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Atavliyeva S, Auganova D, Tarlykov P. Genetic diversity, evolution and drug resistance of Mycobacterium tuberculosis lineage 2. Front Microbiol 2024; 15:1384791. [PMID: 38827149 PMCID: PMC11140050 DOI: 10.3389/fmicb.2024.1384791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 05/01/2024] [Indexed: 06/04/2024] Open
Abstract
Mycobacterium tuberculosis causes a chronic infectious disease called tuberculosis. Phylogenetic lineage 2 (L2) of M. tuberculosis, also known as the East Asian lineage, is associated with high virulence, increased transmissibility, and the spread of multidrug-resistant strains. This review article examines the genomic characteristics of the M. tuberculosis genome and M. tuberculosis lineage 2, such as the unique insertion sequence and spoligotype patterns, as well as MIRU-VNTR typing, and SNP-based barcoding. The review describes the geographical distribution of lineage 2 and its history of origin. In addition, the article discusses recent studies on drug resistance and compensatory mechanisms of M. tuberculosis lineage 2 and its impact on the pathogen's transmissibility and virulence. This review article discusses the importance of establishing a unified classification for lineage 2 to ensure consistency in terminology and criteria across different studies and settings.
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Affiliation(s)
- Sabina Atavliyeva
- Genomics and Proteomics Core Facility, National Center for Biotechnology, Astana, Kazakhstan
| | | | - Pavel Tarlykov
- Genomics and Proteomics Core Facility, National Center for Biotechnology, Astana, Kazakhstan
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2
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Senelle G, Sahal MR, La K, Billard-Pomares T, Marin J, Mougari F, Bridier-Nahmias A, Carbonnelle E, Cambau E, Refrégier G, Guyeux C, Sola C. Towards the reconstruction of a global TB history using a new pipeline "TB-Annotator". Tuberculosis (Edinb) 2023; 143S:102376. [PMID: 38012933 DOI: 10.1016/j.tube.2023.102376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 07/03/2023] [Accepted: 07/10/2023] [Indexed: 11/29/2023]
Abstract
Mycobacterium tuberculosis complex (MTBC) has a population structure consisting of 9 human and animal lineages. The genomic diversity within these lineages is a pathogenesis factor that affects virulence, transmissibility, host response, and antibiotic resistance. Hence it is important to develop improved information systems for tracking and understanding the spreading and evolution of genomes. We present results obtained thanks to a new informatics platform for computational biology of MTBC, that uses a convenience sample from public/private SRAs, designated as TB-Annotator. Version 1 was a first interactive graphic-based web tool based on 15,901 representative genomes. Version 2, still interactive, is a more sophisticated database, developed using the Snakemake Workflow Management System (WMS) that allows an unsupervised global and scalable analysis of the content of the USA National Center for Biotechnology Information Short Read Archives database. This platform analyzes nucleotide variants, the presence/absence of genes, known regions of difference and detect new deletions, the insertion sites of mobile genetic elements, and allows phylogenetic trees to be built, imported in a graphical interface and interactively analyzed between the data and the tree. The objective of TB-Annotator is triple: detect recent epidemiological links, reconstruct distant phylogeographical histories as well as perform more complex phenotypic/genotypic Genome-Wide Association Studies (GWAS). In this paper, we compare the various taxonomic SNPs-based labels and hierarchies previously described in recent reference papers for L1, and present a comparative analysis that allows identification of alias and thus provides the basis of a future unifying naming scheme for L1 sublineages. We present a global phylogenetic tree built with RAxML-NG, and one on L2; at the time of writing, we characterized about 200 sublineages, with many new ones; a detail tree for Modern L2 and a hierarchical scheme allowing to facilitate L2 lineage assignment are also presented.
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Affiliation(s)
- Gaetan Senelle
- FEMTO-ST Institute, UMR 6174, CNRS-Université Bourgogne Franche-Comté (UBFC), France
| | - Muhammed Rabiu Sahal
- Université Paris-Saclay, 91190, Gif-sur-Yvette, France; Université Paris-Cité, IAME, UMR 1137, INSERM, Paris, France
| | - Kevin La
- Université Paris-Cité, IAME, UMR 1137, INSERM, Paris, France; AP-HP, GHU Nord site Bichat, Service de mycobactériologie spécialisée et de référence, Paris, France
| | - Typhaine Billard-Pomares
- Service de microbiologie clinique, Hôpital Avicenne, 93017, Bobigny, France; Université Paris 13, IAME, Inserm, 93017, Bobigny, France
| | - Julie Marin
- Service de microbiologie clinique, Hôpital Avicenne, 93017, Bobigny, France; Université Paris 13, IAME, Inserm, 93017, Bobigny, France
| | - Faiza Mougari
- Université Paris-Cité, IAME, UMR 1137, INSERM, Paris, France; AP-HP, GHU Nord site Bichat, Service de mycobactériologie spécialisée et de référence, Paris, France
| | | | - Etienne Carbonnelle
- Université Paris-Cité, IAME, UMR 1137, INSERM, Paris, France; Service de microbiologie clinique, Hôpital Avicenne, 93017, Bobigny, France; Université Paris 13, IAME, Inserm, 93017, Bobigny, France
| | - Emmanuelle Cambau
- Université Paris-Cité, IAME, UMR 1137, INSERM, Paris, France; AP-HP, GHU Nord site Bichat, Service de mycobactériologie spécialisée et de référence, Paris, France
| | - Guislaine Refrégier
- Université Paris-Saclay, 91190, Gif-sur-Yvette, France; Ecologie Systématique Evolution, Université Paris-Saclay, CNRS, AgroParisTech, UMR ESE, 91405, Orsay, France
| | - Christophe Guyeux
- FEMTO-ST Institute, UMR 6174, CNRS-Université Bourgogne Franche-Comté (UBFC), France
| | - Christophe Sola
- Université Paris-Saclay, 91190, Gif-sur-Yvette, France; Université Paris-Cité, IAME, UMR 1137, INSERM, Paris, France.
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Shitikov E, Bespiatykh D. A revised SNP-based barcoding scheme for typing Mycobacterium tuberculosis complex isolates. mSphere 2023; 8:e0016923. [PMID: 37314207 PMCID: PMC10449489 DOI: 10.1128/msphere.00169-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 04/28/2023] [Indexed: 06/15/2023] Open
Abstract
The development of whole-genome sequencing technologies is gradually leading to a more detailed description of the population structure of the Mycobacterium tuberculosis complex (MTBC). In this study, we correlated previously published classifications on a collection of more than 10,000 genomes and proposed a new, comprehensive nomenclature that unifies the existing ones. In total, we identified 169 lineages and sublineages of M. tuberculosis/M. africanum and 9 animal-adapted species. For the purpose of organizing these genotypes in a more streamlined manner, we stratified them into five hierarchical levels. To represent the classification and compare it with the reference, we compiled a confirmatory data set of 670 high-quality isolates, which includes all genotypes and species of MTBC, and this confirmatory data set can serve as a basis for further studies. We proposed a set of 213 robust barcoding single-nucleotide polymorphisms and a suitable workflow for reliable differentiation of genotypes and species within the complex. This work integrates the results of all the major systematized studies to date to provide an understanding of the global diversity of the MTBC population structure. The results of this work may ultimately help to reliably determine the pathogen genotype and associate it with traits that reflect its prevalence, virulence, vaccination, and treatment efficiency, as well as to reliably find natural features revealed during its spread. IMPORTANCE Through years of research into the Mycobacterium tuberculosis complex (MTBC), a number of ambiguous phylogenetic classifications have emerged, which often overlap with one another. In the present study, we have combined all major studies on MTBC classification and inferred a unified, most complete to date classification and accompanying SNP barcodes.
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Affiliation(s)
- Egor Shitikov
- Department of biomedicine and genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
| | - Dmitry Bespiatykh
- Department of biomedicine and genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, Russia
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Zhu C, Yang T, Yin J, Jiang H, Takiff HE, Gao Q, Liu Q, Li W. The Global Success of Mycobacterium tuberculosis Modern Beijing Family Is Driven by a Few Recently Emerged Strains. Microbiol Spectr 2023; 11:e0333922. [PMID: 37272796 PMCID: PMC10434187 DOI: 10.1128/spectrum.03339-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 05/23/2023] [Indexed: 06/06/2023] Open
Abstract
Strains of the Mycobacterium tuberculosis complex (MTBC) Beijing family aroused concern because they were often found in clusters and appeared to be exceptionally transmissible. However, it was later found that strains of the Beijing family were heterogeneous, and the transmission advantage was restricted to sublineage L2.3 or modern Beijing. In this study, we analyzed the previously published genome sequences of 7,896 L2.3 strains from 51 different countries. Using BEAST software to approximate the temporal emergence of L2.3, our calculations suggest that L2.3 initially emerged in northern East Asia during the early 15th century and subsequently diverged into six phylogenetic clades, identified as L2.3.1 through L2.3.6. Using terminal branch length and genomic clustering as proxies for transmissibility, we found that the six clades displayed distinct population dynamics, with the three recently emerged clades (L2.3.4 to L2.3.6) exhibiting significantly higher transmissibility than the older three clades (L2.3.1 to L2.3.3). Of the Beijing family strains isolated outside East Asia, 83.1% belonged to the clades L2.3.4 to L2.3.6, which were also associated with more cross-border transmission. This work reveals the heterogeneity in sublineage L2.3 and demonstrates that the global success of Beijing family strains is driven by the three recently emerged L2.3 clades. IMPORTANCE The recent population dynamics of the global tuberculosis epidemic are heavily shaped by Mycobacterium tuberculosis complex (MTBC) strains with enhanced transmissibility. The infamous Beijing family strain stands out because it has rapidly spread throughout the world. Identifying the strains responsible for the global expansion and tracing their evolution should help to understand the nature of high transmissibility and develop effective strategies to control transmission. In this study, we found that the L2.3 sublineage diversified into six phylogenetic clades (L2.3.1 to L2.3.6) with various transmission characteristics. Clades L2.3.4 to L2.3.6 exhibited significantly higher transmissibility than clades L2.3.1 to L2.3.3, which helps explain why more than 80% of Beijing family strains collected outside East Asia belong to these three clades. We conclude that the global success of L2.3 was not caused by the entire L2.3 sublineage but rather was due to the rapid expansion of L2.3.4 to L2.3.6. Tracking the transmission of L2.3.4 to L2.3.6 strains can help to formulate targeted TB prevention and control.
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Affiliation(s)
- Chendi Zhu
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | | | - Jinfeng Yin
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Hui Jiang
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Howard E. Takiff
- Instituto Venezolano de Investigaciones Científicas, Instituto Venezolano de Investigaciones Científicas, Caracas, Venezuela
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology (Ministry of Education/National Health Commission/Chinese Academy of Medical Sciences), School of Basic Medical Sciences, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Weimin Li
- Beijing Chest Hospital, Capital Medical University, Beijing, China
- Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
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Davies-Bolorunduro OF, Jaemsai B, Ruangchai W, Phumiphanjarphak W, Aiewsakun P, Palittapongarnpim P. Analysis of whiB7 in Mycobacterium tuberculosis reveals novel AT-hook deletion mutations. Sci Rep 2023; 13:13324. [PMID: 37587174 PMCID: PMC10432532 DOI: 10.1038/s41598-023-40152-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/05/2023] [Indexed: 08/18/2023] Open
Abstract
Mutations in whiB7 have been associated with both hypersusceptibility and resistance to various antibiotics in Mycobacterium tuberculosis (Mtb). Unlocking the secrets of antibiotic resistance in the bacterium, we examined mutations in the coding sequences of whiB7 of over 40,000 diverse Mtb isolates. Our results unveil the dominant c.191delG (Gly64delG) mutation, present in all members of the lineage L1.2.2 and its impact on WhiB7's conserved GVWGG-motif, causing conformational changes and deletion of the C-terminal AT-hook. Excitingly, we discovered six unique mutations associated with partial or total deletion of the AT-hook, specific to certain sublineages. Our findings suggest the selective pressures driving these mutations, underlining the potential of genomics to advance our understanding of Mtb's antibiotic resistance. As tuberculosis remains a global health threat, our study offers valuable insights into the diverse nature and functional consequences of whiB7 mutations, paving the way for the development of novel therapeutic interventions.
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Affiliation(s)
- Olabisi Flora Davies-Bolorunduro
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
- Center for Tuberculosis Research, Microbiology Department, Nigerian Institute of Medical Research, 6 Edmund Crescent, P.M.B 2013, Yaba, 101012, Lagos, Nigeria
| | - Bharkbhoom Jaemsai
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Wuthiwat Ruangchai
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Worakorn Phumiphanjarphak
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Pakorn Aiewsakun
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand
| | - Prasit Palittapongarnpim
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand.
- Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, 10400, Thailand.
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Hang NTL, Hijikata M, Maeda S, Thuong PH, Huan HV, Hoang NP, Tam DB, Anh PT, Huyen NT, Cuong VC, Kobayashi N, Wakabayashi K, Miyabayashi A, Seto S, Keicho N. Host-pathogen relationship in retreated tuberculosis with major rifampicin resistance-conferring mutations. Front Microbiol 2023; 14:1187390. [PMID: 37469437 PMCID: PMC10352910 DOI: 10.3389/fmicb.2023.1187390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/09/2023] [Indexed: 07/21/2023] Open
Abstract
Introduction It is assumed that host defense systems eliminating the pathogen and regulating tissue damage make a strong impact on the outcome of tuberculosis (TB) disease and that these processes are affected by rifampicin (RIF) resistance-conferring mutations of Mycobacterium tuberculosis (Mtb). However, the host responses to the pathogen harboring different mutations have not been studied comprehensively in clinical settings. We analyzed clinico-epidemiological factors and blood transcriptomic signatures associated with major rpoB mutations conferring RIF resistance in a cohort study. Methods Demographic data were collected from 295 active pulmonary TB patients with treatment history in Hanoi, Vietnam. When recruited, drug resistance-conferring mutations and lineage-specific variations were identified using whole-genome sequencing of clinical Mtb isolates. Before starting retreatment, total RNA was extracted from the whole blood of HIV-negative patients infected with Mtb that carried either the rpoB H445Y or rpoB S450L mutation, and the total RNA was subjected to RNA sequencing after age-gender matching. The individual RNA expression levels in the blood sample set were also measured using real-time RT-PCR. Logistic and linear regression models were used to assess possible associations. Results In our cohort, rpoB S450L and rpoB H445Y were major RIF resistance-conferring mutations [32/87 (36.8%) and 15/87 (17.2%), respectively]. H445Y was enriched in the ancient Beijing genotype and was associated with nonsynonymous mutations of Rv1830 that has been reported to regulate antibiotic resilience. H445Y was also more frequently observed in genetically clustered strains and in samples from patients who had received more than one TB treatment episode. According to the RNA sequencing, gene sets involved in the interferon-γ and-α pathways were downregulated in H445Y compared with S450L. The qRT-PCR analysis also confirmed the low expression levels of interferon-inducible genes, including BATF2 and SERPING1, in the H445Y group, particularly in patients with extensive lesions on chest X-ray. Discussion Our study results showed that rpoB mutations as well as Mtb sublineage with additional genetic variants may have significant effects on host response. These findings strengthen the rationale for investigation of host-pathogen interactions to develop countermeasures against epidemics of drug-resistant TB.
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Affiliation(s)
| | - Minako Hijikata
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, JATA, Tokyo, Japan
| | - Shinji Maeda
- Faculty of Pharmaceutical Sciences, Hokkaido University of Science, Sapporo, Hokkaido, Japan
| | | | | | | | - Do Bang Tam
- Department of Biochemistry, Hematology and Blood Transfusion, Hanoi Lung Hospital, Hanoi, Vietnam
| | - Pham Thu Anh
- Tuberculosis Network Management Office, Hanoi Lung Hospital, Hanoi, Vietnam
| | - Nguyen Thu Huyen
- NCGM-BMH Medical Collaboration Center, Hanoi, Vietnam
- Department of Health Policy and Economics, Hanoi University of Public Health, Hanoi, Vietnam
| | | | | | - Keiko Wakabayashi
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, JATA, Tokyo, Japan
| | - Akiko Miyabayashi
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, JATA, Tokyo, Japan
| | - Shintaro Seto
- Department of Pathophysiology and Host Defense, The Research Institute of Tuberculosis, JATA, Tokyo, Japan
| | - Naoto Keicho
- The Research Institute of Tuberculosis, JATA, Tokyo, Japan
- National Center for Global Health and Medicine, Tokyo, Japan
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Mokrousov I, Vyazovaya A, Shitikov E, Badleeva M, Belopolskaya O, Bespiatykh D, Gerasimova A, Ioannidis P, Jiao W, Khromova P, Masharsky A, Naizabayeva D, Papaventsis D, Pasechnik O, Perdigão J, Rastogi N, Shen A, Sinkov V, Skiba Y, Solovieva N, Tafaj S, Valcheva V, Kostyukova I, Zhdanova S, Zhuravlev V, Ogarkov O. Insight into pathogenomics and phylogeography of hypervirulent and highly-lethal Mycobacterium tuberculosis strain cluster. BMC Infect Dis 2023; 23:426. [PMID: 37353765 DOI: 10.1186/s12879-023-08413-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 06/21/2023] [Indexed: 06/25/2023] Open
Abstract
BACKGROUND . The Mycobacterium tuberculosis Beijing genotype is globally spread lineage with important medical properties that however vary among its subtypes. M. tuberculosis Beijing 14717-15-cluster was recently discovered as both multidrug-resistant, hypervirulent, and highly-lethal strain circulating in the Far Eastern region of Russia. Here, we aimed to analyze its pathogenomic features and phylogeographic pattern. RESULTS . The study collection included M. tuberculosis DNA collected between 1996 and 2020 in different world regions. The bacterial DNA was subjected to genotyping and whole genome sequencing followed by bioinformatics and phylogenetic analysis. The PCR-based assay to detect specific SNPs of the Beijing 14717-15-cluster was developed and used for its screening in the global collections. Phylogenomic and phylogeographic analysis confirmed endemic prevalence of the Beijing 14717-15-cluster in the Asian part of Russia, and distant common ancestor with isolates from Korea (> 115 SNPs). The Beijing 14717-15-cluster isolates had two common resistance mutations RpsL Lys88Arg and KatG Ser315Thr and belonged to spoligotype SIT269. The Russian isolates of this cluster were from the Asian Russia while 4 isolates were from the Netherlands and Spain. The cluster-specific SNPs that significantly affect the protein function were identified in silico in genes within different categories (lipid metabolism, regulatory proteins, intermediary metabolism and respiration, PE/PPE, cell wall and cell processes). CONCLUSIONS . We developed a simple method based on real-time PCR to detect clinically significant MDR and hypervirulent Beijing 14717-15-cluster. Most of the identified cluster-specific mutations were previously unreported and could potentially be associated with increased pathogenic properties of this hypervirulent M. tuberculosis strain. Further experimental study to assess the pathobiological role of these mutations is warranted.
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Affiliation(s)
- Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia.
- Henan International Joint Laboratory of Children's Infectious Diseases, Henan Children's Hospital, Children's Hospital, Zhengzhou University, Zhengzhou Children's Hospital, Zhengzhou, China.
| | - Anna Vyazovaya
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Egor Shitikov
- Department of Biomedicine and Genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Maria Badleeva
- Department of Infectious Diseases, Dorji Banzarov Buryat State University, Ulan-Ude, Buryatia, Russia
| | - Olesya Belopolskaya
- Resource Center Bio-bank Center, Research Park of St. Petersburg State University, St. Petersburg, Russia
- Laboratory of Genogeography, Vavilov Institute of General Genetics Russian Academy of Sciences Moscow, Moscow, Russia
| | - Dmitry Bespiatykh
- Department of Biomedicine and Genomics, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russia
| | - Alena Gerasimova
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Panayotis Ioannidis
- National Reference Laboratory for Mycobacteria, Sotiria Chest Diseases Hospital, Athens, Greece
| | - Weiwei Jiao
- National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Polina Khromova
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Aleksey Masharsky
- Resource Center Bio-bank Center, Research Park of St. Petersburg State University, St. Petersburg, Russia
| | - Dinara Naizabayeva
- Laboratory of Molecular Biology, Almaty Branch of National Center for Biotechnology in Central Reference Laboratory, Almaty, Kazakhstan
- Department of Biotechnology, Al-Farabi Kazakh National University, Almaty, Kazakhstan
| | - Dimitrios Papaventsis
- National Reference Laboratory for Mycobacteria, Sotiria Chest Diseases Hospital, Athens, Greece
| | - Oksana Pasechnik
- Department of Public Health, Omsk State Medical University, Omsk, Russia
| | - João Perdigão
- iMed.ULisboa - Instituto de Investigação do Medicamento, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Nalin Rastogi
- WHO Supranational TB Reference Laboratory, Unité de la Tuberculose et des Mycobactéries, Institut Pasteur de la Guadeloupe, Abymes, Guadeloupe, France
| | - Adong Shen
- National Clinical Research Center for Respiratory Diseases, Beijing Key Laboratory of Pediatric Respiratory Infection Disease, Beijing Children's Hospital, Beijing Pediatric Research Institute, Capital Medical University, National Center for Children's Health, Beijing, China
- Henan Children's Hospital, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou Children's Hospital, Zhengzhou, China
| | - Viacheslav Sinkov
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Yuriy Skiba
- Laboratory of Molecular Biology, Almaty Branch of National Center for Biotechnology in Central Reference Laboratory, Almaty, Kazakhstan
| | - Natalia Solovieva
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Silva Tafaj
- National Mycobacteria Reference Laboratory, University Hospital Shefqet Ndroqi, Tirana, Albania
| | - Violeta Valcheva
- Laboratory of Molecular Genetics of Mycobacteria, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Irina Kostyukova
- Bacteriology laboratory, Clinical Tuberculosis Dispensary, Omsk, Russia
| | - Svetlana Zhdanova
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
| | - Viacheslav Zhuravlev
- St. Petersburg Research Institute of Phthisiopulmonology, St. Petersburg, Russia
| | - Oleg Ogarkov
- Department of Epidemiology and Microbiology, Scientific Centre of the Family Health and Human Reproduction Problems, Irkutsk, Russia
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8
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Chaiyachat P, Kaewseekhao B, Chaiprasert A, Kamolwat P, Nonghanphithak D, Phetcharaburanin J, Sirichoat A, Ong RTH, Faksri K. Metabolomic analysis of Mycobacterium tuberculosis reveals metabolic profiles for identification of drug-resistant tuberculosis. Sci Rep 2023; 13:8655. [PMID: 37244948 DOI: 10.1038/s41598-023-35882-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 05/25/2023] [Indexed: 05/29/2023] Open
Abstract
The detection of pre-extensively (pre-XDR) and extensively drug-resistant tuberculosis (XDR-TB) is challenging. Drug-susceptibility tests for some anti-TB drugs, especially ethambutol (ETH) and ethionamide (ETO), are problematic due to overlapping thresholds to differentiate between susceptible and resistant phenotypes. We aimed to identify possible metabolomic markers to detect Mycobacterium tuberculosis (Mtb) strains causing pre-XDR and XDR-TB. The metabolic patterns of ETH- and ETO-resistant Mtb isolates were also investigated. Metabolomics of 150 Mtb isolates (54 pre-XDR, 63 XDR-TB and 33 pan-susceptible; pan-S) were investigated. Metabolomics of ETH and ETO phenotypically resistant subgroups were analyzed using UHPLC-ESI-QTOF-MS/MS. Orthogonal partial least-squares discriminant analysis revealed distinct separation in all pairwise comparisons among groups. Two metabolites (meso-hydroxyheme and itaconic anhydride) were able to differentiate the pre-XDR and XDR-TB groups from the pan-S group with 100% sensitivity and 100% specificity. In comparisons of the ETH and ETO phenotypically resistant subsets, sets of increased (ETH = 15, ETO = 7) and decreased (ETH = 1, ETO = 6) metabolites specific for the resistance phenotype of each drug were found. We demonstrated the potential for metabolomics of Mtb to differentiate among types of DR-TB as well as between isolates that were phenotypically resistant to ETO and ETH. Thus, metabolomics might be further applied for DR-TB diagnosis and patient management.
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Affiliation(s)
- Pratchakan Chaiyachat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Benjawan Kaewseekhao
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Angkana Chaiprasert
- Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Phalin Kamolwat
- Bureau of Tuberculosis, Department of Disease Control, Ministry of Public Health, Nonthaburi, Thailand
| | - Ditthawat Nonghanphithak
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Jutarop Phetcharaburanin
- Department of Systems Biosciences and Computational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Auttawit Sirichoat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand.
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand.
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9
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Prombutara P, Adriansyah Putra Siregar T, Laopanupong T, Kanjanasirirat P, Khumpanied T, Borwornpinyo S, Rai A, Chaiprasert A, Palittapongarnpim P, Ponpuak M. Host cell transcriptomic response to the multidrug-resistant Mycobacterium tuberculosis clonal outbreak Beijing strain reveals its pathogenic features. Virulence 2022; 13:1810-1826. [PMID: 36242542 PMCID: PMC9578452 DOI: 10.1080/21505594.2022.2135268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Abstract
The upsurge of multidrug-resistant infections has rendered tuberculosis the principal cause of death among infectious diseases. A clonal outbreak multidrug-resistant triggering strain of Mycobacterium tuberculosis was identified in Kanchanaburi Province, labelled "MKR superspreader," which was found to subsequently spread to other regions, as revealed by prior epidemiological reports in Thailand. Herein, we showed that the MKR displayed a higher growth rate upon infection into host macrophages in comparison with the H37Rv reference strain. To further elucidate MKR's biology, we utilized RNA-Seq and differential gene expression analyses to identify host factors involved in the intracellular viability of the MKR. A set of host genes function in the cellular response to lipid pathway was found to be uniquely up-regulated in host macrophages infected with the MKR, but not those infected with H37Rv. Within this set of genes, the IL-36 cytokines which regulate host cell cholesterol metabolism and resistance against mycobacteria attracted our interest, as our previous study revealed that the MKR elevated genes associated with cholesterol breakdown during its growth inside host macrophages. Indeed, when comparing macrophages infected with the MKR to H37Rv-infected cells, our RNA-Seq data showed that the expression ratio of IL-36RN, the negative regulator of the IL-36 pathway, to that of IL-36G was greater in macrophages infected with the MKR. Furthermore, the MKR's intracellular survival and increased intracellular cholesterol level in the MKR-infected macrophages were diminished with decreased IL-36RN expression. Overall, our results indicated that IL-36RN could serve as a new target against this emerging multidrug-resistant M. tuberculosis strain.
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Affiliation(s)
- Pinidphon Prombutara
- Omics Sciences and Bioinformatics Center, Faculty of Science, Chulalongkorn University, Bangkok, Thailand.,Microbiome Research Unit for Probiotics in Food and Cosmetics, Faculty of Sciences, Chulalongkorn University, Bangkok, Thailand.,Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Tegar Adriansyah Putra Siregar
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Microbiology, Faculty of Medicine, University of Muhammadiyah Sumatera Utara, Medan, Indonesia
| | - Thanida Laopanupong
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Tanawadee Khumpanied
- Excellent Center for Drug Discovery, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Suparerk Borwornpinyo
- Excellent Center for Drug Discovery, Faculty of Science, Mahidol University, Bangkok, Thailand.,Department of Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Awantika Rai
- School of Biotechnology, KIIT University, Bhubaneswar, India
| | - Angkana Chaiprasert
- Drug-Resistance Tuberculosis Research Fund, Siriraj Foundation, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Prasit Palittapongarnpim
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand.,Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand.,National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pratumthani, Thailand
| | - Marisa Ponpuak
- Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand.,Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
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10
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Merker M, Rasigade JP, Barbier M, Cox H, Feuerriegel S, Kohl TA, Shitikov E, Klaos K, Gaudin C, Antoine R, Diel R, Borrell S, Gagneux S, Nikolayevskyy V, Andres S, Crudu V, Supply P, Niemann S, Wirth T. Transcontinental spread and evolution of Mycobacterium tuberculosis W148 European/Russian clade toward extensively drug resistant tuberculosis. Nat Commun 2022; 13:5105. [PMID: 36042200 PMCID: PMC9426364 DOI: 10.1038/s41467-022-32455-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 08/01/2022] [Indexed: 11/09/2022] Open
Abstract
Transmission-driven multi-/extensively drug resistant (M/XDR) tuberculosis (TB) is the largest single contributor to human mortality due to antimicrobial resistance. A few major clades of the Mycobacterium tuberculosis complex belonging to lineage 2, responsible for high prevalence of MDR-TB in Eurasia, show outstanding transnational distributions. Here, we determined factors underlying the emergence and epidemic spread of the W148 clade by genome sequencing and Bayesian demogenetic analyses of 720 isolates from 23 countries. We dated a common ancestor around 1963 and identified two successive epidemic expansions in the late 1980s and late 1990s, coinciding with major socio-economic changes in the post-Soviet Era. These population expansions favored accumulation of resistance mutations to up to 11 anti-TB drugs, with MDR evolving toward additional resistances to fluoroquinolones and second-line injectable drugs within 20 years on average. Timescaled haplotypic density analysis revealed that widespread acquisition of compensatory mutations was associated with transmission success of XDR strains. Virtually all W148 strains harbored a hypervirulence-associated ppe38 gene locus, and incipient recurrent emergence of prpR mutation-mediated drug tolerance was detected. The outstanding genetic arsenal of this geographically widespread M/XDR strain clade represents a “perfect storm” that jeopardizes the successful introduction of new anti-M/XDR-TB antibiotic regimens. An outbreak of the multidrug-resistant Mycobacterium tuberculosis lineage W148 has spread widely across Russia, Central Asia and Europe. Here, the authors use whole genome sequences of ~700 isolates of this lineage collected over ~20 years to analyze its spread, evolution of drug resistance, and impact of compensatory mutations.
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Affiliation(s)
- Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.,Evolution of the Resistome, Research Center Borstel, Borstel, Germany
| | - Jean-Philippe Rasigade
- EPHE, PSL University, Paris, France.,Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.,Centre International de Recherche en Infectiologie, INSERM U1111, CNRS UMR5308, Université Lyon 1, ENS de Lyon, Lyon, France
| | - Maxime Barbier
- EPHE, PSL University, Paris, France.,Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France
| | - Helen Cox
- Division of Medical Microbiology and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Silke Feuerriegel
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Thomas A Kohl
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany.,German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Egor Shitikov
- Federal Research and Clinical Centre of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Kadri Klaos
- SA TUH United Laboratories, Mycobacteriology, Tartu, Estonia
| | | | - Rudy Antoine
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Centre d'Infection et d'Immunité de Lille, F-59000, Lille, France
| | - Roland Diel
- Institute for Epidemiology, Schleswig-Holstein University Hospital, Kiel, Germany.,Lung Clinic Grosshansdorf, German Center for Lung Research (DZL), Airway Research Center North (ARCN), 22927, Großhansdorf, Germany
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Sönke Andres
- National and WHO Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Valeriu Crudu
- National TB Reference Laboratory, Institute of Phthisiopneumology, Chisinau, Moldova
| | - Philip Supply
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 9017 - CIIL - Centre d'Infection et d'Immunité de Lille, F-59000, Lille, France.
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany. .,German Center for Infection Research, Partner site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany.
| | - Thierry Wirth
- EPHE, PSL University, Paris, France. .,Institut de Systématique, Evolution, Biodiversité, ISYEB, Muséum national d'Histoire naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, Paris, France.
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11
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Netikul T, Thawornwattana Y, Mahasirimongkol S, Yanai H, Maung HMW, Chongsuvivatwong V, Palittapongarnpim P. Whole-genome single nucleotide variant phylogenetic analysis of Mycobacterium tuberculosis Lineage 1 in endemic regions of Asia and Africa. Sci Rep 2022; 12:1565. [PMID: 35091638 PMCID: PMC8799649 DOI: 10.1038/s41598-022-05524-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 01/11/2022] [Indexed: 12/14/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) lineage 1 (L1) contributes considerably to the disease morbidity. While whole genome sequencing (WGS) is increasingly used for studying Mtb, our understanding of genetic diversity of L1 remains limited. Using phylogenetic analysis of WGS data from endemic range in Asia and Africa, we provide an improved genotyping scheme for L1. Mapping deletion patterns of the 68 direct variable repeats (DVRs) in the CRISPR region of the genome onto the phylogeny provided supporting evidence that the CRISPR region evolves primarily by deletion, and hinted at a possible Southeast Asian origin of L1. Both phylogeny and DVR patterns clarified some relationships between different spoligotypes, and highlighted the limited resolution of spoligotyping. We identified a diverse repertoire of drug resistance mutations. Altogether, this study demonstrates the usefulness of WGS data for understanding the genetic diversity of L1, with implications for public health surveillance and TB control. It also highlights the need for more WGS studies in high-burden but underexplored regions.
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Affiliation(s)
- Thidarat Netikul
- Faculty of Medicine, Siam University, Phet Kasem Road, Bangkok, Thailand
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand
| | - Yuttapong Thawornwattana
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | | | - Hideki Yanai
- Fukujuji Hospital and Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Kiyose, 204-8533, Japan
| | - Htet Myat Win Maung
- National TB Control Programme, Department of Public Health, Ministry of Health and Sports, Naypyitaw, 15011, Myanmar
- Epidemiology Unit, Faculty of Medicine, Prince of Songkla University, Had Yai, 90110, Thailand
| | | | - Prasit Palittapongarnpim
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Rama 6 Road, Bangkok, Thailand.
- National Science and Technology Development Agency, Pathumthani, Thailand.
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