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Fuller NM, McQuaid CF, Harker MJ, Weerasuriya CK, McHugh TD, Knight GM. Mathematical models of drug-resistant tuberculosis lack bacterial heterogeneity: A systematic review. PLoS Pathog 2024; 20:e1011574. [PMID: 38598556 PMCID: PMC11060536 DOI: 10.1371/journal.ppat.1011574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 04/30/2024] [Accepted: 03/25/2024] [Indexed: 04/12/2024] Open
Abstract
Drug-resistant tuberculosis (DR-TB) threatens progress in the control of TB. Mathematical models are increasingly being used to guide public health decisions on managing both antimicrobial resistance (AMR) and TB. It is important to consider bacterial heterogeneity in models as it can have consequences for predictions of resistance prevalence, which may affect decision-making. We conducted a systematic review of published mathematical models to determine the modelling landscape and to explore methods for including bacterial heterogeneity. Our first objective was to identify and analyse the general characteristics of mathematical models of DR-mycobacteria, including M. tuberculosis. The second objective was to analyse methods of including bacterial heterogeneity in these models. We had different definitions of heterogeneity depending on the model level. For between-host models of mycobacterium, heterogeneity was defined as any model where bacteria of the same resistance level were further differentiated. For bacterial population models, heterogeneity was defined as having multiple distinct resistant populations. The search was conducted following PRISMA guidelines in five databases, with studies included if they were mechanistic or simulation models of DR-mycobacteria. We identified 195 studies modelling DR-mycobacteria, with most being dynamic transmission models of non-treatment intervention impact in M. tuberculosis (n = 58). Studies were set in a limited number of specific countries, and 44% of models (n = 85) included only a single level of "multidrug-resistance (MDR)". Only 23 models (8 between-host) included any bacterial heterogeneity. Most of these also captured multiple antibiotic-resistant classes (n = 17), but six models included heterogeneity in bacterial populations resistant to a single antibiotic. Heterogeneity was usually represented by different fitness values for bacteria resistant to the same antibiotic (61%, n = 14). A large and growing body of mathematical models of DR-mycobacterium is being used to explore intervention impact to support policy as well as theoretical explorations of resistance dynamics. However, the majority lack bacterial heterogeneity, suggesting that important evolutionary effects may be missed.
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Affiliation(s)
- Naomi M. Fuller
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Antimicrobial Resistance Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Tuberculosis Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Christopher F. McQuaid
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Antimicrobial Resistance Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Tuberculosis Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Martin J. Harker
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Antimicrobial Resistance Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Tuberculosis Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Chathika K. Weerasuriya
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Antimicrobial Resistance Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Tuberculosis Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Timothy D. McHugh
- UCL Centre for Clinical Microbiology, Division of Infection & Immunity, Royal Free Campus, University College London, London, United Kingdom
| | - Gwenan M. Knight
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Centre for Mathematical Modelling of Infectious Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Antimicrobial Resistance Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Tuberculosis Centre, London School of Hygiene and Tropical Medicine, London, United Kingdom
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2
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Morales-Durán N, León-Buitimea A, Morones-Ramírez JR. Unraveling resistance mechanisms in combination therapy: A comprehensive review of recent advances and future directions. Heliyon 2024; 10:e27984. [PMID: 38510041 PMCID: PMC10950705 DOI: 10.1016/j.heliyon.2024.e27984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 03/07/2024] [Accepted: 03/08/2024] [Indexed: 03/22/2024] Open
Abstract
Antimicrobial resistance is a global health threat. Misuse and overuse of antimicrobials are the main drivers in developing drug-resistant bacteria. The emergence of the rapid global spread of multi-resistant bacteria requires urgent multisectoral action to generate novel treatment alternatives. Combination therapy offers the potential to exploit synergistic effects for enhanced antibacterial efficacy of drugs. Understanding the complex dynamics and kinetics of drug interactions in combination therapy is crucial. Therefore, this review outlines the current advances in antibiotic resistance's evolutionary and genetic dynamics in combination therapies-exposed bacteria. Moreover, we also discussed four pivotal future research areas to comprehend better the development of antibiotic resistance in bacteria treated with combination strategies.
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Affiliation(s)
- Nami Morales-Durán
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, 66455, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, 66628, Mexico
| | - Angel León-Buitimea
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, 66455, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, 66628, Mexico
| | - José R. Morones-Ramírez
- Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León (UANL), San Nicolás de los Garza, 66455, Mexico
- Centro de Investigación en Biotecnología y Nanotecnología, Facultad de Ciencias Químicas, Universidad Autónoma de Nuevo León, Parque de Investigación e Innovación Tecnológica, Apodaca, 66628, Mexico
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3
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Biset S, Teferi M, Alamirew H, Birhanu B, Dessie A, Aschale A, Haymanot A, Dejenie S, Gebremedhin T, Abebe W, Adane G. Trends of Mycobacterium tuberculosis and Rifampicin resistance in Northwest Ethiopia: Xpert® MTB/RIF assay results from 2015 to 2021. BMC Infect Dis 2024; 24:238. [PMID: 38389060 PMCID: PMC10882931 DOI: 10.1186/s12879-024-09135-0] [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: 05/02/2023] [Accepted: 02/13/2024] [Indexed: 02/24/2024] Open
Abstract
BACKGROUND Tuberculosis (TB) remains one of the leading causes of morbidity and mortality worldwide, particularly in countries with limited resources. The emergence of drug resistance in mycobacterium tuberculosis (MTB), particularly rifampicin (RIF) resistance, hindered TB control efforts. Continuous surveillance and regular monitoring of drug-resistant TB, including rifampicin resistance (RR), are required for effective TB intervention strategies and prevention and control measures. OBJECTIVE Determine the trend of TB and RR-TB among presumptive TB patients in Northwest Ethiopia. METHOD A retrospective study was conducted at the University of Gondar Comprehensive Specialized Hospital (UoG-CSH). The study included TB registration logbook data from all patients who visited the hospital and were tested for MTB using the Xpert® MTB/RIF assay between 2015 and 2021. The SPSS version 26 software was used to enter, clean, and analyze the laboratory-based data. RESULTS A total of 18,787 patient results were included, with 93.8% (17,615/18787) of them being successful, meaning they were not invalid, error, or aborted. About 10.5% (1846/17615) of the 17,615 results were MTB-positive, with 7.42% (137/1846) RIF resistant. Age, anti-TB treatment history, and diagnosis year were associated with the presence of MTB and RR-MTB. Tuberculosis (TB) prevalence was higher in productive age groups, whereas RR-TB prevalence was higher in the elderly. Regarding diagnosis year, the prevalence of TB and RR-TB showed a declining trend as the year progressed. While MTB was detected in 12.8% (471/3669) of new and 22.2% (151/679) of re-treatment presumptive TB patients, RR-MTB was detected in 8.5% (40/471) of new and 18.5% (28/151) of re-treatment TB cases. CONCLUSION The prevalence of TB and RR-TB in the study area showed a declining trend over the years. While TB was more prevalent in productive age groups (15 to 45 years), RR-TB was more prevalent in older populations (over 45 years), than others. Moreover, patients with a history of anti-TB drug exposure were more likely to be positive for DR-TB, highlighting the need to strengthen DOT programs for proper management of TB treatment.
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Affiliation(s)
- Sirak Biset
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, University of Gondar, Gondar, Ethiopia.
| | - Milto Teferi
- School of Biomedical and Laboratory Sciences, University of Gondar, Gondar, Ethiopia
| | - Haylemesikel Alamirew
- School of Biomedical and Laboratory Sciences, University of Gondar, Gondar, Ethiopia
| | - Biniyam Birhanu
- School of Biomedical and Laboratory Sciences, University of Gondar, Gondar, Ethiopia
| | - Awoke Dessie
- School of Biomedical and Laboratory Sciences, University of Gondar, Gondar, Ethiopia
| | - Abebe Aschale
- School of Biomedical and Laboratory Sciences, University of Gondar, Gondar, Ethiopia
| | - Anmaw Haymanot
- School of Biomedical and Laboratory Sciences, University of Gondar, Gondar, Ethiopia
| | - Selamu Dejenie
- University of Gondar Comprehensive Specialized Hospital, University of Gondar, Gondar, Ethiopia
| | - Teshager Gebremedhin
- University of Gondar Comprehensive Specialized Hospital, University of Gondar, Gondar, Ethiopia
| | - Wondwossen Abebe
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, University of Gondar, Gondar, Ethiopia
| | - Gashaw Adane
- Department of Immunology and Molecular Biology, School of Biomedical and Laboratory Sciences, University of Gondar, Gondar, Ethiopia
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Chaturvedi M, Patel M, Tiwari A, Dwivedi N, Mondal DP, Srivastava AK, Dhand C. An insight to the recent advancements in detection of Mycobacterium tuberculosis using biosensors: A systematic review. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 186:14-27. [PMID: 38052326 DOI: 10.1016/j.pbiomolbio.2023.10.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 07/31/2023] [Accepted: 10/01/2023] [Indexed: 12/07/2023]
Abstract
Since ancient times, Tuberculosis (TB) has been a severe invasive illness that has been prevalent for thousands of years and is also known as "consumption" or phthisis. TB is the most common chronic lung bacterial illness in the world, killing over 2 million people each year, caused by Mycobacterium tuberculosis (MTB). As per the reports of WHO, in spite of technology advancements, the average rate of decline in global TB infections from 2000-2018 was only 1.6% per year, and the worldwide reduction in TB deaths was only 11%. In addition, COVID-19 pandemic has reversed years of global progress in tackling TB with fewer diagnosed cases. The majority of undiagnosed patients of TB are found in low- and middle-income countries where the GeneXpert MTB/RIF assay and sputum smear microscopy have been approved by the WHO as reference procedures for quickly detecting TB. Biosensors, like other cutting-edge technologies, have piqued researchers' interest since they offer a quick and accurate way to identify MTB. Modern integrated technologies allow for the rapid, low-cost, and highly precise detection of analytes in extremely little amounts of sample by biosensors. Here in this review, we outlined the severity of tuberculosis (TB) and the most recent developments in the biosensors sector, as well as their various kinds and benefits for TB detection. The review also emphasizes how widespread TB is and how it needs accurate diagnosis and effective treatment.
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Affiliation(s)
- Mansi Chaturvedi
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; School of Biomolecular Engineering & Biotechnology UTD RGPV, Bhopal, 462033, India
| | - Monika Patel
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Archana Tiwari
- School of Biomolecular Engineering & Biotechnology UTD RGPV, Bhopal, 462033, India
| | - Neeraj Dwivedi
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - D P Mondal
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Avanish Kumar Srivastava
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Chetna Dhand
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal, 462026, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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5
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Mutayoba BK, Ershova J, Lyamuya E, Hoelscher M, Heinrich N, Kilale AM, Range NS, Ngowi BJ, Ntinginya NE, Mfaume SM, Nkiligi E, Doulla B, Lyimo J, Kisonga R, Kingalu A, Lema Y, Kondo Z, Pletschette M. The second national anti-tuberculosis drug resistance survey in Tanzania, 2017-2018. Trop Med Int Health 2022; 27:891-901. [PMID: 36089572 PMCID: PMC9826299 DOI: 10.1111/tmi.13814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
OBJECTIVE To determine the levels and patterns of resistance to first- and second-line anti-tuberculosis (TB) drugs among new and previously treated sputum smear positive pulmonary TB (PTB) patients. METHODS We conducted a nationally representative cross-sectional facility-based survey in June 2017-July 2018 involving 45 clusters selected based on probability proportional to size. The survey aimed to determine the prevalence of anti-TB drug resistance and associated risk factors among smear positive PTB patients in Tanzania. Sputum samples were examined using smear microscopy, Xpert MTB/RIF, culture and drug susceptibility testing (DST). Logistic regression was used to account for missing data and sampling design effects on the estimates and their standard errors. RESULTS We enrolled 1557 TB patients, including 1408 (90.4%) newly diagnosed and 149 (9.6%) previously treated patients. The prevalence of multidrug-resistant TB (MDR-TB) was 0.85% [95% confidence interval (CI): 0.4-1.3] among new cases and 4.6% (95% CI: 1.1-8.2) among previously treated cases. The prevalence of Mycobacterium tuberculosis strains resistant to any of the four first-line anti-TB drugs (isoniazid, rifampicin, streptomycin and ethambutol) was 1.7% among new TB patients and 6.5% among those previously treated. Drug resistance to all first-line drugs was similar (0.1%) in new and previously treated patients. None of the isolates displayed poly-resistance or extensively drug-resistant TB (XDR-TB). The only risk factor for MDR-TB was history of previous TB treatment (odds ratio = 5.7, 95% CI: 1.9-17.2). CONCLUSION The burden of MDR-TB in the country was relatively low with no evidence of XDR-TB. Given the overall small number of MDR-TB cases in this survey, it will be beneficial focusing efforts on intensified case detection including universal DST.
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Affiliation(s)
- Beatrice Kemilembe Mutayoba
- Department of Preventive ServicesMinistry of Health National AIDS Control ProgramDodomaTanzania,Department of Infectious Diseases and Tropical MedicineMedical Center of the University of MunichMunichGermany
| | - Julia Ershova
- Division of Global HIV and TB, Global TB BranchUS Centers for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Eligius Lyamuya
- Department of Microbiology and ImmunologyMuhimbili University of Health and Allied SciencesDar es SalaamTanzania
| | - Michael Hoelscher
- Department of Infectious Diseases and Tropical MedicineMedical Center of the University of MunichMunichGermany
| | - Norbert Heinrich
- Department of Infectious Diseases and Tropical MedicineMedical Center of the University of MunichMunichGermany
| | - Andrew Martin Kilale
- Muhimbili Medical Research CentreNational Institute for Medical ResearchDar es SalaamTanzania
| | - Nyagosya Segere Range
- Muhimbili Medical Research CentreNational Institute for Medical ResearchDar es SalaamTanzania
| | - Benard James Ngowi
- Mbeya College of Health and Allied SciencesUniversity of Dar es SalaamMbeyaTanzania
| | | | - Saidi Mwinjuma Mfaume
- Muhimbili Medical Research CentreNational Institute for Medical ResearchDar es SalaamTanzania
| | - Emmanuel Nkiligi
- National Tuberculosis and Leprosy Program, Department of Preventive ServicesMinistry of HealthDodomaTanzania
| | - Basra Doulla
- National Tuberculosis and Leprosy ProgramCentral Tuberculosis Reference LaboratoryDar es SalaamTanzania
| | - Johnson Lyimo
- National Tuberculosis and Leprosy Program, Department of Preventive ServicesMinistry of HealthDodomaTanzania
| | - Riziki Kisonga
- Kibong'oto Infectious Diseases HospitalKilimanjaroTanzania
| | - Amri Kingalu
- National Tuberculosis and Leprosy Program, Department of Preventive ServicesMinistry of HealthDodomaTanzania
| | - Yakobo Lema
- Muhimbili Medical Research CentreNational Institute for Medical ResearchDar es SalaamTanzania
| | - Zuwena Kondo
- National Tuberculosis and Leprosy Program, Department of Preventive ServicesMinistry of HealthDodomaTanzania
| | - Michel Pletschette
- Department of Infectious Diseases and Tropical MedicineMedical Center of the University of MunichMunichGermany
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Hemez C, Clarelli F, Palmer AC, Bleis C, Abel S, Chindelevitch L, Cohen T, Abel zur Wiesch P. Mechanisms of antibiotic action shape the fitness landscapes of resistance mutations. Comput Struct Biotechnol J 2022; 20:4688-4703. [PMID: 36147681 PMCID: PMC9463365 DOI: 10.1016/j.csbj.2022.08.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 08/12/2022] [Accepted: 08/12/2022] [Indexed: 11/15/2022] Open
Abstract
Antibiotic-resistant pathogens are a major public health threat. A deeper understanding of how an antibiotic's mechanism of action influences the emergence of resistance would aid in the design of new drugs and help to preserve the effectiveness of existing ones. To this end, we developed a model that links bacterial population dynamics with antibiotic-target binding kinetics. Our approach allows us to derive mechanistic insights on drug activity from population-scale experimental data and to quantify the interplay between drug mechanism and resistance selection. We find that both bacteriostatic and bactericidal agents can be equally effective at suppressing the selection of resistant mutants, but that key determinants of resistance selection are the relationships between the number of drug-inactivated targets within a cell and the rates of cellular growth and death. We also show that heterogeneous drug-target binding within a population enables resistant bacteria to evolve fitness-improving secondary mutations even when drug doses remain above the resistant strain's minimum inhibitory concentration. Our work suggests that antibiotic doses beyond this "secondary mutation selection window" could safeguard against the emergence of high-fitness resistant strains during treatment.
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Affiliation(s)
- Colin Hemez
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Graduate Program in Biophysics, Harvard University, Boston, MA 02115, USA
- Corresponding authors at: Broad Institute, 75 Ames St, Room 3035, Cambridge, MA 02412, USA (C. Hemez). Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway (P. Abel zur Wiesch).
| | - Fabrizio Clarelli
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Adam C. Palmer
- Department of Pharmacology, Computational Medicine Program, Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Christina Bleis
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Sören Abel
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Division of Infection Control, Norwegian Institute of Public Health, Oslo 0318, Norway
| | - Leonid Chindelevitch
- Department of Infectious Disease Epidemiology, Imperial College, London SW7 2AZ, UK
| | - Theodore Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT 06520, USA
| | - Pia Abel zur Wiesch
- Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Division of Infection Control, Norwegian Institute of Public Health, Oslo 0318, Norway
- Corresponding authors at: Broad Institute, 75 Ames St, Room 3035, Cambridge, MA 02412, USA (C. Hemez). Department of Pharmacy, UiT – The Arctic University of Norway, 9019 Tromsø, Norway (P. Abel zur Wiesch).
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7
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Soeroto AY, Nurhayati RD, Purwiga A, Lestari BW, Pratiwi C, Santoso P, Kulsum ID, Suryadinata H, Ferdian F. Factors associated with treatment outcome of MDR/RR-TB patients treated with shorter injectable based regimen in West Java Indonesia. PLoS One 2022; 17:e0263304. [PMID: 35089981 PMCID: PMC8797248 DOI: 10.1371/journal.pone.0263304] [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: 08/19/2021] [Accepted: 01/17/2022] [Indexed: 02/07/2023] Open
Abstract
Background and aims Multi drug or rifampicin resistant tuberculosis (MDR/RR-TB) is a major burden to TB prevention and eradication globally. Since 2016, WHO guidelines have included options for treating MDR/RR-TB with a standard regimen of 9 to 11 months duration (the ’shorter regimen’) rather than an individual regimen of at least 20 months. This regimen has been introduced in Indonesia since September 2017. Therefore, we aimed to determine the success rate and factors associated with the treatment outcome of shorter injectable based regimen in West Java province, Indonesia. Methods This was a retrospective cohort study of MDR/RR-TB patients aged over 18 years old who received the shorter injectable based regimen between September 2017 and December 2020. We defined successful outcomes as the combined proportion of patients who were cured or had complete treatment. While, unsuccessful outcomes were defined as the combined proportion of patients who died from any causes, failure, and loss to follow-up (LTFU). Results A total of 315 patients were included in this study. The success rate was 64.5%. Multivariate analysis showed male gender (aRR = 1.18, 95% CI 1.04 to 1.34) increased the chance of successful outcome, while malnutrition (aRR = 0.78, 95% CI 0.68 to 0.89), history of previous TB treatment (aRR = 0.80%CI 0.68 to 0.94), and time of culture conversion >2 months (aRR = 0.72 (95% CI 0.59 to 0.87) decreased the chance of successful outcome. Conclusion History of previous TB treatment, time of culture conversion >2 months, and malnutrition were independent factors that decrease the chance for success rate, while male gender increase the likelihood for success rate of patients treated by the shorter injectable based regimen.
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Affiliation(s)
- Arto Yuwono Soeroto
- Faculty of Medicine, Division of Respirology and Critical Care Medicine, Department of Internal Medicine, Hasan Sadikin General Hospital, Universitas Padjadjaran, Bandung, West Java, Indonesia.,Faculty of Medicine, Department of Internal Medicine, Hasan Sadikin Hospital, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Raden Desy Nurhayati
- Faculty of Medicine, Division of Respirology and Critical Care Medicine, Department of Internal Medicine, Hasan Sadikin General Hospital, Universitas Padjadjaran, Bandung, West Java, Indonesia.,Faculty of Medicine, Department of Internal Medicine, Hasan Sadikin Hospital, Universitas Padjadjaran, Bandung, West Java, Indonesia.,Department of Internal Medicine, Rotinsulu Pulmonary Hospital, Bandung, West Java, Indonesia
| | - Aga Purwiga
- Faculty of Medicine, Department of Internal Medicine, Hasan Sadikin Hospital, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Bony Wiem Lestari
- Faculty of MedicineDepartment of Public Health, Universitas Padjadjaran, Bandung, West Java, Indonesia.,Faculty of Medicine, TB-HIV Research Center, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Chica Pratiwi
- Faculty of Medicine, Department of Internal Medicine, Hasan Sadikin Hospital, Universitas Padjadjaran, Bandung, West Java, Indonesia.,Department of Internal Medicine, Cimacan Hospital, Cianjur, West Java, Indonesia
| | - Prayudi Santoso
- Faculty of Medicine, Division of Respirology and Critical Care Medicine, Department of Internal Medicine, Hasan Sadikin General Hospital, Universitas Padjadjaran, Bandung, West Java, Indonesia.,Faculty of Medicine, Department of Internal Medicine, Hasan Sadikin Hospital, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Iceu Dimas Kulsum
- Faculty of Medicine, Division of Respirology and Critical Care Medicine, Department of Internal Medicine, Hasan Sadikin General Hospital, Universitas Padjadjaran, Bandung, West Java, Indonesia.,Faculty of Medicine, Department of Internal Medicine, Hasan Sadikin Hospital, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Hendarsyah Suryadinata
- Faculty of Medicine, Division of Respirology and Critical Care Medicine, Department of Internal Medicine, Hasan Sadikin General Hospital, Universitas Padjadjaran, Bandung, West Java, Indonesia.,Faculty of Medicine, Department of Internal Medicine, Hasan Sadikin Hospital, Universitas Padjadjaran, Bandung, West Java, Indonesia
| | - Ferdy Ferdian
- Faculty of Medicine, Division of Respirology and Critical Care Medicine, Department of Internal Medicine, Hasan Sadikin General Hospital, Universitas Padjadjaran, Bandung, West Java, Indonesia.,Faculty of Medicine, Department of Internal Medicine, Hasan Sadikin Hospital, Universitas Padjadjaran, Bandung, West Java, Indonesia
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8
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Investigation of the Sensitivity of Mycobacterium Tuberculosis Strains Isolated from Various Clinical Samples in Eastern Turkey to Major Anti-tuberculosis Drugs. JOURNAL OF CONTEMPORARY MEDICINE 2021. [DOI: 10.16899/jcm.841505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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9
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Afkhami S, Villela AD, D’Agostino MR, Jeyanathan M, Gillgrass A, Xing Z. Advancing Immunotherapeutic Vaccine Strategies Against Pulmonary Tuberculosis. Front Immunol 2020; 11:557809. [PMID: 33013927 PMCID: PMC7509172 DOI: 10.3389/fimmu.2020.557809] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/18/2020] [Indexed: 12/21/2022] Open
Abstract
Chemotherapeutic intervention remains the primary strategy in treating and controlling tuberculosis (TB). However, a complex interplay between therapeutic and patient-related factors leads to poor treatment adherence. This in turn continues to give rise to unacceptably high rates of disease relapse and the growing emergence of drug-resistant forms of TB. As such, there is considerable interest in strategies that simultaneously improve treatment outcome and shorten chemotherapy duration. Therapeutic vaccines represent one such approach which aims to accomplish this through boosting and/or priming novel anti-TB immune responses to accelerate disease resolution, shorten treatment duration, and enhance treatment success rates. Numerous therapeutic vaccine candidates are currently undergoing pre-clinical and clinical assessment, showing varying degrees of efficacy. By dissecting the underlying mechanisms/correlates of their successes and/or shortcomings, strategies can be identified to improve existing and future vaccine candidates. This mini-review will discuss the current understanding of therapeutic TB vaccine candidates, and discuss major strategies that can be implemented in advancing their development.
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Affiliation(s)
- Sam Afkhami
- McMaster Immunology Research Center, McMaster University, Hamilton, ON, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Anne Drumond Villela
- McMaster Immunology Research Center, McMaster University, Hamilton, ON, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Michael R. D’Agostino
- McMaster Immunology Research Center, McMaster University, Hamilton, ON, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Mangalakumari Jeyanathan
- McMaster Immunology Research Center, McMaster University, Hamilton, ON, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Amy Gillgrass
- McMaster Immunology Research Center, McMaster University, Hamilton, ON, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Zhou Xing
- McMaster Immunology Research Center, McMaster University, Hamilton, ON, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
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10
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Mathematical model and tool to explore shorter multi-drug therapy options for active pulmonary tuberculosis. PLoS Comput Biol 2020; 16:e1008107. [PMID: 32810158 PMCID: PMC7480878 DOI: 10.1371/journal.pcbi.1008107] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 09/09/2020] [Accepted: 06/30/2020] [Indexed: 12/20/2022] Open
Abstract
Standard treatment for active tuberculosis (TB) requires drug treatment with at least four drugs over six months. Shorter-duration therapy would mean less need for strict adherence, and reduced risk of bacterial resistance. A system pharmacology model of TB infection, and drug therapy was developed and used to simulate the outcome of different drug therapy scenarios. The model incorporated human immune response, granuloma lesions, multi-drug antimicrobial chemotherapy, and bacterial resistance. A dynamic population pharmacokinetic/pharmacodynamic (PK/PD) simulation model including rifampin, isoniazid, pyrazinamide, and ethambutol was developed and parameters aligned with previous experimental data. Population therapy outcomes for simulations were found to be generally consistent with summary results from previous clinical trials, for a range of drug dose and duration scenarios. An online tool developed from this model is released as open source software. The TB simulation tool could support analysis of new therapy options, novel drug types, and combinations, incorporating factors such as patient adherence behavior. A comprehensive in-silico model of pulmonary tuberculosis successfully predicted previous clinical trials and could simulate future therapeutics.
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11
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Ernest JP, Strydom N, Wang Q, Zhang N, Nuermberger E, Dartois V, Savic RM. Development of New Tuberculosis Drugs: Translation to Regimen Composition for Drug-Sensitive and Multidrug-Resistant Tuberculosis. Annu Rev Pharmacol Toxicol 2020; 61:495-516. [PMID: 32806997 DOI: 10.1146/annurev-pharmtox-030920-011143] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Tuberculosis (TB) kills more people than any other infectious disease. Challenges for developing better treatments include the complex pathology due to within-host immune dynamics, interpatient variability in disease severity and drug pharmacokinetics-pharmacodynamics (PK-PD), and the growing emergence of resistance. Model-informed drug development using quantitative and translational pharmacology has become increasingly recognized as a method capable of drug prioritization and regimen optimization to efficiently progress compounds through TB drug development phases. In this review, we examine translational models and tools, including plasma PK scaling, site-of-disease lesion PK, host-immune and bacteria interplay, combination PK-PD models of multidrug regimens, resistance formation, and integration of data across nonclinical and clinical phases.We propose a workflow that integrates these tools with computational platforms to identify drug combinations that have the potential to accelerate sterilization, reduce relapse rates, and limit the emergence of resistance.
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Affiliation(s)
- Jacqueline P Ernest
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, USA;
| | - Natasha Strydom
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, USA;
| | - Qianwen Wang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, USA;
| | - Nan Zhang
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, USA;
| | - Eric Nuermberger
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, Maryland 21231, USA
| | - Véronique Dartois
- Center for Discovery and Innovation, Hackensack Meridian School of Medicine at Seton Hall University, Nutley, New Jersey 07110, USA
| | - Rada M Savic
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California 94158, USA;
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Welekidan LN, Skjerve E, Dejene TA, Gebremichael MW, Brynildsrud O, Agdestein A, Tessema GT, Tønjum T, Yimer SA. Characteristics of pulmonary multidrug-resistant tuberculosis patients in Tigray Region, Ethiopia: A cross-sectional study. PLoS One 2020; 15:e0236362. [PMID: 32797053 PMCID: PMC7428183 DOI: 10.1371/journal.pone.0236362] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 07/03/2020] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is among the top 10 causes of mortality and the first killer among infectious diseases worldwide. One of the factors fuelling the TB epidemic is the global rise of multidrug resistant TB (MDR-TB). The aim of this study was to determine the magnitude and factors associated with MDR-TB in the Tigray Region, Ethiopia. METHOD This study employed a facility-based cross-sectional study design, which was conducted between July 2018 and August 2019. The inclusion criteria for the study participants were GeneXpert-positive who were not under treatment for TB, PTB patients' ≥15 years of age and who provided written informed consent. A total of 300 participants were enrolled in the study, with a structured questionnaire used to collect data on clinical, sociodemographic and behavioral factors. Sputum samples were collected and processed for acid-fast bacilli staining, culture and drug susceptibility testing. Drug susceptibility testing was performed using a line probe assay. Logistic regression was used to analyze associations between outcome and predictor variables. RESULTS The overall proportion of MDR-TB was 16.7% (11.6% and 32.7% for new and previously treated patients, respectively). Of the total MDR-TB isolates, 5.3% were pre-XDR-TB. The proportion of MDR-TB/HIV co-infection was 21.1%. A previous history of TB treatment AOR 3.75; 95% CI (0.7-2.24), cigarette smoking AOR 6.09; CI (1.65-2.50) and patients who had an intermittent fever (AOR = 2.54, 95% CI = 1.21-5.4) were strongly associated with MDR-TB development. CONCLUSIONS The magnitude of MDR-TB observed among new and previously treated patients is very alarming, which calls for an urgent need for intervention. The high proportion of MDR-TB among newly diagnosed cases indicates ongoing transmission, which suggests the need for enhanced TB control program performance to interrupt transmission. The increased proportion of MDR-TB among previously treated cases indicates a need for better patient management to prevent the evolution of drug resistance. Assessing the TB control program performance gaps and an optimal implementation of the WHO recommended priority actions for the management of drug-resistant TB, is imperative to help reduce the current high MDR-TB burden in the study region.
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Affiliation(s)
- Letemichael Negash Welekidan
- Department of Para Clinical Sciences, Norwegian University of Life Sciences, Oslo, Norway
- Department of Production Animal Medicine, Norwegian University of Life Sciences, Oslo, Norway
- Department of Medical Microbiology and Immunology, Division of Biomedical Sciences, College of Health Sciences, Mekelle University, Mekelle, Ethiopia
| | - Eystein Skjerve
- Department of Production Animal Medicine, Norwegian University of Life Sciences, Oslo, Norway
| | - Tsehaye Asmelash Dejene
- Department of Medical Microbiology and Immunology, Division of Biomedical Sciences, College of Health Sciences, Mekelle University, Mekelle, Ethiopia
| | | | - Ola Brynildsrud
- Department of Para Clinical Sciences, Norwegian University of Life Sciences, Oslo, Norway
- Department of Bacteriology and Immunology, Norwegian Institute of Public Health, Oslo, Norway
| | | | | | - Tone Tønjum
- Department of Microbiology, Unit for Genome Dynamics, University of Oslo, Oslo, Norway
- Department of Microbiology, Unit for Genome Dynamics, Oslo University Hospital, Oslo, Norway
| | - Solomon Abebe Yimer
- Department of Bacteriology and Immunology, Norwegian Institute of Public Health, Oslo, Norway
- Department of Microbiology, Unit for Genome Dynamics, University of Oslo, Oslo, Norway
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Soedarsono S, Mertaniasih NM, Sulistyowati T. FIRST LINE ANTI-TUBERCULOSIS DRUG RESISTANCE PATTERN IN MULTIDRUG-RESISTANT PULMONARY TUBERCULOSIS PATIENTS CORRELATE WITH ACID FAST BACILLI MICROSCOPY GRADING. INDONESIAN JOURNAL OF TROPICAL AND INFECTIOUS DISEASE 2020. [DOI: 10.20473/ijtid.v8i2.14294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) is a global public health crisis. Acid-fast bacilli (AFB) gradation in sputum examination is an important component in Pulmonary Tuberculosis (PTB) diagnosis and treatment outcome monitoring. Previously treated pulmonary TB patients with a higher AFB smear gradation may have higher rates of acquired resistance. Patients with a higher AFB grade indicate a higher bacillary load and had higher rates of acquired resistance. This study aims to evaluate the correlation between AFB gradation and first-line anti-TB drug resistance patterns in MDR pulmonary TB patients. This was a retrospective study conducted from August 2009 to April 2018 in Dr. Soetomo Hospital. Sputum samples were taken from MDR PTB patients. Sputum smear examination was done using Ziehl–Neelsen staining and gradation was measured according to IUATLD criteria. Samples with positive smear were evaluated for resistance patterns based on culture and resistance tests using the MGIT 960 BACTEC System. There were 433 sputum samples with AFB positive collected from MDR PTB patients. Resistance to RHES was found in 22 (14%) AFB +1, 19 (15%) AFB +2, and 29 (20%) AFB +3. Resistance to RHS was found in 22 (14%) AFB +1, 12 (9%) AFB +2, and 13 (9%) AFB +3. Resistance to RHE was found in 39 (25%) AFB +1, 38 (29%) AFB +2, and 35 (24%) AFB +3. Resistance to RH was found in 74 (47%) AFB +1, 61 (47%) AFB +2, and 69 (47%) AFB +3. Statistic analysis by Spearman test showed that there was no significant correlation between AFB gradation and first-line anti-TB drug resistance patterns. Acquired resistance to RHES can also found in lower bacillary load AFB +1.
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14
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Stochastic bacterial population dynamics restrict the establishment of antibiotic resistance from single cells. Proc Natl Acad Sci U S A 2020; 117:19455-19464. [PMID: 32703812 PMCID: PMC7431077 DOI: 10.1073/pnas.1919672117] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The emergence of antibiotic resistance poses a critical threat to the efficacy of antibiotic treatments. A resistant bacterial population must originally arise from a single cell that mutates or acquires a resistance gene. This single cell may, by chance, fail to successfully reproduce before it dies, leading to loss of the nascent resistant lineage. Here, we show that antibiotic concentrations that selectively favor resistance are nonetheless sufficient to reduce the chance of outgrowth from a single cell to a very low probability. Our findings suggest that lower antibiotic concentrations than those required to clear a large resistant population may be sufficient to prevent, with high probability, outgrowth of initially rare resistant mutants. A better understanding of how antibiotic exposure impacts the evolution of resistance in bacterial populations is crucial for designing more sustainable treatment strategies. The conventional approach to this question is to measure the range of concentrations over which resistant strain(s) are selectively favored over a sensitive strain. Here, we instead investigate how antibiotic concentration impacts the initial establishment of resistance from single cells, mimicking the clonal expansion of a resistant lineage following mutation or horizontal gene transfer. Using two Pseudomonas aeruginosa strains carrying resistance plasmids, we show that single resistant cells have <5% probability of detectable outgrowth at antibiotic concentrations as low as one-eighth of the resistant strain’s minimum inhibitory concentration (MIC). This low probability of establishment is due to detrimental effects of antibiotics on resistant cells, coupled with the inherently stochastic nature of cell division and death on the single-cell level, which leads to loss of many nascent resistant lineages. Our findings suggest that moderate doses of antibiotics, well below the MIC of resistant strains, may effectively restrict de novo emergence of resistance even though they cannot clear already-large resistant populations.
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15
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Acosta MM, Bram JT, Sim D, Read AF. Effect of drug dose and timing of treatment on the emergence of drug resistance in vivo in a malaria model. Evol Med Public Health 2020; 2020:196-210. [PMID: 33209305 PMCID: PMC7652304 DOI: 10.1093/emph/eoaa016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 05/15/2020] [Accepted: 05/26/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND AND OBJECTIVES There is a significant interest in identifying clinically effective drug treatment regimens that minimize the de novo evolution of antimicrobial resistance in pathogen populations. However, in vivo studies that vary treatment regimens and directly measure drug resistance evolution are rare. Here, we experimentally investigate the role of drug dose and treatment timing on resistance evolution in an animal model. METHODOLOGY In a series of experiments, we measured the emergence of atovaquone-resistant mutants of Plasmodium chabaudi in laboratory mice, as a function of dose or timing of treatment (day post-infection) with the antimalarial drug atovaquone. RESULTS The likelihood of high-level resistance emergence increased with atovaquone dose. When varying the timing of treatment, treating either very early or late in infection reduced the risk of resistance. When we varied starting inoculum, resistance was more likely at intermediate inoculum sizes, which correlated with the largest population sizes at time of treatment. CONCLUSIONS AND IMPLICATIONS (i) Higher doses do not always minimize resistance emergence and can promote the emergence of high-level resistance. (ii) Altering treatment timing affects the risk of resistance emergence, likely due to the size of the population at the time of treatment, although we did not test the effect of immunity whose influence may have been important in the case of late treatment. (iii) Finding the 'right' dose and 'right' time to maximize clinical gains and limit resistance emergence can vary depending on biological context and was non-trivial even in our simplified experiments. LAY SUMMARY In a mouse model of malaria, higher drug doses led to increases in drug resistance. The timing of drug treatment also impacted resistance emergence, likely due to the size of the population at the time of treatment.
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Affiliation(s)
- Mónica M Acosta
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA
| | - Joshua T Bram
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA
| | - Derek Sim
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA
| | - Andrew F Read
- Department of Biology, Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA 16802, USA
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA
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Liu Q, Wei J, Li Y, Wang M, Su J, Lu Y, López MG, Qian X, Zhu Z, Wang H, Gan M, Jiang Q, Fu YX, Takiff HE, Comas I, Li F, Lu X, Fortune SM, Gao Q. Mycobacterium tuberculosis clinical isolates carry mutational signatures of host immune environments. SCIENCE ADVANCES 2020; 6:eaba4901. [PMID: 32524000 PMCID: PMC7259932 DOI: 10.1126/sciadv.aba4901] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/25/2020] [Indexed: 05/12/2023]
Abstract
Mycobacterium tuberculosis (Mtb) infection results in a spectrum of clinical and histopathologic manifestations. It has been proposed that the environmental and immune pressures associated with different contexts of infection have different consequences for the associated bacterial populations, affecting drug susceptibility and the emergence of resistance. However, there is little concrete evidence for this model. We prospectively collected sputum samples from 18 newly diagnosed and treatment-naïve patients with tuberculosis and sequenced 795 colony-derived Mtb isolates. Mutant accumulation rates varied considerably between different bacilli isolated from the same individual, and where high rates of mutation were observed, the mutational spectrum was consistent with reactive oxygen species-induced mutagenesis. Elevated bacterial mutation rates were identified in isolates from HIV-negative but not HIV-positive individuals, suggesting that they were immune-driven. These results support the model that mutagenesis of Mtb in vivo is modulated by the host environment, which could drive the emergence of variants associated with drug resistance in a host-dependent manner.
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Affiliation(s)
- Qingyun Liu
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Fudan University, Shanghai, China
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Jianhao Wei
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yawei Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mei Wang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jun Su
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yonghui Lu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Mariana G. López
- Tuberculosis Genomic Unit, Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Xueqin Qian
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Zhaoqin Zhu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Haiying Wang
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Mingyun Gan
- Molecular Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Qi Jiang
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Fudan University, Shanghai, China
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Yun-Xin Fu
- Department of Biostatistics and Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Howard E. Takiff
- Integrated Mycobacterial Pathogenomics Unit, Institut Pasteur, Paris, France
- Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Iñaki Comas
- Tuberculosis Genomic Unit, Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Feng Li
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Xuemei Lu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- CAS Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Qian Gao
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Fudan University, Shanghai, China
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
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Molecular Detection of Isoniazid and Rifampin Resistance in Mycobacterium tuberculosis Isolates from Lorestan Province, Iran from 2014 to 2017. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2020. [DOI: 10.5812/archcid.81436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Mittal P, Sinha R, Kumar A, Singh P, Ngasainao MR, Singh A, Singh IK. Focusing on DNA Repair and Damage Tolerance Mechanisms in Mycobacterium tuberculosis: An Emerging Therapeutic Theme. Curr Top Med Chem 2020; 20:390-408. [PMID: 31924156 DOI: 10.2174/1568026620666200110114322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/02/2019] [Accepted: 10/10/2019] [Indexed: 11/22/2022]
Abstract
Tuberculosis (TB) is one such disease that has become a nuisance in the world scenario and one of the most deadly diseases of the current times. The etiological agent of tuberculosis, Mycobacterium tuberculosis (M. tb) kills millions of people each year. Not only 1.7 million people worldwide are estimated to harbor M. tb in the latent form but also 5 to 15 percent of which are expected to acquire an infection during a lifetime. Though curable, a long duration of drug regimen and expense leads to low patient adherence. The emergence of multi-, extensive- and total- drug-resistant strains of M. tb further complicates the situation. Owing to high TB burden, scientists worldwide are trying to design novel therapeutics to combat this disease. Therefore, to identify new drug targets, there is a growing interest in targeting DNA repair pathways to fight this infection. Thus, this review aims to explore DNA repair and damage tolerance as an efficient target for drug development by understanding M. tb DNA repair and tolerance machinery and its regulation, its role in pathogenesis and survival, mutagenesis, and consequently, in the development of drug resistance.
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Affiliation(s)
- Pooja Mittal
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Rajesh Sinha
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Amit Kumar
- Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India
| | - Pooja Singh
- Public Health Research Institute, NJMS-Rutgers University, New Jersey, United States
| | - Moses Rinchui Ngasainao
- Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India.,Department of Molecular Ecology, Max-Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Indrakant K Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India.,Department of Molecular Ecology, Max-Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
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Okethwangu D, Birungi D, Biribawa C, Kwesiga B, Turyahabwe S, Ario AR, Zhu BP. Multidrug-resistant tuberculosis outbreak associated with poor treatment adherence and delayed treatment: Arua District, Uganda, 2013-2017. BMC Infect Dis 2019; 19:387. [PMID: 31064332 PMCID: PMC6503550 DOI: 10.1186/s12879-019-4014-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/24/2019] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND In August 2017, the Uganda Ministry of Health was notified of increased cases of multidrug-resistant tuberculosis (MDR-TB) in Arua District, Uganda during 2017. We investigated to identify the scope of the increase and risk factors for infection, evaluate health facilities' capacity to manage MDR-TB, and recommend evidence-based control measures. METHODS We defined an MDR-TB case-patient as a TB patient attending Arua Regional Referral Hospital (ARRH) during 2013-2017 with a sputum sample yielding Mycobacterium tuberculosis resistant to at least rifampicin and isoniazid, confirmed by an approved drug susceptibility test. We reviewed clinical records from ARRH and compared the number of MDR-TB cases during January-August 2017 with the same months in 2013-2016. To identify risk factors specific for MDR-TB among cases with secondary infection, we conducted a case-control study using persons with drug-susceptible TB matched by sub-county of residence as controls. We observed infection prevention and control practices in health facilities and community, and assessed health facilities' capacity to manage TB. RESULTS We identified 33 patients with MDR-TB, of whom 30 were secondary TB infection cases. The number of cases during January-August 2017 was 10, compared with 3-4 cases in January-August from 2013 to 2016 (p = 0.02). Men were more affected than women (6.5 vs 1.6/100,000, p < 0.01), as were cases ≥18 years old compared to those < 18 years (8.7 vs 0.21/100,000, p < 0.01). In the case-control study, poor adherence to first-line anti-TB treatment (aOR = 9.2, 95% CI: 2.3-37) and initiating treatment > 15 months from symptom onset (aOR = 11, 95% CI: 1.5-87) were associated with MDR-TB. All ten facilities assessed reported stockouts of TB commodities. All 15 ambulatory MDR-TB patients we observed were not wearing masks given to them to minimize community infection. The MDR-TB ward at ARRH capacity was 4 patients but there were 11 patients. CONCLUSION The number of cases during January-August in 2017 was significantly higher than during the same months in 2013-2016. Poor adherence to TB drugs and delayed treatment initiation were associated with MDR-TB infection. We recommended strengthening directly-observed treatment strategy, increasing access to treatment services, and increasing the number of beds in the MDR-TB ward at ARRH.
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Affiliation(s)
| | - Doreen Birungi
- Uganda Public Health Fellowship Program, Kampala, Uganda
| | | | - Benon Kwesiga
- Uganda Public Health Fellowship Program, Kampala, Uganda
| | - Stavia Turyahabwe
- National Tuberculosis and Leprosy Program, Ministry of Health, Kampala, Uganda
| | - Alex R. Ario
- Uganda Public Health Fellowship Program, Kampala, Uganda
| | - Bao-Ping Zhu
- US Centers for Disease Control and Prevention, Kampala, Uganda
- Division of Global Health Protection, Center for Global Health, US Centers for Disease Control and Prevention, Atlanta, GA USA
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20
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Competing evolutionary paths in growing populations with applications to multidrug resistance. PLoS Comput Biol 2019; 15:e1006866. [PMID: 30986219 PMCID: PMC6483269 DOI: 10.1371/journal.pcbi.1006866] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 04/25/2019] [Accepted: 02/13/2019] [Indexed: 11/19/2022] Open
Abstract
Investigating the emergence of a particular cell type is a recurring theme in models of growing cellular populations. The evolution of resistance to therapy is a classic example. Common questions are: when does the cell type first occur, and via which sequence of steps is it most likely to emerge? For growing populations, these questions can be formulated in a general framework of branching processes spreading through a graph from a root to a target vertex. Cells have a particular fitness value on each vertex and can transition along edges at specific rates. Vertices represent cell states, say genotypes or physical locations, while possible transitions are acquiring a mutation or cell migration. We focus on the setting where cells at the root vertex have the highest fitness and transition rates are small. Simple formulas are derived for the time to reach the target vertex and for the probability that it is reached along a given path in the graph. We demonstrate our results on several scenarios relevant to the emergence of drug resistance, including: the orderings of resistance-conferring mutations in bacteria and the impact of imperfect drug penetration in cancer. How long does it take for a treatment naive, growing bacterial colony to be able to survive exposure to a cocktail of antibiotics? En route to multidrug resistance, what order did the drugs become impotent in? Questions such as these that pertain to the emergence of a significant cell type in a growing population arise frequently. They are often investigated via mathematical modelling but biologically insightful results are challenging to obtain. Here we outline a general framework of a stochastically growing population spreading through a graph to study such questions and provide simple formulas as answers. The significant cell type appears upon the population reaching a target vertex. Due to their simplicity, the derived formulas are widely accessible and can be used to guide and develop intuition on a range of biological scenarios. We demonstrate this on several settings including: how a region where drugs cannot penetrate affects the emergence of resistance, and, the ordering of mutations that leads to drugs being ineffective.
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Reid MJA, Arinaminpathy N, Bloom A, Bloom BR, Boehme C, Chaisson R, Chin DP, Churchyard G, Cox H, Ditiu L, Dybul M, Farrar J, Fauci AS, Fekadu E, Fujiwara PI, Hallett TB, Hanson CL, Harrington M, Herbert N, Hopewell PC, Ikeda C, Jamison DT, Khan AJ, Koek I, Krishnan N, Motsoaledi A, Pai M, Raviglione MC, Sharman A, Small PM, Swaminathan S, Temesgen Z, Vassall A, Venkatesan N, van Weezenbeek K, Yamey G, Agins BD, Alexandru S, Andrews JR, Beyeler N, Bivol S, Brigden G, Cattamanchi A, Cazabon D, Crudu V, Daftary A, Dewan P, Doepel LK, Eisinger RW, Fan V, Fewer S, Furin J, Goldhaber-Fiebert JD, Gomez GB, Graham SM, Gupta D, Kamene M, Khaparde S, Mailu EW, Masini EO, McHugh L, Mitchell E, Moon S, Osberg M, Pande T, Prince L, Rade K, Rao R, Remme M, Seddon JA, Selwyn C, Shete P, Sachdeva KS, Stallworthy G, Vesga JF, Vilc V, Goosby EP. Building a tuberculosis-free world: The Lancet Commission on tuberculosis. Lancet 2019; 393:1331-1384. [PMID: 30904263 DOI: 10.1016/s0140-6736(19)30024-8] [Citation(s) in RCA: 216] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Revised: 12/20/2018] [Accepted: 12/25/2018] [Indexed: 11/22/2022]
Affiliation(s)
- Michael J A Reid
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA; Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA, USA.
| | - Nimalan Arinaminpathy
- School of Public Health, Imperial College London, London, UK; Faculty of Medicine, Imperial College London, London, UK
| | - Amy Bloom
- Tuberculosis Division, United States Agency for International Development, Washington, DC, USA
| | - Barry R Bloom
- Department of Global Health and Population, Harvard University, Cambridge, MA, USA
| | | | - Richard Chaisson
- Departments of Medicine, Epidemiology, and International Health, Johns Hopkins School of Medicine, Baltimore, MA, USA
| | | | | | - Helen Cox
- Department of Pathology, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Mark Dybul
- Department of Medicine, Centre for Global Health and Quality, Georgetown University, Washington, DC, USA
| | | | - Anthony S Fauci
- National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Maryland, MA, USA
| | | | - Paula I Fujiwara
- Department of Tuberculosis and HIV, The International Union Against Tuberculosis and Lung Disease, Paris, France
| | - Timothy B Hallett
- School of Public Health, Imperial College London, London, UK; Faculty of Medicine, Imperial College London, London, UK
| | | | | | - Nick Herbert
- Global TB Caucus, Houses of Parliament, London, UK
| | - Philip C Hopewell
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Chieko Ikeda
- Department of GLobal Health, Ministry of Heath, Labor and Welfare, Tokyo, Japan
| | - Dean T Jamison
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA; Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Aamir J Khan
- Interactive Research & Development, Karachi, Pakistan
| | - Irene Koek
- Global Health Bureau, United States Agency for International Development, Washington, DC, USA
| | - Nalini Krishnan
- Resource Group for Education and Advocacy for Community Health, Chennai, India
| | - Aaron Motsoaledi
- South African National Department of Health, Pretoria, South Africa
| | - Madhukar Pai
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada; McGill International TB Center, McGill University, Montreal, QC, Canada
| | - Mario C Raviglione
- University of Milan, Milan, Italy; Global Studies Institute, University of Geneva, Geneva, Switzerland
| | - Almaz Sharman
- Academy of Preventive Medicine of Kazakhstan, Almaty, Kazakhstan
| | - Peter M Small
- Global Health Institute, School of Medicine, Stony Brook University, Stony Brook, NY, USA
| | | | - Zelalem Temesgen
- Department of Infectious Diseases, Mayo Clinic, Rochester, MI, USA
| | - Anna Vassall
- Department of Global Health and Development, Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, UK; Amsterdam Institute for Global Health and Development, University of Amsterdam, Amsterdam, Netherlands
| | | | | | - Gavin Yamey
- Center for Policy Impact in Global Health, Duke Global Health Institute, Duke University, Durham, NC, USA
| | - Bruce D Agins
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA; Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Sofia Alexandru
- Institutul de Ftiziopneumologie Chiril Draganiuc, Chisinau, Moldova
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, CA, USA
| | - Naomi Beyeler
- Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Stela Bivol
- Center for Health Policies and Studies, Chisinau, Moldova
| | - Grania Brigden
- Department of Tuberculosis and HIV, The International Union Against Tuberculosis and Lung Disease, Paris, France
| | - Adithya Cattamanchi
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Danielle Cazabon
- McGill International TB Center, McGill University, Montreal, QC, Canada
| | - Valeriu Crudu
- Center for Health Policies and Studies, Chisinau, Moldova
| | - Amrita Daftary
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada; McGill International TB Center, McGill University, Montreal, QC, Canada
| | - Puneet Dewan
- Bill & Melinda Gates Foundation, New Delhi, India
| | - Laurie K Doepel
- National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Maryland, MA, USA
| | - Robert W Eisinger
- National Institute of Allergy and Infectious Diseases, US National Institutes of Health, Maryland, MA, USA
| | - Victoria Fan
- T H Chan School of Public Health, Harvard University, Cambridge, MA, USA; Office of Public Health Studies, University of Hawaii, Mānoa, HI, USA
| | - Sara Fewer
- Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA, USA
| | - Jennifer Furin
- Division of Infectious Diseases & HIV Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jeremy D Goldhaber-Fiebert
- Centers for Health Policy and Primary Care and Outcomes Research, Stanford University, Stanford, CA, USA
| | - Gabriela B Gomez
- Department of Global Health and Development, Faculty of Public Health and Policy, London School of Hygiene and Tropical Medicine, London, UK
| | - Stephen M Graham
- Department of Tuberculosis and HIV, The International Union Against Tuberculosis and Lung Disease, Paris, France; Department of Paediatrics, Center for International Child Health, University of Melbourne, Melbourne, VIC, Australia; Burnet Institute, Melbourne, VIC, Australia
| | - Devesh Gupta
- Revised National TB Control Program, New Delhi, India
| | - Maureen Kamene
- National Tuberculosis, Leprosy and Lung Disease Program, Ministry of Health, Nairobi, Kenya
| | | | - Eunice W Mailu
- National Tuberculosis, Leprosy and Lung Disease Program, Ministry of Health, Nairobi, Kenya
| | | | - Lorrie McHugh
- Office of the Secretary-General's Special Envoy on Tuberculosis, United Nations, Geneva, Switzerland
| | - Ellen Mitchell
- International Institute of Social Studies, Erasmus University Rotterdam, The Hague, Netherland
| | - Suerie Moon
- Department of Global Health and Population, Harvard University, Cambridge, MA, USA; Global Health Centre, The Graduate Institute Geneva, Geneva, Switzerland
| | | | - Tripti Pande
- McGill International TB Center, McGill University, Montreal, QC, Canada
| | - Lea Prince
- Centers for Health Policy and Primary Care and Outcomes Research, Stanford University, Stanford, CA, USA
| | | | - Raghuram Rao
- Ministry of Health and Family Welfare, New Delhi, India
| | - Michelle Remme
- International Institute for Global Health, United Nations University, Kuala Lumpur, Malaysia
| | - James A Seddon
- Department of Medicine, Imperial College London, London, UK; Faculty of Medicine, Imperial College London, London, UK; Department of Paediatrics and Child Health, Stellenbosch University, Stellenbosch, South Africa
| | - Casey Selwyn
- Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Priya Shete
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | | | | | - Juan F Vesga
- School of Public Health, Imperial College London, London, UK; Faculty of Medicine, Imperial College London, London, UK
| | | | - Eric P Goosby
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA; Institute for Global Health Sciences, University of California San Francisco, San Francisco, CA, USA
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Divala TH, Corbett EL, Stagg HR, Nliwasa M, Sloan DJ, French N, Fielding KL. Effect of the duration of antimicrobial exposure on the development of antimicrobial resistance (AMR) for macrolide antibiotics: protocol for a systematic review with a network meta-analysis. Syst Rev 2018; 7:246. [PMID: 30580758 PMCID: PMC6304229 DOI: 10.1186/s13643-018-0917-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 12/13/2018] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND Antimicrobial resistance generates a huge health and economic burden and has the potential to become the leading cause of death globally, but its underlying drivers are yet to be fully described. The association between a microbe's exposure to antimicrobials and subsequent development of, or selection for, resistance is well documented, as are the exacerbating microbial and human factors. However, the nature and extent of this risk, and how it varies by antimicrobial class and duration of treatment, is poorly defined. The goal of our systematic review and network meta-analysis is to determine the relationship between the duration of antimicrobial exposure and selection for resistance. We will use macrolides as the antimicrobial class of interest and Streptococcus pneumoniae carriage as an indicator organism. Our secondary outcomes include duration of symptoms, risk of treatment failure and recurrence, and descriptions of resistance mechanisms. METHODS We will conduct a systematic review, selecting studies if they are published randomised controlled trials (RCTs) which report the relationship between taking a macrolide for any indication and incidence of resistant Streptococcus pneumoniae in patients of any age group. We will use a predefined search strategy to identify studies meeting these eligibility criteria in MEDLINE, Embase, Global Health and the Cochrane Central Register of RCTs. Two authors will independently screen titles and abstracts, review the full texts and undertake data extraction. We will use the Cochrane Collaboration's tool to assess the quality of included RCTs. If feasible, we will perform pair-wise meta-analysis modelling to determine the relationship between the duration of macrolide treatment and development of macrolide resistant Streptococcus pneumoniae. If the identified studies meet the assumptions for a network meta-analysis (NMA), we will additionally model this relationship using indirect comparisons. Our protocol utilises reporting guidance by Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) and the extensions for protocols (PRISMA-P) and network meta-analyses (PRISMA for NMA). Our review will also report to these standards. DISCUSSION Establishing the relationship between the duration of antimicrobial exposure and development of, or selection for, resistance will inform the design of antimicrobial prescriptions, treatment guidelines and the behaviour of both physicians and patients. This work will therefore be a strong contribution towards the full realisation of current antimicrobial resistance stewardship strategies. SYSTEMATIC REVIEW REGISTRATION PROSPERO CRD42018089275.
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Affiliation(s)
- Titus H. Divala
- London School of Hygiene & Tropical Medicine, Keppel Street, Bloomsbury, London, WC1E 7HT UK
- Helse Nord Tuberculosis Initiative, University of Malawi College of Medicine, Blantyre, Malawi
| | - Elizabeth L. Corbett
- London School of Hygiene & Tropical Medicine, Keppel Street, Bloomsbury, London, WC1E 7HT UK
- Helse Nord Tuberculosis Initiative, University of Malawi College of Medicine, Blantyre, Malawi
- Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Helen R. Stagg
- Usher Institute for Population Health Sciences and Informatics, University of Edinburgh, Edinburgh, EH8 9AG UK
| | - Marriott Nliwasa
- London School of Hygiene & Tropical Medicine, Keppel Street, Bloomsbury, London, WC1E 7HT UK
- Helse Nord Tuberculosis Initiative, University of Malawi College of Medicine, Blantyre, Malawi
| | - Derek J. Sloan
- School of Medicine, University of St Andrews, St Andrews, UK
| | - Neil French
- Institute of Infection & Global Health, University of Liverpool, Liverpool, UK
| | - Katherine L. Fielding
- London School of Hygiene & Tropical Medicine, Keppel Street, Bloomsbury, London, WC1E 7HT UK
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Nguyen QH, Contamin L, Nguyen TVA, Bañuls A. Insights into the processes that drive the evolution of drug resistance in Mycobacterium tuberculosis. Evol Appl 2018; 11:1498-1511. [PMID: 30344622 PMCID: PMC6183457 DOI: 10.1111/eva.12654] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 05/25/2018] [Accepted: 05/27/2018] [Indexed: 01/01/2023] Open
Abstract
At present, the successful transmission of drug-resistant Mycobacterium tuberculosis, including multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains, in human populations, threatens tuberculosis control worldwide. Differently from many other bacteria, M. tuberculosis drug resistance is acquired mainly through mutations in specific drug resistance-associated genes. The panel of mutations is highly diverse, but depends on the affected gene and M. tuberculosis genetic background. The variety of genetic profiles observed in drug-resistant clinical isolates underlines different evolutionary trajectories towards multiple drug resistance, although some mutation patterns are prominent. This review discusses the intrinsic processes that may influence drug resistance evolution in M. tuberculosis, such as mutation rate, drug resistance-associated mutations, fitness cost, compensatory mutations and epistasis. This knowledge should help to better predict the risk of emergence of highly resistant M. tuberculosis strains and to develop new tools and strategies to limit the development and spread of MDR and XDR strains.
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Affiliation(s)
- Quang Huy Nguyen
- Department of Pharmacological, Medical and Agronomical BiotechnologyUniversity of Science and Technology of HanoiVietnam Academy of Science and Technology (VAST)HanoiVietnam
- Institute of Research for DevelopmentUMR MIVEGEC (CNRS‐IRD‐University of Montpellier)MontpellierFrance
- LMI Drug Resistance in South East Asia (LMI DRISA)University of Science and Technology of HanoiVietnam Academy of Science and Technology (VAST)HanoiVietnam
| | - Lucie Contamin
- Institute of Research for DevelopmentUMR MIVEGEC (CNRS‐IRD‐University of Montpellier)MontpellierFrance
- LMI Drug Resistance in South East Asia (LMI DRISA)University of Science and Technology of HanoiVietnam Academy of Science and Technology (VAST)HanoiVietnam
- Department of BacteriologyNational Institute of Hygiene and Epidemiology (NIHE)HanoiVietnam
| | - Thi Van Anh Nguyen
- Department of BacteriologyNational Institute of Hygiene and Epidemiology (NIHE)HanoiVietnam
| | - Anne‐Laure Bañuls
- Institute of Research for DevelopmentUMR MIVEGEC (CNRS‐IRD‐University of Montpellier)MontpellierFrance
- LMI Drug Resistance in South East Asia (LMI DRISA)University of Science and Technology of HanoiVietnam Academy of Science and Technology (VAST)HanoiVietnam
- Department of BacteriologyNational Institute of Hygiene and Epidemiology (NIHE)HanoiVietnam
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24
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Pienaar E, Linderman JJ, Kirschner DE. Emergence and selection of isoniazid and rifampin resistance in tuberculosis granulomas. PLoS One 2018; 13:e0196322. [PMID: 29746491 PMCID: PMC5944939 DOI: 10.1371/journal.pone.0196322] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 04/11/2018] [Indexed: 12/15/2022] Open
Abstract
Drug resistant tuberculosis is increasing world-wide. Resistance against isoniazid (INH), rifampicin (RIF), or both (multi-drug resistant TB, MDR-TB) is of particular concern, since INH and RIF form part of the standard regimen for TB disease. While it is known that suboptimal treatment can lead to resistance, it remains unclear how host immune responses and antibiotic dynamics within granulomas (sites of infection) affect emergence and selection of drug-resistant bacteria. We take a systems pharmacology approach to explore resistance dynamics within granulomas. We integrate spatio-temporal host immunity, INH and RIF dynamics, and bacterial dynamics (including fitness costs and compensatory mutations) in a computational framework. We simulate resistance emergence in the absence of treatment, as well as resistance selection during INH and/or RIF treatment. There are four main findings. First, in the absence of treatment, the percentage of granulomas containing resistant bacteria mirrors the non-monotonic bacterial dynamics within granulomas. Second, drug-resistant bacteria are less frequently found in non-replicating states in caseum, compared to drug-sensitive bacteria. Third, due to a steeper dose response curve and faster plasma clearance of INH compared to RIF, INH-resistant bacteria have a stronger influence on treatment outcomes than RIF-resistant bacteria. Finally, under combination therapy with INH and RIF, few MDR bacteria are able to significantly affect treatment outcomes. Overall, our approach allows drug-specific prediction of drug resistance emergence and selection in the complex granuloma context. Since our predictions are based on pre-clinical data, our approach can be implemented relatively early in the treatment development process, thereby enabling pro-active rather than reactive responses to emerging drug resistance for new drugs. Furthermore, this quantitative and drug-specific approach can help identify drug-specific properties that influence resistance and use this information to design treatment regimens that minimize resistance selection and expand the useful life-span of new antibiotics.
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Affiliation(s)
- Elsje Pienaar
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jennifer J. Linderman
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Denise E. Kirschner
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
- * E-mail:
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25
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Drug-resistant Mycobacterium tuberculosis: Epidemiology and role of morphological alterations. J Glob Antimicrob Resist 2018; 12:192-196. [DOI: 10.1016/j.jgar.2017.10.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 09/30/2017] [Accepted: 10/07/2017] [Indexed: 02/03/2023] Open
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Pienaar E, Sarathy J, Prideaux B, Dietzold J, Dartois V, Kirschner DE, Linderman JJ. Comparing efficacies of moxifloxacin, levofloxacin and gatifloxacin in tuberculosis granulomas using a multi-scale systems pharmacology approach. PLoS Comput Biol 2017; 13:e1005650. [PMID: 28817561 PMCID: PMC5560534 DOI: 10.1371/journal.pcbi.1005650] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 06/26/2017] [Indexed: 12/19/2022] Open
Abstract
Granulomas are complex lung lesions that are the hallmark of tuberculosis (TB). Understanding antibiotic dynamics within lung granulomas will be vital to improving and shortening the long course of TB treatment. Three fluoroquinolones (FQs) are commonly prescribed as part of multi-drug resistant TB therapy: moxifloxacin (MXF), levofloxacin (LVX) or gatifloxacin (GFX). To date, insufficient data are available to support selection of one FQ over another, or to show that these drugs are clinically equivalent. To predict the efficacy of MXF, LVX and GFX at a single granuloma level, we integrate computational modeling with experimental datasets into a single mechanistic framework, GranSim. GranSim is a hybrid agent-based computational model that simulates granuloma formation and function, FQ plasma and tissue pharmacokinetics and pharmacodynamics and is based on extensive in vitro and in vivo data. We treat in silico granulomas with recommended daily doses of each FQ and compare efficacy by multiple metrics: bacterial load, sterilization rates, early bactericidal activity and efficacy under non-compliance and treatment interruption. GranSim reproduces in vivo plasma pharmacokinetics, spatial and temporal tissue pharmacokinetics and in vitro pharmacodynamics of these FQs. We predict that MXF kills intracellular bacteria more quickly than LVX and GFX due in part to a higher cellular accumulation ratio. We also show that all three FQs struggle to sterilize non-replicating bacteria residing in caseum. This is due to modest drug concentrations inside caseum and high inhibitory concentrations for this bacterial subpopulation. MXF and LVX have higher granuloma sterilization rates compared to GFX; and MXF performs better in a simulated non-compliance or treatment interruption scenario. We conclude that MXF has a small but potentially clinically significant advantage over LVX, as well as LVX over GFX. We illustrate how a systems pharmacology approach combining experimental and computational methods can guide antibiotic selection for TB. Tuberculosis (TB) is caused by infection with the bacterium Mycobacterium tuberculosis (Mtb) and kills 1.5 million people each year. TB requires at least 6 months of treatment with up to four drugs, and is characterized by formation of granulomas in patient lungs. Granulomas are spherical collections of host cells and bacteria. Fluoroquinolones (FQs) are a class of drug that could help shorten TB treatment. Three FQs that are used to treat TB are: moxifloxacin (MXF), levofloxacin (LVX) or gatifloxacin (GFX). To date, it is unclear if one FQ is better than the others at treating TB, in part because little is known about how these drugs distribute and work inside the lung granulomas. We use computer simulations of Mtb infection and FQ treatment within granulomas to predict which FQ is better and why. Our computer model is calibrated to multiple experimental data sets. We compare the three FQs by multiple metrics, and predict that MXF is better than LVX and GFX because it kills bacteria more quickly, and it works better when patients miss doses. However, all three FQs are unable to kill a part of the bacterial population living in the center of granulomas. Our results can now inform future experimental studies.
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Affiliation(s)
- Elsje Pienaar
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Jansy Sarathy
- Public Health Research Institute and New Jersey Medical School, Rutgers, Newark, New Jersey, United States of America
| | - Brendan Prideaux
- Public Health Research Institute and New Jersey Medical School, Rutgers, Newark, New Jersey, United States of America
| | - Jillian Dietzold
- Department of Medicine, Division of Infectious Disease, New Jersey Medical School, Rutgers University, Newark, New Jersey, United States of America
| | - Véronique Dartois
- Public Health Research Institute and New Jersey Medical School, Rutgers, Newark, New Jersey, United States of America
| | - Denise E. Kirschner
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Jennifer J. Linderman
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- * E-mail:
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27
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Kirschner D, Pienaar E, Marino S, Linderman JJ. A review of computational and mathematical modeling contributions to our understanding of Mycobacterium tuberculosis within-host infection and treatment. ACTA ACUST UNITED AC 2017; 3:170-185. [PMID: 30714019 DOI: 10.1016/j.coisb.2017.05.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Tuberculosis (TB) is an ancient and deadly disease characterized by complex host-pathogen dynamics playing out over multiple time and length scales and physiological compartments. Computational modeling can be used to integrate various types of experimental data and suggest new hypotheses, mechanisms, and therapeutic approaches to TB. Here, we offer a first-time comprehensive review of work on within-host TB models that describe the immune response of the host to infection, including the formation of lung granulomas. The models include systems of ordinary and partial differential equations and agent-based models as well as hybrid and multi-scale models that are combinations of these. Many aspects of M. tuberculosis infection, including host dynamics in the lung (typical site of infection for TB), granuloma formation, roles of cytokine and chemokine dynamics, and bacterial nutrient availability have been explored. Finally, we survey applications of these within-host models to TB therapy and prevention and suggest future directions to impact this global disease.
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Affiliation(s)
- Denise Kirschner
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI
| | - Elsje Pienaar
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI
| | - Simeone Marino
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI
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28
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Sharma A, Hill A, Kurbatova E, van der Walt M, Kvasnovsky C, Tupasi TE, Caoili JC, Gler MT, Volchenkov GV, Kazennyy BY, Demikhova OV, Bayona J, Contreras C, Yagui M, Leimane V, Cho SN, Kim HJ, Kliiman K, Akksilp S, Jou R, Ershova J, Dalton T, Cegielski P. Estimating the future burden of multidrug-resistant and extensively drug-resistant tuberculosis in India, the Philippines, Russia, and South Africa: a mathematical modelling study. THE LANCET. INFECTIOUS DISEASES 2017; 17:707-715. [PMID: 28499828 DOI: 10.1016/s1473-3099(17)30247-5] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 02/17/2017] [Accepted: 03/28/2017] [Indexed: 12/26/2022]
Abstract
BACKGROUND Multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis are emerging worldwide. The Green Light Committee initiative supported programmatic management of drug-resistant tuberculosis in 90 countries. We used estimates from the Preserving Effective TB Treatment Study to predict MDR and XDR tuberculosis trends in four countries with a high burden of MDR tuberculosis: India, the Philippines, Russia, and South Africa. METHODS We calibrated a compartmental model to data from drug resistance surveys and WHO tuberculosis reports to forecast estimates of incident MDR and XDR tuberculosis and the percentage of incident MDR and XDR tuberculosis caused by acquired drug resistance, assuming no fitness cost of resistance from 2000 to 2040 in India, the Philippines, Russia, and South Africa. FINDINGS The model forecasted the percentage of MDR tuberculosis among incident cases of tuberculosis to increase, reaching 12·4% (95% prediction interval 9·4-16·2) in India, 8·9% (4·5-11·7) in the Philippines, 32·5% (27·0-35·8) in Russia, and 5·7% (3·0-7·6) in South Africa in 2040. It also predicted the percentage of XDR tuberculosis among incident MDR tuberculosis to increase, reaching 8·9% (95% prediction interval 5·1-12·9) in India, 9·0% (4·0-14·7) in the Philippines, 9·0% (4·8-14·2) in Russia, and 8·5% (2·5-14·7) in South Africa in 2040. Acquired drug resistance would cause less than 30% of incident MDR tuberculosis during 2000-40. Acquired drug resistance caused 80% of incident XDR tuberculosis in 2000, but this estimate would decrease to less than 50% by 2040. INTERPRETATION MDR and XDR tuberculosis were forecast to increase in all four countries despite improvements in acquired drug resistance shown by the Green Light Committee-supported programmatic management of drug-resistant tuberculosis. Additional control efforts beyond improving acquired drug resistance rates are needed to stop the spread of MDR and XDR tuberculosis in countries with a high burden of MDR tuberculosis. FUNDING US Agency for International Development and US Centers for Disease Control and Prevention, Division of Tuberculosis Elimination.
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Affiliation(s)
- Aditya Sharma
- US Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Andrew Hill
- US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | | | | | | | | | | | | | | | - Olga V Demikhova
- Central Tuberculosis Research Institute, Russian Academy of Medical Sciences, Moscow, Russia
| | | | | | | | - Vaira Leimane
- Riga East University Hospital Centre of Tuberculosis and Lung Diseases, Latvia
| | - Sang Nae Cho
- International Tuberculosis Research Center, Changwon and Yonsei University College of Medicine, Seoul, South Korea
| | - Hee Jin Kim
- Korean Institute of Tuberculosis, Seoul, South Korea
| | | | | | - Ruwen Jou
- Taiwan Centers for Disease Control, Taipei, Taiwan
| | - Julia Ershova
- US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Tracy Dalton
- US Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Peter Cegielski
- US Centers for Disease Control and Prevention, Atlanta, GA, USA
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29
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Acquisition of Rifampin Resistance in Pulmonary Tuberculosis. Antimicrob Agents Chemother 2017; 61:AAC.02220-16. [PMID: 28167550 DOI: 10.1128/aac.02220-16] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/28/2017] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis strains with spontaneous mutations conferring resistance to rifampin (RIF) are exceedingly rare, and fixed drug combinations typically prevent augmentation of resistance to single drugs. Fourteen newly diagnosed tuberculosis patients were treated with RIF alone for 14 days, and bacterial loads, including mutation frequencies, were determined. A statistical model estimated that 1% of the remaining viable mycobacteria could be RIF resistant after 30 days of monotherapy. This indicates that temporal and spatial windows of RIF monotherapy due to uneven drug distribution within lung lesions could contribute to the acquisition of resistance to RIF.
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30
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Eshetie S, Gizachew M, Dagnew M, Kumera G, Woldie H, Ambaw F, Tessema B, Moges F. Multidrug resistant tuberculosis in Ethiopian settings and its association with previous history of anti-tuberculosis treatment: a systematic review and meta-analysis. BMC Infect Dis 2017; 17:219. [PMID: 28320336 PMCID: PMC5360058 DOI: 10.1186/s12879-017-2323-y] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 03/14/2017] [Indexed: 12/26/2022] Open
Abstract
Background Efforts to control the global burden of tuberculosis (TB) have been jeopardized by the rapid evolution of multi-drug resistant Mycobacterium tuberculosis (MTB), which is resistant to at least isoniazid and rifampicin. Previous studies have documented variable prevalences of multidrug-resistant tuberculosis (MDR-TB) and its risk factors in Ethiopia. Therefore, this meta-analysis is aimed, firstly, to determine the pooled prevalence of MDR-TB among newly diagnosed and previously treated TB cases, and secondly, to measure the association between MDR-TB and a history of previous anti-TB drugs treatment. Methods PubMed, Embase and Google Scholar databases were searched. Studies that reported a prevalence of MDR-TB among new and previously treated TB patients were selected. Studies or surveys conducted at national or sub-national level, with reported MDR-TB prevalence or sufficient data to calculate prevalence were considered for the analysis. Two authors searched and reviewed the studies for eligibility and extracted the data in pre-defined forms. Forest plots of all prevalence estimates were performed and summary estimates were also calculated using random effects models. Associations between previous TB treatment and MDR-MTB infection were examined through subgroup analyses stratified by new and previously treated patients. Results We identified 16 suitable studies and found an overall prevalence of MDR-TB among newly diagnosed and previously treated TB patients to be 2% (95% CI 1% - 2%) and 15% (95% CI 12% - 17%), respectively. The observed difference was statistically significant (P < 0.001) and there was an odds ratio of 8.1 (95% CI 7.5–8.7) for previously treated TB patients to develop a MDR-MTB infection compared to newly diagnosed cases. For the past 10 years (2006 to 2014) the overall MDR-TB prevalence showed a stable time trend. Conclusions The burden of MDR-TB remains high in Ethiopian settings, especially in previously treated TB cases. Previous TB treatment was the most powerful predictor for MDR-MTB infection. Strict compliance with anti-TB regimens and improving case detection rate are the necessary steps to tackle the problem in Ethiopia.
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Affiliation(s)
- Setegn Eshetie
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar Northwest, Ethiopia.
| | - Mucheye Gizachew
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar Northwest, Ethiopia
| | - Mulat Dagnew
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar Northwest, Ethiopia
| | - Gemechu Kumera
- Department of Human Nutrition, College of Health Sciences, Debre Markos University, Debre Markos, Ethiopia
| | - Haile Woldie
- Department of Human Nutrition, Institute of Public Health, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Fekadu Ambaw
- Department of Nursing, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Belay Tessema
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar Northwest, Ethiopia.,WHO/TDR Clinical Research and Development Fellow at FIND, Geneva, Switzerland
| | - Feleke Moges
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Sciences, University of Gondar, Gondar Northwest, Ethiopia
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31
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Dheda K, Gumbo T, Maartens G, Dooley KE, McNerney R, Murray M, Furin J, Nardell EA, London L, Lessem E, Theron G, van Helden P, Niemann S, Merker M, Dowdy D, Van Rie A, Siu GKH, Pasipanodya JG, Rodrigues C, Clark TG, Sirgel FA, Esmail A, Lin HH, Atre SR, Schaaf HS, Chang KC, Lange C, Nahid P, Udwadia ZF, Horsburgh CR, Churchyard GJ, Menzies D, Hesseling AC, Nuermberger E, McIlleron H, Fennelly KP, Goemaere E, Jaramillo E, Low M, Jara CM, Padayatchi N, Warren RM. The epidemiology, pathogenesis, transmission, diagnosis, and management of multidrug-resistant, extensively drug-resistant, and incurable tuberculosis. THE LANCET. RESPIRATORY MEDICINE 2017; 5:S2213-2600(17)30079-6. [PMID: 28344011 DOI: 10.1016/s2213-2600(17)30079-6] [Citation(s) in RCA: 377] [Impact Index Per Article: 53.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 10/24/2016] [Accepted: 12/08/2016] [Indexed: 12/25/2022]
Abstract
Global tuberculosis incidence has declined marginally over the past decade, and tuberculosis remains out of control in several parts of the world including Africa and Asia. Although tuberculosis control has been effective in some regions of the world, these gains are threatened by the increasing burden of multidrug-resistant (MDR) and extensively drug-resistant (XDR) tuberculosis. XDR tuberculosis has evolved in several tuberculosis-endemic countries to drug-incurable or programmatically incurable tuberculosis (totally drug-resistant tuberculosis). This poses several challenges similar to those encountered in the pre-chemotherapy era, including the inability to cure tuberculosis, high mortality, and the need for alternative methods to prevent disease transmission. This phenomenon mirrors the worldwide increase in antimicrobial resistance and the emergence of other MDR pathogens, such as malaria, HIV, and Gram-negative bacteria. MDR and XDR tuberculosis are associated with high morbidity and substantial mortality, are a threat to health-care workers, prohibitively expensive to treat, and are therefore a serious public health problem. In this Commission, we examine several aspects of drug-resistant tuberculosis. The traditional view that acquired resistance to antituberculous drugs is driven by poor compliance and programmatic failure is now being questioned, and several lines of evidence suggest that alternative mechanisms-including pharmacokinetic variability, induction of efflux pumps that transport the drug out of cells, and suboptimal drug penetration into tuberculosis lesions-are likely crucial to the pathogenesis of drug-resistant tuberculosis. These factors have implications for the design of new interventions, drug delivery and dosing mechanisms, and public health policy. We discuss epidemiology and transmission dynamics, including new insights into the fundamental biology of transmission, and we review the utility of newer diagnostic tools, including molecular tests and next-generation whole-genome sequencing, and their potential for clinical effectiveness. Relevant research priorities are highlighted, including optimal medical and surgical management, the role of newer and repurposed drugs (including bedaquiline, delamanid, and linezolid), pharmacokinetic and pharmacodynamic considerations, preventive strategies (such as prophylaxis in MDR and XDR contacts), palliative and patient-orientated care aspects, and medicolegal and ethical issues.
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Affiliation(s)
- Keertan Dheda
- Lung Infection and Immunity Unit, Department of Medicine, Division of Pulmonology and UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa.
| | - Tawanda Gumbo
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, USA
| | - Gary Maartens
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Kelly E Dooley
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Ruth McNerney
- Lung Infection and Immunity Unit, Department of Medicine, Division of Pulmonology and UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | - Megan Murray
- Department of Global Health and Social Medicine, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jennifer Furin
- Department of Global Health and Social Medicine, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Edward A Nardell
- TH Chan School of Public Health, Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Leslie London
- School of Public Health and Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Grant Theron
- SA MRC Centre for Tuberculosis Research/DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg, South Africa
| | - Paul van Helden
- SA MRC Centre for Tuberculosis Research/DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg, South Africa
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Schleswig-Holstein, Germany; German Centre for Infection Research (DZIF), Partner Site Borstel, Borstel, Schleswig-Holstein, Germany
| | - Matthias Merker
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Schleswig-Holstein, Germany
| | - David Dowdy
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Annelies Van Rie
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; International Health Unit, Epidemiology and Social Medicine, Faculty of Medicine, University of Antwerp, Antwerp, Belgium
| | - Gilman K H Siu
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China
| | - Jotam G Pasipanodya
- Center for Infectious Diseases Research and Experimental Therapeutics, Baylor Research Institute, Baylor University Medical Center, Dallas, TX, USA
| | - Camilla Rodrigues
- Department of Microbiology, P.D. Hinduja National Hospital & Medical Research Centre, Mumbai, India
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases and Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Frik A Sirgel
- SA MRC Centre for Tuberculosis Research/DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg, South Africa
| | - Aliasgar Esmail
- Lung Infection and Immunity Unit, Department of Medicine, Division of Pulmonology and UCT Lung Institute, University of Cape Town, Groote Schuur Hospital, Cape Town, South Africa
| | - Hsien-Ho Lin
- Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Sachin R Atre
- Center for Clinical Global Health Education (CCGHE), Johns Hopkins University, Baltimore, MD, USA; Medical College, Hospital and Research Centre, Pimpri, Pune, India
| | - H Simon Schaaf
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Kwok Chiu Chang
- Tuberculosis and Chest Service, Centre for Health Protection, Department of Health, Hong Kong SAR, China
| | - Christoph Lange
- Division of Clinical Infectious Diseases, German Center for Infection Research, Research Center Borstel, Borstel, Schleswig-Holstein, Germany; International Health/Infectious Diseases, University of Lübeck, Lübeck, Germany; Department of Medicine, Karolinska Institute, Stockholm, Sweden; Department of Medicine, University of Namibia School of Medicine, Windhoek, Namibia
| | - Payam Nahid
- Division of Pulmonary and Critical Care, San Francisco General Hospital, University of California, San Francisco, CA, USA
| | - Zarir F Udwadia
- Pulmonary Department, Hinduja Hospital & Research Center, Mumbai, India
| | | | - Gavin J Churchyard
- Aurum Institute, Johannesburg, South Africa; School of Public Health, University of Witwatersrand, Johannesburg, South Africa; Advancing Treatment and Care for TB/HIV, South African Medical Research Council, Johannesburg, South Africa
| | - Dick Menzies
- Montreal Chest Institute, McGill University, Montreal, QC, Canada
| | - Anneke C Hesseling
- Desmond Tutu TB Centre, Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Eric Nuermberger
- Center for Tuberculosis Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Helen McIlleron
- Division of Clinical Pharmacology, Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Kevin P Fennelly
- Pulmonary Clinical Medicine Section, Division of Intramural Research, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Eric Goemaere
- MSF South Africa, Cape Town, South Africa; School of Public Health and Family Medicine, University of Cape Town, Cape Town, South Africa
| | | | - Marcus Low
- Treatment Action Campaign, Johannesburg, South Africa
| | | | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), MRC HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Robin M Warren
- SA MRC Centre for Tuberculosis Research/DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Tygerberg, South Africa
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32
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Gomez JE, Kaufmann-Malaga BB, Wivagg CN, Kim PB, Silvis MR, Renedo N, Ioerger TR, Ahmad R, Livny J, Fishbein S, Sacchettini JC, Carr SA, Hung DT. Ribosomal mutations promote the evolution of antibiotic resistance in a multidrug environment. eLife 2017; 6. [PMID: 28220755 PMCID: PMC5319836 DOI: 10.7554/elife.20420] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 01/20/2017] [Indexed: 12/17/2022] Open
Abstract
Antibiotic resistance arising via chromosomal mutations is typically specific to a particular antibiotic or class of antibiotics. We have identified mutations in genes encoding ribosomal components in Mycobacterium smegmatis that confer resistance to several structurally and mechanistically unrelated classes of antibiotics and enhance survival following heat shock and membrane stress. These mutations affect ribosome assembly and cause large-scale transcriptomic and proteomic changes, including the downregulation of the catalase KatG, an activating enzyme required for isoniazid sensitivity, and upregulation of WhiB7, a transcription factor involved in innate antibiotic resistance. Importantly, while these ribosomal mutations have a fitness cost in antibiotic-free medium, in a multidrug environment they promote the evolution of high-level, target-based resistance. Further, suppressor mutations can then be easily acquired to restore wild-type growth. Thus, ribosomal mutations can serve as stepping-stones in an evolutionary path leading to the emergence of high-level, multidrug resistance. DOI:http://dx.doi.org/10.7554/eLife.20420.001 The rise of antibiotic resistant bacteria is challenging clinicians, and some infections are now resistant to almost all of the drugs that are currently available. Some types of bacteria – such as mycobacteria, which include the bacteria that cause tuberculosis and leprosy – can only acquire antibiotic resistance from mutations that alter their existing genes. The process by which bacteria develop resistance to multiple drugs is generally viewed as a stepwise accumulation of different mutations. However, the role of individual mutations that increase a bacterium’s resistance to multiple antibiotics has not been fully explored. Gomez, Kaufmann-Malaga et al. exposed bacteria from the species Mycobacterium smegmatis, a cousin of the bacterium that causes tuberculosis, to a mixture of relatively low concentrations of different antibiotics that should kill the bacteria relatively slowly. Hundreds of small bacteria cultures were grown in parallel, and only a fraction of them developed antibiotic-resistant members. Gomez, Kaufmann-Malaga et al. identified mutations in these bacteria that unexpectedly gave the bacteria resistance to several unrelated classes of antibiotics. Individual mutants carried single mutations in different components of the ribosome, a complex molecular machine that helps to build proteins inside cells. As well as increasing their resistance to antibiotics, these mutations also reduced the growth rate of the bacteria. This meant that when the bacteria were grown in an antibiotic-free environment they survived less well than non-mutant bacteria. However, the mutations gave the bacteria an advantage in environments that contained many different antibiotics, as they could more easily develop mutations that made them more resistant to other drugs. Thus, the mutant bacteria can serve as stepping-stones toward the development of high-level resistance to multiple drugs. Further work will now explore whether this phenomenon occurs in a range of other bacterial species, including the bacteria that cause tuberculosis. While new antibiotics are desperately needed, a better understanding of how bacteria evolve the ability to resist the effects of antibiotics will help us to preserve the usefulness of existing and future drugs. DOI:http://dx.doi.org/10.7554/eLife.20420.002
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Affiliation(s)
- James E Gomez
- The Broad Institute of MIT and Harvard, Cambridge, United States
| | - Benjamin B Kaufmann-Malaga
- The Broad Institute of MIT and Harvard, Cambridge, United States.,Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, United States
| | - Carl N Wivagg
- The Broad Institute of MIT and Harvard, Cambridge, United States.,Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States
| | - Peter B Kim
- The Broad Institute of MIT and Harvard, Cambridge, United States
| | - Melanie R Silvis
- The Broad Institute of MIT and Harvard, Cambridge, United States
| | - Nikolai Renedo
- The Broad Institute of MIT and Harvard, Cambridge, United States
| | - Thomas R Ioerger
- Department of Computer Science, Texas A&M University, College Station, United States
| | - Rushdy Ahmad
- The Broad Institute of MIT and Harvard, Cambridge, United States
| | - Jonathan Livny
- The Broad Institute of MIT and Harvard, Cambridge, United States
| | - Skye Fishbein
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, United States
| | - James C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, United States
| | - Steven A Carr
- The Broad Institute of MIT and Harvard, Cambridge, United States
| | - Deborah T Hung
- The Broad Institute of MIT and Harvard, Cambridge, United States.,Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, United States.,Department of Genetics, Harvard Medical School, Boston, United States
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33
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Maitre T, Aubry A, Jarlier V, Robert J, Veziris N, Bernard C, Sougakoff W, Brossier F, Cambau E, Mougari F, Raskine L. Multidrug and extensively drug-resistant tuberculosis. Med Mal Infect 2017; 47:3-10. [DOI: 10.1016/j.medmal.2016.07.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 07/18/2016] [Indexed: 11/16/2022]
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34
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Alexander HK, Mayer SI, Bonhoeffer S. Population Heterogeneity in Mutation Rate Increases the Frequency of Higher-Order Mutants and Reduces Long-Term Mutational Load. Mol Biol Evol 2017; 34:419-436. [PMID: 27836985 PMCID: PMC5850754 DOI: 10.1093/molbev/msw244] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Mutation rate is a crucial evolutionary parameter that has typically been treated as a constant in population genetic analyses. However, the propensity to mutate is likely to vary among co-existing individuals within a population, due to genetic polymorphisms, heterogeneous environmental influences, and random physiological fluctuations. We review the evidence for mutation rate heterogeneity and explore its consequences by extending classic population genetic models to allow an arbitrary distribution of mutation rate among individuals, either with or without inheritance. With this general new framework, we rigorously establish the effects of heterogeneity at various evolutionary timescales. In a single generation, variation of mutation rate about the mean increases the probability of producing zero or many simultaneous mutations on a genome. Over multiple generations of mutation and selection, heterogeneity accelerates the appearance of both deleterious and beneficial multi-point mutants. At mutation-selection balance, higher-order mutant frequencies are likewise boosted, while lower-order mutants exhibit subtler effects; nonetheless, population mean fitness is always enhanced. We quantify the dependencies on moments of the mutation rate distribution and selection coefficients, and clarify the role of mutation rate inheritance. While typical methods of estimating mutation rate will recover only the population mean, analyses assuming mutation rate is fixed to this mean could underestimate the potential for multi-locus adaptation, including medically relevant evolution in pathogenic and cancerous populations. We discuss the potential to empirically parameterize mutation rate distributions, which have to date hardly been quantified.
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Affiliation(s)
- Helen K. Alexander
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Switzerland
| | - Stephanie I. Mayer
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Switzerland
| | - Sebastian Bonhoeffer
- Institute of Integrative Biology, Department of Environmental Systems Science, ETH Zürich, Switzerland
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35
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Ayabina D, Hendon-Dunn C, Bacon J, Colijn C. Diverse drug-resistant subpopulations of Mycobacterium tuberculosis are sustained in continuous culture. J R Soc Interface 2016; 13:rsif.2016.0745. [PMID: 27807274 PMCID: PMC5134024 DOI: 10.1098/rsif.2016.0745] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 10/11/2016] [Indexed: 01/09/2023] Open
Abstract
Drug resistance to tuberculosis (TB) has become more widespread over the past decade. As such, understanding the emergence and fitness of antibiotic-resistant subpopulations is crucial for the development of new interventions. Here we use a simple mathematical model to explain the differences in the response to isoniazid (INH) of Mycobacterium tuberculosis cells cultured under two growth rates in a chemostat. We obtain posterior distributions of model parameters consistent with data using a Markov chain Monte Carlo (MCMC) method. We explore the dynamics of diverse INH-resistant subpopulations consistent with these data in a multi-population model. We find that the simple model captures the qualitative behaviour of the cultures under both dilution rates and also present testable predictions about how diversity is maintained in such cultures.
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Affiliation(s)
- Diepreye Ayabina
- Department of Mathematics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
| | - Charlotte Hendon-Dunn
- Public Health England, National Infection Service, Porton Down, Salisbury SP4 0JG, UK
| | - Joanna Bacon
- Public Health England, National Infection Service, Porton Down, Salisbury SP4 0JG, UK
| | - Caroline Colijn
- Department of Mathematics, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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36
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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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37
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Mieras L, Anthony R, van Brakel W, Bratschi MW, van den Broek J, Cambau E, Cavaliero A, Kasang C, Perera G, Reichman L, Richardus JH, Saunderson P, Steinmann P, Yew WW. Negligible risk of inducing resistance in Mycobacterium tuberculosis with single-dose rifampicin as post-exposure prophylaxis for leprosy. Infect Dis Poverty 2016; 5:46. [PMID: 27268059 PMCID: PMC4897814 DOI: 10.1186/s40249-016-0140-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 04/28/2016] [Indexed: 12/02/2022] Open
Abstract
Post-exposure prophylaxis (PEP) for leprosy is administered as one single dose of rifampicin (SDR) to the contacts of newly diagnosed leprosy patients. SDR reduces the risk of developing leprosy among contacts by around 60 % in the first 2–3 years after receiving SDR. In countries where SDR is currently being implemented under routine programme conditions in defined areas, questions were raised by health authorities and professional bodies about the possible risk of inducing rifampicin resistance among the M. tuberculosis strains circulating in these areas. This issue has not been addressed in scientific literature to date. To produce an authoritative consensus statement about the risk that SDR would induce rifampicin-resistant tuberculosis, a meeting was convened with tuberculosis (TB) and leprosy experts. The experts carefully reviewed and discussed the available evidence regarding the mechanisms and risk factors for the development of (multi) drug-resistance in M. tuberculosis with a view to the special situation of the use of SDR as PEP for leprosy. They concluded that SDR given to contacts of leprosy patients, in the absence of symptoms of active TB, poses a negligible risk of generating resistance in M. tuberculosis in individuals and at the population level. Thus, the benefits of SDR prophylaxis in reducing the risk of developing leprosy in contacts of new leprosy patients far outweigh the risks of generating drug resistance in M. tuberculosis.
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Affiliation(s)
- Liesbeth Mieras
- Netherlands Leprosy Relief, P.O. Box 95005, 1090 HA, Amsterdam, The Netherlands.
| | | | - Wim van Brakel
- Netherlands Leprosy Relief, P.O. Box 95005, 1090 HA, Amsterdam, The Netherlands
| | | | | | | | | | - Christa Kasang
- The German Leprosy and Tuberculosis Relief Association, Würzburg, Germany
| | | | - Lee Reichman
- New Jersey Medical School Global Tuberculosis Institute, New Jersey, USA
| | | | | | - Peter Steinmann
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Wing Wai Yew
- Chinese University of Hong Kong, Hong Kong, China
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38
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Abstract
Tuberculosis (TB), caused byMycobacterium tuberculosis(M.tb.), is one of the most prevalent and serious infectious diseases worldwide with an estimated annual global mortality of 1.4 million in 2010.
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Affiliation(s)
- Saurabh K. Srivastava
- Plant Research International
- Wageningen UR
- 6708 PB Wageningen
- The Netherlands
- Laboratory of Organic Chemistry
| | - Cees J. M. van Rijn
- Laboratory of Organic Chemistry
- Wageningen UR
- 6703 HB Wageningen
- The Netherlands
| | - Maarten A. Jongsma
- Plant Research International
- Wageningen UR
- 6708 PB Wageningen
- The Netherlands
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39
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Dynamics of Mycobacteriophage-Mycobacterial Host Interaction: Evidence for Secondary Mechanisms for Host Lethality. Appl Environ Microbiol 2015; 82:124-33. [PMID: 26475112 DOI: 10.1128/aem.02700-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 10/12/2015] [Indexed: 12/15/2022] Open
Abstract
Mycobacteriophages infect mycobacteria, resulting in their death. Therefore, the possibility of using them as therapeutic agents against the deadly mycobacterial disease tuberculosis (TB) is of great interest. To obtain better insight into the dynamics of mycobacterial inactivation by mycobacteriophages, this study was initiated using mycobacteriophage D29 and Mycobacterium smegmatis as the phage-host system. Here, we implemented a goal-oriented iterative cycle of experiments on one hand and mathematical modeling combined with Monte Carlo simulations on the other. This integrative approach lends valuable insight into the detailed kinetics of bacterium-phage interactions. We measured time-dependent changes in host viability during the growth of phage D29 in M. smegmatis at different multiplicities of infection (MOI). The predictions emerging out of theoretical analyses were further examined using biochemical and cell biological assays. In a phage-host interaction system where multiple rounds of infection are allowed to take place, cell counts drop more rapidly than expected if cell lysis is considered the only mechanism for cell death. The phenomenon could be explained by considering a secondary factor for cell death in addition to lysis. Further investigations reveal that phage infection leads to the increased production of superoxide radicals, which appears to be the secondary factor. Therefore, mycobacteriophage D29 can function as an effective antimycobacterial agent, the killing potential of which may be amplified through secondary mechanisms.
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Lin YJ, Liao CM. Quantifying the impact of drug combination regimens on TB treatment efficacy and multidrug resistance probability. J Antimicrob Chemother 2015; 70:3273-82. [PMID: 26311836 DOI: 10.1093/jac/dkv247] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 07/21/2015] [Indexed: 11/13/2022] Open
Abstract
OBJECTIVES TB patients' non-adherence to the multidrug treatment regimen is thought to be the main cause of the emergence of drug resistance. The purpose of this study was to quantify the impacts of two-drug combination regimens and non-adherence to these regimens on treatment efficacy and drug resistance probability. METHODS A drug treatment modelling strategy was developed by incorporating a pharmacokinetic/pharmacodynamic model into a bacterial population dynamic model to explore the dynamics of TB bacilli and evolution of resistance during multidrug combination therapy, with an emphasis on non-adherence. A Hill-equation-based pharmacodynamic model was used to assess the bactericidal efficacy of single drugs and to estimate drug interactions. RESULTS Non-adherence to the treatment regimen increased treatment duration by nearly 1.6- and 3.4-fold relative to compliance with treatment. Symptom-based intermittent treatment, a form of non-adherence, might lead to treatment failure and accelerated growth and evolution of resistant mutants, resulting in a dramatically higher probability of 4.17 × 10(-3) (95% CI 2.10 × 10(-4)-1.28 × 10(-2)) for the emergence of MDR TB. Overall, determination of the optimal treatment regimen depended on the different types of medication adherence. CONCLUSIONS Our model not only predicts evolutionary dynamics, but also quantifies treatment efficacy. More broadly, our model provides a quantitative framework for improving treatment protocols and establishing an emergence threshold of resistance that can be used to prevent drug resistance.
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Affiliation(s)
- Yi-Jun Lin
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei, Taiwan 10617, Republic of China
| | - Chung-Min Liao
- Department of Bioenvironmental Systems Engineering, National Taiwan University, Taipei, Taiwan 10617, Republic of China
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41
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Migliori GB, Lienhardt C, Weyer K, van der Werf MJ, Blasi F, Raviglione MC. Ensuring rational introduction and responsible use of new TB tools: outcome of an ERS multisector consultation. Eur Respir J 2015; 44:1412-7. [PMID: 25435528 DOI: 10.1183/09031936.00132114] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Giovanni Battista Migliori
- WHO Collaborating Centre for TB and lung diseases, Fondazione S. Maugeri, Care and Research Institute, Tradate, Italy
| | | | - Karin Weyer
- Global TB Programme, World Health Organization, Geneva, Switzerland
| | | | - Francesco Blasi
- Dept of Pathophysiology and Transplantation, University of Milan, IRCCS Fondazione Cà Granda, Milan, Italy
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42
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Cox HS, Furin JJ, Mitnick CD, Daniels C, Cox V, Goemaere E. The need to accelerate access to new drugs for multidrug-resistant tuberculosis. Bull World Health Organ 2015; 93:491-7. [PMID: 26170507 PMCID: PMC4490806 DOI: 10.2471/blt.14.138925] [Citation(s) in RCA: 12] [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: 03/19/2014] [Revised: 02/24/2015] [Accepted: 03/04/2015] [Indexed: 11/27/2022] Open
Abstract
Approximately half a million people are thought to develop multidrug-resistant tuberculosis annually. Barely 20% of these people currently receive recommended treatment and only about 10% are successfully treated. Poor access to treatment is probably driving the current epidemic, via ongoing transmission. Treatment scale-up is hampered by current treatment regimens, which are lengthy, expensive, poorly tolerated and difficult to administer in the settings where most patients reside. Although new drugs provide an opportunity to improve treatment regimens, current and planned clinical trials hold little promise for developing regimens that will facilitate prompt treatment scale-up. In this article we argue that clinical trials, while necessary, should be complemented by timely, large-scale, operational research that will provide programmatic data on the use of new drugs and regimens while simultaneously improving access to life-saving treatment. Perceived risks - such as the rapid development of resistance to new drugs - need to be balanced against the high levels of mortality and transmission that will otherwise persist. Doubling access to treatment and increasing treatment success could save approximately a million lives over the next decade.
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Affiliation(s)
- Helen S Cox
- Department of Medical Microbiology and the Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Anzio Road, Observatory 7925, South Africa
| | - Jennifer J Furin
- Tuberculosis Research Unit, Case Western Reserve University, Cleveland, United States of America (USA)
| | - Carole D Mitnick
- Department of Global Health and Social Medicine, Harvard Medical School and Partners In Health, Boston, USA
| | | | - Vivian Cox
- Khayelitsha Programme, Médecins Sans Frontières, Cape Town, South Africa
| | - Eric Goemaere
- Southern African Medical Unit, Médecins Sans Frontières, Johannesburg, South Africa
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43
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Parida SK, Axelsson-Robertson R, Rao MV, Singh N, Master I, Lutckii A, Keshavjee S, Andersson J, Zumla A, Maeurer M. Totally drug-resistant tuberculosis and adjunct therapies. J Intern Med 2015; 277:388-405. [PMID: 24809736 DOI: 10.1111/joim.12264] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The first cases of totally drug-resistant (TDR) tuberculosis (TB) were reported in Italy 10 years ago; more recently, cases have also been reported in Iran, India and South Africa. Although there is no consensus on terminology, it is most commonly described as 'resistance to all first- and second-line drugs used to treat TB'. Mycobacterium tuberculosis (M.tb) acquires drug resistance mutations in a sequential fashion under suboptimal drug pressure due to monotherapy, inadequate dosing, treatment interruptions and drug interactions. The treatment of TDR-TB includes antibiotics with disputed or minimal effectiveness against M.tb, and the fatality rate is high. Comorbidities such as diabetes and infection with human immunodeficiency virus further impact on TB treatment options and survival rates. Several new drug candidates with novel modes of action are under late-stage clinical evaluation (e.g., delamanid, bedaquiline, SQ109 and sutezolid). 'Repurposed' antibiotics have also recently been included in the treatment of extensively drug resistant TB. However, because of mutations in M.tb, drugs will not provide a cure for TB in the long term. Adjunct TB therapies, including therapeutic vaccines, vitamin supplementation and/or repurposing of drugs targeting biologically and clinically relevant molecular pathways, may achieve better clinical outcomes in combination with standard chemotherapy. Here, we review broader perspectives of drug resistance in TB and potential adjunct treatment options.
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Affiliation(s)
- S K Parida
- Therapeutic Immunology Division, Department of Laboratory Medicine, Karolinska Institutet, Stockholm, Sweden
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44
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Chang HH, Cohen T, Grad YH, Hanage WP, O'Brien TF, Lipsitch M. Origin and proliferation of multiple-drug resistance in bacterial pathogens. Microbiol Mol Biol Rev 2015; 79:101-16. [PMID: 25652543 PMCID: PMC4402963 DOI: 10.1128/mmbr.00039-14] [Citation(s) in RCA: 134] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
SUMMARY Many studies report the high prevalence of multiply drug-resistant (MDR) strains. Because MDR infections are often significantly harder and more expensive to treat, they represent a growing public health threat. However, for different pathogens, different underlying mechanisms are traditionally used to explain these observations, and it is unclear whether each bacterial taxon has its own mechanism(s) for multidrug resistance or whether there are common mechanisms between distantly related pathogens. In this review, we provide a systematic overview of the causes of the excess of MDR infections and define testable predictions made by each hypothetical mechanism, including experimental, epidemiological, population genomic, and other tests of these hypotheses. Better understanding the cause(s) of the excess of MDR is the first step to rational design of more effective interventions to prevent the origin and/or proliferation of MDR.
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Affiliation(s)
- Hsiao-Han Chang
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Ted Cohen
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, USA
| | - Yonatan H Grad
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - William P Hanage
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Thomas F O'Brien
- The World Health Organization Collaborating Centre for Surveillance of Antimicrobial Resistance, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Marc Lipsitch
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA
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45
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Warner DF, Koch A, Mizrahi V. Diversity and disease pathogenesis in Mycobacterium tuberculosis. Trends Microbiol 2015; 23:14-21. [DOI: 10.1016/j.tim.2014.10.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 10/13/2014] [Accepted: 10/17/2014] [Indexed: 12/11/2022]
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46
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Plazzotta G, Cohen T, Colijn C. Magnitude and sources of bias in the detection of mixed strain M. tuberculosis infection. J Theor Biol 2014; 368:67-73. [PMID: 25553967 PMCID: PMC7011203 DOI: 10.1016/j.jtbi.2014.12.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2014] [Revised: 12/11/2014] [Accepted: 12/16/2014] [Indexed: 11/26/2022]
Abstract
High resolution tests for genetic variation reveal that individuals may simultaneously host more than one distinct strain of Mycobacterium tuberculosis. Previous studies find that this phenomenon, which we will refer to as “mixed infection”, may affect the outcomes of treatment for infected individuals and may influence the impact of population-level interventions against tuberculosis. In areas where the incidence of TB is high, mixed infections have been found in nearly 20% of patients; these studies may underestimate the actual prevalence of mixed infection given that tests may not be sufficiently sensitive for detecting minority strains. Specific reasons for failing to detect mixed infections would include low initial numbers of minority strain cells in sputum, stochastic growth in culture and the physical division of initial samples into parts (typically only one of which is genotyped). In this paper, we develop a mathematical framework that models the study designs aimed to detect mixed infections. Using both a deterministic and a stochastic approach, we obtain posterior estimates of the prevalence of mixed infection. We find that the posterior estimate of the prevalence of mixed infection may be substantially higher than the fraction of cases in which it is detected. We characterize this bias in terms of the sensitivity of the genotyping method and the relative growth rates and initial population sizes of the different strains collected in sputum.
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Affiliation(s)
| | - Ted Cohen
- Brigham and Women׳s Hospital, Harvard School of Public Health, United States
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47
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Alexander HK, Martin G, Martin OY, Bonhoeffer S. Evolutionary rescue: linking theory for conservation and medicine. Evol Appl 2014; 7:1161-79. [PMID: 25558278 PMCID: PMC4275089 DOI: 10.1111/eva.12221] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 09/16/2014] [Indexed: 02/01/2023] Open
Abstract
Evolutionary responses that rescue populations from extinction when drastic environmental changes occur can be friend or foe. The field of conservation biology is concerned with the survival of species in deteriorating global habitats. In medicine, in contrast, infected patients are treated with chemotherapeutic interventions, but drug resistance can compromise eradication of pathogens. These contrasting biological systems and goals have created two quite separate research communities, despite addressing the same central question of whether populations will decline to extinction or be rescued through evolution. We argue that closer integration of the two fields, especially of theoretical understanding, would yield new insights and accelerate progress on these applied problems. Here, we overview and link mathematical modelling approaches in these fields, suggest specific areas with potential for fruitful exchange, and discuss common ideas and issues for empirical testing and prediction.
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Affiliation(s)
- Helen K Alexander
- Institute for Integrative Biology, D-USYS, ETH Zürich Zürich, Switzerland
| | - Guillaume Martin
- Institut des Sciences de l'Evolution, UMR 5554, Université Montpellier 2 - CNRS - IRD Montpellier Cedex, France
| | - Oliver Y Martin
- Institute for Integrative Biology, D-USYS, ETH Zürich Zürich, Switzerland
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48
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Emergence of resistance to atovaquone-proguanil in malaria parasites: insights from computational modeling and clinical case reports. Antimicrob Agents Chemother 2014; 58:4504-14. [PMID: 24867967 DOI: 10.1128/aac.02550-13] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The usefulness of atovaquone-proguanil (AP) as an antimalarial treatment is compromised by the emergence of atovaquone resistance during therapy. However, the origin of the parasite mitochondrial DNA (mtDNA) mutation conferring atovaquone resistance remains elusive. Here, we report a patient-based stochastic model that tracks the intrahost emergence of mutations in the multicopy mtDNA during the first erythrocytic parasite cycles leading to the malaria febrile episode. The effect of mtDNA copy number, mutation rate, mutation cost, and total parasite load on the mutant parasite load per patient was evaluated. Computer simulations showed that almost any infected patient carried, after four to seven erythrocytic cycles, de novo mutant parasites at low frequency, with varied frequencies of parasites carrying varied numbers of mutant mtDNA copies. A large interpatient variability in the size of this mutant reservoir was found; this variability was due to the different parameters tested but also to the relaxed replication and partitioning of mtDNA copies during mitosis. We also report seven clinical cases in which AP-resistant infections were treated by AP. These provided evidence that parasiticidal drug concentrations against AP-resistant parasites were transiently obtained within days after treatment initiation. Altogether, these results suggest that each patient carries new mtDNA mutant parasites that emerge before treatment but are killed by high starting drug concentrations. However, because the size of this mutant reservoir is highly variable from patient to patient, we propose that some patients fail to eliminate all of the mutant parasites, repeatedly producing de novo AP treatment failures.
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49
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Liu HS, Tan WB, Yang N, Yang YY, Cheng P, Liu LJ, Wang WJ, Zhu CL. Effects of Ribosomal Protein L39-L on the Drug Resistance Mechanisms of Lung Cancer A549 Cells. Asian Pac J Cancer Prev 2014; 15:3093-7. [DOI: 10.7314/apjcp.2014.15.7.3093] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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50
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Koch A, Mizrahi V, Warner DF. The impact of drug resistance on Mycobacterium tuberculosis physiology: what can we learn from rifampicin? Emerg Microbes Infect 2014; 3:e17. [PMID: 26038512 PMCID: PMC3975073 DOI: 10.1038/emi.2014.17] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 12/12/2013] [Accepted: 12/30/2013] [Indexed: 01/08/2023]
Abstract
The emergence of drug-resistant pathogens poses a major threat to public health. Although influenced by multiple factors, high-level resistance is often associated with mutations in target-encoding or related genes. The fitness cost of these mutations is, in turn, a key determinant of the spread of drug-resistant strains. Rifampicin (RIF) is a frontline anti-tuberculosis agent that targets the rpoB-encoded β subunit of the DNA-dependent RNA polymerase (RNAP). In Mycobacterium tuberculosis (Mtb), RIF resistance (RIF(R)) maps to mutations in rpoB that are likely to impact RNAP function and, therefore, the ability of the organism to cause disease. However, while numerous studies have assessed the impact of RIF(R) on key Mtb fitness indicators in vitro, the consequences of rpoB mutations for pathogenesis remain poorly understood. Here, we examine evidence from diverse bacterial systems indicating very specific effects of rpoB polymorphisms on cellular physiology, and consider these observations in the context of Mtb. In addition, we discuss the implications of these findings for the propagation of clinically relevant RIF(R) mutations. While our focus is on RIF, we also highlight results which suggest that drug-independent effects might apply to a broad range of resistance-associated mutations, especially in an obligate pathogen increasingly linked with multidrug resistance.
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Affiliation(s)
- Anastasia Koch
- Medical Research Council/National Health Laboratory Service/University of Cape Town Molecular Mycobacteriology Research Unit, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Institute of Infectious Disease and Molecular Medicine and Department of Clinical Laboratory Sciences, University of Cape Town , Cape Town 7701, South Africa
| | - Valerie Mizrahi
- Medical Research Council/National Health Laboratory Service/University of Cape Town Molecular Mycobacteriology Research Unit, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Institute of Infectious Disease and Molecular Medicine and Department of Clinical Laboratory Sciences, University of Cape Town , Cape Town 7701, South Africa
| | - Digby F Warner
- Medical Research Council/National Health Laboratory Service/University of Cape Town Molecular Mycobacteriology Research Unit, Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis Research, Institute of Infectious Disease and Molecular Medicine and Department of Clinical Laboratory Sciences, University of Cape Town , Cape Town 7701, South Africa
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