-genome sequencing (WGS) is increasingly used to aid the understanding of pathogen transmission. A first step in analyzing WGS data is usually to define "transmission clusters," sets of cases that are potentially linked by direct transmission. This is often done by including two cases in the same cluster if they are separated by fewer single-nucleotide polymorphisms (SNPs) than a specified threshold. However, there is little agreement as to what an appropriate threshold should be. We propose a probabilistic alternative, suggesting that the key inferential target for transmission clusters is the number of transmissions separating cases. We characterize this by combining the number of SNP differences and the length of time over which those differences have accumulated, using information about case timing, molecular clock, and transmission processes. Our framework has the advantage of allowing for variable mutation rates across the genome and can incorporate other epidemiological data. We use two tuberculosis studies to illustrate the impact of our approach: with British Columbia data by using spatial divisions; with Republic of Moldova data by incorporating antibiotic resistance. Simulation results indicate that our transmission-based method is better in identifying direct transmissions than a SNP threshold, with dissimilarity between clusterings of on average 0.27 bits compared with 0.37 bits for the SNP-threshold method and 0.84 bits for randomly permuted data. These results show that it is likely to outperform the SNP-threshold method where clock rates are variable and sample collection times are spread out. We implement the method in the R package transcluster.
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Affiliation(s)
- James Stimson
- Department of Mathematics, Imperial College London, London, UK
| | - Jennifer Gardy
- British Columbia Centre for Disease Control, Communicable Disease Prevention and Control Services, Vancouver, Canada.,School of Population and Public Health, University of British Columbia, Vancouver, Canada
| | - Barun Mathema
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, USA
| | - Valeriu Crudu
- Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Ted Cohen
- Yale University School of Public Health, New Haven
| | - Caroline Colijn
- Department of Mathematics, Imperial College London, London, UK.,Department of Mathematics, Simon Fraser University, Vancouver, Canada
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181
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Simple Assay for Detection of the Central Asia Outbreak Clade of the Mycobacterium tuberculosis Beijing Genotype. J Clin Microbiol 2019; 57:JCM.00215-19. [PMID: 31043465 DOI: 10.1128/jcm.00215-19] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 04/24/2019] [Indexed: 11/20/2022] Open
Abstract
The Central Asia outbreak (CAO) clade is a branch of the Mycobacterium tuberculosis Beijing genotype that is associated with multidrug resistance, increased transmissibility, and epidemic spread in parts of the former Soviet Union. Furthermore, migration flows bring these strains far beyond their areas of origin. We aimed to find a specific molecular marker of the Beijing CAO clade and develop a simple and affordable method for its detection. Based on the bioinformatics analysis of the large M. tuberculosis whole-genome sequencing (WGS) data set (n = 1,398), we identified an IS6110 insertion in the Rv1359-Rv1360 intergenic region as a specific molecular marker of the CAO clade. We further designed and optimized a multiplex PCR method to detect this insertion. The method was validated in silico with the recently published WGS data set from Central Asia (n = 277) and experimentally with M. tuberculosis isolates from European and Asian parts of Russia, the former Soviet Union, and East Asia (n = 319). The developed molecular assay may be recommended for rapid screening of retrospective collections and for prospective surveillance when comprehensive but expensive WGS is not available or practical. The assay may be especially useful in high multidrug-resistant tuberculosis (MDR-TB) burden countries of the former Soviet Union and in countries with respective immigrant communities.
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182
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Klotoe BJ, Kacimi S, Costa-Conceicão E, Gomes HM, Barcellos RB, Panaiotov S, Haj Slimene D, Sikhayeva N, Sengstake S, Schuitema AR, Akhalaia M, Alenova A, Zholdybayeva E, Tarlykov P, Anthony R, Refrégier G, Sola C. Genomic characterization of MDR/XDR-TB in Kazakhstan by a combination of high-throughput methods predominantly shows the ongoing transmission of L2/Beijing 94-32 central Asian/Russian clusters. BMC Infect Dis 2019; 19:553. [PMID: 31234780 PMCID: PMC6592005 DOI: 10.1186/s12879-019-4201-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 06/18/2019] [Indexed: 12/27/2022] Open
Abstract
Background Kazakhstan remains a high-burden TB prevalence country with a concomitent high-burden of multi-drug resistant tuberculosis. For this reason, we performed an in depth genetic diversity and population structure characterization of Mycobacterium tuberculosis complex (MTC) genetic diversity in Kazakhstan with both patient and community benefit. Methods A convenience sample of 700 MTC DNA cultures extracts from 630 tuberculosis patients recruited from 12 out of 14 regions in Kazakhstan, between 2010 and 2015, was independently studied by high-throughput hybridization-based methods, TB-SPRINT (59-Plex, n = 700), TB-SNPID (50-Plex, n = 543). DNA from 391 clinical isolates was successfully typed by two methods. To resolve the population structure of drug-resistant clades in more detail two complementary assays were run on the L2 isolates: an IS6110-NTF insertion site typing assay and a SigE SNP polymorphism assay. Results Strains belonged to L2/Beijing and L4/Euro-American sublineages; L2/Beijing prevalence totaled almost 80%. 50% of all samples were resistant to RIF and to INH., Subtyping showed that: (1) all L2/Beijing were “modern” Beijing and (2) most of these belonged to the previously described 94–32 sublineage (Central Asian/Russian), (3) at least two populations of the Central Asian/Russian sublineages are circulating in Kazakhstan, with different evolutionary dynamics. Conclusions For the first time, the global genetic diversity and population structure of M. tuberculosis genotypes circulating in Kazakhstan was obtained and compared to previous local studies. Results suggest a region-specific spread of a very limited number of L2/Beijing clonal complexes in Kazakhstan many strongly associated with an MDR phenotype. Electronic supplementary material The online version of this article (10.1186/s12879-019-4201-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- B J Klotoe
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - S Kacimi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - E Costa-Conceicão
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - H M Gomes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.,Laboratory of Molecular Biology Applied to Mycobacteria, FIOCRUZ, Rio de Janeiro, Brazil
| | - R B Barcellos
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.,Center of Scientific and Technological Development (CDCT), Secretary of Health of Rio Grande do Sul State (SES/RS), Porto Alegre, Brazil
| | - S Panaiotov
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.,National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| | - D Haj Slimene
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.,Institut Pasteur de Tunisie, Tunis, Tunisie
| | - N Sikhayeva
- National Centre for Biotechnology, Astana, Kazakhstan
| | - S Sengstake
- Royal Tropical Institute (KIT), Amsterdam, The Netherlands
| | - A R Schuitema
- Royal Tropical Institute (KIT), Amsterdam, The Netherlands
| | - M Akhalaia
- Foundation for Innovative New Diagnostics (FIND), Geneva, Switzerland
| | - A Alenova
- National Centre for Tuberculosis Problems, Almaty, Kazakhstan
| | | | - P Tarlykov
- National Centre for Biotechnology, Astana, Kazakhstan
| | - R Anthony
- Royal Tropical Institute (KIT), Amsterdam, The Netherlands
| | - G Refrégier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - C Sola
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
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183
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Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nat Rev Microbiol 2019; 17:533-545. [DOI: 10.1038/s41579-019-0214-5] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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184
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Konstantynovska O, Rekrotchuk M, Hrek I, Rohozhyn A, Rudova N, Poteiko P, Gerilovych A, Bortz E, Solodiankin O. Severe Clinical Outcomes of Tuberculosis in Kharkiv Region, Ukraine, Are Associated with Beijing Strains of Mycobacterium tuberculosis. Pathogens 2019; 8:pathogens8020075. [PMID: 31185670 PMCID: PMC6631893 DOI: 10.3390/pathogens8020075] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/02/2019] [Accepted: 06/06/2019] [Indexed: 11/16/2022] Open
Abstract
Genotypic variation in Beijing lineages of Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis (TB), has been associated with hyper virulence and the spread of extensively and multiple drug (X/MDR) resistant MTB strains in Eastern Europe, Central Asia, and East Asia. The clinical outcomes of 215 new cases of TB among the population of the Kharkiv region of Eastern Ukraine were analyzed to uncover factors associated with severe infection. Infecting MTB strains were profiled by 5 locus exact tandem repeats (ETRs) and 15 locus mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR) genotyping. Among diverse MTB genotypes discovered in Ukraine, the Beijing genotype (MIRU-VNTR 42425) was significantly associated with risk factors for severe outcomes of disease in the study population, including TB/HIV co-infection and treatment failure. Strain replacement (superinfection) was observed in 10 patients, suggesting repeated exposure to novel MTB strains in hospital or community settings. Inclusion of MTB genotyping data may identify at-risk patients and improve treatment adherence to prevent X/MDR development for effective public health response against tuberculosis in Ukraine.
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Affiliation(s)
| | - Mariia Rekrotchuk
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine (NSC IECVM), 61023 Kharkiv, Ukraine.
| | - Ivan Hrek
- Kharkiv Medical Academy of Postgraduate Education, 61176 Kharkiv, Ukraine.
| | - Anton Rohozhyn
- Kharkiv Medical Academy of Postgraduate Education, 61176 Kharkiv, Ukraine.
| | - Nataliia Rudova
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine (NSC IECVM), 61023 Kharkiv, Ukraine.
| | - Petro Poteiko
- Kharkiv Medical Academy of Postgraduate Education, 61176 Kharkiv, Ukraine.
| | - Anton Gerilovych
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine (NSC IECVM), 61023 Kharkiv, Ukraine.
| | - Eric Bortz
- Department of Biological Sciences, University of Alaska Anchorage, Anchorage, AK 99508, USA.
| | - Oleksii Solodiankin
- National Scientific Center Institute of Experimental and Clinical Veterinary Medicine (NSC IECVM), 61023 Kharkiv, Ukraine.
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185
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Cui Z, Lin D, Chongsuvivatwong V, Graviss EA, Chaiprasert A, Palittapongarnpim P, Lin M, Ou J, Zhao J. Hot and Cold Spot Areas of Household Tuberculosis Transmission in Southern China: Effects of Socio-Economic Status and Mycobacterium tuberculosis Genotypes. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16101863. [PMID: 31137811 PMCID: PMC6572207 DOI: 10.3390/ijerph16101863] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 05/19/2019] [Accepted: 05/23/2019] [Indexed: 11/16/2022]
Abstract
The aims of the study were: (1) compare sociodemographic characteristics among active tuberculosis (TB) cases and their household contacts in cold and hot spot transmission areas, and (2) quantify the influence of locality, genotype and potential determinants on the rates of latent tuberculosis infection (LTBI) among household contacts of index TB cases. Parallel case-contact studies were conducted in two geographic areas classified as "cold" and "hot" spots based on TB notification and spatial clustering between January and June 2018 in Guangxi, China, using data from field contact investigations, whole genome sequencing, tuberculin skin tests (TSTs), and chest radiographs. Beijing family strains accounted for 64.6% of Mycobacterium tuberculosis (Mtb) strains transmitted in hot spots, and 50.7% in cold spots (p-value = 0.02). The positive TST rate in hot spot areas was significantly higher than that observed in cold spot areas (p-value < 0.01). Living in hot spots (adjusted odds ratio (aOR) = 1.75, 95%, confidence interval (CI): 1.22, 2.50), Beijing family genotype (aOR = 1.83, 95% CI: 1.19, 2.81), living in the same room with an index case (aOR = 2.29, 95% CI: 1.5, 3.49), travelling time from home to a medical facility (aOR = 4.78, 95% CI: 2.96, 7.72), history of Bacillus Calmette-Guérin vaccination (aOR = 2.02, 95% CI: 1.13 3.62), and delay in diagnosis (aOR = 2.56, 95% CI: 1.13, 5.80) were significantly associated with positive TST results among household contacts of TB cases. The findings of this study confirmed the strong transmissibility of the Beijing genotype family strains and this genotype's important role in household transmission. We found that an extended traveling time from home to the medical facility was an important socioeconomic factor for Mtb transmission in the family. It is still necessary to improve the medical facility infrastructure and management, especially in areas with a high TB prevalence.
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Affiliation(s)
- Zhezhe Cui
- Department of Tuberculosis Control, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning 530028, China.
- Epidemiology Unit, Faculty of Medicine, Prince of Songkla University, Songkhla 90110, Thailand.
| | - Dingwen Lin
- Department of Tuberculosis Control, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning 530028, China.
| | | | - Edward A Graviss
- Department of Pathology and Genomic Medicine, The Center for Molecular and Translational Human Infectious Diseases Research, Houston Methodist Research Institute, Houston, TX 77030, USA.
| | - Angkana Chaiprasert
- Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
| | | | - Mei Lin
- Department of Tuberculosis Control, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning 530028, China.
| | - Jing Ou
- Department of Tuberculosis Control, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning 530028, China.
| | - Jinming Zhao
- Department of Tuberculosis Control, Guangxi Zhuang Autonomous Region Center for Disease Control and Prevention, Nanning 530028, China.
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186
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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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187
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Bespyatykh JA, Vinogradova ТI, Manicheva OA, Zabolotnykh NV, Dogonadze MZ, Vitovskaya ML, Guliaev AS, Zhuravlev VY, Shitikov EA, Ilina EN. In vivo virulence of Beijing genotype Mycobacterium tuberculosis. ACTA ACUST UNITED AC 2019. [DOI: 10.15789/2220-7619-2019-1-173-182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- J. A. Bespyatykh
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency
| | | | | | | | | | | | - A. S. Guliaev
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency
| | | | - E. A. Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency
| | - E. N. Ilina
- Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency
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188
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Mycobacterium tuberculosis. Bundesgesundheitsblatt Gesundheitsforschung Gesundheitsschutz 2019; 61:100-115. [PMID: 29356839 DOI: 10.1007/s00103-017-2660-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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189
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Cohen KA, Manson AL, Abeel T, Desjardins CA, Chapman SB, Hoffner S, Birren BW, Earl AM. Extensive global movement of multidrug-resistant M. tuberculosis strains revealed by whole-genome analysis. Thorax 2019; 74:882-889. [PMID: 31048508 PMCID: PMC6788793 DOI: 10.1136/thoraxjnl-2018-211616] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 01/28/2019] [Accepted: 02/25/2019] [Indexed: 11/22/2022]
Abstract
Background While the international spread of multidrug-resistant (MDR) Mycobacterium tuberculosis strains is an acknowledged public health threat, a broad and more comprehensive examination of the global spread of MDR-tuberculosis (TB) using whole-genome sequencing has not yet been performed. Methods In a global dataset of 5310 M. tuberculosis whole-genome sequences isolated from five continents, we performed a phylogenetic analysis to identify and characterise clades of MDR-TB with respect to geographic dispersion. Results Extensive international dissemination of MDR-TB was observed, with identification of 32 migrant MDR-TB clades with descendants isolated in 17 unique countries. Relatively recent movement of strains from both Beijing and non-Beijing lineages indicated successful global spread of varied genetic backgrounds. Migrant MDR-TB clade members shared relatively recent common ancestry, with a median estimate of divergence of 13–27 years. Migrant extensively drug-resistant (XDR)-TB clades were not observed, although development of XDR-TB within migratory MDR-TB clades was common. Conclusions Application of genomic techniques to investigate global MDR migration patterns revealed extensive global spread of MDR clades between countries of varying TB burden. Further expansion of genomic studies to incorporate isolates from diverse global settings into a single analysis, as well as data sharing platforms that facilitate genomic data sharing across country lines, may allow for future epidemiological analyses to monitor for international transmission of MDR-TB. In addition, efforts to perform routine whole-genome sequencing on all newly identified M. tuberculosis, like in England, will serve to better our understanding of the transmission dynamics of MDR-TB globally.
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Affiliation(s)
- Keira A Cohen
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Abigail L Manson
- Broad Institute of Harvard and M.I.T, Cambridge, Massachusetts, USA
| | - Thomas Abeel
- Broad Institute of Harvard and M.I.T, Cambridge, Massachusetts, USA.,Delft Bioinformatics Lab, Technische Universiteit Delft Faculteit Technische Natuurwetenschappen, Delft, Netherlands
| | | | - Sinead B Chapman
- Broad Institute of Harvard and M.I.T, Cambridge, Massachusetts, USA
| | - Sven Hoffner
- Department of Public Health Sciences, Karolinska Institute, Stockholm, Sweden
| | - Bruce W Birren
- Broad Institute of Harvard and M.I.T, Cambridge, Massachusetts, USA
| | - Ashlee M Earl
- Broad Institute of Harvard and M.I.T, Cambridge, Massachusetts, USA
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190
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Rutaihwa LK, Menardo F, Stucki D, Gygli SM, Ley SD, Malla B, Feldmann J, Borrell S, Beisel C, Middelkoop K, Carter EJ, Diero L, Ballif M, Jugheli L, Reither K, Fenner L, Brites D, Gagneux S. Multiple Introductions of Mycobacterium tuberculosis Lineage 2–Beijing Into Africa Over Centuries. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00112] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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191
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Nikolayevskyy V, Niemann S, Anthony R, van Soolingen D, Tagliani E, Ködmön C, van der Werf MJ, Cirillo DM. Role and value of whole genome sequencing in studying tuberculosis transmission. Clin Microbiol Infect 2019; 25:1377-1382. [PMID: 30980928 DOI: 10.1016/j.cmi.2019.03.022] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 03/16/2019] [Accepted: 03/19/2019] [Indexed: 11/15/2022]
Abstract
BACKGROUND Tuberculosis (TB) remains a serious public health threat worldwide. Theoretically ultimate resolution of whole genome sequencing (WGS) for Mycobacterium tuberculosis complex (MTBC) strain classification makes this technology very attractive for epidemiological investigations. OBJECTIVES To summarize the evidence available in peer-reviewed publications on the role and place of WGS in detection of TB transmission. SOURCES A total of 69 peer-reviewed publications identified in Pubmed database. CONTENT Evidence from >30 publications suggests that a cut-off value of fewer than six single nucleotide polymorphisms between strains efficiently excludes cases that are not the result of recent transmission and could be used for the identification of drug-sensitive isolates involved in direct human-to-human TB transmission. Sensitivity of WGS to identify epidemiologically linked isolates is high, reaching 100% in eight studies with specificity (17%-95%) highly dependent on the settings. Drug resistance and specific phylogenetic lineages may be associated with accelerated mutation rates affecting genetic distances. WGS can be potentially used to distinguish between true relapses and re-infections but in high-incidence low-diversity settings this would require consideration of epidemiological links and minority alleles. Data from four studies looking into within-host diversity highlight a need for developing criteria for acceptance or rejection of WGS relatedness results depending on the proportion of minority alleles. IMPLICATIONS WGS will potentially allow for more targeted public health actions preventing unnecessary investigations of false clusters. Consensus on standardization of raw data quality control processing criteria, analytical pipelines and reporting language is yet to be reached.
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Affiliation(s)
- V Nikolayevskyy
- Public Health England, London, UK; Imperial College, London, UK.
| | - S Niemann
- Molecular and Experimental Mycobacteriology, National Reference Centre for Mycobacteria, Research Centre, Borstel, Germany; German Centre for Infection Research, Borstel site, Germany
| | - R Anthony
- Tuberculosis Reference Laboratory, Infectious Diseases Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - D van Soolingen
- Tuberculosis Reference Laboratory, Infectious Diseases Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - E Tagliani
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - C Ködmön
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - M J van der Werf
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - D M Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
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192
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An integrated whole genome analysis of Mycobacterium tuberculosis reveals insights into relationship between its genome, transcriptome and methylome. Sci Rep 2019; 9:5204. [PMID: 30914757 PMCID: PMC6435705 DOI: 10.1038/s41598-019-41692-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 03/14/2019] [Indexed: 01/01/2023] Open
Abstract
Human tuberculosis disease (TB), caused by Mycobacterium tuberculosis (Mtb), is a complex disease, with a spectrum of outcomes. Genomic, transcriptomic and methylation studies have revealed differences between Mtb lineages, likely to impact on transmission, virulence and drug resistance. However, so far no studies have integrated sequence-based genomic, transcriptomic and methylation characterisation across a common set of samples, which is critical to understand how DNA sequence and methylation affect RNA expression and, ultimately, Mtb pathogenesis. Here we perform such an integrated analysis across 22 M. tuberculosis clinical isolates, representing ancient (lineage 1) and modern (lineages 2 and 4) strains. The results confirm the presence of lineage-specific differential gene expression, linked to specific SNP-based expression quantitative trait loci: with 10 eQTLs involving SNPs in promoter regions or transcriptional start sites; and 12 involving potential functional impairment of transcriptional regulators. Methylation status was also found to have a role in transcription, with evidence of differential expression in 50 genes across lineage 4 samples. Lack of methylation was associated with three novel variants in mamA, likely to cause loss of function of this enzyme. Overall, our work shows the relationship of DNA sequence and methylation to RNA expression, and differences between ancient and modern lineages. Further studies are needed to verify the functional consequences of the identified mechanisms of gene expression regulation.
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193
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Saelens JW, Viswanathan G, Tobin DM. Mycobacterial Evolution Intersects With Host Tolerance. Front Immunol 2019; 10:528. [PMID: 30967867 PMCID: PMC6438904 DOI: 10.3389/fimmu.2019.00528] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/27/2019] [Indexed: 12/12/2022] Open
Abstract
Over the past 200 years, tuberculosis (TB) has caused more deaths than any other infectious disease, likely infecting more people than it has at any other time in human history. Mycobacterium tuberculosis (Mtb), the etiologic agent of TB, is an obligate human pathogen that has evolved through the millennia to become an archetypal human-adapted pathogen. This review focuses on the evolutionary framework by which Mtb emerged as a specialized human pathogen and applies this perspective to the emergence of specific lineages that drive global TB burden. We consider how evolutionary pressures, including transmission dynamics, host tolerance, and human population patterns, may have shaped the evolution of diverse mycobacterial genomes.
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Affiliation(s)
- Joseph W. Saelens
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
| | - Gopinath Viswanathan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
| | - David M. Tobin
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
- Department of Immunology, Duke University School of Medicine, Durham, NC, United States
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194
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Transmission dynamics study of tuberculosis isolates with whole genome sequencing in southern Sweden. Sci Rep 2019; 9:4931. [PMID: 30894568 PMCID: PMC6426893 DOI: 10.1038/s41598-019-39971-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 02/06/2019] [Indexed: 11/17/2022] Open
Abstract
Epidemiological contact tracing complemented with genotyping of clinical Mycobacterium tuberculosis isolates is important for understanding disease transmission. In Sweden, tuberculosis (TB) is mostly reported in migrant and homeless where epidemiologic contact tracing could pose a problem. This study compared epidemiologic linking with genotyping in a low burden country. Mycobacterium tuberculosis isolates (n = 93) collected at Scania University Hospital in Southern Sweden were analysed with the standard genotyping method mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR) and the results were compared with whole genome sequencing (WGS). Using a maximum of twelve single nucleotide polymorphisms (SNPs) as the upper threshold of genomic relatedness noted among hosts, we identified 18 clusters with WGS comprising 52 patients with overall pairwise genetic maximum distances ranging from zero to nine SNPs. MIRU-VNTR and WGS clustered the same isolates, although the distribution differed depending on MIRU-VNTR limitations. Both genotyping techniques identified clusters where epidemiologic linking was insufficient, although WGS had higher correlation with epidemiologic data. To summarize, WGS provided better resolution of transmission than MIRU-VNTR in a setting with low TB incidence. WGS predicted epidemiologic links better which could consolidate and correct the epidemiologically linked cases, avoiding thus false clustering.
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195
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A Mycobacterium tuberculosis Beijing strain persists at high rates and extends its geographic boundaries 20 years after importation. Sci Rep 2019; 9:4687. [PMID: 30886337 PMCID: PMC6423232 DOI: 10.1038/s41598-019-40525-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 02/04/2019] [Indexed: 11/15/2022] Open
Abstract
Transmission of Beijing Mycobacterium tuberculosis can be investigated based on genotypic analysis of clinical isolates. A Beijing strain began to spread on Gran Canaria Island, Spain, at the end of the last century. In 1996, only 3 years after its importation to the island, its frequency had increased to 27.1% of all the isolates. The strain was tracked during the following years, and the most recent data obtained corresponded to 2007-8, when its presence continued to be alarming (21%). In the current study, we updated data on the distribution of this strain 20 years (2013–2014) after it was first detected on the island and extended the analysis for the first time to all the mycobacteriology laboratories covering the population of the Canary Island archipelago. Rapid updating was enabled by means of 2 different strain-specific PCRs: one targeting a peculiar feature of the strain, which was identified based on an IS6110 copy mapping in the Rv2180c gene, and a newly defined strain-specific single nucleotide polymorphism, which was identified by whole-genome sequencing. The results showed that the strain has remained highly prevalent (20.90% of all isolates), has spread throughout the neighbouring islands, and has also reached high representativeness in them (11–32%).
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196
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Garzon-Chavez D, Zurita J, Mora-Pinargote C, Franco-Sotomayor G, Leon-Benitez M, Granda-Pardo JC, Trueba G, Garcia-Bereguiain MA, de Waard JH. Prevalence, Drug Resistance, and Genotypic Diversity of the Mycobacterium tuberculosis Beijing Family in Ecuador. Microb Drug Resist 2019; 25:931-937. [PMID: 30883259 DOI: 10.1089/mdr.2018.0429] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Beijing family, the most successful Mycobacterium tuberculosis lineage, is considered hypervirulent, associated with clustering and has a strong association with multidrug-resistant tuberculosis. The Beijing strains have spread worldwide and also to Latin America. Genotyping of a countrywide collection of 380 M. tuberculosis strains from Ecuador, with 24-loci mycobacterial interspersed repetitive units-variable number tandem repeats (MIRU-VNTR), revealed only six Beijing strains, but four of these were MDR-TB. There was no clustering as all six strains had very distinct MIRU-VNTR profiles that have not been reported in the rest of Latin America. Although active transmission for Beijing has been described for the neighboring countries Peru and Colombia, there is no evidence that Beijing strains in Ecuador are more frequently transmitted than other strains. Moreover, the low prevalence (1.6%) of the Beijing sublineage in Ecuador challenges the concept of hyperadaptability and transmissibility of the Beijing strains in our country.
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Affiliation(s)
- Daniel Garzon-Chavez
- 1 Instituto de Microbiología and Colegio de Ciencias de la Salud, Universidad San Francisco de Quito, Quito, Ecuador
| | - Jeannete Zurita
- 2 Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador.,3 Zurita & Zurita Laboratorios, Unidad de Investigaciones en Biomedicina, Quito, Ecuador
| | - Carlos Mora-Pinargote
- 4 Laboratorio Para Investigaciones Biomedicas, Facultad de Ciencias de la Vida, Escuela Superior Politecnica del Litoral, Guayaquil, Ecuador
| | - Greta Franco-Sotomayor
- 5 Instituto de Salud Pública e Investigacion Leopoldo Izquieta Perez, Guayaquil, Ecuador
| | - Margarita Leon-Benitez
- 5 Instituto de Salud Pública e Investigacion Leopoldo Izquieta Perez, Guayaquil, Ecuador
| | | | - Gabriel Trueba
- 1 Instituto de Microbiología and Colegio de Ciencias de la Salud, Universidad San Francisco de Quito, Quito, Ecuador
| | - Miguel Angel Garcia-Bereguiain
- 4 Laboratorio Para Investigaciones Biomedicas, Facultad de Ciencias de la Vida, Escuela Superior Politecnica del Litoral, Guayaquil, Ecuador.,6 One Health Research Group, Facultad de Ciencias de la Salud, Universidad de Las Américas, Quito, Ecuador.,7 Escuela de Ciencias Biologicas e Ingeniería, Universidad Yachay Tech, Urcuqui, Ecuador
| | - Jacobus H de Waard
- 6 One Health Research Group, Facultad de Ciencias de la Salud, Universidad de Las Américas, Quito, Ecuador.,7 Escuela de Ciencias Biologicas e Ingeniería, Universidad Yachay Tech, Urcuqui, Ecuador.,8 Laboratorio de Tuberculosis, Instituto de Biomedicina, Hospital Vargas, Universidad Central de Venezuela, Caracas, Venezuela
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197
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Bespyatykh J, Smolyakov A, Guliaev A, Shitikov E, Arapidi G, Butenko I, Dogonadze M, Manicheva O, Ilina E, Zgoda V, Govorun V. Proteogenomic analysis of Mycobacterium tuberculosis Beijing B0/W148 cluster strains. J Proteomics 2019; 192:18-26. [DOI: 10.1016/j.jprot.2018.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 06/29/2018] [Accepted: 07/10/2018] [Indexed: 10/28/2022]
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198
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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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199
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Genetic Diversity of Multi- and Extensively Drug-Resistant Mycobacterium tuberculosis Isolates in the Capital of Iran, Revealed by Whole-Genome Sequencing. J Clin Microbiol 2019; 57:JCM.01477-18. [PMID: 30404943 DOI: 10.1128/jcm.01477-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/01/2018] [Indexed: 01/23/2023] Open
Abstract
The emergence and spread of multidrug resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains is a critical global health problem. Between 2014 and 2018, 606 MTBC strains were isolated from 13,892 suspected pulmonary tuberculosis (TB) patients in Tehran, Iran, including 16 (2.6%) MDR-TB cases. A combination of phenotypic and genotypic methods (whole-genome sequencing) was employed for the identification of additional drug resistances and strain-to-strain genetic distances as a marker for recent transmission events. MDR and extensively drug-resistant (XDR) TB cases were almost exclusively infected by lineage 2/Beijing strains (14/16, P < 0.001). We further showed that recent transmission and/or recent introduction of lineage 2/Beijing strains contribute to high XDR-TB rates among all MDR-TB cases and should be considered an emerging threat for TB control in Tehran. In addition, the extensive pre-existing drug resistance profiles of MDR/XDR strains will further challenge TB diagnostics in the region.
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Early ancient sublineages of Mycobacterium tuberculosis Beijing genotype: unexpected clues from phylogenomics of the pathogen and human history. Clin Microbiol Infect 2018; 25:1039.e1-1039.e6. [PMID: 30528901 DOI: 10.1016/j.cmi.2018.11.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 11/20/2018] [Accepted: 11/24/2018] [Indexed: 11/23/2022]
Abstract
OBJECTIVE The Mycobacterium tuberculosis Beijing family is an epidemiologically important lineage subdivided into large-scale phylogenetic sublineages: ancient, endemic in East Asia, and global modern. Here, we analysed ancient sublineages of the Beijing genotype in the Omsk region of southwestern Siberia, an intriguing area at the intersection of European Russia, Siberia, and Central Asia. METHODS The study included 423 M. tuberculosis strains isolated in 2013-2017 and subjected to drug susceptibility testing, genotyping, and whole genome sequencing. RESULTS The Beijing genotype constituted 280 out of 423 strains. Forty Beijing strains belonged to the early ancient sublineage (wild type mutT4-48). Of these, 11 belonged to the 14717-15 MIRU-VNTR cluster and had intact RD181, 29 belonged to the 1071-32 cluster and had the RD181 deletion. Thirty-nine ancient strains were multidrug-resistant (MDR) and 20 pre-extensively drug resistant (XDR)/XDR. Comparison with global data demonstrated that these clones circulate mainly in Asian Russia with certain phylogenetic affinity to strains from Japan, Korea, and northeastern China. The genome-wide analysis revealed 29-37 single nucleotide polymorphism distances between isolates from different Russian regions within these two clusters. CONCLUSIONS Based on phylogenetic, phylogeographic, genomic, and historical data, we hypothesize that these two clones or their direct ancestors were probably brought to Russia ∼70 years ago after the Second World War with Japanese prisoners of war and, until recently, were mainly circulating in Siberia and the Far East. Their elevated prevalence in Omsk along with the extremely strong association with not only MDR but also pre-XDR/XDR also observed in other locations highlight their epidemic potential and the need for monitoring and attention from health authorities.
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