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Li YF, Kong XL, Song WM, Li YM, Li YY, Fang WW, Yang JY, Yu CB, Li HC, Liu Y. Genomic analysis of lineage-specific transmission of multidrug resistance tuberculosis in China. Emerg Microbes Infect 2024; 13:2294858. [PMID: 38126135 PMCID: PMC10866052 DOI: 10.1080/22221751.2023.2294858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
OBJECTIVES We investigated the genetic diversities and lineage-specific transmission dynamics of multidrug-resistant tuberculosis (MDR-TB), with the goal of determining the potential factors driving the MDR epidemics in China. METHODS We curated a large nationwide Mycobacterium tuberculosis (M. tuberculosis) whole genome sequence data set, including 1313 MDR strains. We reconstructed the phylogeny and mapped the transmission networks of MDR-TB across China using Bayesian inference. To identify drug-resistance variants linked to enhanced transmissibility, we employed ordinary least-squares (OLS) regression analysis. RESULT The majority of MDR-TB strains in China belong to lineage 2.2.1. Transmission chain analysis has indicated that the repeated and frequent transmission of L2.2.1 plays a central role in the establishment of MDR epidemic in China, but no occurrence of a large predominant MDR outbreak was detected. Using OLS regression, the most common single nucleotide polymorphisms (SNPs) associated with resistance to isoniazid (katG_p.Ser315Thr and katG_p.Ser315Asn) and rifampicin (rpoB_p.Ser450Leu, rpoB_p.His445Tyr, rpoB_p.His445Arg, rpoB_p.His445Asp, and rpoB_p.His445Asn) were more likely to be found in L2 clustered strains. Several putative compensatory mutations in rpoA, rpoC, and katG were significantly associated with clustering. The eastern, central, and southern regions of China had a high level of connectivity for the migration of L2 MDR strains throughout the country. The skyline plot showed distinct population size expansion dynamics for MDR-TB lineages in China. CONCLUSION MDR-TB epidemic in China is predominantly driven by the spread of highly transmissible Beijing strains. A range of drug-resistance mutations of L2 MDR-TB strains displayed minimal fitness costs and may facilitate their transmission.
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Affiliation(s)
- Yi-fan Li
- Department of Respiratory and Critical Care Medicine, The Third Affiliated Hospital of Shandong First Medical University, Jinan, People’s Republic of China
| | - Xiang-long Kong
- Shandong Artificial Intelligence Institute Qilu University of Technology (Shandong Academy of Sciences), Jinan, People’s Republic of China
| | - Wan-mei Song
- Department of Respiratory Medicine, Ruijin Hospital Affiliated to Shanghai Jiaotong University, Shanghai, People’s Republic of China
| | - Ya-meng Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
- Department of Respiratory and Critical Care Medicine, Shandong University of Traditional Chinese Medicine, Jinan, People’s Republic of China
| | - Ying-Ying Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
- Department of Respiratory and Critical Care Medicine, Shandong University of Traditional Chinese Medicine, Jinan, People’s Republic of China
| | - Wei-wei Fang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
| | - Jie-yu Yang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
| | - Chun-Bao Yu
- Center for Integrative and Translational Medicine, Shandong Public Health Clinical Center, Jinan, People’s Republic of China
| | - Huai-chen Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
| | - Yao Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
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Li Y, Li Y, Liu Y, Kong X, Tao N, Hou Y, Wang T, Han Q, Zhang Y, Long F, Li H. Iron-related gene mutations driving global Mycobacterium tuberculosis transmission revealed by whole-genome sequencing. BMC Genomics 2024; 25:249. [PMID: 38448842 PMCID: PMC10916221 DOI: 10.1186/s12864-024-10152-1] [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: 11/29/2023] [Accepted: 02/21/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND Iron plays a crucial role in the growth of Mycobacterium tuberculosis (M. tuberculosis). However, the precise regulatory mechanism governing this system requires further elucidation. Additionally, limited studies have examined the impact of gene mutations related to iron on the transmission of M. tuberculosis globally. This research aims to investigate the correlation between mutations in iron-related genes and the worldwide transmission of M. tuberculosis. RESULTS A total of 13,532 isolates of M. tuberculosis were included in this study. Among them, 6,104 (45.11%) were identified as genomic clustered isolates, while 8,395 (62.04%) were classified as genomic clade isolates. Our results showed that a total of 12 single nucleotide polymorphisms (SNPs) showed a positive correlation with clustering, such as Rv1469 (ctpD, C758T), Rv3703c (etgB, G1122T), and Rv3743c (ctpJ, G676C). Additionally, seven SNPs, including Rv0104 (T167G, T478G), Rv0211 (pckA, A302C), Rv0283 (eccB3, C423T), Rv1436 (gap, G654T), ctpD C758T, and etgB C578A, demonstrated a positive correlation with transmission clades across different countries. Notably, our findings highlighted the positive association of Rv0104 T167G, pckA A302C, eccB3 C423T, ctpD C758T, and etgB C578A with transmission clades across diverse regions. Furthermore, our analysis identified 78 SNPs that exhibited significant associations with clade size. CONCLUSIONS Our study reveals the link between iron-related gene SNPs and M. tuberculosis transmission, offering insights into crucial factors influencing the pathogenicity of the disease. This research holds promise for targeted strategies in prevention and treatment, advancing research and interventions in this field.
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Affiliation(s)
- Yameng Li
- Clinical Department of Integrated Traditional Chinese and Western Medicine , The First Clinical Medical College of Shandong University of Traditional Chinese Medicine, 250014, Jinan, Shandong, People's Republic of China
| | - Yifan Li
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Shandong First Medical University (Affiliated Hospital of Shandong Academy of Medical Sciences), 250031, Jinan, Shandong, People's Republic of China
| | - Yao Liu
- Department of Pulmonary and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021, Jinan, Shandong, People's Republic of China
| | - Xianglong Kong
- Artificial Intelligence Institute, Qilu University of Technology (Shandong Academy of Sciences), 250011, Jinan, Shandong, People's Republic of China
| | - Ningning Tao
- Department of Pulmonary and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021, Jinan, Shandong, People's Republic of China
| | - Yawei Hou
- Institute of Chinese Medical Literature and Culture of Shandong University of Traditional Chinese Medicine, 250355, Jinan, Shandong, People's Republic of China
| | - Tingting Wang
- Clinical Department of Integrated Traditional Chinese and Western Medicine , The First Clinical Medical College of Shandong University of Traditional Chinese Medicine, 250014, Jinan, Shandong, People's Republic of China
| | - Qilin Han
- Shandong First Medical University & Shandong Academy of Medical Sciences, 250117, Jinan, Shandong, People's Republic of China
| | - Yuzhen Zhang
- Shandong First Medical University & Shandong Academy of Medical Sciences, 250117, Jinan, Shandong, People's Republic of China
| | - Fei Long
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Shandong First Medical University (Affiliated Hospital of Shandong Academy of Medical Sciences), 250031, Jinan, Shandong, People's Republic of China.
| | - Huaichen Li
- Clinical Department of Integrated Traditional Chinese and Western Medicine , The First Clinical Medical College of Shandong University of Traditional Chinese Medicine, 250014, Jinan, Shandong, People's Republic of China.
- Department of Pulmonary and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 250021, Jinan, Shandong, People's Republic of China.
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Jin M, He B, Cai X, Lei Z, Sun T. Research progress of nanoparticle targeting delivery systems in bacterial infections. Colloids Surf B Biointerfaces 2023; 229:113444. [PMID: 37453264 DOI: 10.1016/j.colsurfb.2023.113444] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/28/2023] [Accepted: 07/05/2023] [Indexed: 07/18/2023]
Abstract
Bacterial infection is a huge threat to the health of human beings and animals. The abuse of antibiotics have led to the occurrence of bacterial multidrug resistance, which have become a difficult problem in the treatment of clinical infections. Given the outstanding advantages of nanodrug delivery systems in cancer treatment, many scholars have begun to pay attention to their application in bacterial infections. However, due to the similarity of the microenvironment between bacterial infection lesions and cancer sites, the targeting and accuracy of traditional microenvironment-responsive nanocarriers are questionable. Therefore, finding new specific targets has become a new development direction of nanocarriers in bacterial prevention and treatment. This article reviews the infectious microenvironment induced by bacteria and a series of virulence factors of common pathogenic bacteria and their physiological functions, which may be used as potential targets to improve the targeting accuracy of nanocarriers in lesions.
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Affiliation(s)
- Ming Jin
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China; Hubei Key Laboratory of Nanomedicine for Neurodegenerative Diseases, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Bin He
- Institute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Sciences, China
| | - Xiaoli Cai
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China; Hubei Key Laboratory of Nanomedicine for Neurodegenerative Diseases, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Zhixin Lei
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China; Hubei Key Laboratory of Nanomedicine for Neurodegenerative Diseases, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China.
| | - Taolei Sun
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China; Hubei Key Laboratory of Nanomedicine for Neurodegenerative Diseases, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China.
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Ruaro-Moreno M, Monterrubio-López GP, Reyes-Gastellou A, Castelán-Vega JA, Jiménez-Alberto A, Aparicio-Ozores G, Delgadillo-Gutiérrez K, González-Y-Merchand JA, Ribas-Aparicio RM. Design of a Multi-Epitope Vaccine against Tuberculosis from Mycobacterium tuberculosis PE_PGRS49 and PE_PGRS56 Proteins by Reverse Vaccinology. Microorganisms 2023; 11:1647. [PMID: 37512820 PMCID: PMC10385543 DOI: 10.3390/microorganisms11071647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/12/2023] [Accepted: 06/14/2023] [Indexed: 07/30/2023] Open
Abstract
Tuberculosis is a disease caused by Mycobacterium tuberculosis, representing the second leading cause of death by an infectious agent worldwide. The available vaccine against this disease has insufficient coverage and variable efficacy, accounting for a high number of cases worldwide. In fact, an estimated third of the world's population has a latent infection. Therefore, developing new vaccines is crucial to preventing it. In this study, the highly antigenic PE_PGRS49 and PE_PGRS56 proteins were analyzed. These proteins were used for predicting T- and B-cell epitopes and for human leukocyte antigen (HLA) protein binding efficiency. Epitopes GGAGGNGSLSS, FAGAGGQGGLGG, GIGGGTQSATGLG (PE_PGRS49), and GTGWNGGKGDTG (PE_PGRS56) were selected based on their best physicochemical, antigenic, non-allergenic, and non-toxic properties and coupled to HLA I and HLA II structures for in silico assays. A construct with an adjuvant (RS09) plus each epitope joined by GPGPG linkers was designed, and the stability of the HLA-coupled construct was further evaluated by molecular dynamics simulations. Although experimental and in vivo studies are still necessary to ensure its protective effect against the disease, this study shows that the vaccine construct is dynamically stable and potentially effective against tuberculosis.
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Affiliation(s)
- Maritriny Ruaro-Moreno
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
| | - Gloria Paulina Monterrubio-López
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
| | - Abraham Reyes-Gastellou
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
| | - Juan Arturo Castelán-Vega
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
| | - Alicia Jiménez-Alberto
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
| | - Gerardo Aparicio-Ozores
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
| | - Karen Delgadillo-Gutiérrez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
| | - Jorge Alberto González-Y-Merchand
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
| | - Rosa María Ribas-Aparicio
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico; (M.R.-M.); (G.P.M.-L.); (A.R.-G.); (G.A.-O.); (K.D.-G.)
- Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City 11340, Mexico;
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Dekhil N, Mardassi H. Genomic changes underpinning the emergence of a successful Mycobacterium tuberculosis Latin American and Mediterranean clonal complex. Front Microbiol 2023; 14:1159994. [PMID: 37425998 PMCID: PMC10325029 DOI: 10.3389/fmicb.2023.1159994] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/26/2023] [Indexed: 07/11/2023] Open
Abstract
Introduction The Latin American and Mediterranean sublineage (L4.3/LAM) is the most common generalist sublineage of Mycobacterium tuberculosis lineage 4 (L4), yet certain L4.3/LAM genotypes appear to be confined to particular geographic regions. This is typically the case of a L4.3/LAM clonal complex (CC), TUN4.3_CC1, which is the most preponderant in Tunisia (61.5% of L4.3/LAM). Methods Here, we used whole-genome sequencing data of 346 globally distributed L4 clinical strains, including 278 L4.3/LAM isolates, to reconstruct the evolutionary history of TUN4.3_CC1 and delineate critical genomic changes underpinning its success. Results and Discussion Phylogenomic coupled to phylogeographic analyses indicated that TUN4.3_CC1 has evolved locally, being confined mainly to North Africa. Maximum likelihood analyses using the site and branch-site models of the PAML package disclosed strong evidence of positive selection in the gene category "cell wall and cell processes" of TUN4.3_CC1. Collectively, the data indicate that TUN4.3_CC1 has inherited several mutations, which could have potentially contributed to its evolutionary success. Of particular interest are amino acid replacements at the esxK and eccC2 genes of the ESX/Type VII secretion system, which were found to be specific to TUN4.3_CC1, being common to almost all isolates. Because of its homoplastic nature, the esxK mutation could potentially have endowed TUN4.3_CC1 with a selective advantage. Moreover, we noticed the occurrence of additional, previously described homoplasic nonsense mutations in ponA1 and Rv0197. The mutation in the latter gene, a putative oxido-reductase, has previously been shown to be correlated with enhanced transmissibility in vivo. In sum, our findings unveiled several features underpinning the success of a locally evolved L4.3/LAM clonal complex, lending further support to the critical role of genes encoded by the ESX/type VII secretion system.
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Chandra P, Grigsby SJ, Philips JA. Immune evasion and provocation by Mycobacterium tuberculosis. Nat Rev Microbiol 2022; 20:750-766. [PMID: 35879556 PMCID: PMC9310001 DOI: 10.1038/s41579-022-00763-4] [Citation(s) in RCA: 244] [Impact Index Per Article: 81.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/20/2022] [Indexed: 02/07/2023]
Abstract
Mycobacterium tuberculosis, the causative agent of tuberculosis, has infected humans for millennia. M. tuberculosis is well adapted to establish infection, persist in the face of the host immune response and be transmitted to uninfected individuals. Its ability to complete this infection cycle depends on it both evading and taking advantage of host immune responses. The outcome of M. tuberculosis infection is often a state of equilibrium characterized by immunological control and bacterial persistence. Recent data have highlighted the diverse cell populations that respond to M. tuberculosis infection and the dynamic changes in the cellular and intracellular niches of M. tuberculosis during the course of infection. M. tuberculosis possesses an arsenal of protein and lipid effectors that influence macrophage functions and inflammatory responses; however, our understanding of the role that specific bacterial virulence factors play in the context of diverse cellular reservoirs and distinct infection stages is limited. In this Review, we discuss immune evasion and provocation by M. tuberculosis during its infection cycle and describe how a more detailed molecular understanding is crucial to enable the development of novel host-directed therapies, disease biomarkers and effective vaccines.
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Affiliation(s)
- Pallavi Chandra
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Steven J Grigsby
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA
| | - Jennifer A Philips
- Division of Infectious Diseases, Department of Medicine, Washington University School of Medicine, St Louis, MO, USA.
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, USA.
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Walker TM, Choisy M, Dedicoat M, Drennan PG, Wyllie D, Yang-Turner F, Crook DW, Robinson ER, Walker AS, Smith EG, Peto TE. Mycobacterium tuberculosis transmission in Birmingham, UK, 2009-19: An observational study. THE LANCET REGIONAL HEALTH. EUROPE 2022; 17:100361. [PMID: 35345560 PMCID: PMC8956939 DOI: 10.1016/j.lanepe.2022.100361] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Background Over 10-years of whole-genome sequencing (WGS) of Mycobacterium tuberculosis in Birmingham presents an opportunity to explore epidemiological trends and risk factors for transmission in new detail. Methods Between 1st January 2009 and 15th June 2019, we obtained the first WGS isolate from every patient resident in a postcode district covered by Birmingham's centralised tuberculosis service. Data on patients' sex, country of birth, social risk-factors, anatomical locus of disease, and strain lineage were collected. Poisson harmonic regression was used to assess seasonal variation in case load and a mixed-effects multivariable Cox proportionate hazards model was used to assess risk factors for a future case arising in clusters defined by a 5 single nucleotide polymorphism (SNP) threshold, and by 12 SNPs in a sensitivity analysis. Findings 511/1653 (31%) patients were genomically clustered with another. A seasonal variation in diagnoses was observed, peaking in spring, but only among clustered cases. Risk-factors for a future clustered case included UK-birth (aHR=2·03 (95%CI 1·35-3·04), p < 0·001), infectious (pulmonary/laryngeal/miliary) tuberculosis (aHR=3·08 (95%CI 1·98-4·78), p < 0·001), and M. tuberculosis lineage 3 (aHR=1·91 (95%CI 1·03-3·56), p = 0·041) and 4 (aHR=2·27 (95%CI 1·21-4·26), p = 0·011), vs. lineage 1. Similar results pertained to 12 SNP clusters, for which social risk-factors were also significant (aHR 1·72 (95%CI 1·02-2·93), p = 0·044). There was marked heterogeneity in transmission patterns between postcode districts. Interpretation There is seasonal variation in the diagnosis of genomically clustered, but not non-clustered, cases. Risk factors for clustering include UK-birth, infectious forms of tuberculosis, and infection with lineage 3 or 4. Funding Wellcome Trust, MRC, UKHSA.
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Affiliation(s)
- Timothy M. Walker
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, UK
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam
| | - Marc Choisy
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, UK
- Oxford University Clinical Research Unit, Ho Chi Minh City, Viet Nam
| | - Martin Dedicoat
- University Hospitals Birmingham NHS Foundation Trust, Birmingham, UK
| | - Philip G. Drennan
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, UK
- Oxford University Hospitals NHS Foundation Trust, UK
| | - David Wyllie
- TB Unit and National Mycobacterial Reference Service, UK Health Security Agency, UK
| | - Fan Yang-Turner
- NIHR Oxford Biomedical Research Centre, University of Oxford, UK
| | - Derrick W. Crook
- Oxford University Hospitals NHS Foundation Trust, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, UK
| | - Esther R. Robinson
- TB Unit and National Mycobacterial Reference Service, UK Health Security Agency, UK
| | - A. Sarah Walker
- NIHR Oxford Biomedical Research Centre, University of Oxford, UK
| | - E. Grace Smith
- TB Unit and National Mycobacterial Reference Service, UK Health Security Agency, UK
| | - Timothy E.A. Peto
- Oxford University Hospitals NHS Foundation Trust, UK
- NIHR Oxford Biomedical Research Centre, University of Oxford, UK
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Coll F, Gouliouris T, Bruchmann S, Phelan J, Raven KE, Clark TG, Parkhill J, Peacock SJ. PowerBacGWAS: a computational pipeline to perform power calculations for bacterial genome-wide association studies. Commun Biol 2022; 5:266. [PMID: 35338232 PMCID: PMC8956664 DOI: 10.1038/s42003-022-03194-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 02/25/2022] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies (GWAS) are increasingly being applied to investigate the genetic basis of bacterial traits. However, approaches to perform power calculations for bacterial GWAS are limited. Here we implemented two alternative approaches to conduct power calculations using existing collections of bacterial genomes. First, a sub-sampling approach was undertaken to reduce the allele frequency and effect size of a known and detectable genotype-phenotype relationship by modifying phenotype labels. Second, a phenotype-simulation approach was conducted to simulate phenotypes from existing genetic variants. We implemented both approaches into a computational pipeline (PowerBacGWAS) that supports power calculations for burden testing, pan-genome and variant GWAS; and applied it to collections of Enterococcus faecium, Klebsiella pneumoniae and Mycobacterium tuberculosis. We used this pipeline to determine sample sizes required to detect causal variants of different minor allele frequencies (MAF), effect sizes and phenotype heritability, and studied the effect of homoplasy and population diversity on the power to detect causal variants. Our pipeline and user documentation are made available and can be applied to other bacterial populations. PowerBacGWAS can be used to determine sample sizes required to find statistically significant associations, or the associations detectable with a given sample size. We recommend to perform power calculations using existing genomes of the bacterial species and population of study.
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Affiliation(s)
- Francesc Coll
- Department of Infection Biology, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
| | - Theodore Gouliouris
- Department of Medicine, University of Cambridge, Cambridge, UK
- Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | | | - Jody Phelan
- Department of Infection Biology, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Kathy E Raven
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Taane G Clark
- Department of Infection Biology, Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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Payros D, Alonso H, Malaga W, Volle A, Mazères S, Déjean S, Valière S, Moreau F, Balor S, Stella A, Combes-Soia L, Burlet-Schiltz O, Bouchez O, Nigou J, Astarie-Dequeker C, Guilhot C. Rv0180c contributes to Mycobacterium tuberculosis cell shape and to infectivity in mice and macrophages. PLoS Pathog 2021; 17:e1010020. [PMID: 34724002 PMCID: PMC8584747 DOI: 10.1371/journal.ppat.1010020] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 11/11/2021] [Accepted: 10/08/2021] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium tuberculosis, the main causative agent of human tuberculosis, is transmitted from person to person via small droplets containing very few bacteria. Optimizing the chance to seed in the lungs is therefore a major adaptation to favor survival and dissemination in the human population. Here we used TnSeq to identify genes important for the early events leading to bacterial seeding in the lungs. Beside several genes encoding known virulence factors, we found three new candidates not previously described: rv0180c, rv1779c and rv1592c. We focused on the gene, rv0180c, of unknown function. First, we found that deletion of rv0180c in M. tuberculosis substantially reduced the initiation of infection in the lungs of mice. Next, we established that Rv0180c enhances entry into macrophages through the use of complement-receptor 3 (CR3), a major phagocytic receptor for M. tuberculosis. Silencing CR3 or blocking the CR3 lectin site abolished the difference in entry between the wild-type parental strain and the Δrv0180c::km mutant. However, we detected no difference in the production of both CR3-known carbohydrate ligands (glucan, arabinomannan, mannan), CR3-modulating lipids (phthiocerol dimycocerosate), or proteins in the capsule of the Δrv0180c::km mutant in comparison to the wild-type or complemented strains. By contrast, we established that Rv0180c contributes to the functionality of the bacterial cell envelope regarding resistance to toxic molecule attack and cell shape. This alteration of bacterial shape could impair the engagement of membrane receptors that M. tuberculosis uses to invade host cells, and open a new perspective on the modulation of bacterial infectivity. The epidemic efficiency of tuberculosis bacilli is determined by their capacity to transmit via aerosol. Currently, the bacterial functions that favor Mycobacterium tuberculosis seeding in the lung of naïve host remain mostly unknown. Here we implemented a genome-wide approach to identify M. tuberculosis mutants deficient for seeding and early replication in the lung of mice. In addition to genes known to encode virulence factors, we identified three genes not previously described. We used complementary approaches to characterize the phenotype of a M. tuberculosis mutant with insertion within the rv0180c gene. We found that this mutant is impaired for seeding in the lung of mice and for invasion and replication in human macrophages. In macrophages, the defect relies on a lack of engagement of CR3 receptor. Although we did not detect any difference between the wild type strain and the rv0180c mutant with regard to potential CR3-ligand, we found that the bacterial cell envelope is altered in the rv0180c mutant. Our study provides new insight into bacterial genes required for early interaction of M. tuberculosis with the host and perspective to understand the bacterial functions enhancing infectivity.
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Affiliation(s)
- Delphine Payros
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Henar Alonso
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Wladimir Malaga
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Arnaud Volle
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Serge Mazères
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Sébastien Déjean
- Institut de Mathématiques de Toulouse, UMR5219, Université de Toulouse, CNRS, UPS, Toulouse, France
| | | | - Flavie Moreau
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Stéphanie Balor
- Plateforme de Microscopie Électronique Intégrative (METi), Centre de Biologie Intégrative (CBI), CNRS, Toulouse, France
| | - Alexandre Stella
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Lucie Combes-Soia
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Odile Burlet-Schiltz
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | | | - Jérôme Nigou
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Catherine Astarie-Dequeker
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
- * E-mail: (CAD); (CG)
| | - Christophe Guilhot
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
- * E-mail: (CAD); (CG)
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10
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Alame Emane AK, Guo X, Takiff HE, Liu S. Highly transmitted M. tuberculosis strains are more likely to evolve MDR/XDR and cause outbreaks, but what makes them highly transmitted? Tuberculosis (Edinb) 2021; 129:102092. [PMID: 34102584 DOI: 10.1016/j.tube.2021.102092] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 05/10/2021] [Accepted: 05/17/2021] [Indexed: 11/17/2022]
Abstract
Multi-Drug-Resistant strains of Mycobacterium tuberculosis (MDR-TB) are a serious obstacle to global TB eradication. While most MDR-TB strains are infrequently transmitted, a few cause large transmission clusters that contribute substantially to local MDR-TB burdens. Here we examine whether the known mutations in these strains can explain their success. Drug resistance mutations differ in fitness costs and strains can also acquire compensatory mutations (CM) to restore fitness, but some highly transmitted MDR strains have no CM. The acquisition of resistance mutations that maintain high transmissibility seems to occur by chance and are more likely in strains that are intrinsically highly transmitted and cause many cases. Modern Beijing lineage strains have caused several large outbreaks, but MDR outbreaks are also caused by ancient Beijing and lineage 4 strains, suggesting the lineage is less important than the characteristics of the individual strain. The development of fluoroquinolone resistance appears to represent another level of selection, in which strains must surmount unknown fitness costs of gyrA mutations. The genetic determinants of high transmission are poorly defined but may involve genes encoding proteins involved in molybdenum acquisition and the Esx systems. In addition, strains eliciting lower cytokine responses and producing more caseating granulomas may have advantages for transmission. Successful MDR/XDR strains generally evolve from highly transmitted drug sensitive parent strains due to selection pressures from deficiencies in local TB control programs. Until TB incidence is considerably reduced, there will likely be highly transmitted strains that develop resistance to any new antibiotic.
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Affiliation(s)
- Amel Kevin Alame Emane
- Shenzhen Nanshan Center for Chronic Disease Control, 7 Huaming Road, Nanshan, Shenzhen City, Guangdong Province, China.
| | - Xujun Guo
- Shenzhen Nanshan Center for Chronic Disease Control, 7 Huaming Road, Nanshan, Shenzhen City, Guangdong Province, China.
| | - Howard E Takiff
- Shenzhen Nanshan Center for Chronic Disease Control, 7 Huaming Road, Nanshan, Shenzhen City, Guangdong Province, China; Integrated Mycobacterial Pathogenomics Unit, Institut Pasteur, 28 Rue du Dr Roux, Paris, 75015, France; Laboratorio de Genética Molecular, CMBC, IVIC, Km. 11 Carr. Panamericana, Caracas, Venezuela.
| | - Shengyuan Liu
- Shenzhen Nanshan Center for Chronic Disease Control, 7 Huaming Road, Nanshan, Shenzhen City, Guangdong Province, China.
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11
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Ektefaie Y, Dixit A, Freschi L, Farhat MR. Globally diverse Mycobacterium tuberculosis resistance acquisition: a retrospective geographical and temporal analysis of whole genome sequences. LANCET MICROBE 2021; 2:e96-e104. [PMID: 33912853 PMCID: PMC8078851 DOI: 10.1016/s2666-5247(20)30195-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Background Mycobacterium tuberculosis whole genome sequencing (WGS) data can provide insights into temporal and geographical trends in resistance acquisition and inform public health interventions. We aimed to use a large clinical collection of M tuberculosis WGS and resistance phenotype data to study how, when, and where resistance was acquired on a global scale. Methods We did a retrospective analysis of WGS data. We curated a set of clinical M tuberculosis isolates with high-quality sequencing and culture-based drug susceptibility data (spanning four lineages and 52 countries in Africa, Asia, the Americas, and Europe) using public databases and literature curation. For inclusion, sequence quality criteria and country of origin data were required. We constructed geographical and lineage specific M tuberculosis phylogenies and used Bayesian molecular dating with BEAST, version 1.10.4, to infer the most recent common susceptible ancestor age for 4869 instances of resistance to ten drugs. Findings Between Jan 1, 1987, and Sept 12, 2014, of 10 299 M tuberculosis clinical isolates, 8550 were curated, of which 6099 (71%) from 15 countries met criteria for molecular dating. The number of independent resistance acquisition events was lower than the number of resistant isolates across all countries, suggesting ongoing transmission of drug resistance. Ancestral age distributions supported the presence of old resistance, 20 years or more before, in most countries. A consistent order of resistance acquisition was observed globally starting with resistance to isoniazid, but resistance ancestral age varied by country. We found a direct correlation between gross domestic product per capita and resistance age (r 2=0·47; p=0·014). Amplification of fluoroquinolone and second-line injectable resistance among multidrug-resistant isolates is estimated to have occurred very recently (median ancestral age 4·7 years [IQR 1·9-9·8] before sample collection). We found the sensitivity of commercial molecular diagnostics for second-line resistance to vary significantly by country (p<0·0003). Interpretation Our results highlight that both resistance transmission and amplification are contributing to disease burden globally but vary by country. The observation that wealthier nations are more likely to have old resistance (most recent common susceptible ancestor >20 years before isolation) suggests that programmatic improvements can reduce resistance amplification, but that fit resistant strains can circulate for decades subsequently implies the need for continued surveillance.
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Affiliation(s)
- Yasha Ektefaie
- Department of BioEngineering, University of California Berkeley, Berkeley, CA, USA
| | - Avika Dixit
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Luca Freschi
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
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12
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Lees JA, Mai TT, Galardini M, Wheeler NE, Horsfield ST, Parkhill J, Corander J. Improved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions. mBio 2020; 11:e01344-20. [PMID: 32636251 PMCID: PMC7343994 DOI: 10.1128/mbio.01344-20] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 06/05/2020] [Indexed: 12/19/2022] Open
Abstract
Discovery of genetic variants underlying bacterial phenotypes and the prediction of phenotypes such as antibiotic resistance are fundamental tasks in bacterial genomics. Genome-wide association study (GWAS) methods have been applied to study these relations, but the plastic nature of bacterial genomes and the clonal structure of bacterial populations creates challenges. We introduce an alignment-free method which finds sets of loci associated with bacterial phenotypes, quantifies the total effect of genetics on the phenotype, and allows accurate phenotype prediction, all within a single computationally scalable joint modeling framework. Genetic variants covering the entire pangenome are compactly represented by extended DNA sequence words known as unitigs, and model fitting is achieved using elastic net penalization, an extension of standard multiple regression. Using an extensive set of state-of-the-art bacterial population genomic data sets, we demonstrate that our approach performs accurate phenotype prediction, comparable to popular machine learning methods, while retaining both interpretability and computational efficiency. Compared to those of previous approaches, which test each genotype-phenotype association separately for each variant and apply a significance threshold, the variants selected by our joint modeling approach overlap substantially.IMPORTANCE Being able to identify the genetic variants responsible for specific bacterial phenotypes has been the goal of bacterial genetics since its inception and is fundamental to our current level of understanding of bacteria. This identification has been based primarily on painstaking experimentation, but the availability of large data sets of whole genomes with associated phenotype metadata promises to revolutionize this approach, not least for important clinical phenotypes that are not amenable to laboratory analysis. These models of phenotype-genotype association can in the future be used for rapid prediction of clinically important phenotypes such as antibiotic resistance and virulence by rapid-turnaround or point-of-care tests. However, despite much effort being put into adapting genome-wide association study (GWAS) approaches to cope with bacterium-specific problems, such as strong population structure and horizontal gene exchange, current approaches are not yet optimal. We describe a method that advances methodology for both association and generation of portable prediction models.
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Affiliation(s)
- John A Lees
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - T Tien Mai
- Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Marco Galardini
- Biological Design Center, Boston University, Boston, Massachusetts, USA
| | - Nicole E Wheeler
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Samuel T Horsfield
- MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, Imperial College London, London, United Kingdom
| | - Julian Parkhill
- Department of Veterinary Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jukka Corander
- Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, University of Oslo, Oslo, Norway
- Centre for Genomic Pathogen Surveillance, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
- Helsinki Institute of Information Technology, Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
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13
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Homoplastic single nucleotide polymorphisms contributed to phenotypic diversity in Mycobacterium tuberculosis. Sci Rep 2020; 10:8024. [PMID: 32415151 PMCID: PMC7229016 DOI: 10.1038/s41598-020-64895-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 04/20/2020] [Indexed: 12/16/2022] Open
Abstract
Homoplastic mutations are mutations independently occurring in different clades of an organism. The homoplastic changes may be a result of convergence evolution due to selective pressures. Reports on the analysis of homoplastic mutations in Mycobacterium tuberculosis have been limited. Here we characterized the distribution of homoplastic single nucleotide polymorphisms (SNPs) among genomes of 1,170 clinical M. tuberculosis isolates. They were present in all functional categories of genes, with pe/ppe gene family having the highest ratio of homoplastic SNPs compared to the total SNPs identified in the same functional category. Among the pe/ppe genes, the homoplastic SNPs were common in a relatively small number of homologous genes, including ppe18, the protein of which is a component of a promising candidate vaccine, M72/AS01E. The homoplastic SNPs in ppe18 were particularly common among M. tuberculosis Lineage 1 isolates, suggesting the need for caution in extrapolating the results of the vaccine trial to the population where L1 is endemic in Asia. As expected, homoplastic SNPs strongly associated with drug resistance. Most of these mutations are already well known. However, a number of novel mutations associated with streptomycin resistance were identified, which warrants further investigation. A SNP in the intergenic region upstream of Rv0079 (DATIN) was experimentally shown to increase transcriptional activity of the downstream gene, suggesting that intergenic homoplastic SNPs should have effects on the physiology of the bacterial cells. Our study highlights the potential of homoplastic mutations to produce phenotypic changes. Under selective pressure and during interaction with the host, homoplastic mutations may confer advantages to M. tuberculosis and deserve further characterization.
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14
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Sobkowiak B, Banda L, Mzembe T, Crampin AC, Glynn JR, Clark TG. Bayesian reconstruction of Mycobacterium tuberculosis transmission networks in a high incidence area over two decades in Malawi reveals associated risk factors and genomic variants. Microb Genom 2020; 6:e000361. [PMID: 32234123 PMCID: PMC7276699 DOI: 10.1099/mgen.0.000361] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 03/12/2020] [Indexed: 11/21/2022] Open
Abstract
Understanding host and pathogen factors that influence tuberculosis (TB) transmission can inform strategies to eliminate the spread of Mycobacterium tuberculosis (Mtb). Determining transmission links between cases of TB is complicated by a long and variable latency period and undiagnosed cases, although methods are improving through the application of probabilistic modelling and whole-genome sequence analysis. Using a large dataset of 1857 whole-genome sequences and comprehensive metadata from Karonga District, Malawi, over 19 years, we reconstructed Mtb transmission networks using a two-step Bayesian approach that identified likely infector and recipient cases, whilst robustly allowing for incomplete case sampling. We investigated demographic and pathogen genomic variation associated with transmission and clustering in our networks. We found that whilst there was a significant decrease in the proportion of infectors over time, we found higher transmissibility and large transmission clusters for lineage 2 (Beijing) strains. By performing evolutionary convergence testing (phyC) and genome-wide association analysis (GWAS) on transmitting versus non-transmitting cases, we identified six loci, PPE54, accD2, PE_PGRS62, rplI, Rv3751 and Rv2077c, that were associated with transmission. This study provides a framework for reconstructing large-scale Mtb transmission networks. We have highlighted potential host and pathogen characteristics that were linked to increased transmission in a high-burden setting and identified genomic variants that, with validation, could inform further studies into transmissibility and TB eradication.
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Affiliation(s)
- Benjamin Sobkowiak
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Present address: Division of Respiratory Medicine, University of British Columbia, Vancouver, Canada, and British Columbia Centre for Disease Control, Vancouver, Canada
| | - Louis Banda
- Malawi Epidemiology and Intervention Research Unit, Malawi
| | - Themba Mzembe
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Amelia C. Crampin
- Institute of Health and Wellbeing, University of Glasgow, Glasgow, UK
| | - Judith R. Glynn
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
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15
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Raze D, Segers J, Mille C, Slupek S, Lecher S, Coutte L, Antoine R, Ducrocq L, Rouanet C, Appelmelk BJ, Locht C. Coordinate regulation of virulence and metabolic genes by the transcription factor HbhR in Mycobacterium marinum. Mol Microbiol 2019; 113:52-67. [PMID: 31587365 DOI: 10.1111/mmi.14400] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2019] [Indexed: 12/17/2022]
Abstract
The heparin-binding hemagglutinin (HBHA) is a multifunctional protein involved in adherence of Mycobacterium tuberculosis to non-phagocytic cells and in the formation of intracytosolic lipid inclusions. We demonstrate that the expression of hbhA is regulated by a transcriptional repressor, named HbhR, in Mycobacterium marinum. The hbhR gene, located upstream of hbhA, was identified by screening a transposon insertion library and detailed analysis of a mutant overproducing HBHA. HbhR was found to repress both hbhA and hbhR transcription by binding to the promoter regions of both genes. Complementation restored production of HBHA. RNA-seq analyses comparing the mutant and parental strains uncovered 27 genes, including hbhA, that were repressed and 20 genes activated by HbhR. Among the former, the entire locus of genes coding for a type-VII secretion system, including esxA, esxB and pe-ppe paralogs, as well as the gene coding for PspA, present in intracellular lipid vesicles, was identified, as was katG, a gene involved in the sensitivity to isoniazid. The latter category contains genes that play a role in diverse functions, such as metabolism and resistance to oxidative conditions. Thus, HbhR appears to be a master regulator, linking the transcriptional regulation of virulence, metabolic and antibiotic sensitivity genes in M. marinum.
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Affiliation(s)
- Dominique Raze
- CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, INSERM, Institut Pasteur de Lille, U1019 - UMR 8204, Lille, F-59000, France
| | - Jérôme Segers
- CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, INSERM, Institut Pasteur de Lille, U1019 - UMR 8204, Lille, F-59000, France
| | - Céline Mille
- CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, INSERM, Institut Pasteur de Lille, U1019 - UMR 8204, Lille, F-59000, France
| | - Stéphanie Slupek
- CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, INSERM, Institut Pasteur de Lille, U1019 - UMR 8204, Lille, F-59000, France
| | - Sophie Lecher
- CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, INSERM, Institut Pasteur de Lille, U1019 - UMR 8204, Lille, F-59000, France
| | - Loïc Coutte
- CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, INSERM, Institut Pasteur de Lille, U1019 - UMR 8204, Lille, F-59000, France
| | - Rudy Antoine
- CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, INSERM, Institut Pasteur de Lille, U1019 - UMR 8204, Lille, F-59000, France
| | - Lucie Ducrocq
- CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, INSERM, Institut Pasteur de Lille, U1019 - UMR 8204, Lille, F-59000, France
| | - Carine Rouanet
- CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, INSERM, Institut Pasteur de Lille, U1019 - UMR 8204, Lille, F-59000, France
| | - Ben J Appelmelk
- Molecular Microbiology/Medical Microbiology and Infection Control, Amsterdam University Medical Centers, Amsterdam, The Netherlands
| | - Camille Locht
- CIIL - Center for Infection and Immunity of Lille, Univ. Lille, CNRS, INSERM, Institut Pasteur de Lille, U1019 - UMR 8204, Lille, F-59000, France
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16
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Abubakar I, Gupta RK, Rangaka MX, Lipman M. Update in Tuberculosis and Nontuberculous Mycobacteria 2017. Am J Respir Crit Care Med 2019. [PMID: 29537298 DOI: 10.1164/rccm.201801-0106up] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
| | | | | | - Marc Lipman
- 2 UCL-TB and UCL Respiratory, University College London, London, United Kingdom; and.,3 Royal Free London NHS Foundation Trust, London, United Kingdom
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17
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Koeken VACM, Verrall AJ, Ardiansyah E, Apriani L, Dos Santos JC, Kumar V, Alisjahbana B, Hill PC, Joosten LAB, van Crevel R, van Laarhoven A. IL-32 and its splice variants are associated with protection against Mycobacterium tuberculosis infection and skewing of Th1/Th17 cytokines. J Leukoc Biol 2019; 107:113-118. [PMID: 31378983 PMCID: PMC6972663 DOI: 10.1002/jlb.4ab0219-071r] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 07/02/2019] [Accepted: 07/17/2019] [Indexed: 12/11/2022] Open
Abstract
Studies in IL‐32 transgenic mice and in vitro suggest that IL‐32 may have protective effects against Mycobacterium tuberculosis, but so far there are barely any studies in humans. We studied the role of IL‐32 and its splice variants in tuberculosis (TB) in vivo and in vitro. Blood transcriptional analysis showed lower total IL‐32 mRNA levels in pulmonary TB patients compared to patients with latent TB infection and healthy controls. Also, among Indonesian household contacts who were heavily exposed to an infectious TB patient, IL‐32 mRNA levels were higher among those who remained uninfected compared to those who became infected with M. tuberculosis. In peripheral blood mononuclear cells from healthy donors, we found that IL‐32γ, the most potent isoform, was down‐regulated upon M. tuberculosis stimulation. This decrease in IL‐32γ was mirrored by an increase of another splice variant, IL‐32β. Also, a higher IL‐32γ/IL‐32β ratio correlated with IFN‐γ production, whereas a lower ratio correlated with production of IL‐1Ra, IL‐6, and IL‐17. These data suggest that IL‐32 contributes to protection against M. tuberculosis infection, and that this effect may depend on the relative abundance of different IL‐32 isoforms.
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Affiliation(s)
- Valerie A C M Koeken
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS), and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Ayesha J Verrall
- Department of Pathology and Molecular Medicine, University of Otago, Wellington, Wellington, New Zealand
| | - Edwin Ardiansyah
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS), and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands.,Faculty of Medicine, TB-HIV Research Center, Universitas Padjadjaran, Bandung, Indonesia
| | - Lika Apriani
- Faculty of Medicine, TB-HIV Research Center, Universitas Padjadjaran, Bandung, Indonesia
| | - Jéssica C Dos Santos
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS), and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Vinod Kumar
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS), and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Bachti Alisjahbana
- Faculty of Medicine, TB-HIV Research Center, Universitas Padjadjaran, Bandung, Indonesia
| | - Philip C Hill
- Department of Preventive and Social Medicine, Centre for International Health, University of Otago, Dunedin, New Zealand
| | - Leo A B Joosten
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS), and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Reinout van Crevel
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS), and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
| | - Arjan van Laarhoven
- Department of Internal Medicine, Radboud Institute of Molecular Life Sciences (RIMLS), and Radboud Center of Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, The Netherlands
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18
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Dixit A, Freschi L, Vargas R, Calderon R, Sacchettini J, Drobniewski F, Galea JT, Contreras C, Yataco R, Zhang Z, Lecca L, Kolokotronis SO, Mathema B, Farhat MR. Whole genome sequencing identifies bacterial factors affecting transmission of multidrug-resistant tuberculosis in a high-prevalence setting. Sci Rep 2019; 9:5602. [PMID: 30944370 PMCID: PMC6447560 DOI: 10.1038/s41598-019-41967-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/20/2019] [Indexed: 11/09/2022] Open
Abstract
Whole genome sequencing (WGS) can elucidate Mycobacterium tuberculosis (Mtb) transmission patterns but more data is needed to guide its use in high-burden settings. In a household-based TB transmissibility study in Peru, we identified a large MIRU-VNTR Mtb cluster (148 isolates) with a range of resistance phenotypes, and studied host and bacterial factors contributing to its spread. WGS was performed on 61 of the 148 isolates. We compared transmission link inference using epidemiological or genomic data and estimated the dates of emergence of the cluster and antimicrobial drug resistance (DR) acquisition events by generating a time-calibrated phylogeny. Using a set of 12,032 public Mtb genomes, we determined bacterial factors characterizing this cluster and under positive selection in other Mtb lineages. Four of the 61 isolates were distantly related and the remaining 57 isolates diverged ca. 1968 (95%HPD: 1945-1985). Isoniazid resistance arose once and rifampin resistance emerged subsequently at least three times. Emergence of other DR types occurred as recently as within the last year of sampling. We identified five cluster-defining SNPs potentially contributing to transmissibility. In conclusion, clusters (as defined by MIRU-VNTR typing) may be circulating for decades in a high-burden setting. WGS allows for an enhanced understanding of transmission, drug resistance, and bacterial fitness factors.
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Affiliation(s)
- Avika Dixit
- Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | | | | | | | | | | | | | | | | | - Zibiao Zhang
- Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Leonid Lecca
- Harvard Medical School, Boston, MA, USA
- Socios En Salud, Lima, Peru
| | | | - Barun Mathema
- Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Maha R Farhat
- Harvard Medical School, Boston, MA, USA
- Massachussetts General Hospital, Boston, MA, USA
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19
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Oppong YEA, Phelan J, Perdigão J, Machado D, Miranda A, Portugal I, Viveiros M, Clark TG, Hibberd ML. Genome-wide analysis of Mycobacterium tuberculosis polymorphisms reveals lineage-specific associations with drug resistance. BMC Genomics 2019; 20:252. [PMID: 30922221 PMCID: PMC6440112 DOI: 10.1186/s12864-019-5615-3] [Citation(s) in RCA: 31] [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: 04/11/2018] [Accepted: 03/15/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Continuing evolution of the Mycobacterium tuberculosis (Mtb) complex genomes associated with resistance to anti-tuberculosis drugs is threatening tuberculosis disease control efforts. Both multi- and extensively drug resistant Mtb (MDR and XDR, respectively) are increasing in prevalence, but the full set of Mtb genes involved are not known. There is a need for increased sensitivity of genome-wide approaches in order to elucidate the genetic basis of anti-microbial drug resistance and gain a more detailed understanding of Mtb genome evolution in a context of widespread antimicrobial therapy. Population structure within the Mtb complex, due to clonal expansion, lack of lateral gene transfer and low levels of recombination between lineages, may be reducing statistical power to detect drug resistance associated variants. RESULTS To investigate the effect of lineage-specific effects on the identification of drug resistance associations, we applied genome-wide association study (GWAS) and convergence-based (PhyC) methods to multiple drug resistance phenotypes of a global dataset of Mtb lineages 2 and 4, using both lineage-wise and combined approaches. We identify both well-established drug resistance variants and novel associations; uniquely identifying associations for both lineage-specific and -combined GWAS analyses. We report 17 potential novel associations between antimicrobial resistance phenotypes and Mtb genomic variants. CONCLUSIONS For GWAS, both lineage-specific and -combined analyses are useful, whereas PhyC may perform better in contexts of greater diversity. Unique associations with XDR in lineage-specific analyses provide evidence of diverging evolutionary trajectories between lineages 2 and 4 in response to antimicrobial drug therapy.
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Affiliation(s)
- Yaa E. A. Oppong
- Pathogen Molecular Biology Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - Jody Phelan
- Pathogen Molecular Biology Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
| | - João Perdigão
- iMed.ULisboa – Research Institute for Medicines, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Diana Machado
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, UNL, Lisbon, Portugal
| | - Anabela Miranda
- National Mycobacterium Reference Laboratory, Porto, Portugal
| | - Isabel Portugal
- iMed.ULisboa – Research Institute for Medicines, Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Miguel Viveiros
- Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, UNL, Lisbon, Portugal
| | - Taane G. Clark
- Pathogen Molecular Biology Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
- Faculty of Epidemiology and Population Health, LSHTM, London, UK
| | - Martin L. Hibberd
- Pathogen Molecular Biology Department, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT UK
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20
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Verma S, Bhatt K, Lovey A, Ribeiro-Rodrigues R, Durbin J, Jones-López EC, Palaci M, Vinhas SA, Alland D, Dietze R, Ellner JJ, Salgame P. Transmission phenotype of Mycobacterium tuberculosis strains is mechanistically linked to induction of distinct pulmonary pathology. PLoS Pathog 2019; 15:e1007613. [PMID: 30840702 PMCID: PMC6422314 DOI: 10.1371/journal.ppat.1007613] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 03/18/2019] [Accepted: 02/02/2019] [Indexed: 12/19/2022] Open
Abstract
In a study of household contacts (HHC), households were categorized into High (HT) and Low (LT) transmission groups based on the proportion of HHC with a positive tuberculin skin test. The Mycobacterium tuberculosis (Mtb) strains from HT and LT index cases of the households were designated Mtb-HT and Mtb-LT, respectively. We found that C3HeB/FeJ mice infected with Mtb-LT strains exhibited significantly higher bacterial burden compared to Mtb-HT strains and also developed diffused inflammatory lung pathology. In stark contrast, a significant number of mice infected with Mtb-HT strains developed caseating granulomas, a lesion type with high potential to cavitate. None of the Mtb-HT infected animals developed diffused inflammatory lung pathology. A link was observed between increased in vitro replication of Mtb-LT strains and their ability to induce significantly high lipid droplet formation in macrophages. These results support that distinct early interactions of Mtb-HT and Mtb-LT strains with macrophages and subsequent differential trajectories in pathological disease may be the mechanism underlying their transmission potential.
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Affiliation(s)
- Sheetal Verma
- Rutgers University-New Jersey Medical School, Department of Medicine, Centre for Emerging Pathogens, Newark, New Jersey, United States of America
| | - Kamlesh Bhatt
- Rutgers University-New Jersey Medical School, Department of Medicine, Centre for Emerging Pathogens, Newark, New Jersey, United States of America
| | - Arianne Lovey
- Rutgers University-New Jersey Medical School, Department of Medicine, Centre for Emerging Pathogens, Newark, New Jersey, United States of America
| | - Rodrigo Ribeiro-Rodrigues
- Cellular and Molecular Immunology Laboratory, Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, Brazil
| | - Joan Durbin
- Rutgers University-New Jersey Medical School, Department of Pathology, Newark, New Jersey, United States of America
| | - Edward C. Jones-López
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Moises Palaci
- Mycobacteriology Laboratory, Núcleo de Doenças de Infecciosas, Universidade Federal do Espírito Santo, Vitória, Brazil
| | - Solange A. Vinhas
- Mycobacteriology Laboratory, Núcleo de Doenças de Infecciosas, Universidade Federal do Espírito Santo, Vitória, Brazil
| | - David Alland
- Rutgers University-New Jersey Medical School, Department of Medicine, Centre for Emerging Pathogens, Newark, New Jersey, United States of America
| | - Reynaldo Dietze
- Núcleo de Doenças Infecciosas, Universidade Federal do Espírito Santo, Vitória, Brazil
- Global Health & Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Lisbon, Portugal
| | - Jerrold J. Ellner
- Section of Infectious Diseases, Department of Medicine, Boston Medical Center and Boston University School of Medicine, Boston, Massachusetts, United States of America
| | - Padmini Salgame
- Rutgers University-New Jersey Medical School, Department of Medicine, Centre for Emerging Pathogens, Newark, New Jersey, United States of America
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21
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Wiens KE, Woyczynski LP, Ledesma JR, Ross JM, Zenteno-Cuevas R, Goodridge A, Ullah I, Mathema B, Djoba Siawaya JF, Biehl MH, Ray SE, Bhattacharjee NV, Henry NJ, Reiner RC, Kyu HH, Murray CJL, Hay SI. Global variation in bacterial strains that cause tuberculosis disease: a systematic review and meta-analysis. BMC Med 2018; 16:196. [PMID: 30373589 PMCID: PMC6206891 DOI: 10.1186/s12916-018-1180-x] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Accepted: 09/24/2018] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND The host, microbial, and environmental factors that contribute to variation in tuberculosis (TB) disease are incompletely understood. Accumulating evidence suggests that one driver of geographic variation in TB disease is the local ecology of mycobacterial genotypes or strains, and there is a need for a comprehensive and systematic synthesis of these data. The objectives of this study were to (1) map the global distribution of genotypes that cause TB disease and (2) examine whether any epidemiologically relevant clinical characteristics were associated with those genotypes. METHODS We performed a systematic review of PubMed and Scopus to create a comprehensive dataset of human TB molecular epidemiology studies that used representative sampling techniques. The methods were developed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). We extracted and synthesized data from studies that reported prevalence of bacterial genotypes and from studies that reported clinical characteristics associated with those genotypes. RESULTS The results of this study are twofold. First, we identified 206 studies for inclusion in the study, representing over 200,000 bacterial isolates collected over 27 years in 85 countries. We mapped the genotypes and found that, consistent with previously published maps, Euro-American lineage 4 and East Asian lineage 2 strains are widespread, and West African lineages 5 and 6 strains are geographically restricted. Second, 30 studies also reported transmission chains and 4 reported treatment failure associated with genotypes. We performed a meta-analysis and found substantial heterogeneity across studies. However, based on the data available, we found that lineage 2 strains may be associated with increased risk of transmission chains, while lineages 5 and 6 strains may be associated with reduced risk, compared with lineage 4 strains. CONCLUSIONS This study provides the most comprehensive systematic analysis of the evidence for diversity in bacterial strains that cause TB disease. The results show both geographic and epidemiological differences between strains, which could inform our understanding of the global burden of TB. Our findings also highlight the challenges of collecting the clinical data required to inform TB diagnosis and treatment. We urge future national TB programs and research efforts to prioritize and reinforce clinical data collection in study designs and results dissemination.
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Affiliation(s)
- Kirsten E Wiens
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA
| | - Lauren P Woyczynski
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA
| | - Jorge R Ledesma
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA
| | - Jennifer M Ross
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA
- Departments of Global Health and Medicine, University of Washington, Seattle, WA, USA
| | | | - Amador Goodridge
- Tuberculosis Biomarker Research Unit, Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), City of Knowledge, Panama, Panama
| | - Irfan Ullah
- Gomal Centre of Biochemistry and Biotechnology, Gomal University, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
- Programmatic Management of Drug-Resistant TB Unit, BSL-II TB Culture Laboratory, Mufti Mehmood Memorial Teaching Hospital, Dera Ismail Khan, Khyber Pakhtunkhwa, Pakistan
| | - Barun Mathema
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Joel Fleury Djoba Siawaya
- Unité de Recherche et de Diagnostics Spécialisés, Laboratoire National de Santé Publique, Libreville, Gabon
- Centre Hospitalier Universitaire Mère-Enfant Fondation Jeanne EBORI, Libreville, Gabon
| | - Molly H Biehl
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA
| | - Sarah E Ray
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA
| | - Natalia V Bhattacharjee
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA
| | - Nathaniel J Henry
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA
| | - Robert C Reiner
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA
| | - Hmwe H Kyu
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA
| | - Christopher J L Murray
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA
| | - Simon I Hay
- Institute for Health Metrics and Evaluation, University of Washington, 2301 5th Ave, Suite 600, Seattle, WA, 98121, USA.
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22
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Large-scale genomic analysis shows association between homoplastic genetic variation in Mycobacterium tuberculosis genes and meningeal or pulmonary tuberculosis. BMC Genomics 2018; 19:122. [PMID: 29402222 PMCID: PMC5800017 DOI: 10.1186/s12864-018-4498-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 01/28/2018] [Indexed: 12/03/2022] Open
Abstract
Background Meningitis is the most severe manifestation of tuberculosis. It is largely unknown why some people develop pulmonary TB (PTB) and others TB meningitis (TBM); we examined if the genetic background of infecting M. tuberculosis strains may be relevant. Methods We whole-genome sequenced M. tuberculosis strains isolated from 322 HIV-negative tuberculosis patients from Indonesia and compared isolates from patients with TBM (n = 106) and PTB (n = 216). Using a phylogeny-adjusted genome-wide association method to count homoplasy events we examined phenotype-related changes at specific loci or genes in parallel branches of the phylogenetic tree. Enrichment scores for the TB phenotype were calculated on single nucleotide polymorphism (SNP), gene, and pathway level. Genetic associations were validated in an independent set of isolates. Results Strains belonged to the East-Asian lineage (36.0%), Euro-American lineage (61.5%), and Indo-Oceanic lineage (2.5%). We found no association between lineage and phenotype (Chi-square = 4.556; p = 0.207). Large genomic differences were observed between isolates; the minimum pairwise genetic distance varied from 17 to 689 SNPs. Using the phylogenetic tree, based on 28,544 common variable positions, we selected 54 TBM and 54 PTB isolates in terminal branch sets with distinct phenotypes. Genetic variation in Rv0218, and absence of Rv3343c, and nanK were significantly associated with disease phenotype in these terminal branch sets, and confirmed in the validation set of 214 unpaired isolates. Conclusions Using homoplasy counting we identified genetic variation in three separate genes to be associated with the TB phenotype, including one (Rv0218) which encodes a secreted protein that could play a role in host-pathogen interaction by altering pathogen recognition or acting as virulence effector. Electronic supplementary material The online version of this article (10.1186/s12864-018-4498-z) contains supplementary material, which is available to authorized users.
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23
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Kalsum S, Braian C, Koeken VACM, Raffetseder J, Lindroth M, van Crevel R, Lerm M. The Cording Phenotype of Mycobacterium tuberculosis Induces the Formation of Extracellular Traps in Human Macrophages. Front Cell Infect Microbiol 2017; 7:278. [PMID: 28695112 PMCID: PMC5483443 DOI: 10.3389/fcimb.2017.00278] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 06/06/2017] [Indexed: 12/14/2022] Open
Abstract
The causative agent of tuberculosis, Mycobacterium tuberculosis, shares several characteristics with organisms that produce biofilms during infections. One of these is the ability to form tight bundles also known as cords. However, little is known of the physiological relevance of the cording phenotype. In this study, we investigated whether cord-forming M. tuberculosis induce the formation of macrophage extracellular traps (METs) in human monocyte-derived macrophages. Macrophages have previously been shown to produce extracellular traps in response to various stimuli. We optimized bacterial culturing conditions that favored the formation of the cord-forming phenotype as verified by scanning electron microscopy. Microscopy analysis of METs formation during experimental infection of macrophages with M. tuberculosis revealed that cord-forming M. tuberculosis induced significantly more METs compared to the non-cording phenotype. Deletion of early secreted antigenic target-6 which is an important virulence factor of M. tuberculosis, abrogated the ability of the bacteria to induce METs. The release of extracellular DNA from host cells during infection may represent a defense mechanism against pathogens that are difficult to internalize, including cord-forming M. tuberculosis.
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Affiliation(s)
- Sadaf Kalsum
- Division of Microbiology and Molecular Medicine, Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping UniversityLinköping, Sweden
| | - Clara Braian
- Division of Microbiology and Molecular Medicine, Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping UniversityLinköping, Sweden
| | - Valerie A C M Koeken
- Division of Microbiology and Molecular Medicine, Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping UniversityLinköping, Sweden.,Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical CenterNijmegen, Netherlands
| | - Johanna Raffetseder
- Division of Microbiology and Molecular Medicine, Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping UniversityLinköping, Sweden
| | - Margaretha Lindroth
- Division of Microbiology and Molecular Medicine, Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping UniversityLinköping, Sweden
| | - Reinout van Crevel
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical CenterNijmegen, Netherlands
| | - Maria Lerm
- Division of Microbiology and Molecular Medicine, Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping UniversityLinköping, Sweden
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24
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Grandjean L. Investigating the Pathogen Genomic Determinants of Tuberculosis Transmission. Am J Respir Crit Care Med 2017; 195:1418-1420. [PMID: 28569581 DOI: 10.1164/rccm.201701-0053ed] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Louis Grandjean
- 1 Institute of Child Health University College London London, United Kingdom
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