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Windels EM, Wampande EM, Joloba ML, Boom WH, Goig GA, Cox H, Hella J, Borrell S, Gagneux S, Brites D, Stadler T. HIV co-infection is associated with reduced Mycobacterium tuberculosis transmissibility in sub-Saharan Africa. PLoS Pathog 2024; 20:e1011675. [PMID: 38696531 DOI: 10.1371/journal.ppat.1011675] [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: 09/12/2023] [Revised: 05/14/2024] [Accepted: 04/10/2024] [Indexed: 05/04/2024] Open
Abstract
Persons living with HIV are known to be at increased risk of developing tuberculosis (TB) disease upon infection with Mycobacterium tuberculosis (Mtb). However, it has remained unclear how HIV co-infection affects subsequent Mtb transmission from these patients. Here, we customized a Bayesian phylodynamic framework to estimate the effects of HIV co-infection on the Mtb transmission dynamics from sequence data. We applied our model to four Mtb genomic datasets collected in sub-Saharan African countries with a generalized HIV epidemic. Our results confirm that HIV co-infection is a strong risk factor for developing active TB. Additionally, we demonstrate that HIV co-infection is associated with a reduced effective reproductive number for TB. Stratifying the population by CD4+ T-cell count yielded similar results, suggesting that, in this context, CD4+ T-cell count is not a better predictor of Mtb transmissibility than HIV infection status alone. Together, our genome-based analyses complement observational household contact studies, and more firmly establish the negative association between HIV co-infection and Mtb transmissibility.
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Affiliation(s)
- Etthel M Windels
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | | | - W Henry Boom
- Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio, United States of America
| | - Galo A Goig
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Helen Cox
- University of Cape Town, Cape Town, South Africa
| | - Jerry Hella
- Ifakara Health Institute, Dar es Salaam, Tanzania
| | - 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
| | - Daniela Brites
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Tanja Stadler
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Dekhil N, Mardassi H. On the onset and dispersal of a major MDR TB clone among HIV-negative patients, Tunisia. Antimicrob Resist Infect Control 2024; 13:18. [PMID: 38355557 PMCID: PMC10865554 DOI: 10.1186/s13756-023-01360-7] [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: 07/26/2023] [Accepted: 12/28/2023] [Indexed: 02/16/2024] Open
Abstract
BACKGROUND To carry out a whole genome sequencing (WGS)-based investigation on the emergence and spread of the largest multidrug-resistant tuberculosis (MDR TB) outbreak that has been thriving among HIV-negative patients, Tunisia, since the early 2000s. METHODS We performed phylogeographic analyses and molecular dating based on a WGS dataset representing 68 unique Mycobacterium tuberculosis isolates, covering almost the entire MDR TB outbreak for the time period 2001-2016. RESULTS The data indicate that the ancestor of the MDR TB outbreak emerged in the region of Bizerte, as early as 1974 (95% CI 1951-1985), from where it spread to other regions by 1992 (95% CI 1980-1996). Analysis of a minimum spanning tree based on core genome Multilocus Sequence Typing (cgMLST) uncovered the early spill-over of the fitness-compensated MDR TB strain from the prison into the general population. Indeed, cases with history of incarceration were found to be directly or indirectly linked to up to 22 new outbreak cases (32.35%) among the non-imprisoned population. By around 2008, the MDR TB outbreak strain had acquired additional resistance, leading to an XDR phenotype. CONCLUSIONS WGS allowed refining our understanding of the emergence and evolution of the largest MDR TB outbreak in Tunisia, whose causative strain has been circulating silently for almost 26 years before. Our study lends further support to the critical role of prisons-related cases in the early spread of the outbreak among the general population. The shift to an XDR phenotype of such an epidemic clone prompts an urgent need to undertake drastic control measures.
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Affiliation(s)
- Naira Dekhil
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Pasteur Institute, Tunis, University of Tunis El Manar, Tunis, Tunisia.
| | - Helmi Mardassi
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Pasteur Institute, Tunis, University of Tunis El Manar, Tunis, Tunisia.
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Ilesanmi A, Odeniran OM, Tatsipie L, Osam Duodu E, Ankrah PK. The Role of Proline-Proline-Glutamic Acid (PPE) Proteins in Mycobacterium tuberculosis Virulence: Mechanistic Insights and Therapeutic Implications. Cureus 2024; 16:e51955. [PMID: 38333477 PMCID: PMC10852204 DOI: 10.7759/cureus.51955] [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] [Accepted: 01/09/2024] [Indexed: 02/10/2024] Open
Abstract
For decades, tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), has remained a global health challenge. Central to this issue are the proline-proline-glutamic acid (PPE) proteins, which play a pivotal role in the pathogenesis and persistence of MTB. This article explores the molecular mechanisms of PPE proteins and their roles in facilitating MTB's evasion of the host's immune system while enhancing virulence and transmission. Focusing on the structural and functional aspects of PPE proteins, this review provides a detailed analysis of antigenic variation, a crucial mechanism allowing MTB to elude immune detection. It also probes the genetic diversity of these PPE proteins and their complex interactions with host immunity, offering insights into the challenges they pose for therapeutic development. This review delves into the potential of targeting PPE proteins in novel therapeutic strategies, discussing the prospects of drug and vaccine development. The evidence reviewed in this article underscores the pressing need for innovative approaches to combat TB, especially in the face of increasing drug resistance. Ultimately, this review article highlights the untapped potential of PPE proteins in revolutionizing TB treatment, paving the way for breakthroughs in drug and vaccine development.
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Affiliation(s)
- Ajibola Ilesanmi
- Center for Human Systems Immunology, Duke University, Durham, USA
| | | | - Lenora Tatsipie
- Drug Development, Pharmaceutical Product Development, Wilmington, USA
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Torres Ortiz A, Kendall M, Storey N, Hatcher J, Dunn H, Roy S, Williams R, Williams C, Goldstein RA, Didelot X, Harris K, Breuer J, Grandjean L. Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks. eLife 2023; 12:e84384. [PMID: 37732733 PMCID: PMC10602588 DOI: 10.7554/elife.84384] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 09/20/2023] [Indexed: 09/22/2023] Open
Abstract
Accurate inference of who infected whom in an infectious disease outbreak is critical for the delivery of effective infection prevention and control. The increased resolution of pathogen whole-genome sequencing has significantly improved our ability to infer transmission events. Despite this, transmission inference often remains limited by the lack of genomic variation between the source case and infected contacts. Although within-host genetic diversity is common among a wide variety of pathogens, conventional whole-genome sequencing phylogenetic approaches exclusively use consensus sequences, which consider only the most prevalent nucleotide at each position and therefore fail to capture low-frequency variation within samples. We hypothesized that including within-sample variation in a phylogenetic model would help to identify who infected whom in instances in which this was previously impossible. Using whole-genome sequences from SARS-CoV-2 multi-institutional outbreaks as an example, we show how within-sample diversity is partially maintained among repeated serial samples from the same host, it can transmitted between those cases with known epidemiological links, and how this improves phylogenetic inference and our understanding of who infected whom. Our technique is applicable to other infectious diseases and has immediate clinical utility in infection prevention and control.
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Affiliation(s)
- Arturo Torres Ortiz
- Department of Infectious Diseases, Imperial College LondonLondonUnited Kingdom
- Department of Infection, Immunity and Inflammation, University College LondonLondonUnited Kingdom
| | - Michelle Kendall
- Department of Statistics, University of WarwickCoventryUnited Kingdom
| | - Nathaniel Storey
- Department of Microbiology, Great Ormond Street HospitalLondonUnited Kingdom
| | - James Hatcher
- Department of Microbiology, Great Ormond Street HospitalLondonUnited Kingdom
| | - Helen Dunn
- Department of Microbiology, Great Ormond Street HospitalLondonUnited Kingdom
| | - Sunando Roy
- Department of Infection, Immunity and Inflammation, University College LondonLondonUnited Kingdom
| | | | | | | | - Xavier Didelot
- Department of Statistics, University of WarwickCoventryUnited Kingdom
| | - Kathryn Harris
- Department of Microbiology, Great Ormond Street HospitalLondonUnited Kingdom
- Department of Virology, East & South East London Pathology Partnership, Royal London Hospital, Barts Health NHS TrustLondonUnited Kingdom
| | - Judith Breuer
- Department of Infection, Immunity and Inflammation, University College LondonLondonUnited Kingdom
| | - Louis Grandjean
- Department of Infection, Immunity and Inflammation, University College LondonLondonUnited Kingdom
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Lin H, Zhang R, Wu Z, Li M, Wu J, Shen X, Yang C. Assessing the spatial heterogeneity of tuberculosis in a population with internal migration in China: a retrospective population-based study. Front Public Health 2023; 11:1155146. [PMID: 37325311 PMCID: PMC10266412 DOI: 10.3389/fpubh.2023.1155146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/11/2023] [Indexed: 06/17/2023] Open
Abstract
Background Internal migrants pose a critical threat to eliminating Tuberculosis (TB) in many high-burden countries. Understanding the influential pattern of the internal migrant population in the incidence of tuberculosis is crucial for controlling and preventing the disease. We used epidemiological and spatial data to analyze the spatial distribution of tuberculosis and identify potential risk factors for spatial heterogeneity. Methods We conducted a population-based, retrospective study and identified all incident bacterially-positive TB cases between January 1st, 2009, and December 31st, 2016, in Shanghai, China. We used Getis-Ord Gi* statistics and spatial relative risk methods to explore spatial heterogeneity and identify regions with spatial clusters of TB cases, and then used logistic regression method to estimate individual-level risk factors for notified migrant TB and spatial clusters. A hierarchical Bayesian spatial model was used to identify the attributable location-specific factors. Results Overall, 27,383 bacterially-positive tuberculosis patients were notified for analysis, with 42.54% (11,649) of them being migrants. The age-adjusted notification rate of TB among migrants was much higher than among residents. Migrants (aOR, 1.85; 95%CI, 1.65-2.08) and active screening (aOR, 3.13; 95%CI, 2.60-3.77) contributed significantly to the formation of TB high-spatial clusters. With the hierarchical Bayesian modeling, the presence of industrial parks (RR, 1.420; 95%CI, 1.023-1.974) and migrants (RR, 1.121; 95%CI, 1.007-1.247) were the risk factors for increased TB disease at the county level. Conclusion We identified a significant spatial heterogeneity of tuberculosis in Shanghai, one of the typical megacities with massive migration. Internal migrants play an essential role in the disease burden and the spatial heterogeneity of TB in urban settings. Optimized disease control and prevention strategies, including targeted interventions based on the current epidemiological heterogeneity, warrant further evaluation to fuel the TB eradication process in urban China.
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Affiliation(s)
- Honghua Lin
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Rui Zhang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Zheyuan Wu
- Division of TB and HIV/AIDS Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
- Shanghai Institutes of Preventive Medicine, Shanghai, China
| | - Minjuan Li
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Jiamei Wu
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Xin Shen
- Division of TB and HIV/AIDS Prevention, Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
- Shanghai Institutes of Preventive Medicine, Shanghai, China
| | - Chongguang Yang
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
- School of Public Health, Yale University, New Haven, CT, United States
- Nanshan District Center for Disease Control and Prevention, Shenzhen, Guangdong Province, China
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Drug Resistance of Mycobacterium tuberculosis Based on Whole-Genome Sequencing in the Yi Ethnic Group, Sichuan Province, China. J Immunol Res 2023; 2023:4431209. [PMID: 36726492 PMCID: PMC9886460 DOI: 10.1155/2023/4431209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/11/2022] [Accepted: 11/24/2022] [Indexed: 01/25/2023] Open
Abstract
This study investigated drug-resistant tuberculosis (DR-TB) in the Yi ethnic group. The study was designed to identify risk factors for DR-TB and its relationship with HIV/AIDS. To establish the resistance to antituberculosis drugs, whole-genome sequencing (WGS) was performed using culture-positive Mycobacterium tuberculosis samples collected from people of the Yi ethnic group from March 2019 to March 2021. Baseline characteristics were obtained from China's tuberculosis surveillance system. A total of 116 M. tuberculosis strains were included in the final analysis. Lineage 2.2 (75.86%) was the dominant sublineage, followed by lineage 4.5 (18.97%) and lineage 4.4 (5.17%). The rates of rifampicin-resistant (RR-TB), multidrug-resistant (MDR-TB), and preextensively drug-resistant TB (pre-XDR-TB) were 18.97%, 10.34%, and 6.03%, respectively. Drug-resistant strains were not found in the elderly (age ≥ 65 years). The proportions of RR/MDR-TB and pre-XDR-TB cases among re-treatment patients were higher than those among new patients (χ 2 = 12.155, P = 0.003; χ 2 = 22.495, P = 0.001, respectively). The pre-XDR-TB case proportions were higher among female patients than among males and higher among referred patients (χ 2 = 5.456, P = 0.032; χ 2 = 15.134, P = 0.002, respectively). The rates of RR/MDR-TB and pre-XDR-TB did not differ appreciably among groups with different HIV infection statuses nor lineage populations. DR-TB poses a serious challenge to the Yi ethnic group. Re-treatment patients, women, and referred patients were at high risk of MDR/RR-TB or pre-XDR-TB while HIV and lineage 2 had negligible association with drug resistance. Whole-genome sequencing should be used to guide the design of treatment regimens and to tailor public interventions.
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Chao E, Chato C, Vender R, Olabode AS, Ferreira RC, Poon AFY. Molecular source attribution. PLoS Comput Biol 2022; 18:e1010649. [PMID: 36395093 PMCID: PMC9671344 DOI: 10.1371/journal.pcbi.1010649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Elisa Chao
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Connor Chato
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Reid Vender
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- School of Medicine, Queen’s University, Kingston, Ontario, Canada
| | - Abayomi S. Olabode
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Roux-Cil Ferreira
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Art F. Y. Poon
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- * E-mail:
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Shaik J, Pillay M, Moodley J, Jeena P. Predominance of the Mycobacterium tuberculosis Beijing strain amongst children from a high tuberculosis burden township in South Africa. Tuberculosis (Edinb) 2022; 136:102250. [PMID: 36055152 DOI: 10.1016/j.tube.2022.102250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/18/2022] [Accepted: 08/24/2022] [Indexed: 10/15/2022]
Abstract
The objective was to determine the molecular epidemiology and drug susceptibility patterns of Mycobacterium tuberculosis (MTB) of children and their household contacts (HHC) in Umlazi, a high TB-burden township in South Africa. Sixty eight MTBRifPLUS positive TB-infected children (TIC) (≤14 years) and 111 HHC were enrolled. Drug susceptibility testing (DST) was performed on sputum samples using the proportion method and GenoType® MTBDR. Genotyping of MTB was conducted using IS6110-restriction fragment length polymorphism (RFLP) and spoligotyping. Rifampicin (RIF) susceptibility was observed in 67/68 TIC. GenoType® MTBDRplus and phenotypic DST identified drug resistant strains in five of 16 culture-confirmed TIC. The Beijing strain was identified in six and the F15/LAM4/KZN strain in one of the 13 TIC respectively. Four patients with unknown RFLP strains belonged to spoligoclades S, T1, T3 variant and X2. The S-lineage and an unknown strain were identified in two HHC. MDR-TB and pre-XDR-TB were identified in one HHC each. Household transmission could not be determined as none of the culture-confirmed TIC resided with the six culture-confirmed contacts. The predominance of the hypervirulent Beijing strain and presence of drug-resistant strains must be considered in the implementation of effective TB control strategies and development of efficacious vaccines.
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Affiliation(s)
- Junaid Shaik
- Department of Paediatrics and Child Health, School of Clinical Medicine, College of Health Sciences, University of Kwa-Zulu Natal, South Africa; Faculty of Health Sciences, Durban University of Technology, South Africa; Doctoral Research Office, MANCOSA, Samora Machel Street, Durban, South Africa.
| | - Manormoney Pillay
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, South Africa
| | - Julie Moodley
- Medical Microbiology, National Health Laboratory Service, Inkosi Albert Luthuli Central Hospital, South Africa
| | - Prakash Jeena
- Medical Microbiology, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, South Africa
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Ortiz AT, Kendall M, Storey N, Hatcher J, Dunn H, Roy S, Williams R, Williams C, Goldstein RA, Didelot X, Harris K, Breuer J, Grandjean L. Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.06.07.495142. [PMID: 35702156 PMCID: PMC9196117 DOI: 10.1101/2022.06.07.495142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Accurate inference of who infected whom in an infectious disease outbreak is critical for the delivery of effective infection prevention and control. The increased resolution of pathogen whole-genome sequencing has significantly improved our ability to infer transmission events. Despite this, transmission inference often remains limited by the lack of genomic variation between the source case and infected contacts. Although within-host genetic diversity is common among a wide variety of pathogens, conventional whole-genome sequencing phylogenetic approaches to reconstruct outbreaks exclusively use consensus sequences, which consider only the most prevalent nucleotide at each position and therefore fail to capture low frequency variation within samples. We hypothesized that including within-sample variation in a phylogenetic model would help to identify who infected whom in instances in which this was previously impossible. Using whole-genome sequences from SARS-CoV-2 multi-institutional outbreaks as an example, we show how within-sample diversity is stable among repeated serial samples from the same host, is transmitted between those cases with known epidemiological links, and how this improves phylogenetic inference and our understanding of who infected whom. Our technique is applicable to other infectious diseases and has immediate clinical utility in infection prevention and control.
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Affiliation(s)
| | - Michelle Kendall
- Department of Statistics, University of Warwick, Coventry, CV4 7AL
| | - Nathaniel Storey
- Department of Microbiology, Great Ormond Street Hospital, London WC1N 3JH
| | - James Hatcher
- Department of Microbiology, Great Ormond Street Hospital, London WC1N 3JH
| | - Helen Dunn
- Department of Microbiology, Great Ormond Street Hospital, London WC1N 3JH
| | - Sunando Roy
- Department of Infection, Immunity and Inflammation, Institute of Child Health, UCL, London WC1N 1EH
| | - Rachel Williams
- UCL Genomics, Institute of Child Health, UCL, London WC1N 1EH
| | | | | | - Xavier Didelot
- Department of Statistics, University of Warwick, Coventry, CV4 7AL
| | - Kathryn Harris
- Department of Microbiology, Great Ormond Street Hospital, London WC1N 3JH
- Department of Virology, East South East London Pathology Partnership, Royal London Hospital, Barts Health NHS Trust, London E12ES
| | - Judith Breuer
- Department of Infection, Immunity and Inflammation, Institute of Child Health, UCL, London WC1N 1EH
| | - Louis Grandjean
- Department of Infection, Immunity and Inflammation, Institute of Child Health, UCL, London WC1N 1EH
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Nelson KN, Talarico S, Poonja S, McDaniel CJ, Cilnis M, Chang AH, Raz K, Noboa WS, Cowan L, Shaw T, Posey J, Silk BJ. Mutation of Mycobacterium tuberculosis and Implications for Using Whole-Genome Sequencing for Investigating Recent Tuberculosis Transmission. Front Public Health 2022; 9:790544. [PMID: 35096744 PMCID: PMC8793027 DOI: 10.3389/fpubh.2021.790544] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/09/2021] [Indexed: 11/26/2022] Open
Abstract
Tuberculosis (TB) control programs use whole-genome sequencing (WGS) of Mycobacterium tuberculosis (Mtb) for detecting and investigating TB case clusters. Existence of few genomic differences between Mtb isolates might indicate TB cases are the result of recent transmission. However, the variable and sometimes long duration of latent infection, combined with uncertainty in the Mtb mutation rate during latency, can complicate interpretation of WGS results. To estimate the association between infection duration and single nucleotide polymorphism (SNP) accumulation in the Mtb genome, we first analyzed pairwise SNP differences among TB cases from Los Angeles County, California, with strong epidemiologic links. We found that SNP distance alone was insufficient for concluding that cases are linked through recent transmission. Second, we describe a well-characterized cluster of TB cases in California to illustrate the role of genomic data in conclusions regarding recent transmission. Longer presumed latent periods were inconsistently associated with larger SNP differences. Our analyses suggest that WGS alone cannot be used to definitively determine that a case is attributable to recent transmission. Methods for integrating clinical, epidemiologic, and genomic data can guide conclusions regarding the likelihood of recent transmission, providing local public health practitioners with better tools for monitoring and investigating TB transmission.
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Affiliation(s)
- Kristin N Nelson
- Rollins School of Public Health, Emory University, Atlanta, GA, United States
| | - Sarah Talarico
- Division of Tuberculosis Elimination, National Center for HIV/AIDS (Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome), Viral Hepatitis, STD (Sexually Transmitted Diseases), and Tuberculosis (TB) Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Shameer Poonja
- Los Angeles County Department of Public Health, Los Angeles, CA, United States
| | - Clinton J McDaniel
- Division of Tuberculosis Elimination, National Center for HIV/AIDS (Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome), Viral Hepatitis, STD (Sexually Transmitted Diseases), and Tuberculosis (TB) Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Martin Cilnis
- TB Control Branch, California Department of Public Health, Richmond, CA, United States
| | - Alicia H Chang
- Los Angeles County Department of Public Health, Los Angeles, CA, United States
| | - Kala Raz
- Division of Tuberculosis Elimination, National Center for HIV/AIDS (Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome), Viral Hepatitis, STD (Sexually Transmitted Diseases), and Tuberculosis (TB) Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Wendy S Noboa
- Los Angeles County Department of Public Health, Los Angeles, CA, United States
| | - Lauren Cowan
- Division of Tuberculosis Elimination, National Center for HIV/AIDS (Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome), Viral Hepatitis, STD (Sexually Transmitted Diseases), and Tuberculosis (TB) Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Tambi Shaw
- TB Control Branch, California Department of Public Health, Richmond, CA, United States
| | - James Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS (Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome), Viral Hepatitis, STD (Sexually Transmitted Diseases), and Tuberculosis (TB) Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
| | - Benjamin J Silk
- Division of Tuberculosis Elimination, National Center for HIV/AIDS (Human Immunodeficiency Virus/Acquired Immunodeficiency Syndrome), Viral Hepatitis, STD (Sexually Transmitted Diseases), and Tuberculosis (TB) Prevention, Centers for Disease Control and Prevention, Atlanta, GA, United States
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11
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Yokobori N, López B, Ritacco V. The host-pathogen-environment triad: Lessons learned through the study of the multidrug-resistant Mycobacterium tuberculosis M strain. Tuberculosis (Edinb) 2022; 134:102200. [PMID: 35339874 DOI: 10.1016/j.tube.2022.102200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 03/13/2022] [Accepted: 03/18/2022] [Indexed: 10/18/2022]
Abstract
Multidrug-resistant tuberculosis is one of the major obstacles that face the tuberculosis eradication efforts. Drug-resistant Mycobacterium tuberculosis clones were initially disregarded as a public health threat, because they were assumed to have paid a high fitness cost in exchange of resistance acquisition. However, some genotypes manage to overcome the impact of drug-resistance conferring mutations, retain transmissibility and cause large outbreaks. In Argentina, the HIV-AIDS epidemics fuelled the expansion of the so-called M strain in the early 1990s, which is responsible for the largest recorded multidrug-resistant tuberculosis cluster of Latin America. The aim of this work is to review the knowledge gathered after nearly three decades of multidisciplinary research on epidemiological, microbiological and immunological aspects of this highly successful strain. Collectively, our results indicate that the successful transmission of the M strain could be ascribed to its unaltered virulence, low Th1/Th17 response, a low fitness cost imposed by the resistance conferring mutations and a high resistance to host-related stress. In the early 2000s, the incident cases due to the M strain steadily declined and stabilized in the latest years. Improvements in the management, diagnosis and treatment of multidrug-resistant tuberculosis along with societal factors such as the low domestic and international mobility of the patients affected by this strain probably contributed to the outbreak containment. This stresses the importance of sustaining the public health interventions to avoid the resurgence of this conspicuous multidrug-resistant strain.
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Affiliation(s)
- Noemí Yokobori
- Servicio de Micobacterias, Instituto Nacional de Enfermedades Infecciosas, ANLIS "Dr. C. G. Malbrán", Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina.
| | - Beatriz López
- Departamento de Bacteriología, Instituto Nacional de Enfermedades Infecciosas, ANLIS "Dr. C. G. Malbrán", Buenos Aires, Argentina.
| | - Viviana Ritacco
- Servicio de Micobacterias, Instituto Nacional de Enfermedades Infecciosas, ANLIS "Dr. C. G. Malbrán", Buenos Aires, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas, Argentina.
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Methods Combining Genomic and Epidemiological Data in the Reconstruction of Transmission Trees: A Systematic Review. Pathogens 2022; 11:pathogens11020252. [PMID: 35215195 PMCID: PMC8875843 DOI: 10.3390/pathogens11020252] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 11/17/2022] Open
Abstract
In order to better understand transmission dynamics and appropriately target control and preventive measures, studies have aimed to identify who-infected-whom in actual outbreaks. Numerous reconstruction methods exist, each with their own assumptions, types of data, and inference strategy. Thus, selecting a method can be difficult. Following PRISMA guidelines, we systematically reviewed the literature for methods combing epidemiological and genomic data in transmission tree reconstruction. We identified 22 methods from the 41 selected articles. We defined three families according to how genomic data was handled: a non-phylogenetic family, a sequential phylogenetic family, and a simultaneous phylogenetic family. We discussed methods according to the data needed as well as the underlying sequence mutation, within-host evolution, transmission, and case observation. In the non-phylogenetic family consisting of eight methods, pairwise genetic distances were estimated. In the phylogenetic families, transmission trees were inferred from phylogenetic trees either simultaneously (nine methods) or sequentially (five methods). While a majority of methods (17/22) modeled the transmission process, few (8/22) took into account imperfect case detection. Within-host evolution was generally (7/8) modeled as a coalescent process. These practical and theoretical considerations were highlighted in order to help select the appropriate method for an outbreak.
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Sánchez-Corrales L, Tovar-Aguirre OL, Galeano-Vanegas NF, Castaño Jiménez PA, Martínez-Vega RA, Maldonado-Londoño CE, Hernández-Botero JS, Siller-López F. Phylogenomic analysis and Mycobacterium tuberculosis antibiotic resistance prediction by whole-genome sequencing from clinical isolates of Caldas, Colombia. PLoS One 2021; 16:e0258402. [PMID: 34618869 PMCID: PMC8496870 DOI: 10.1371/journal.pone.0258402] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 09/25/2021] [Indexed: 12/30/2022] Open
Abstract
Mycobacterium tuberculosis (M. tuberculosis) was the pathogen responsible for the highest number of deaths from infectious diseases in the world, before the arrival of the COVID-19 pandemic. Whole genome sequencing (WGS) has contributed to the understanding of genetic diversity, the mechanisms involved in drug resistance and the transmission dynamics of this pathogen. The object of this study is to use WGS for the epidemiological and molecular characterization of M. tuberculosis clinical strains from Chinchiná, Caldas, a small town in Colombia with a high incidence of TB. Sputum samples were obtained during the first semester of 2020 from six patients and cultured in solid Löwenstein-Jensen medium. DNA extraction was obtained from positive culture samples and WGS was performed with the Illumina HiSeq 2500 platform for subsequent bioinformatic analysis. M. tuberculosis isolates were typified as Euro-American lineage 4 with a predominance of the Harlem and LAM sublineages. All samples were proven sensitive to antituberculosis drugs by genomic analysis, although no phenotype antimicrobial tests were performed on the samples, unreported mutations were identified that could require further analysis. The present study provides preliminary data for the construction of a genomic database line and the follow-up of lineages in this region.
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Affiliation(s)
- Lusayda Sánchez-Corrales
- Maestría en Investigación en Enfermedades Infecciosas, Universidad de Santander, Bucaramanga, Santander, Colombia
| | | | - Narmer Fernando Galeano-Vanegas
- Instituto de Investigación en Microbiología y Biotecnología Agroindustrial, Universidad Católica de Manizales, Manizales, Caldas, Colombia
- Departamento de Biotecnología, BIOS Centro de Bioinformática y Biología Computacional, Manizales, Caldas, Colombia
| | | | | | | | - Johan Sebastián Hernández-Botero
- Grupo de Investigación Médica, Escuela de Medicina, Universidad de Manizales, Manizales, Caldas, Colombia
- Grupo de Resistencia Antibiótica de Manizales, Manizales, Caldas, Colombia
| | - Fernando Siller-López
- Programa de Bacteriología, Universidad Católica de Manizales, Manizales, Caldas, Colombia
- Programa de Microbiología, Universidad Libre, Pereira, Risaralda, Colombia
- * E-mail:
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Can miRNA Indicate Risk of Illness after Continuous Exposure to M. tuberculosis? Int J Mol Sci 2021; 22:ijms22073674. [PMID: 33916069 PMCID: PMC8036329 DOI: 10.3390/ijms22073674] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 12/21/2022] Open
Abstract
The role of regulatory elements such as small ncRNAs and their mechanisms are poorly understood in infectious diseases. Tuberculosis is one of the oldest infectious diseases of humans and it is still a challenge to prevent and treat. Control of the infection, as well as its diagnosis, are still complex and current treatments used are linked to several side effects. This study aimed to identify possible biomarkers for tuberculosis by applying NGS techniques to obtain global miRNA expression profiles from 22 blood samples of infected patients with tuberculosis (n = 9), their respective healthy physicians (n = 6) and external healthy individuals as controls (n = 7). Samples were run through a pipeline consisting of differential expression, target genes, gene set enrichment and miRNA-gene network analyses. We observed 153 altered miRNAs, among which only three DEmiRNAs (hsa-let-7g-5p, hsa-miR-486-3p and hsa-miR-4732-5p) were found between the investigated patients and their respective physicians. These DEmiRNAs are suggested to play an important role in granuloma regulation and their immune physiopathology. Our results indicate that miRNAs may be involved in immune modulation by regulating gene expression in cells of the immune system. Our findings encourage the application of miRNAs as potential biomarkers for tuberculosis.
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15
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Wedekind SIS, Shenker NS. Antiviral Properties of Human Milk. Microorganisms 2021; 9:715. [PMID: 33807146 PMCID: PMC8066736 DOI: 10.3390/microorganisms9040715] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/22/2021] [Accepted: 03/25/2021] [Indexed: 12/29/2022] Open
Abstract
Humans have always coexisted with viruses, with both positive and negative consequences. Evolutionary pressure on mammals has selected intrinsic properties of lactation and milk to support the relatively immunocompromised neonate from environmental pathogens, as well as support the normal development of diverse immune responses. Human milk supports both adaptive and innate immunity, with specific constituents that drive immune learning and maturation, and direct protection against microorganisms. Viruses constitute one of the most ancient pressures on human evolution, and yet there is a lack of awareness by both public and healthcare professionals of the complexity of human milk as an adaptive response beyond the production of maternal antibodies. This review identifies and describes the specific antiviral properties of human milk and describes how maternal support of infants through lactation is protective beyond antibodies.
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Affiliation(s)
| | - Natalie S. Shenker
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK;
- Human Milk Foundation, Daniel Hall Building, Rothamsted Institute, Harpenden AL5 2JQ, UK
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16
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Hoffmann J, Chedid C, Ocheretina O, Masetti C, Joseph P, Mabou MM, Mathon JE, Francois EM, Gebelin J, Babin FX, Raskine L, Pape JW. Drug-resistant TB prevalence study in 5 health institutions in Haiti. PLoS One 2021; 16:e0248707. [PMID: 33735224 PMCID: PMC7971505 DOI: 10.1371/journal.pone.0248707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/04/2021] [Indexed: 11/19/2022] Open
Abstract
Objectives Tuberculosis (TB) is the leading infectious cause of death in the world. Multi-drug resistant TB (MDR-TB) is a major public health problem as treatment is long, costly, and associated to poor outcomes. Here, we report epidemiological data on the prevalence of drug-resistant TB in Haiti. Methods This cross-sectional prevalence study was conducted in five health centers across Haiti. Adult, microbiologically confirmed pulmonary TB patients were included. Molecular genotyping (rpoB gene sequencing and spoligotyping) and phenotypic drug susceptibility testing were used to characterize rifampin-resistant MTB isolates detected by Xpert MTB/RIF. Results Between April 2016 and February 2018, 2,777 patients were diagnosed with pulmonary TB by Xpert MTB/RIF screening and positive MTB cultures. A total of 74 (2.7%) patients were infected by a drug-resistant (DR-TB) M. tuberculosis strain. Overall HIV prevalence was 14.1%. Patients with HIV infection were at a significantly higher risk for infection with DR-TB strains compared to pan-susceptible strains (28.4% vs. 13.7%, adjusted odds ratio 2.6, 95% confidence interval 1.5–4.4, P = 0.001). Among the detected DR-TB strains, T1 (29.3%), LAM9 (13.3%), and H3 (10.7%) were the most frequent clades. In comparison with previous spoligotypes studies with data collected in 2000–2002 and in 2008–2009 on both sensitive and resistant strains of TB in Haiti, we observed a significant increase in the prevalence of the drug-resistant MTB Spoligo-International-Types (SIT) 137 (X2 clade: 8.1% vs. 0.3% in 2000–02 and 0.9% in 2008–09, p<0.001), 5 (T1 clade: 6.8% vs 1.9 in 2000–02 and 1.7% in 2008–09, P = 0.034) and 455 (T1 clade: 5.4% vs 1.6% and 1.1%, P = 0.029). Newly detected spoligotypes (SIT 6, 7, 373, 909 and 1624) were also recorded. Conclusion This study describes the genotypic and phenotypic characteristics of DR-TB strains circulating in Haiti from April 2016 to February 2018. Newly detected MTB clades harboring multi-drug resistance patterns among the Haitian population as well as the higher risk of MDR-TB infection in HIV-positive people highlights the epidemiological relevance of these surveillance data. The importance of detecting RIF-resistant patients, as proxy for MDR-TB in peripheral sites via molecular techniques, is particularly important to provide adequate patient case management, prevent the transmission of resistant strains in the community and to contribute to the surveillance of resistant strains.
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Affiliation(s)
- Jonathan Hoffmann
- Fondation Mérieux, Direction Médicale et Scientifique, Lyon, France
- * E-mail:
| | - Carole Chedid
- Fondation Mérieux, Direction Médicale et Scientifique, Lyon, France
- Département de Biologie, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Oksana Ocheretina
- Division of Infectious Diseases, Department of Medicine, Center for Global Health, Weill Cornell Medical College, New York, New York, United States of America
- Les Centres GHESKIO, Port-au-Prince, Haiti
| | - Chloé Masetti
- Fondation Mérieux, Direction des Opérations Internationales, Lyon, France
| | | | | | | | | | - Juliane Gebelin
- Fondation Mérieux, Direction des Opérations Internationales, Lyon, France
| | | | - Laurent Raskine
- Fondation Mérieux, Direction des Opérations Internationales, Lyon, France
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17
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Didelot X, Kendall M, Xu Y, White PJ, McCarthy N. Genomic Epidemiology Analysis of Infectious Disease Outbreaks Using TransPhylo. Curr Protoc 2021; 1:e60. [PMID: 33617114 PMCID: PMC7995038 DOI: 10.1002/cpz1.60] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Comparing the pathogen genomes from several cases of an infectious disease has the potential to help us understand and control outbreaks. Many methods exist to reconstruct a phylogeny from such genomes, which represents how the genomes are related to one another. However, such a phylogeny is not directly informative about transmission events between individuals. TransPhylo is a software tool implemented as an R package designed to bridge the gap between pathogen phylogenies and transmission trees. TransPhylo is based on a combined model of transmission between hosts and pathogen evolution within each host. It can simulate both phylogenies and transmission trees jointly under this combined model. TransPhylo can also reconstruct a transmission tree based on a dated phylogeny, by exploring the space of transmission trees compatible with the phylogeny. A transmission tree can be represented as a coloring of a phylogeny where each color represents a different host of the pathogen, and TransPhylo provides convenient ways to plot these colorings and explore the results. This article presents the basic protocols that can be used to make the most of TransPhylo. © 2021 The Authors. Basic Protocol 1: First steps with TransPhylo Basic Protocol 2: Simulation of outbreak data Basic Protocol 3: Inference of transmission Basic Protocol 4: Exploring the results of inference.
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Affiliation(s)
- Xavier Didelot
- School of Life Sciences and Department of StatisticsUniversity of WarwickUnited Kingdom
| | - Michelle Kendall
- School of Life Sciences and Department of StatisticsUniversity of WarwickUnited Kingdom
| | - Yuanwei Xu
- Center for Computational Biology, Institute of Cancer and Genomic SciencesUniversity of BirminghamUnited Kingdom
| | - Peter J. White
- Department of Infectious Disease Epidemiology, School of Public HealthImperial College LondonUnited Kingdom
- Medical Research Council Centre for Global Infectious Disease Analysis, School of Public HealthImperial College LondonUnited Kingdom
- National Institute for Health Research Health Protection Research Unit in Modelling and Health Economics, School of Public HealthImperial College LondonUnited Kingdom
- Modelling and Economics Unit, National Infection ServicePublic Health EnglandLondonUnited Kingdom
| | - Noel McCarthy
- Warwick Medical SchoolUniversity of WarwickUnited Kingdom
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19
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Acosta F, Norman A, Sambrano D, Batista V, Mokrousov I, Shitikov E, Jurado J, Mayrena M, Luque O, Garay M, Solís L, Muñoz P, Folkvardsen DB, Lillebaek T, Pérez-Lago L, Goodridge A, García de Viedma D. Probable long-term prevalence for a predominant Mycobacterium tuberculosis clone of a Beijing genotype in Colon, Panama. Transbound Emerg Dis 2020; 68:2229-2238. [PMID: 33048439 DOI: 10.1111/tbed.13875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 09/24/2020] [Accepted: 10/06/2020] [Indexed: 11/26/2022]
Abstract
Beijing genotype Mycobacterium tuberculosis strains associate with increased virulence, resistance and/or higher transmission rates. This study describes a specific Beijing strain predominantly identified in the Panamanian province of Colon with one of the highest incidences of tuberculosis in the country. Retrospective mycobacterial interspersed repetitive unit/variable number of tandem repeats analysis of 42 isolates collected between January and August 2018 allowed to identify a cluster (Beijing A) with 17 (40.5%) Beijing isolates. Subsequent prospective strain-specific PCR-based surveillance from September 2019 to March 2020 confirmed the predominance of the Beijing A strain (44.1%) in this province. Whole-genome sequencing revealed higher-than-expected diversity within the cluster, suggesting long-term prevalence of this strain and low number of cases caused by recent transmission. The Beijing A strain belongs to the Asian African 3 (Bmyc13, L2.2.5) branch of the modern Beijing sublineage, with their closest isolates corresponding to cases from Vietnam, probably introduced in Panama between 2000 and 2012.
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Affiliation(s)
- Fermin Acosta
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Anders Norman
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Dilcia Sambrano
- Unidad de Investigaciones de Biomarcadores de Tuberculosis, Centro de Biología Celular y Molecular de Enfermedades-Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), Ciudad del Saber, Panama, Panama
| | - Victoria Batista
- Unidad de Investigaciones de Biomarcadores de Tuberculosis, Centro de Biología Celular y Molecular de Enfermedades-Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), Ciudad del Saber, Panama, Panama
| | - Igor Mokrousov
- Laboratory of Molecular Epidemiology and Evolutionary Genetics, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Egor Shitikov
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | | | | | - Odemaris Luque
- Programa de Control de Tuberculosis, Ministerio de Salud, Colón, Panama
| | - Maybis Garay
- Unidad de Investigaciones de Biomarcadores de Tuberculosis, Centro de Biología Celular y Molecular de Enfermedades-Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), Ciudad del Saber, Panama, Panama
| | - Laura Solís
- Programa de Control de Tuberculosis, Ministerio de Salud, Colón, Panama
| | - Patricia Muñoz
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Centro de Investigación Biomédica en Red Enfermedades Respiratorias (CIBERES), Spain.,Departamento de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Dorte B Folkvardsen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Troels Lillebaek
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark.,Global Health Section, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Laura Pérez-Lago
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Amador Goodridge
- Unidad de Investigaciones de Biomarcadores de Tuberculosis, Centro de Biología Celular y Molecular de Enfermedades-Instituto de Investigaciones Científicas y Servicios de Alta Tecnología (INDICASAT-AIP), Ciudad del Saber, Panama, Panama
| | - Darío García de Viedma
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Centro de Investigación Biomédica en Red Enfermedades Respiratorias (CIBERES), Spain
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20
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Han L, Lu Y, Wang X, Zhang S, Wang Y, Wu F, Zhang W, Wang X, Zhang L. Regulatory role and mechanism of the inhibition of the Mcl-1 pathway during apoptosis and polarization of H37Rv-infected macrophages. Medicine (Baltimore) 2020; 99:e22438. [PMID: 33080678 PMCID: PMC7572003 DOI: 10.1097/md.0000000000022438] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Myeloid cell leukemia-1 (Mcl-1) plays an important role in the clearance of Mycobacterium tuberculosis (MTB) infection. It has the effect of anti-apoptosis, protecting macrophages that have engulfed pathogens and preventing pathogen clearance. Meanwhile, the MAPK signaling pathway plays a significant role in regulating Mcl-1 expression during tuberculosis infection. In the case of latent infection and active infection, the apoptosis and polarization of macrophages have a great influence during MTB infection, so we discussed the effect of Mcl-1 on apoptosis and polarization. Then, further discussed its mechanism. METHODS An infected RAW264.7 macrophage model was established to investigate the regulatory role and mechanism of the Mcl-1 pathway inhibition during apoptosis and polarization of H37Rv infection. First, Mcl-1 protein and mRNA was identified by western blotting and Real-Time Polymerase Chain Reaction (RT-PCR). RAW264.7 macrophage apoptosis was detected by flow cytometry. RT-PCR was utilized to detect Bax, Caspase-3, Cyt-c and Bcl-2 mRNA expression. Next, Then the expression levels of inflammation factors CD86, CD206, iNOS, Fizz1, IL-6, IL-10, TNF-α, and TGF-β was detected by ELISA. SEM was used to observe macrophages phenotype. Finally, Bax, Bcl-2 and Bcl-xl the expression was detected by western blotting. Confocal microscopy was used to analyze mitochondrial membrane potential using the JC-10 kit. RESULTS In this study, we found that inhibiting the Mcl-1 expression signaling pathway led to infection by different virulence Mycobacterium tuberculosis, as well as changes in Mcl-1 protein and mRNA expression. Concomitantly macrophage apoptosis rate also changed, While, two phenotypic states of M1 and M2 appeared in the infected cells. We also found that the mitochondrial pathway was activated, the expression of its related genes Bax, casepase3, and Cyt-c, increased, whereas that of Bcl-2 decreased, and the mitochondrial membrane depolarization function was changed. CONCLUSIONS We found that Mcl-1 affected the apoptosis and polarization of macrophages infected by Mycobacterium tuberculosis, mainly M1 in the early stage and M2 in the later stage. In addition, mitochondria played a crucial role in this process.
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Affiliation(s)
- Ling Han
- Department of Pathophysiology, the Key Laboratories for Xinjiang Endemic and Ethnic Diseases, Medical College of Shihezi University
| | - Yang Lu
- Department of Pathophysiology, the Key Laboratories for Xinjiang Endemic and Ethnic Diseases, Medical College of Shihezi University
| | - Xiaofang Wang
- Department of Pathophysiology, the Key Laboratories for Xinjiang Endemic and Ethnic Diseases, Medical College of Shihezi University
| | - Shujun Zhang
- Department of Pathophysiology, the Key Laboratories for Xinjiang Endemic and Ethnic Diseases, Medical College of Shihezi University
| | - Yingzi Wang
- Department of Pathophysiology, the Key Laboratories for Xinjiang Endemic and Ethnic Diseases, Medical College of Shihezi University
| | - Fang Wu
- Department of Pathophysiology, the Key Laboratories for Xinjiang Endemic and Ethnic Diseases, Medical College of Shihezi University
| | - Wanjiang Zhang
- Department of Pathophysiology, the Key Laboratories for Xinjiang Endemic and Ethnic Diseases, Medical College of Shihezi University
| | - Xinmin Wang
- Department of Urinary Surgery, The First Affiliated Hospital, Medical College of Shihezi University, Shihezi, Xinjiang, China
| | - Le Zhang
- Department of Pathophysiology, the Key Laboratories for Xinjiang Endemic and Ethnic Diseases, Medical College of Shihezi University
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21
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HIV Coinfection Is Associated with Low-Fitness rpoB Variants in Rifampicin-Resistant Mycobacterium tuberculosis. Antimicrob Agents Chemother 2020; 64:AAC.00782-20. [PMID: 32718966 PMCID: PMC7508592 DOI: 10.1128/aac.00782-20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/23/2020] [Indexed: 12/22/2022] Open
Abstract
We analyzed 312 drug-resistant genomes of Mycobacterium tuberculosis isolates collected from HIV-coinfected and HIV-negative TB patients from nine countries with a high tuberculosis burden. We found that rifampicin-resistant M. tuberculosis strains isolated from HIV-coinfected patients carried disproportionally more resistance-conferring mutations in rpoB that are associated with a low fitness in the absence of the drug, suggesting these low-fitness rpoB variants can thrive in the context of reduced host immunity.
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22
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Tilahun M, Shimelis E, Wogayehu T, Assefa G, Wondimagegn G, Mekonnen A, Hailu T, Bobosha K, Aseffa A. Molecular detection of multidrug resistance pattern and associated gene mutations in M. tuberculosis isolates from newly diagnosed pulmonary tuberculosis patients in Addis Ababa, Ethiopia. PLoS One 2020; 15:e0236054. [PMID: 32750053 PMCID: PMC7402498 DOI: 10.1371/journal.pone.0236054] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/27/2020] [Indexed: 12/23/2022] Open
Abstract
INTRODUCTION Multi-drug resistance is a major challenge in the control of tuberculosis. Despite newer modalities for diagnosis and treatment, people are still suffering from this disease. Understanding the common gene mutations conferring rifampicin and isoniazid resistance is crucial for the implementation of effective molecular tools at local and national levels. Hence, this study aimed to evaluate the molecular detection of rifampicin and isoniazid-resistant gene mutations in M.tuberculosis isolates in Addis Ababa, Ethiopia. METHOD Health Center-based cross-sectional study was conducted between January and September 2017 in Addis Ababa, Ethiopia. The collected sputum samples were processed for mycobacterial isolation and Region of difference 9 based polymerase chain reaction for species identification. To characterize the rifampicin and isoniazid-resistant M. tuberculosis isolates, a molecular genetic assay (GenoType MTBDRplus) was used; the assay is based on DNA-STRIP technology. RESULT Culture positivity was confirmed in 82.6% (190/230) of smear-positive newly diagnosed pulmonary tuberculosis cases enrolled in the study. From 190 isolates 93.2% were sensitive for both rifampicin and isoniazid, and 6.8% of the isolates were resistant to at least one of the tested anti-TB drugs. Gene mutations were observed in all studied multidrug resistance-associated gene loci (rpoB, katG, and inhA). Two isolates exhibited heteroresistance, a mutated, as well as wild type sequences, were detected in the respective strains. MDR-TB case was observed in 1.1% (2/190) of the cases. All the MDR-TB cases were positive for HIV and found to have a history of prior hospital admission. CONCLUSION In our finding a relatively high prevalence of any drug resistance was observed and the overall prevalence of multidrug-resistant tuberculosis was 1.1%.The majority of drug-resistant isolates demonstrated common mutations. Heteroresistant strains were detected, signaling the existence of an M.tuberculosis population with variable responses to anti-tuberculosis drugs or of mixed infections.
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Affiliation(s)
- Melaku Tilahun
- Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia
- Department of Biology, Arba Minch University (AMU), College of Natural Sciences, Arba Minch, Ethiopia
- * E-mail: (MT); (ES)
| | - Ezra Shimelis
- Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia
- School of Public Health, College of Health Sciences, Addis Ababa University (AAU), Black Lion Hospital, Addis Ababa, Ethiopia
- * E-mail: (MT); (ES)
| | - Teklu Wogayehu
- Department of Biology, Arba Minch University (AMU), College of Natural Sciences, Arba Minch, Ethiopia
| | - Gebeyehu Assefa
- Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia
| | | | | | - Tsegaye Hailu
- Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia
| | - Kidist Bobosha
- Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia
| | - Abraham Aseffa
- Armauer Hansen Research Institute (AHRI), Addis Ababa, Ethiopia
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Grandjean L, Monteserin J, Gilman R, Pauschardt J, Rokadiya S, Bonilla C, Ritacco V, Vidal JR, Parkhill J, Peacock S, Moore DA, Balloux F. Association between bacterial homoplastic variants and radiological pathology in tuberculosis. Thorax 2020; 75:584-591. [PMID: 32546574 PMCID: PMC7361023 DOI: 10.1136/thoraxjnl-2019-213281] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 03/23/2020] [Accepted: 03/23/2020] [Indexed: 01/09/2023]
Abstract
BACKGROUND Understanding how pathogen genetic factors contribute to pathology in TB could enable tailored treatments to the most pathogenic and infectious strains. New strategies are needed to control drug-resistant TB, which requires longer and costlier treatment. We hypothesised that the severity of radiological pathology on the chest radiograph in TB disease was associated with variants arising independently, multiple times (homoplasies) in the Mycobacterium tuberculosis genome. METHODS We performed whole genome sequencing (Illumina HiSeq2000 platform) on M. tuberculosis isolates from 103 patients with drug-resistant TB in Lima between 2010 and 2013. Variables including age, sex, HIV status, previous TB disease and the percentage of lung involvement on the pretreatment chest radiograph were collected from health posts of the national TB programme. Genomic variants were identified using standard pipelines. RESULTS Two mutations were significantly associated with more widespread radiological pathology in a multivariable regression model controlling for confounding variables (Rv2828c.141, RR 1.3, 95% CI 1.21 to 1.39, p<0.01; rpoC.1040 95% CI 1.77 to 2.16, RR 1.9, p<0.01). The rpoB.450 mutation was associated with less extensive radiological pathology (RR 0.81, 95% CI 0.69 to 0.94, p=0.03), suggestive of a bacterial fitness cost for this mutation in vivo. Patients with a previous episode of TB disease and those between 10 and 30 years of age also had significantly increased radiological pathology. CONCLUSIONS This study is the first to compare the M. tuberculosis genome to radiological pathology on the chest radiograph. We identified two variants significantly positively associated with more widespread radiological pathology and one with reduced pathology. Prospective studies are warranted to determine whether mutations associated with increased pathology also predict the spread of drug-resistant TB.
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Affiliation(s)
- Louis Grandjean
- Department of Medicine, Imperial College London, London, UK .,Laboratorio de Investigacion y Enfermedades Infecciosas, Cayetano Heredia Pervuvian University, Lima, Peru.,Institute of Child Health, UCL Division of Infection and Immunity, London, UK
| | - Joha Monteserin
- Instituto Nacional de Enfermedades Infecciosas INEI-ANLIS, Administración Nacional de Laboratorios e Institutos de Salud Dr Carlos G Malbrán, Buenos Aires, Argentina
| | - Robert Gilman
- Laboratorio de Investigacion y Enfermedades Infecciosas, Cayetano Heredia Pervuvian University, Lima, Peru.,Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, USA
| | - Julia Pauschardt
- Laboratorio de Investigacion y Enfermedades Infecciosas, Cayetano Heredia Pervuvian University, Lima, Peru
| | - Sakib Rokadiya
- Faculty of Medicine, Imperial College London, London, UK
| | - Cesar Bonilla
- Unidad Tecnica de Tuberculosis MDR, Ministerio de Salud, Lima, Peru
| | - Viviana Ritacco
- Instituto Nacional de Enfermedades Infecciosas INEI-ANLIS, Administración Nacional de Laboratorios e Institutos de Salud Dr Carlos G Malbrán, Buenos Aires, Argentina
| | - Julia Rios Vidal
- Unidad Tecnica de Tuberculosis MDR, Ministerio de Salud, Lima, Peru
| | - Julian Parkhill
- Pathogen Genomics Group, Wellcome Trust Sanger Institute, Cambridge, UK
| | - Sharon Peacock
- Faculty of Medicine, University of Cambridge, Cambridge, UK
| | - David Aj Moore
- TB Centre, London School of Hygiene and Tropical Medicine, London, UK
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Gul S, Khalil R, Zaheer Ul-Haq, Mubarak MS. Computational Overview of Mycobacterial Thymidine Monophosphate Kinase. Curr Pharm Des 2020; 26:1676-1681. [PMID: 32242781 DOI: 10.2174/1381612826666200403114152] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/30/2019] [Indexed: 11/22/2022]
Abstract
Tuberculosis (TB) ranks among the diseases with the highest morbidity rate with significantly high prevalence in developing countries. Globally, tuberculosis poses the most substantial burden of mortality. Further, a partially treated tuberculosis patient is worse than untreated; they may lead to standing out as a critical obstacle to global tuberculosis control. The emergence of multi-drug resistant (MDR) and extremely drug-resistant (XDR) strains, and co-infection of HIV further worsen the situation. The present review article discusses validated targets of the bacterial enzyme thymidine monophosphate kinase (TMPK). TMPKMTB enzyme belongs to the nucleoside monophosphate kinases (NMPKs) family. It is involved in phosphorylation of TMP to TDP, and TDP is phosphorylated to TTP. This review highlights structure elucidation of TMP enzymes and their inhibitors study on TMP scaffold, and it also discusses different techniques; including molecular docking, virtual screening, 3DPharmacophore, QSAR for finding anti-tubercular agents.
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Affiliation(s)
- Sana Gul
- Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi-75210, Pakistan
| | - Ruqaiya Khalil
- Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi-75210, Pakistan
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, ICCBS, University of Karachi, Karachi-75210, Pakistan
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25
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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: 14] [Impact Index Per Article: 3.5] [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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26
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Monteserin J, Pérez-Lago L, Yokobori N, Paul R, Rodríguez Maus S, Simboli N, Eldholm V, López B, García de Viedma D, Ritacco V. Trends of Two Epidemic Multidrug-Resistant Strains of Mycobacterium tuberculosis in Argentina Disclosed by Tailored Molecular Strategy. Am J Trop Med Hyg 2020; 101:1308-1311. [PMID: 31628738 DOI: 10.4269/ajtmh.19-0397] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Two Mycobacterium tuberculosis strains-M (sublineage 4.1) and Ra (sublineage 4.3)-have long prevailed in Argentina among patients with multidrug-resistant tuberculosis (MDR-TB). Recently, budget constraints have hampered the surveillance of MDR-TB transmission. Based on whole-genome sequence analysis, we used M- and Ra-specific single nucleotide polymorphisms to tailor two multiplex allele-specific polymerase chain reactions (PCRs), which we applied to 252 stored isolates (95% of all newly diagnosed MDR-TB cases countrywide, 2015-2017). Compared with the latest data available (2007-2009), the M strain has receded (80/324 to 20/252, P < 0.0001), particularly among cross-border migrants (12/58 to 0/53, P = 0.0003) and HIV-infected people (30/97 to 7/74, P = 0.0007), but it still accounts for 4/12 new cases of extensively drug-resistant TB. Differently, the Ra strain remained stable in frequency (39/324 to 33/252) and contributed marginally to the extensive drug-resistance load (1/12). Our novel strategy disclosed recent trends of the two major MDR-TB strains, providing meaningful data to allocate control interventions more efficiently.
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Affiliation(s)
- Johana Monteserin
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.,Instituto Nacional de Enfermedades Infecciosas ANLIS, Buenos Aires, Argentina
| | - Laura Pérez-Lago
- Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Noemí Yokobori
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.,Instituto Nacional de Enfermedades Infecciosas ANLIS, Buenos Aires, Argentina
| | - Roxana Paul
- Instituto Nacional de Enfermedades Infecciosas ANLIS, Buenos Aires, Argentina
| | - Sandra Rodríguez Maus
- Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Norberto Simboli
- Instituto Nacional de Enfermedades Infecciosas ANLIS, Buenos Aires, Argentina
| | | | - Beatriz López
- Instituto Nacional de Enfermedades Infecciosas ANLIS, Buenos Aires, Argentina
| | - Darío García de Viedma
- Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades Respiratorias, CIBERES, Madrid, Spain
| | - Viviana Ritacco
- Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.,Instituto Nacional de Enfermedades Infecciosas ANLIS, Buenos Aires, Argentina
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27
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Singh A, Prasad R, Balasubramanian V, Gupta N. Drug-Resistant Tuberculosis and HIV Infection: Current Perspectives. HIV AIDS (Auckl) 2020; 12:9-31. [PMID: 32021483 PMCID: PMC6968813 DOI: 10.2147/hiv.s193059] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 12/09/2019] [Indexed: 01/26/2023] Open
Abstract
Drug-resistant tuberculosis (DR-TB), including multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB), is considered a potential obstacle for elimination of TB globally. HIV coinfection with M/XDR-TB further complicates the scenario, and is a potential threat with challenging management. Reports have shown poor outcomes and alarmingly high mortality rates among people living with HIV (PLHIV) coinfected with M/XDR-TB. This coinfection is also responsible for all forms of M/XDR-TB epidemics or outbreaks. Better outcomes with reductions in mortality have been reported with concomitant treatment containing antiretroviral drugs for the HIV component and antitubercular drugs for the DR-TB component. Early and rapid diagnosis with genotypic tests, prompt treatment with appropriate regimens based on drug-susceptibility testing, preference for shorter regimens fortified with newer drugs, a patient-centric approach, and strong infection-control measures are all essential components in the management of M/XDR-TB in people living with HIV.
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Affiliation(s)
- Abhijeet Singh
- Department of Pulmonary Medicine, Vallabhbhai Patel Chest Institute, University of Delhi, New Delhi, Delhi110007, India
| | - Rajendra Prasad
- Department of Pulmonary Medicine, Vallabhbhai Patel Chest Institute, University of Delhi, New Delhi, Delhi110007, India
- Department of Pulmonary Medicine, King George Medical University, Lucknow, Uttar Pradesh226003, India
| | - Viswesvaran Balasubramanian
- Department of Pulmonary Medicine, Vallabhbhai Patel Chest Institute, University of Delhi, New Delhi, Delhi110007, India
| | - Nikhil Gupta
- Department of Internal Medicine, Ram Manohar Lohia Institute of Medical Sciences, Lucknow, Uttar Pradesh226010, India
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28
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Pre-detection history of extensively drug-resistant tuberculosis in KwaZulu-Natal, South Africa. Proc Natl Acad Sci U S A 2019; 116:23284-23291. [PMID: 31659018 PMCID: PMC6859317 DOI: 10.1073/pnas.1906636116] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Antimicrobial-resistant (AMR) infections pose a major threat to global public health. Similar to other AMR pathogens, both historical and ongoing drug-resistant tuberculosis (TB) epidemics are characterized by transmission of a limited number of predominant Mycobacterium tuberculosis (Mtb) strains. Understanding how these predominant strains achieve sustained transmission, particularly during the critical period before they are detected via clinical or public health surveillance, can inform strategies for prevention and containment. In this study, we employ whole-genome sequence (WGS) data from TB clinical isolates collected in KwaZulu-Natal, South Africa to examine the pre-detection history of a successful strain of extensively drug-resistant (XDR) TB known as LAM4/KZN, first identified in a widely reported cluster of cases in 2005. We identify marked expansion of this strain concurrent with the onset of the generalized HIV epidemic 12 y prior to 2005, localize its geographic origin to a location in northeastern KwaZulu-Natal ∼400 km away from the site of the 2005 outbreak, and use protein structural modeling to propose a mechanism for how strain-specific rpoB mutations offset fitness costs associated with rifampin resistance in LAM4/KZN. Our findings highlight the importance of HIV coinfection, high preexisting rates of drug-resistant TB, human migration, and pathoadaptive evolution in the emergence and dispersal of this critical public health threat. We propose that integrating whole-genome sequencing into routine public health surveillance can enable the early detection and local containment of AMR pathogens before they achieve widespread dispersal.
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29
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Saldanha N, Runwal K, Ghanekar C, Gaikwad S, Sane S, Pujari S. High prevalence of multi drug resistant tuberculosis in people living with HIV in Western India. BMC Infect Dis 2019; 19:391. [PMID: 31068153 PMCID: PMC6507020 DOI: 10.1186/s12879-019-4042-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 04/29/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Most studies assessing drug resistant tuberculosis (DRTB) in human immunodeficiency virus (HIV) co-infected patients in India have used conventional culture- based systems to diagnose DRTB that have a longer turnaround time leading to risk of amplification of resistance to an empirical regimen. We determined the prevalence of DRTB amongst people living with HIV (PLHIV) using the line probe assay and determined risk factors associated with the presence of multi drug resistant tuberculosis (MDRTB). METHODS A Cross-sectional study was undertaken at Poona Hospital and Research Center (PHRC) and the Institute of Infectious Diseases, two tertiary level private care centers in Pune, India. Consenting PLHIV with confirmed Pulmonary TB (PTB) and/or extra-pulmonary TB (EPTB) diagnosed based on detection of Mycobacterium TB by line probe assay (Geno Type MTBDRplus version 2) on clinical specimens were included. Those with documented past history of DRTB were excluded. Resistance against anti-TB drugs was determined by the same assay. The prevalence of any form of drug resistant TB (DRTB), MDRTB, Rifampicin resistant TB (RRTB) and Isoniazid (INH) mono-resistant TB were determined as the proportion of these amongst all included PLHIV-TB. A multivariate analysis was conducted to determine risk factors that were statistically associated with MDRTB, DRTB, RRTB and INH mono-resistant TB. RESULTS Two hundred PLHIV were recruited. The prevalence (95% CI) of MDRTB, INH mono- resistance and RR resistance was 12.5% (7.9-17.1%), 9% (6.9-11.2%) and 2.5% (1.4-3.6%), respectively. The prevalence (95% CI) of MDRTB among new and relapsed patients was 8.8% (6.5-11.1%) and 23.1% (17.2-28.9%), respectively. Tuberculosis relapse was the only factor significantly associated with MDRTB, DRTB and INH mono-resistant TB. CONCLUSION We document a high prevalence of drug resistance to anti-TB drugs including MDRTB among PLHIV in our setting using Geno Type MTBDRplus directly on clinical specimens. This validates the WHO recommendation of performing routine rapid molecular resistance testing prior to initiating anti-TB treatment among all PLHIV with presumptive TB. Using rapid molecular testing especially Geno Type MTBDRplus (that detects resistance to INH and Rifampicin simultaneously) reduces the turn-around time helping in optimizing treatment.
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Affiliation(s)
- Neil Saldanha
- Consultant Biostatistician, Poona Hospital and Research Center, Pune, India.
| | - Kiran Runwal
- Consultant Biostatistician, Poona Hospital and Research Center, Pune, India
| | - Charulata Ghanekar
- Consultant Biostatistician, Poona Hospital and Research Center, Pune, India
| | | | - Shrivallabh Sane
- Consultant Biostatistician, Poona Hospital and Research Center, Pune, India
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30
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Nikolayevskyy V, Niemann S, Anthony R, van Soolingen D, Tagliani E, Ködmön C, van der Werf MJ, Cirillo DM. Role and value of whole genome sequencing in studying tuberculosis transmission. Clin Microbiol Infect 2019; 25:1377-1382. [PMID: 30980928 DOI: 10.1016/j.cmi.2019.03.022] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 03/16/2019] [Accepted: 03/19/2019] [Indexed: 11/15/2022]
Abstract
BACKGROUND Tuberculosis (TB) remains a serious public health threat worldwide. Theoretically ultimate resolution of whole genome sequencing (WGS) for Mycobacterium tuberculosis complex (MTBC) strain classification makes this technology very attractive for epidemiological investigations. OBJECTIVES To summarize the evidence available in peer-reviewed publications on the role and place of WGS in detection of TB transmission. SOURCES A total of 69 peer-reviewed publications identified in Pubmed database. CONTENT Evidence from >30 publications suggests that a cut-off value of fewer than six single nucleotide polymorphisms between strains efficiently excludes cases that are not the result of recent transmission and could be used for the identification of drug-sensitive isolates involved in direct human-to-human TB transmission. Sensitivity of WGS to identify epidemiologically linked isolates is high, reaching 100% in eight studies with specificity (17%-95%) highly dependent on the settings. Drug resistance and specific phylogenetic lineages may be associated with accelerated mutation rates affecting genetic distances. WGS can be potentially used to distinguish between true relapses and re-infections but in high-incidence low-diversity settings this would require consideration of epidemiological links and minority alleles. Data from four studies looking into within-host diversity highlight a need for developing criteria for acceptance or rejection of WGS relatedness results depending on the proportion of minority alleles. IMPLICATIONS WGS will potentially allow for more targeted public health actions preventing unnecessary investigations of false clusters. Consensus on standardization of raw data quality control processing criteria, analytical pipelines and reporting language is yet to be reached.
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Affiliation(s)
- V Nikolayevskyy
- Public Health England, London, UK; Imperial College, London, UK.
| | - S Niemann
- Molecular and Experimental Mycobacteriology, National Reference Centre for Mycobacteria, Research Centre, Borstel, Germany; German Centre for Infection Research, Borstel site, Germany
| | - R Anthony
- Tuberculosis Reference Laboratory, Infectious Diseases Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - D van Soolingen
- Tuberculosis Reference Laboratory, Infectious Diseases Research, Diagnostics and Laboratory Surveillance, National Institute for Public Health and the Environment, Bilthoven, the Netherlands
| | - E Tagliani
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - C Ködmön
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - M J van der Werf
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - D M Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
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31
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Transmission of drug-resistant tuberculosis in HIV-endemic settings. THE LANCET. INFECTIOUS DISEASES 2018; 19:e77-e88. [PMID: 30554996 DOI: 10.1016/s1473-3099(18)30537-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 08/10/2018] [Accepted: 08/10/2018] [Indexed: 12/17/2022]
Abstract
The emergence and expansion of the multidrug-resistant tuberculosis epidemic is a threat to the global control of tuberculosis. Multidrug-resistant tuberculosis is the result of the selection of resistance-conferring mutations during inadequate antituberculosis treatment. However, HIV has a profound effect on the natural history of tuberculosis, manifesting in an increased rate of disease progression, leading to increased transmission and amplification of multidrug-resistant tuberculosis. Interventions specific to HIV-endemic areas are urgently needed to block tuberculosis transmission. These interventions should include a combination of rapid molecular diagnostics and improved chemotherapy to shorten the duration of infectiousness, implementation of infection control measures, and active screening of multidrug-resistant tuberculosis contacts, with prophylactic regimens for individuals without evidence of disease. Development and improvement of the efficacy of interventions will require a greater understanding of the factors affecting the transmission of multidrug-resistant tuberculosis in HIV-endemic settings, including population-based molecular epidemiology studies. In this Series article, we review what we know about the transmission of multidrug-resistant tuberculosis in settings with high burdens of HIV and define the research priorities required to develop more effective interventions, to diminish ongoing transmission and the amplification of drug resistance.
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32
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Balloux F, Brønstad Brynildsrud O, van Dorp L, Shaw LP, Chen H, Harris KA, Wang H, Eldholm V. From Theory to Practice: Translating Whole-Genome Sequencing (WGS) into the Clinic. Trends Microbiol 2018; 26:1035-1048. [PMID: 30193960 PMCID: PMC6249990 DOI: 10.1016/j.tim.2018.08.004] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Revised: 07/20/2018] [Accepted: 08/10/2018] [Indexed: 12/12/2022]
Abstract
Hospitals worldwide are facing an increasing incidence of hard-to-treat infections. Limiting infections and providing patients with optimal drug regimens require timely strain identification as well as virulence and drug-resistance profiling. Additionally, prophylactic interventions based on the identification of environmental sources of recurrent infections (e.g., contaminated sinks) and reconstruction of transmission chains (i.e., who infected whom) could help to reduce the incidence of nosocomial infections. WGS could hold the key to solving these issues. However, uptake in the clinic has been slow. Some major scientific and logistical challenges need to be solved before WGS fulfils its potential in clinical microbial diagnostics. In this review we identify major bottlenecks that need to be resolved for WGS to routinely inform clinical intervention and discuss possible solutions.
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Affiliation(s)
- Francois Balloux
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK; These authors made equal contributions.
| | - Ola Brønstad Brynildsrud
- Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, Oslo 0456, Norway; These authors made equal contributions
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK; These authors made equal contributions
| | - Liam P Shaw
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK
| | - Hongbin Chen
- UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK; Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Kathryn A Harris
- Great Ormond Street Hospital NHS Foundation Trust, Department of Microbiology, Virology & Infection Prevention & Control, London WC1N 3JH, UK
| | - Hui Wang
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing, 100044, China
| | - Vegard Eldholm
- Infectious Diseases and Environmental Health, Norwegian Institute of Public Health, Lovisenberggata 8, Oslo 0456, Norway
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33
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Ayabina D, Ronning JO, Alfsnes K, Debech N, Brynildsrud OB, Arnesen T, Norheim G, Mengshoel AT, Rykkvin R, Dahle UR, Colijn C, Eldholm V. Genome-based transmission modelling separates imported tuberculosis from recent transmission within an immigrant population. Microb Genom 2018; 4. [PMID: 30216147 PMCID: PMC6249437 DOI: 10.1099/mgen.0.000219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In many countries the incidence of tuberculosis (TB) is low and is largely shaped by immigrant populations from high-burden countries. This is the case in Norway, where more than 80 % of TB cases are found among immigrants from high-incidence countries. A variable latent period, low rates of evolution and structured social networks make separating import from within-border transmission a major conundrum to TB control efforts in many low-incidence countries. Clinical Mycobacterium tuberculosis isolates belonging to an unusually large genotype cluster associated with people born in the Horn of Africa have been identified in Norway over the last two decades. We modelled transmission based on whole-genome sequence data to estimate infection times for individual patients. By contrasting these estimates with time of arrival in Norway, we estimate on a case-by-case basis whether patients were likely to have been infected before or after arrival. Independent import was responsible for the majority of cases, but we estimate that about one-quarter of the patients had contracted TB in Norway. This study illuminates the transmission dynamics within an immigrant community. Our approach is broadly applicable to many settings where TB control programmes can benefit from understanding when and where patients acquired TB.
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Affiliation(s)
- Diepreye Ayabina
- 1Department of Mathematics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Janne O Ronning
- 2Infection Control and Environmental Health, Norwegian Institute of Public Health, Lovisengerggata 8, 0456 Oslo, Norway
| | - Kristian Alfsnes
- 2Infection Control and Environmental Health, Norwegian Institute of Public Health, Lovisengerggata 8, 0456 Oslo, Norway
| | - Nadia Debech
- 2Infection Control and Environmental Health, Norwegian Institute of Public Health, Lovisengerggata 8, 0456 Oslo, Norway
| | - Ola B Brynildsrud
- 2Infection Control and Environmental Health, Norwegian Institute of Public Health, Lovisengerggata 8, 0456 Oslo, Norway
| | - Trude Arnesen
- 2Infection Control and Environmental Health, Norwegian Institute of Public Health, Lovisengerggata 8, 0456 Oslo, Norway
| | - Gunnstein Norheim
- 2Infection Control and Environmental Health, Norwegian Institute of Public Health, Lovisengerggata 8, 0456 Oslo, Norway
| | - Anne-Torunn Mengshoel
- 2Infection Control and Environmental Health, Norwegian Institute of Public Health, Lovisengerggata 8, 0456 Oslo, Norway
| | - Rikard Rykkvin
- 2Infection Control and Environmental Health, Norwegian Institute of Public Health, Lovisengerggata 8, 0456 Oslo, Norway
| | - Ulf R Dahle
- 2Infection Control and Environmental Health, Norwegian Institute of Public Health, Lovisengerggata 8, 0456 Oslo, Norway
| | - Caroline Colijn
- 1Department of Mathematics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Vegard Eldholm
- 2Infection Control and Environmental Health, Norwegian Institute of Public Health, Lovisengerggata 8, 0456 Oslo, Norway
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Direct Whole-Genome Sequencing of Sputum Accurately Identifies Drug-Resistant Mycobacterium tuberculosis Faster than MGIT Culture Sequencing. J Clin Microbiol 2018; 56:JCM.00666-18. [PMID: 29848567 PMCID: PMC6062781 DOI: 10.1128/jcm.00666-18] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 05/25/2018] [Indexed: 11/20/2022] Open
Abstract
The current methods available to diagnose antimicrobial-resistant Mycobacterium tuberculosis infections require a positive culture or only test a limited number of resistance-associated mutations. A rapid accurate identification of antimicrobial resistance enables the prompt initiation of effective treatment. Here, we determine the utility of whole-genome sequencing (WGS) of M. tuberculosis directly from routinely obtained diagnostic sputum samples to provide a comprehensive resistance profile compared to that from mycobacterial growth indicator tube (MGIT) WGS. We sequenced M. tuberculosis from 43 sputum samples by targeted DNA enrichment using the Agilent SureSelectXT kit, and 43 MGIT positive samples from each participant. Thirty two (74%) sputum samples and 43 (100%) MGIT samples generated whole genomes. The times to antimicrobial resistance profiles and concordance were compared with Xpert MTB/RIF and phenotypic resistance testing from cultures of the same samples. Antibiotic susceptibility could be predicted from WGS of sputum within 5 days of sample receipt and up to 24 days earlier than WGS from MGIT culture and up to 31 days earlier than phenotypic testing. Direct sputum results could be reduced to 3 days with faster hybridization and if only regions encoding drug resistance are sequenced. We show that direct sputum sequencing has the potential to provide comprehensive resistance detection significantly faster than MGIT whole-genome sequencing or phenotypic testing of resistance from cultures in a clinical setting. This improved turnaround time enables prompt appropriate treatment with associated patient and health service benefits. Improvements in sample preparation are necessary to ensure comparable sensitivities and complete resistance profile predictions in all cases.
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Abbate JL, Ezenwa VO, Guégan JF, Choisy M, Nacher M, Roche B. Disentangling complex parasite interactions: Protection against cerebral malaria by one helminth species is jeopardized by co-infection with another. PLoS Negl Trop Dis 2018; 12:e0006483. [PMID: 29746467 PMCID: PMC5963812 DOI: 10.1371/journal.pntd.0006483] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 05/22/2018] [Accepted: 04/30/2018] [Indexed: 12/24/2022] Open
Abstract
Multi-species interactions can often have non-intuitive consequences. However, the study of parasite interactions has rarely gone beyond the effects of pairwise combinations of species, and the outcomes of multi-parasite interactions are poorly understood. We investigated the effects of co-infection by four gastrointestinal helminth species on the development of cerebral malaria among Plasmodium falciparum-infected patients. We characterized associations among the helminth parasite infra-community, and then tested for independent (direct) and co-infection dependent (indirect) effects of helminths on cerebral malaria risk. We found that infection by Ascaris lumbricoides and Trichuris trichiura were both associated with direct reductions in cerebral malaria risk. However, the benefit of T. trichiura infection was halved in the presence of hookworm, revealing a strong indirect effect. Our study suggests that the outcome of interactions between two parasite species can be significantly modified by a third, emphasizing the critical role that parasite community interactions play in shaping infection outcomes.
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Affiliation(s)
- Jessica L Abbate
- UMMISCO, IRD / Sorbonne Université, Bondy, France.,MIVEGEC, IRD, CNRS, Université Montpellier, Montpellier, France
| | - Vanessa O Ezenwa
- Odum School of Ecology and Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States of America
| | | | - Marc Choisy
- MIVEGEC, IRD, CNRS, Université Montpellier, Montpellier, France.,Oxford University Clinical Research Unit, Hanoi, Vietnam
| | - Mathieu Nacher
- CIC INSERM 1424, Centre Hospitalier de Cayenne, Cayenne, French Guiana.,EA3593, Ecosystèmes Amazoniens et Pathologie Tropicale, Université de Guyane, Cayenne, French Guiana
| | - Benjamin Roche
- UMMISCO, IRD / Sorbonne Université, Bondy, France.,MIVEGEC, IRD, CNRS, Université Montpellier, Montpellier, France.,Departamento de Etología, Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
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Yokobori N, López B, Monteserin J, Paul R, Von Groll A, Martin A, Marquina-Castillo B, Palomino JC, Hernández-Pando R, Sasiain MDC, Ritacco V. Performance of a highly successful outbreak strain of Mycobacterium tuberculosis in a multifaceted approach to bacterial fitness assessment. Int J Med Microbiol 2018; 308:349-357. [DOI: 10.1016/j.ijmm.2018.01.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 12/19/2017] [Accepted: 01/23/2018] [Indexed: 10/18/2022] Open
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Major genotype families and epidemic clones of Mycobacterium tuberculosis in Omsk region, Western Siberia, Russia, marked by a high burden of tuberculosis-HIV coinfection. Tuberculosis (Edinb) 2017. [PMID: 29523319 DOI: 10.1016/j.tube.2017.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This population-based study characterized Mycobacterium tuberculosis isolates from HIV-positive and HIV-negative tuberculosis (TB) patients in the Omsk region in Western Siberia, Russia. We sought to gain insight into the major genotype families and epidemic and endemic clones of M. tuberculosis in the area with a high burden and adverse trend of TB/HIV coinfection. The study collection included M. tuberculosis isolates from 207 newly-diagnosed patients with pulmonary TB; 55 (26.5%) of patients were HIV-infected. The M. tuberculosis isolates were subjected to drug susceptibility testing and molecular typing based on spoligotyping and analysis of the robust genotype and cluster-specific markers. Patients with disseminated TB disease were more prevalent in the HIV-positive (34.5%) than in the HIV-negative group (4.6%) (P < .001). The Beijing genotype was predominant (62.3% of isolates), and its major subtypes were 94-32-cluster (Central Asian/Russian strain, n = 80) and B0/W148-cluster (successful Russian strain, n = 28). The main non-Beijing families were represented by Latin-American Mediterranean (14.5%), T family (11.1%), Ural (5.8%), and Haarlem (3.9%). Under multivariate logistic regression analysis, MDR was associated with Beijing genotype and not associated with HIV coinfection status (P < .001). Beijing genotype isolates were found more frequently in TB/HIV patients than in TB HIV-negative patients (74.5% versus 57.9%, respectively; P = .031). The non-Beijing genotypes were mainly drug susceptible except for the drug-resistant Ural SIT262 isolates. To summarize, the alarming situation in the Omsk region in Siberia regarding TB/HIV coinfection is seriously influenced by the active circulation of M. tuberculosis isolates of MDR-associated Beijing genotype. Among the non-Beijing families, emergence of the drug-resistant Ural family strains of spoligotype SIT262 warrants attention.
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Koch AS, Brites D, Stucki D, Evans JC, Seldon R, Heekes A, Mulder N, Nicol M, Oni T, Mizrahi V, Warner DF, Parkhill J, Gagneux S, Martin DP, Wilkinson RJ. The Influence of HIV on the Evolution of Mycobacterium tuberculosis. Mol Biol Evol 2017; 34:1654-1668. [PMID: 28369607 PMCID: PMC5455964 DOI: 10.1093/molbev/msx107] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
HIV significantly affects the immunological environment during tuberculosis coinfection, and therefore may influence the selective landscape upon which M. tuberculosis evolves. To test this hypothesis whole genome sequences were determined for 169 South African M. tuberculosis strains from HIV-1 coinfected and uninfected individuals and analyzed using two Bayesian codon-model based selection analysis approaches: FUBAR which was used to detect persistent positive and negative selection (selection respectively favoring and disfavoring nonsynonymous substitutions); and MEDS which was used to detect episodic directional selection specifically favoring nonsynonymous substitutions within HIV-1 infected individuals. Among the 25,251 polymorphic codon sites analyzed, FUBAR revealed that 189-fold more were detectably evolving under persistent negative selection than were evolving under persistent positive selection. Three specific codon sites within the genes celA2b, katG, and cyp138 were identified by MEDS as displaying significant evidence of evolving under directional selection influenced by HIV-1 coinfection. All three genes encode proteins that may indirectly interact with human proteins that, in turn, interact functionally with HIV proteins. Unexpectedly, epitope encoding regions were enriched for sites displaying weak evidence of directional selection influenced by HIV-1. Although the low degree of genetic diversity observed in our M. tuberculosis data set means that these results should be interpreted carefully, the effects of HIV-1 on epitope evolution in M. tuberculosis may have implications for the design of M. tuberculosis vaccines that are intended for use in populations with high HIV-1 infection rates.
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Affiliation(s)
- Anastasia S Koch
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, and Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Daniela Brites
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - David Stucki
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Joanna C Evans
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Ronnett Seldon
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Alexa Heekes
- Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Nicola Mulder
- Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Mark Nicol
- University of Cape Town, and National Health Laboratory Service, Cape Town, South Africa
| | - Tolu Oni
- Division of Public Health Medicine, School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa.,The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Valerie Mizrahi
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Digby F Warner
- Molecular Mycobacteriology Research Unit, Institute of Infectious Disease and Molecular Medicine and Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Julian Parkhill
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Darren P Martin
- Division of Computational Biology, Department of Integrated Biology Sciences and Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Disease and Molecular Medicine, and Department of Medicine, University of Cape Town, Cape Town, South Africa.,Department of Medicine, Imperial College, London, United Kingdom.,Francis Crick Institute, London, United Kingdom
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Yang G, Luo T, Sun C, Yuan J, Peng X, Zhang C, Zhai X, Bao L. PPE27 in Mycobacterium smegmatis Enhances Mycobacterial Survival and Manipulates Cytokine Secretion in Mouse Macrophages. J Interferon Cytokine Res 2017; 37:421-431. [PMID: 28829246 DOI: 10.1089/jir.2016.0126] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Guoping Yang
- Laboratory of Infection and Immunity, School of Basic Medical Science, West China Center of Medical Sciences, Sichuan University, Chengdu, China
| | - Tao Luo
- Laboratory of Infection and Immunity, School of Basic Medical Science, West China Center of Medical Sciences, Sichuan University, Chengdu, China
| | - Changfeng Sun
- Laboratory of Infection and Immunity, School of Basic Medical Science, West China Center of Medical Sciences, Sichuan University, Chengdu, China
| | - Jinning Yuan
- Laboratory of Infection and Immunity, School of Basic Medical Science, West China Center of Medical Sciences, Sichuan University, Chengdu, China
| | - Xuan Peng
- Laboratory of Infection and Immunity, School of Basic Medical Science, West China Center of Medical Sciences, Sichuan University, Chengdu, China
| | - Chunxi Zhang
- Laboratory of Infection and Immunity, School of Basic Medical Science, West China Center of Medical Sciences, Sichuan University, Chengdu, China
| | - Xiaoqian Zhai
- Laboratory of Infection and Immunity, School of Basic Medical Science, West China Center of Medical Sciences, Sichuan University, Chengdu, China
| | - Lang Bao
- Laboratory of Infection and Immunity, School of Basic Medical Science, West China Center of Medical Sciences, Sichuan University, Chengdu, China
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40
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Picard C, Dallot S, Brunker K, Berthier K, Roumagnac P, Soubeyrand S, Jacquot E, Thébaud G. Exploiting Genetic Information to Trace Plant Virus Dispersal in Landscapes. ANNUAL REVIEW OF PHYTOPATHOLOGY 2017; 55:139-160. [PMID: 28525307 DOI: 10.1146/annurev-phyto-080516-035616] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
During the past decade, knowledge of pathogen life history has greatly benefited from the advent and development of molecular epidemiology. This branch of epidemiology uses information on pathogen variation at the molecular level to gain insights into a pathogen's niche and evolution and to characterize pathogen dispersal within and between host populations. Here, we review molecular epidemiology approaches that have been developed to trace plant virus dispersal in landscapes. In particular, we highlight how virus molecular epidemiology, nourished with powerful sequencing technologies, can provide novel insights at the crossroads between the blooming fields of landscape genetics, phylogeography, and evolutionary epidemiology. We present existing approaches and their limitations and contributions to the understanding of plant virus epidemiology.
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Affiliation(s)
- Coralie Picard
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Sylvie Dallot
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Kirstyn Brunker
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, G12 8QQ, United Kingdom
| | | | - Philippe Roumagnac
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | | | - Emmanuel Jacquot
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
| | - Gaël Thébaud
- UMR BGPI, INRA, Montpellier SupAgro, CIRAD, 34398, Montpellier Cedex 5, France;
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41
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Rifat D, Campodónico VL, Tao J, Miller JA, Alp A, Yao Y, Karakousis PC. In vitro and in vivo fitness costs associated with Mycobacterium tuberculosis RpoB mutation H526D. Future Microbiol 2017; 12:753-765. [PMID: 28343421 DOI: 10.2217/fmb-2017-0022] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM There is controversy regarding the potential fitness costs of rifampicin (RIF) resistance-conferring mutations in the Mycobacterium tuberculosis (Mtb) rpoB gene. We characterized the pathogenicity of an Mtb RpoB H526D mutant. MATERIALS & METHODS A mutant containing the RpoB H526D mutation was isolated from wild-type Mtb grown on RIF-containing plates and complemented for determination of in vitro and in vivo fitness costs. RESULTS The RpoB H526D mutant showed reduced survival relative to control strains during progressive hypoxia and delayed growth following resuscitation from nutrient starvation (p < 0.05), which was associated with reduced expression of the resuscitation-promoting factor genes rpfB, rpfC and rpfE. Relative to the isogenic wild-type strain, the mutant showed significantly attenuated growth and long-term survival as well as reduced inflammation in mouse lungs. Conclusion & future perspective: Our data suggest that RpoB H526D mutation confers a fitness cost during growth-limiting conditions in vitro and in mouse lungs.
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Affiliation(s)
- Dalin Rifat
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore MD 21287, USA
| | - Victoria L Campodónico
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore MD 21287, USA
| | - Jing Tao
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore MD 21287, USA.,Department of Microbiology & Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - James A Miller
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore MD 21287, USA
| | - Alpaslan Alp
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore MD 21287, USA.,Department of Medical Microbiology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Yufeng Yao
- Department of Microbiology & Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Petros C Karakousis
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore MD 21287, USA.,Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore MD 21205, USA
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42
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Scott L, da Silva P, Boehme CC, Stevens W, Gilpin CM. Diagnosis of opportunistic infections: HIV co-infections - tuberculosis. Curr Opin HIV AIDS 2017; 12:129-138. [PMID: 28059955 PMCID: PMC6024079 DOI: 10.1097/coh.0000000000000345] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PURPOSE OF REVIEW Tuberculosis (TB) incidence has declined ∼1.5% annually since 2000, but continued to affect 10.4 million individuals in 2015, with 1/3 remaining undiagnosed or underreported. The diagnosis of TB among those co-infected with HIV is challenging as TB remains the leading cause of death in such individuals. Accurate and rapid diagnosis of active TB will avert mortality in both adults and children, reduce transmission, and assist in timeous decisions for antiretroviral therapy initiation. This review describes advances in diagnosing TB, especially among HIV co-infected individuals, highlights national program's uptake, and impact on patient care. RECENT FINDINGS The TB diagnostic landscape has been transformed over the last 5 years. Molecular diagnostics such as Xpert MTB/RIF, which simultaneously detects Mycobacterium tuberculosis (MTB) resistance to rifampicin, has revolutionized TB control programs. WHO endorsed the use of Xpert MTB/RIF in 2010 for use in HIV/TB co-infected patients, and later in 2013 for use as the initial diagnostic test for all adults and children with signs and symptoms of pulmonary TB. Line probe assays (LPAs) are recommended for the detection of rifampicin and isoniazid resistance in sputum smear-positive specimens and mycobacterial cultures. A second-line line probe assay has been recommended for the diagnosis of extensively drug-resistant (XDR)-TB Assays such as the urine lateral flow (LF)-lipoarabinomannan (LAM), can be used at the point of care (POC) and have a niche role to supplement the diagnosis of TB in seriously ill HIV-infected, hospitalized patients with low CD4 cell counts of less than 100 cells/μl. Polyvalent platforms such as the m2000 (Abbott Molecular) and GeneXpert (Cepheid) offer potential for integration of HIV and TB testing services. While the Research and Development (R&D) pipeline appears to be rich at first glance, there are actually few leads for true POC tests that would allow for earlier TB diagnosis or rapid, comprehensive drug susceptibility testing, especially when considering the very high attrition rates observed between biomarker discovery and product market entry. SUMMARY In this review, we describe diagnostic strategies specifically for HIV and TB co-infected individuals. Molecular diagnostics in particular within the past 5 years have revolutionized and 'disrupted' this field. They lend themselves to integration of services with platforms capable of polyvalent testing. Impact on patient care is, however, still debatable. What has been highlighted is the need for health system strengthening and for true POC testing that can be used in active case finding.
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Affiliation(s)
- Lesley Scott
- aDepartment of Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, Gauteng, South Africa bNational Priority Programs, National Health Laboratory Service, Johannesburg, Gauteng, South Africa cFoundation for Innovative New Diagnostics, Geneva dGlobal TB Program, WHO, Geneva, Switzerland
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43
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Tientcheu LD, Koch A, Ndengane M, Andoseh G, Kampmann B, Wilkinson RJ. Immunological consequences of strain variation within the Mycobacterium tuberculosis complex. Eur J Immunol 2017; 47:432-445. [PMID: 28150302 PMCID: PMC5363233 DOI: 10.1002/eji.201646562] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/26/2017] [Accepted: 01/31/2017] [Indexed: 11/11/2022]
Abstract
In 2015, there were an estimated 10.4 million new cases of tuberculosis (TB) globally, making it one of the leading causes of death due to an infectious disease. TB is caused by members of the Mycobacterium tuberculosis complex (MTBC), with human disease resulting from infection by M. tuberculosis sensu stricto and M. africanum. Recent progress in genotyping techniques, in particular the increasing availability of whole genome sequence data, has revealed previously under appreciated levels of genetic diversity within the MTBC. Several studies have shown that this genetic diversity may translate into differences in TB transmission, clinical manifestations of disease, and host immune responses. This suggests the existence of MTBC genotype‐dependent host–pathogen interactions which may influence the outcome of infection and progression of disease. In this review, we highlight the studies demonstrating differences in innate and adaptive immunological outcomes consequent on MTBC genetic diversity, and discuss how these differences in immune response might influence the development of TB vaccines, diagnostics and new therapies.
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Affiliation(s)
- Leopold D Tientcheu
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia.,Department of Biochemistry, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
| | - Anastasia Koch
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, Observatory, Republic of South Africa
| | - Mthawelenga Ndengane
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, Observatory, Republic of South Africa
| | - Genevieve Andoseh
- Department of Biochemistry, Faculty of Science, University of Yaoundé 1, Yaoundé, Cameroon
| | - Beate Kampmann
- Vaccines and Immunity Theme, Medical Research Council Unit, The Gambia, Banjul, The Gambia.,Department of Medicine, Imperial College, London, United Kingdom
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine and Department of Medicine, University of Cape Town, Observatory, Republic of South Africa.,Department of Medicine, Imperial College, London, United Kingdom.,The Francis Crick Institute, London, United Kingdom
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Whole-Genome Sequencing of Mycobacterium tuberculosis Provides Insight into the Evolution and Genetic Composition of Drug-Resistant Tuberculosis in Belarus. J Clin Microbiol 2016; 55:457-469. [PMID: 27903602 PMCID: PMC5277515 DOI: 10.1128/jcm.02116-16] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 11/18/2016] [Indexed: 01/01/2023] Open
Abstract
The emergence and spread of drug-resistant Mycobacterium tuberculosis (DR-TB) are critical global health issues. Eastern Europe has some of the highest incidences of DR-TB, particularly multidrug-resistant (MDR) and extensively drug-resistant (XDR) TB. To better understand the genetic composition and evolution of MDR- and XDR-TB in the region, we sequenced and analyzed the genomes of 138 M. tuberculosis isolates from 97 patients sampled between 2010 and 2013 in Minsk, Belarus. MDR and XDR-TB isolates were significantly more likely to belong to the Beijing lineage than to the Euro-American lineage, and known resistance-conferring loci accounted for the majority of phenotypic resistance to first- and second-line drugs in MDR and XDR-TB. Using a phylogenomic approach, we estimated that the majority of MDR-TB was due to the recent transmission of already-resistant M. tuberculosis strains rather than repeated de novo evolution of resistance within patients, while XDR-TB was acquired through both routes. Longitudinal sampling of M. tuberculosis from 34 patients with treatment failure showed that most strains persisted genetically unchanged during treatment or acquired resistance to fluoroquinolones. HIV+ patients were significantly more likely to have multiple infections over time than HIV− patients, highlighting a specific need for careful infection control in these patients. These data provide a better understanding of the genomic composition, transmission, and evolution of MDR- and XDR-TB in Belarus and will enable improved diagnostics, treatment protocols, and prognostic decision-making.
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45
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Genomic diversity in autopsy samples reveals within-host dissemination of HIV-associated Mycobacterium tuberculosis. Nat Med 2016; 22:1470-1474. [PMID: 27798613 DOI: 10.1038/nm.4205] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 09/14/2016] [Indexed: 12/31/2022]
Abstract
Mycobacterium tuberculosis remains a leading cause of death worldwide, especially among individuals infected with HIV. Whereas phylogenetic analysis has revealed M. tuberculosis spread throughout history and in local outbreaks, much less is understood about its dissemination within the body. Here we report genomic analysis of 2,693 samples collected post mortem from lung and extrapulmonary biopsies of 44 subjects in KwaZulu-Natal, South Africa, who received minimal antitubercular treatment and most of whom were HIV seropositive. We found that purifying selection occurred within individual patients, without the need for patient-to-patient transmission. Despite negative selection, mycobacteria diversified within individuals to form sublineages that co-existed for years. These sublineages, as well as distinct strains from mixed infections, were differentially distributed throughout the lung, suggesting temporary barriers to pathogen migration. As a consequence, samples taken from the upper airway often captured only a fraction of the population diversity, challenging current methods of outbreak tracing and resistance diagnostics. Phylogenetic analysis indicated that dissemination from the lungs to extrapulmonary sites was as frequent as between lung sites, supporting the idea of similar migration routes within and between organs, at least in subjects with HIV. Genomic diversity therefore provides a record of pathogen diversification and repeated dissemination across the body.
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46
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Walker TM, Merker M, Kohl TA, Crook DW, Niemann S, Peto TEA. Whole genome sequencing for M/XDR tuberculosis surveillance and for resistance testing. Clin Microbiol Infect 2016; 23:161-166. [PMID: 27789378 DOI: 10.1016/j.cmi.2016.10.014] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 10/11/2016] [Accepted: 10/12/2016] [Indexed: 11/28/2022]
Abstract
Whole genome sequencing (WGS) can help to relate Mycobacterium tuberculosis genomes to one another to assess genetic relatedness and infer the likelihood of transmission between cases. The same sequence data are now increasingly being used to predict drug resistance and susceptibility. Controlling the spread of tuberculosis and providing patients with the correct treatment are central to the World Health Organization's target to 'End TB' by 2035, for which the global prevalence of drug-resistant tuberculosis remains one of the main obstacles to success. So far, WGS has been applied largely to drug-susceptible strains for the purposes of understanding transmission, leaving a number of analytical considerations before transferring what has been learnt from drug-susceptible disease to drug-resistant tuberculosis. We discuss these potential problems here, alongside some of the challenges to characterizing the Mycobacterium tuberculosis 'resistome'-the optimal knowledge-base required for WGS-based assays to successfully direct individualized treatment regimens through the prediction of drug resistance and susceptibility in the future.
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Affiliation(s)
- T M Walker
- Department of Microbiology and Infectious Diseases, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
| | - M Merker
- Molecular Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany
| | - T A Kohl
- Molecular Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany
| | - D W Crook
- Department of Microbiology and Infectious Diseases, Nuffield Department of Medicine, University of Oxford, Oxford, UK; National Institute of Health Oxford Biomedical Research Centre, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - S Niemann
- Molecular Mycobacteriology, Forschungszentrum Borstel, Leibniz-Zentrum für Medizin und Biowissenschaften, Borstel, Germany; German Center for Infection Research, Borstel Site, Borstel, Germany
| | - T E A Peto
- Department of Microbiology and Infectious Diseases, Nuffield Department of Medicine, University of Oxford, Oxford, UK; National Institute of Health Oxford Biomedical Research Centre, University of Oxford, John Radcliffe Hospital, Oxford, UK
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