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Sy KTL, Leavitt SV, de Vos M, Dolby T, Bor J, Horsburgh CR, Warren RM, Streicher EM, Jenkins HE, Jacobson KR. Spatial heterogeneity of extensively drug resistant-tuberculosis in Western Cape Province, South Africa. Sci Rep 2022; 12:10844. [PMID: 35760977 PMCID: PMC9237070 DOI: 10.1038/s41598-022-14581-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 06/09/2022] [Indexed: 02/04/2023] Open
Abstract
Tuberculosis (TB) remains a leading infectious disease killer globally. Treatment outcomes are especially poor among people with extensively drug-resistant (XDR) TB, until recently defined as rifampicin-resistant (RR) TB with resistance to an aminoglycoside (amikacin) and a fluoroquinolone (ofloxacin). We used laboratory TB test results from Western Cape province, South Africa between 2012 and 2015 to identify XDR-TB and pre-XDR-TB (RR-TB with resistance to one second-line drug) spatial hotspots. We mapped the percentage and count of individuals with RR-TB that had XDR-TB and pre-XDR-TB across the province and in Cape Town, as well as amikacin-resistant and ofloxacin-resistant TB. We found the percentage of pre-XDR-TB and the count of XDR-TB/pre-XDR-TB highly heterogeneous with geographic hotspots within RR-TB high burden areas, and found hotspots in both percentage and count of amikacin-resistant and ofloxacin-resistant TB. The spatial distribution of percentage ofloxacin-resistant TB hotspots was similar to XDR-TB hotspots, suggesting that fluoroquinolone-resistace is often the first step to additional resistance. Our work shows that interventions used to reduce XDR-TB incidence may need to be targeted within spatial locations of RR-TB, and further research is required to understand underlying drivers of XDR-TB transmission in these locations.
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Affiliation(s)
- Karla Therese L Sy
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
| | - Sarah V Leavitt
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Margaretha de Vos
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research/South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Tania Dolby
- National Health Laboratory Service, Cape Town, South Africa
| | - Jacob Bor
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - C Robert Horsburgh
- Department of Epidemiology, Boston University School of Public Health, Boston, MA, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- Department of Global Health, Boston University School of Public Health, Boston, MA, USA
- Section of Infectious Diseases, School of Medicine and Boston Medical Center, Boston University, Boston, MA, USA
| | - Robin M Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research/South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Elizabeth M Streicher
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research/South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Helen E Jenkins
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Karen R Jacobson
- Section of Infectious Diseases, School of Medicine and Boston Medical Center, Boston University, Boston, MA, USA.
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Effectiveness of Isoniazid Preventive Therapy to Reduce Tuberculosis Incidence in the Context of Antiretroviral Therapy. J Acquir Immune Defic Syndr 2020; 84:e14-e17. [DOI: 10.1097/qai.0000000000002339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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3
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Chisompola NK, Streicher EM, Muchemwa CMK, Warren RM, Sampson SL. Molecular epidemiology of drug resistant Mycobacterium tuberculosis in Africa: a systematic review. BMC Infect Dis 2020; 20:344. [PMID: 32404119 PMCID: PMC7222473 DOI: 10.1186/s12879-020-05031-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 04/14/2020] [Indexed: 11/24/2022] Open
Abstract
Background The burden of drug resistant tuberculosis in Africa is largely driven by the emergence and spread of multidrug resistant (MDR) and extensively drug resistant (XDR) Mycobacterium tuberculosis strains. MDR-TB is defined as resistance to isoniazid and rifampicin, while XDR-TB is defined as MDR-TB with added resistance to any of the second line injectable drugs and any fluoroquinolone. The highest burden of drug resistant TB is seen in countries further experiencing an HIV epidemic. The molecular mechanisms of drug resistance as well as the evolution of drug resistant TB strains have been widely studied using various genotyping tools. The study aimed to analyse the drug resistant lineages in circulation and transmission dynamics of these lineages in Africa by describing outbreaks, nosocomial transmission and migration. Viewed as a whole, this can give a better insight into the transmission dynamics of drug resistant TB in Africa. Methods A systematic review was performed on peer reviewed original research extracted from PubMed reporting on the lineages associated with drug resistant TB from African countries, and their association with outbreaks, nosocomial transmission and migration. The search terms “Tuberculosis AND drug resistance AND Africa AND (spoligotyping OR molecular epidemiology OR IS6110 OR MIRU OR DNA fingerprinting OR RFLP OR VNTR OR WGS)” were used to identify relevant articles reporting the molecular epidemiology of drug resistant TB in Africa. Results Diverse genotypes are associated with drug resistant TB in Africa, with variations in strain predominance within the continent. Lineage 4 predominates across Africa demonstrating the ability of “modern strains” to adapt and spread easily. Most studies under review reported primary drug resistance as the predominant type of transmission. Drug resistant TB strains are associated with community and nosocomial outbreaks involving MDR- and XDR-TB strains. The under-use of molecular epidemiological tools is of concern, resulting in gaps in knowledge of the transmission dynamics of drug resistant TB on the continent. Conclusions Genetic diversity of M. tuberculosis strains has been demonstrated across Africa implying that diverse genotypes are driving the epidemiology of drug resistant TB across the continent.
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Affiliation(s)
- Namaunga Kasumu Chisompola
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa. .,Department of Basic Medical Sciences, Michael Chilufya Sata School of Medicine, Copperbelt University, Ndola, Zambia.
| | - Elizabeth Maria Streicher
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | | | - Robin Mark Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Samantha Leigh Sampson
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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4
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Boffa J, Mayan M, Ndlovu S, Fisher D, Staples S, Sauve R, Williamson T. When prevention is dangerous: perceptions of isoniazid preventive therapy in KwaZulu-Natal, South Africa. Public Health Action 2019; 9:24-31. [PMID: 30963039 DOI: 10.5588/pha.18.0040] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 01/30/2019] [Indexed: 11/10/2022] Open
Abstract
Setting In 2011, the South African government began to offer isoniazid preventive therapy (IPT) through the public health system to presumptively treat latent tuberculous infection (LTBI) among people living with human immunodeficiency virus. Objective To describe IPT perceptions and experiences in three Zulu communities in KwaZulu-Natal Province, South Africa. Design Using a combination of community-based research and ethnographic methods, we undertook 17 individual and group interviews between October 2014 and May 2015. Interviews transcripts were analysed using qualitative content analysis and validated with grass-roots community advisors. Results Participants reported multiple ways in which IPT was perceived as dangerous: when costs related to pill collection or consumption were unsustainable, or when daily pill consumption resulted in stigma or was seen to introduce excess dirt or toxins, 'ukungcola', in the body. Theories on dirt are evoked to describe how IPT was perceived as 'matter out of place' when given to people who believed themselves to be healthy, suggesting that under the current TB aetiological model in Zulu culture, 'prevention as tablet' may not fit. Conclusion Implementing IPT without understanding the realities of community stakeholders can unintentionally undermine TB control efforts by worsening the situation for people who already encounter numerous daily problems.
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Affiliation(s)
- J Boffa
- Department of Global Health, Stellenbosch University, Cape Town, South Africa.,Research Institute, McGill University Health Centre, McGill University, Montreal, Quebec, Canada
| | - M Mayan
- Community University Partnerships, Faculty of Extension, University of Edmonton, Alberta, Canada
| | - S Ndlovu
- Izimbali Zesizwe, Pietermaritzburg, South Africa
| | - D Fisher
- Department of Community Health Sciences, Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Department of Medicine, Cumming School of Medicine, University of Calgary, Alberta, Canada
| | - S Staples
- Tuberculosis and HIV Investigative Network (THINK), Durban, South Africa
| | - R Sauve
- Department of Community Health Sciences, Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada.,Tuberculosis and HIV Investigative Network (THINK), Durban, South Africa
| | - T Williamson
- Department of Community Health Sciences, Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
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Optimal Management of Drug-Resistant Tuberculosis and Human Immunodeficiency Virus: an Update. CURRENT TREATMENT OPTIONS IN INFECTIOUS DISEASES 2018. [DOI: 10.1007/s40506-018-0145-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Smith CM, Trienekens SCM, Anderson C, Lalor MK, Brown T, Story A, Fry H, Hayward AC, Maguire H. Twenty years and counting: epidemiology of an outbreak of isoniazid-resistant tuberculosis in England and Wales, 1995 to 2014. ACTA ACUST UNITED AC 2017; 22:30467. [PMID: 28251890 PMCID: PMC5356435 DOI: 10.2807/1560-7917.es.2017.22.8.30467] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 09/19/2016] [Indexed: 11/24/2022]
Abstract
An outbreak of isoniazid-resistant tuberculosis first identified in London has now been ongoing for 20 years, making it the largest drug-resistant outbreak of tuberculosis documented to date worldwide. We identified culture-confirmed cases with indistinguishable molecular strain types and extracted demographic, clinical, microbiological and social risk factor data from surveillance systems. We summarised changes over time and used kernel-density estimation and k-function analysis to assess geographic clustering. From 1995 to 2014, 508 cases were reported, with a declining trend in recent years. Overall, 70% were male (n = 360), 60% born in the United Kingdom (n = 306), 39% white (n = 199), and 26% black Caribbean (n = 134). Median age increased from 25 years in the first 5 years to 42 in the last 5. Approximately two thirds of cases reported social risk factors: 45% drug use (n = 227), 37% prison link (n = 189), 25% homelessness (n = 125) and 13% alcohol dependence (n = 64). Treatment was completed at 12 months by 52% of cases (n = 206), and was significantly lower for those with social risk factors (p < 0.05), but increased over time for all patients (p < 0.05). The outbreak remained focused in north London throughout. Control of this outbreak requires continued efforts to prevent and treat further active cases through targeted screening and enhanced case management.
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Affiliation(s)
- Catherine M Smith
- Farr Institute of Health Informatics Research, Department of Infectious Disease Informatics, University College London, London, United Kingdom.,These authors contributed equally to this work
| | - Suzan C M Trienekens
- These authors contributed equally to this work.,Field Epidemiology Service, Liverpool, United Kingdom.,Field Epidemiology Training Programme, Public Health England, London, United Kingdom.,European Programme for Intervention Epidemiology Training, European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Charlotte Anderson
- Field Epidemiology Service - South East and London, Public Health England, London, United Kingdom
| | - Maeve K Lalor
- Public Health England TB Section, Centre for Infectious Disease Surveillance and Control, Colindale, London, United Kingdom.,Research Department Infection and Population Health, Centre for Infectious Disease Epidemiology, University College London, London, United Kingdom
| | - Tim Brown
- Public Health England National Mycobacterium Reference Laboratory, Whitechapel, London, United Kingdom
| | - Alistair Story
- Farr Institute of Health Informatics Research, Department of Infectious Disease Informatics, University College London, London, United Kingdom.,Find and Treat, University College Hospitals NHS Foundation Trust, London, United Kingdom
| | - Hannah Fry
- Centre for Advanced Spatial Analysis, University College London, London, United Kingdom
| | - Andrew C Hayward
- Farr Institute of Health Informatics Research, Department of Infectious Disease Informatics, University College London, London, United Kingdom
| | - Helen Maguire
- Field Epidemiology Service - South East and London, Public Health England, London, United Kingdom.,Research Department Infection and Population Health, Centre for Infectious Disease Epidemiology, University College London, London, United Kingdom
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van Cutsem G, Isaakidis P, Farley J, Nardell E, Volchenkov G, Cox H. Infection Control for Drug-Resistant Tuberculosis: Early Diagnosis and Treatment Is the Key. Clin Infect Dis 2016; 62 Suppl 3:S238-43. [PMID: 27118853 PMCID: PMC4845888 DOI: 10.1093/cid/ciw012] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Multidrug-resistant (MDR) tuberculosis, "Ebola with wings," is a significant threat to tuberculosis control efforts. Previous prevailing views that resistance was mainly acquired through poor treatment led to decades of focus on drug-sensitive rather than drug-resistant (DR) tuberculosis, driven by the World Health Organization's directly observed therapy, short course strategy. The paradigm has shifted toward recognition that most DR tuberculosis is transmitted and that there is a need for increased efforts to control DR tuberculosis. Yet most people with DR tuberculosis are untested and untreated, driving transmission in the community and in health systems in high-burden settings. The risk of nosocomial transmission is high for patients and staff alike. Lowering transmission risk for MDR tuberculosis requires a combination approach centered on rapid identification of active tuberculosis disease and tuberculosis drug resistance, followed by rapid initiation of appropriate treatment and adherence support, complemented by universal tuberculosis infection control measures in healthcare facilities. It also requires a second paradigm shift, from the classic infection control hierarchy to a novel, decentralized approach across the continuum from early diagnosis and treatment to community awareness and support. A massive scale-up of rapid diagnosis and treatment is necessary to control the MDR tuberculosis epidemic. This will not be possible without intense efforts toward the implementation of decentralized, ambulatory models of care. Increasing political will and resources need to be accompanied by a paradigm shift. Instead of focusing on diagnosed cases, recognition that transmission is driven largely by undiagnosed, untreated cases, both in the community and in healthcare settings, is necessary. This article discusses this comprehensive approach, strategies available, and associated challenges.
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Affiliation(s)
- Gilles van Cutsem
- Médecins Sans Frontières Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa
| | | | - Jason Farley
- School of Nursing, Johns Hopkins University, Baltimore, Maryland
| | - Ed Nardell
- Division of Global Health Equity, Brigham and Women's Hospital, Boston, Massachusetts
| | - Grigory Volchenkov
- Department of Tuberculosis Control, Vladimir Oblast Tuberculosis Dispensary, Russian Federation
| | - Helen Cox
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Family Medicine, University of Cape Town, South Africa Division of Medical Microbiology and Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
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Said HM, Kushner N, Omar SV, Dreyer AW, Koornhof H, Erasmus L, Gardee Y, Rukasha I, Shashkina E, Beylis N, Kaplan G, Fallows D, Ismail NA. A Novel Molecular Strategy for Surveillance of Multidrug Resistant Tuberculosis in High Burden Settings. PLoS One 2016; 11:e0146106. [PMID: 26752297 PMCID: PMC4713439 DOI: 10.1371/journal.pone.0146106] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 12/14/2015] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND In South Africa and other high prevalence countries, transmission is a significant contributor to rising rates of multidrug resistant tuberculosis (MDR-TB). Thus, there is a need to develop an early detection system for transmission clusters suitable for high burden settings. We have evaluated the discriminatory power and clustering concordance of a novel and simple genotyping approach, combining spoligotyping with pncA sequencing (SpoNC), against two well-established methods: IS6110-RFLP and 24-loci MIRU-VNTR. METHODS A total of 216 MDR-TB isolates collected from January to June 2010 from the NHLS Central TB referral laboratory in Braamfontein, Johannesburg, representing a diversity of strains from South Africa, were included. The isolates were submitted for genotyping, pncA sequencing and analysis to the Centre for Tuberculosis in South Africa and the Public Health Research Institute Tuberculosis Center at Rutgers University in the United States. Clustering rates, Hunter-Gaston Discriminatory Indexes (HGI) and Wallace coefficients were compared between the methods. RESULTS Overall clustering rates were high by both IS6110-RFLP (52.8%) and MIRU-VNTR (45.8%), indicative of on-going transmission. Both 24-loci MIRU-VNTR and IS6110-RFLP had similar HGI (0.972 and 0.973, respectively), with close numbers of unique profiles (87 vs. 70), clustered isolates (129 vs. 146), and cluster sizes (2 to 26 vs. 2 to 25 isolates). Spoligotyping alone was the least discriminatory (80.1% clustering, HGI 0.903), with 28 unique types. However, the discriminatory power of spoligotyping was improved when combined with pncA sequencing using the SpoNC approach (61.8% clustering, HGI 0.958). A high proportion of MDR-TB isolates had mutations in pncA (68%, n = 145), and pncA mutations were significantly associated with clustering (p = 0.007 and p = 0.0013 by 24-loci MIRU-VNTR and IS6110-RFLP, respectively), suggesting high rates of resistance to pyrazinamide among all MDR-TB cases and particularly among clustered cases. CONCLUSION We conclude that SpoNC provides good discrimination for MDR-TB surveillance and early identification of outbreaks in South Africa, with 24-loci MIRU-VNTR applied for pncA wild-type strains as needed.
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Affiliation(s)
- Halima M. Said
- Centre for Tuberculosis, National Institute of Communicable Diseases, Sandringham, South Africa
- * E-mail:
| | - Nicole Kushner
- Public Health Research Institute, Rutgers University, Newark, New Jersey, United States of America
| | - Shaheed V. Omar
- Centre for Tuberculosis, National Institute of Communicable Diseases, Sandringham, South Africa
| | - Andries W. Dreyer
- Centre for Tuberculosis, National Institute of Communicable Diseases, Sandringham, South Africa
| | - Hendrik Koornhof
- Centre for Tuberculosis, National Institute of Communicable Diseases, Sandringham, South Africa
| | - Linda Erasmus
- Centre for Tuberculosis, National Institute of Communicable Diseases, Sandringham, South Africa
| | - Yasmin Gardee
- Centre for Tuberculosis, National Institute of Communicable Diseases, Sandringham, South Africa
| | - Ivy Rukasha
- Centre for Tuberculosis, National Institute of Communicable Diseases, Sandringham, South Africa
| | - Elena Shashkina
- Public Health Research Institute, Rutgers University, Newark, New Jersey, United States of America
| | - Natalie Beylis
- National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
| | - Gilla Kaplan
- The Bill & Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Dorothy Fallows
- Public Health Research Institute, Rutgers University, Newark, New Jersey, United States of America
| | - Nazir A. Ismail
- Centre for Tuberculosis, National Institute of Communicable Diseases, Sandringham, South Africa
- Department of Medical Microbiology, Faculty of Health Science, University of Pretoria, Pretoria, South Africa
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Primary Capreomycin Resistance Is Common and Associated With Early Mortality in Patients With Extensively Drug-Resistant Tuberculosis in KwaZulu-Natal, South Africa. J Acquir Immune Defic Syndr 2015; 69:536-43. [PMID: 25886924 DOI: 10.1097/qai.0000000000000650] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
BACKGROUND Capreomycin is a key antimycobacterial drug in treatment of extensively drug-resistant tuberculosis (XDR-TB). Drug-susceptibility testing (DST) for capreomycin is not routinely performed in newly diagnosed XDR-TB in South Africa. We performed this study to assess the prevalence, clinical significance, and molecular epidemiology of capreomycin resistance in newly diagnosed patients with XDR-TB in KwaZulu-Natal, South Africa. METHODS Retrospective cohort study of consecutive patients with XDR-TB admitted to a TB referral hospital without previous XDR-TB treatment. A subset of isolates had extended DST (including capreomycin), mutational analysis, and IS6110 restriction fragment length polymorphism assays. RESULTS A total of 216 eligible patients with XDR-TB were identified. The majority were treated with capreomycin (72%), were young (median age: 35.5 years), and were female (56%). One hundred five (76%) were HIV+, and 109 (66%) were on antiretroviral therapy. A subset of 52 patients had full DST. A total of 47/52 (90.4%) patients with XDR-TB were capreomycin resistant. Capreomycin-resistant patients experienced worse mortality and culture conversion than capreomycin susceptible, although this difference was not statistically significant. The A1401G mutation in the rrs gene was associated with capreomycin resistance. The majority of capreomycin-resistant strains were F15/LAM4/KZN lineage (80%), and clustering was common in these isolates (92.5%). CONCLUSIONS Capreomycin resistance is common in patients with XDR-TB in KwaZulu-Natal, is predominantly because of ongoing province-wide transmission of a highly resistant strain, and is associated with high mortality. Capreomycin should be included in routine DST in all patients with XDR-TB. New drug regimens that do not include injectable agents should be operationally tested as empiric treatment in XDR-TB.
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Cohen KA, Abeel T, Manson McGuire A, Desjardins CA, Munsamy V, Shea TP, Walker BJ, Bantubani N, Almeida DV, Alvarado L, Chapman SB, Mvelase NR, Duffy EY, Fitzgerald MG, Govender P, Gujja S, Hamilton S, Howarth C, Larimer JD, Maharaj K, Pearson MD, Priest ME, Zeng Q, Padayatchi N, Grosset J, Young SK, Wortman J, Mlisana KP, O'Donnell MR, Birren BW, Bishai WR, Pym AS, Earl AM. Evolution of Extensively Drug-Resistant Tuberculosis over Four Decades: Whole Genome Sequencing and Dating Analysis of Mycobacterium tuberculosis Isolates from KwaZulu-Natal. PLoS Med 2015; 12:e1001880. [PMID: 26418737 PMCID: PMC4587932 DOI: 10.1371/journal.pmed.1001880] [Citation(s) in RCA: 195] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 08/20/2015] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND The continued advance of antibiotic resistance threatens the treatment and control of many infectious diseases. This is exemplified by the largest global outbreak of extensively drug-resistant (XDR) tuberculosis (TB) identified in Tugela Ferry, KwaZulu-Natal, South Africa, in 2005 that continues today. It is unclear whether the emergence of XDR-TB in KwaZulu-Natal was due to recent inadequacies in TB control in conjunction with HIV or other factors. Understanding the origins of drug resistance in this fatal outbreak of XDR will inform the control and prevention of drug-resistant TB in other settings. In this study, we used whole genome sequencing and dating analysis to determine if XDR-TB had emerged recently or had ancient antecedents. METHODS AND FINDINGS We performed whole genome sequencing and drug susceptibility testing on 337 clinical isolates of Mycobacterium tuberculosis collected in KwaZulu-Natal from 2008 to 2013, in addition to three historical isolates, collected from patients in the same province and including an isolate from the 2005 Tugela Ferry XDR outbreak, a multidrug-resistant (MDR) isolate from 1994, and a pansusceptible isolate from 1995. We utilized an array of whole genome comparative techniques to assess the relatedness among strains, to establish the order of acquisition of drug resistance mutations, including the timing of acquisitions leading to XDR-TB in the LAM4 spoligotype, and to calculate the number of independent evolutionary emergences of MDR and XDR. Our sequencing and analysis revealed a 50-member clone of XDR M. tuberculosis that was highly related to the Tugela Ferry XDR outbreak strain. We estimated that mutations conferring isoniazid and streptomycin resistance in this clone were acquired 50 y prior to the Tugela Ferry outbreak (katG S315T [isoniazid]; gidB 130 bp deletion [streptomycin]; 1957 [95% highest posterior density (HPD): 1937-1971]), with the subsequent emergence of MDR and XDR occurring 20 y (rpoB L452P [rifampicin]; pncA 1 bp insertion [pyrazinamide]; 1984 [95% HPD: 1974-1992]) and 10 y (rpoB D435G [rifampicin]; rrs 1400 [kanamycin]; gyrA A90V [ofloxacin]; 1995 [95% HPD: 1988-1999]) prior to the outbreak, respectively. We observed frequent de novo evolution of MDR and XDR, with 56 and nine independent evolutionary events, respectively. Isoniazid resistance evolved before rifampicin resistance 46 times, whereas rifampicin resistance evolved prior to isoniazid only twice. We identified additional putative compensatory mutations to rifampicin in this dataset. One major limitation of this study is that the conclusions with respect to ordering and timing of acquisition of mutations may not represent universal patterns of drug resistance emergence in other areas of the globe. CONCLUSIONS In the first whole genome-based analysis of the emergence of drug resistance among clinical isolates of M. tuberculosis, we show that the ancestral precursor of the LAM4 XDR outbreak strain in Tugela Ferry gained mutations to first-line drugs at the beginning of the antibiotic era. Subsequent accumulation of stepwise resistance mutations, occurring over decades and prior to the explosion of HIV in this region, yielded MDR and XDR, permitting the emergence of compensatory mutations. Our results suggest that drug-resistant strains circulating today reflect not only vulnerabilities of current TB control efforts but also those that date back 50 y. In drug-resistant TB, isoniazid resistance was overwhelmingly the initial resistance mutation to be acquired, which would not be detected by current rapid molecular diagnostics employed in South Africa that assess only rifampicin resistance.
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Affiliation(s)
- Keira A. Cohen
- Division of Pulmonary and Critical Care Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, United States of America
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa
| | - Thomas Abeel
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands
| | | | | | - Vanisha Munsamy
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa
| | - Terrance P. Shea
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Bruce J. Walker
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | | | - Deepak V. Almeida
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa
- Center for Tuberculosis Research, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Lucia Alvarado
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Sinéad B. Chapman
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Nomonde R. Mvelase
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- National Health Laboratory Service, Durban, South Africa
| | - Eamon Y. Duffy
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa
| | - Michael G. Fitzgerald
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Pamla Govender
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa
| | - Sharvari Gujja
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Susanna Hamilton
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Clinton Howarth
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jeffrey D. Larimer
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Kashmeel Maharaj
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa
| | - Matthew D. Pearson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Margaret E. Priest
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Qiandong Zeng
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
| | - Jacques Grosset
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa
- Center for Tuberculosis Research, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Sarah K. Young
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Jennifer Wortman
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Koleka P. Mlisana
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- National Health Laboratory Service, Durban, South Africa
| | - Max R. O'Donnell
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Division of Pulmonary, Allergy, and Critical Care Medicine, Columbia University College of Physicians and Surgeons, New York, United States of America
- Department of Epidemiology, Columbia Mailman School of Public Health, New York, United States of America
| | - Bruce W. Birren
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - William R. Bishai
- Center for Tuberculosis Research, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Alexander S. Pym
- KwaZulu-Natal Research Institute for TB and HIV (K-RITH), Durban, South Africa
- * E-mail: (ASP); (AME)
| | - Ashlee M. Earl
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
- * E-mail: (ASP); (AME)
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12
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Maama-Maime LB, Mareka M, Ershova JV, Tlali TE, Kao K, Phalatse M, Polansky L, Beres LK, Letsie M, Holtz TH. Antituberculosis Drug Resistance Survey in Lesotho, 2008-2009: Lessons Learned. PLoS One 2015. [PMID: 26207630 PMCID: PMC4514631 DOI: 10.1371/journal.pone.0133808] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SETTING Drug resistance is an increasing threat to tuberculosis (TB) control worldwide. The World Health Organization advises monitoring for drug resistance, with either ongoing surveillance or periodic surveys. METHODS The antituberculosis drug resistance survey was conducted in Lesotho in 2008-2009. Basic demographic and TB history information was collected from individuals with positive sputum smear results at 17 diagnostic facilities. Additional sputum sample was sent to the national TB reference laboratory for culture and drug susceptibility testing. RESULTS Among 3441 eligible smear-positive persons, 1121 (32.6%) were not requested to submit sputum for culture. Among 2320 persons submitted sputum, 1164 (50.2%) were not asked for clinical information or did not have valid sputum samples for testing. In addition, 445/2320 (19.2%) were excluded from analysis because of other laboratory or data management reasons. Among 984/3441 (28.6%) persons who had data available for analysis, MDR-TB was present in 24/773 (3.1%) of new and 25/195 (12.8%) of retreatment TB cases. Logistical, operational and data management challenges affected survey results. CONCLUSION MDR-TB is prevalent in Lesotho, but limitations reduced the reliability of our findings. Multiple lessons learned during this survey can be applied to improve the next drug resistance survey in Lesotho and other resource constrained countries may learn how to avoid these bottlenecks.
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Affiliation(s)
| | - Mathabo Mareka
- Laboratory Services, Ministry of Health, Maseru, Lesotho
| | - Julia V. Ershova
- Centers for Disease Control and Prevention, Atlanta, United States of America
- * E-mail:
| | | | - Kekeletso Kao
- Laboratory Services, Ministry of Health, Maseru, Lesotho
| | | | - Lauren Polansky
- Centers for Disease Control and Prevention, Atlanta, United States of America
| | | | | | - Timothy H. Holtz
- Centers for Disease Control and Prevention, Atlanta, United States of America
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13
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Lim JR, Gandhi NR, Mthiyane T, Mlisana K, Moodley J, Jaglal P, Ramdin N, Brust JCM, Ismail N, Rustomjee R, Shah NS. Incidence and Geographic Distribution of Extensively Drug-Resistant Tuberculosis in KwaZulu-Natal Province, South Africa. PLoS One 2015; 10:e0132076. [PMID: 26147963 PMCID: PMC4493033 DOI: 10.1371/journal.pone.0132076] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 06/09/2015] [Indexed: 11/18/2022] Open
Abstract
South Africa is experiencing a widespread drug-resistant tuberculosis epidemic, although data are limited regarding the current situation. This study finds that the extensively drug-resistant tuberculosis (XDR-TB) incidence in KwaZulu-Natal increased to 3.5 cases/100,000 (776 cases) in 2011-2012. XDR-TB cases are widely distributed geographically, with the majority of districts experiencing a rise in incidence.
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Affiliation(s)
- Jennifer R. Lim
- Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, United States of America
| | - Neel R. Gandhi
- Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, United States of America
- Emory University Rollins School of Public Health, Atlanta, Georgia, United States of America
- * E-mail:
| | | | - Koleka Mlisana
- University of KwaZulu-Natal, Durban, South Africa
- National Health Laboratory Service, Durban, South Africa
| | - Julie Moodley
- National Health Laboratory Service, Durban, South Africa
| | - Prenika Jaglal
- National Health Laboratory Service, Durban, South Africa
| | - Neeshan Ramdin
- Centre for Tuberculosis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - James C. M. Brust
- Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, United States of America
| | - Nazir Ismail
- Centre for Tuberculosis, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | | | - N. Sarita Shah
- Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York, United States of America
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14
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Upadhya D, Moll AP, Brooks RP, Friedland G, Shenoi SV. What motivates use of community-based human immunodeficiency virus testing in rural South Africa? Int J STD AIDS 2015; 27:662-71. [PMID: 26134323 DOI: 10.1177/0956462415592789] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 06/01/2015] [Indexed: 11/17/2022]
Abstract
Despite substantial progress in implementing HIV testing, challenges remain in achieving widespread uptake particularly in rural resource-limited settings. We sought to understand motivations for HIV testing in a community-based HIV testing programme in rural South Africa. We conducted a questionnaire survey in participants undergoing voluntary HIV testing within an ongoing community-based integrated HIV/tuberculosis intensive case finding programme at congregate rural settings. Participants responded to a six-item non-mutually exclusive motivations survey which included the topics of feeling ill, recent HIV exposure, risky lifestyle, illness in a family member, and pregnancy. Among 2068 respondents completing the survey, 1393 (67.4%) were women, median age was 40 years (IQR 19-56), and 1235 (59.7%) were first-time testers. Among all testers, 142 (6.9%) were HIV-positive with median CD4 count was 346 cells/mm(3) (IQR 218-542). Community-based testing for HIV is acceptable and meets the needs of community members in rural South Africa. Motivations for HIV testing at the community level are complex and differ according to gender, age, site of community testing, and HIV status. These differences can be utilised to improve the focus and yield of community-based HIV screening.
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Affiliation(s)
- Devesh Upadhya
- Department of Internal Medicine, Baylor School of Medicine, Baylor, TX, USA
| | - Anthony P Moll
- Church of Scotland Hospital, ARV Programme, Tugela Ferry, South Africa
| | - Ralph P Brooks
- Department of Internal Medicine, Section of Infectious Diseases, AIDS Program, Yale University School of Medicine, New Haven, CT, USA
| | - Gerald Friedland
- Department of Internal Medicine, Section of Infectious Diseases, AIDS Program, Yale University School of Medicine, New Haven, CT, USA
| | - Sheela V Shenoi
- Department of Internal Medicine, Section of Infectious Diseases, AIDS Program, Yale University School of Medicine, New Haven, CT, USA
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15
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Pires GM, Folgosa E, Nquobile N, Gitta S, Cadir N. Mycobacterium tuberculosis resistance to antituberculosis drugs in Mozambique. J Bras Pneumol 2014; 40:142-7. [PMID: 24831398 PMCID: PMC4083649 DOI: 10.1590/s1806-37132014000200007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 01/20/2014] [Indexed: 11/23/2022] Open
Abstract
OBJECTIVE: To determine the drug resistance profile of Mycobacterium
tuberculosis in Mozambique. METHODS: We analyzed secondary data from the National Tuberculosis Referral Laboratory, in
the city of Maputo, Mozambique, and from the Beira Regional Tuberculosis Referral
Laboratory, in the city of Beira, Mozambique. The data were based on
culture-positive samples submitted to first-line drug susceptibility testing (DST)
between January and December of 2011. We attempted to determine whether the
frequency of DST positivity was associated with patient type or provenance. RESULTS: During the study period, 641 strains were isolated in culture and submitted to
DST. We found that 374 (58.3%) were resistant to at least one antituberculosis
drug and 280 (43.7%) were resistant to multiple antituberculosis drugs. Of the 280
multidrug-resistant tuberculosis cases, 184 (65.7%) were in previously treated
patients, most of whom were from southern Mozambique. Two (0.71%) of the cases of
multidrug-resistant tuberculosis were confirmed to be cases of extensively
drug-resistant tuberculosis. Multidrug-resistant tuberculosis was most common in
males, particularly those in the 21-40 year age bracket. CONCLUSIONS: M. tuberculosis resistance to antituberculosis
drugs is high in Mozambique, especially in previously treated patients. The
frequency of M. tuberculosis strains that were
resistant to isoniazid, rifampin, and streptomycin in combination was found to be
high, particularly in samples from previously treated patients.
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Affiliation(s)
| | - Elena Folgosa
- National Institute of Health, Ministry of Health, Maputo, Mozambique
| | - Ndlovu Nquobile
- National Institute of Health, Ministry of Health, Maputo, Mozambique
| | - Sheba Gitta
- National Institute of Health, Ministry of Health, Maputo, Mozambique
| | - Nureisha Cadir
- National Institute of Health, Ministry of Health, Maputo, Mozambique
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16
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Thomas TA, Heysell SK, Moodley P, Montreuil R, Ha X, Friedland G, Bamber SA, Moll AP, Gandhi N, Brant WE, Sturm W, Shah S. Intensified specimen collection to improve tuberculosis diagnosis in children from Rural South Africa, an observational study. BMC Infect Dis 2014; 14:11. [PMID: 24400822 PMCID: PMC3890632 DOI: 10.1186/1471-2334-14-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 01/06/2014] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND In drug-resistant TB settings, specimen collection is critical for drug-susceptibility testing (DST). This observational study included multiple specimen types collected from pediatric TB suspects with the aim to determine diagnostic yield and inform clinical practice in children with drug-resistant and drug-susceptible TB. METHODS From 03/2009-07/2010, TB suspects aged ≥6 months and ≤12 years were recruited among outpatient and inpatient settings. Subjects were new TB suspects or had persistent symptoms despite ≥2 months of TB treatment. The protocol included collection of a single blood and urine specimen, a single sputum induction and, if inpatients and <5 years of age, collection of 3 gastric aspirates (GA). Samples were cultured on solid and/or liquid media. DST was by 1% proportion method. RESULTS Among 118 children with possible, probable or confirmed TB, the mean age was 4.9 years [SD 3.2] and 64 (62%) of those tested were HIV-positive. Eight (7%) subjects were culture-positive from at least one specimen; yield did not differ by HIV status or TB treatment history. Among those with positive cultures, 7/8 (88%) were from induced sputum, 5/6 (83%) from GA, 3/8 (38%) from blood, and 3/7 (43%) from urine. In subjects with both induced sputum and GA collection, sputum provided one additional case compared to GA. Multidrug resistant (MDR)-TB was detected by urine culture alone in one child >5 years old. Pan-resistant extensively drug resistant (XDR)-TB was identified by cultures from all sites in one subject. CONCLUSIONS TB was cultured from HIV-positive and -negative children, and allowed for identification of MDR and XDR-TB cases. Urine and induced sputum each provided an additional TB diagnosis and, when compared to GA, may be considered a less invasive, same-day method of specimen collection for childhood TB suspects. This study illustrates the continued challenges and limitations of available strategies for pediatric TB diagnostics.
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Affiliation(s)
- Tania A Thomas
- Division of Infectious Diseases & International Health, University of Virginia, PO Box 801337, Charlottesville, VA 22908-1337, USA
| | - Scott K Heysell
- Division of Infectious Diseases & International Health, University of Virginia, PO Box 801337, Charlottesville, VA 22908-1337, USA
| | | | - Romualde Montreuil
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Xia Ha
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | | | | | - Neel Gandhi
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
| | - William E Brant
- Department of Radiology and Medical Imaging, University of Virginia, Charlottesville, VA, USA
| | - Willem Sturm
- University of KwaZulu-Natal, Durban, KZN, South Africa
| | - Sarita Shah
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, USA
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17
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Tang S, Tan S, Yao L, Li F, Li L, Guo X, Liu Y, Hao X, Li Y, Ding X, Zhang Z, Tong L, Huang J. Risk factors for poor treatment outcomes in patients with MDR-TB and XDR-TB in China: retrospective multi-center investigation. PLoS One 2013; 8:e82943. [PMID: 24349402 PMCID: PMC3857781 DOI: 10.1371/journal.pone.0082943] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 11/07/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND The treatment of patients with MDR- and XDR-TB is usually more complex, toxic and costly and less effective than treatment of other forms of TB. However, there is little information available on risk factors for poor outcomes in patients with MDR- and XDR-TB in China. METHODOLOGY/PRINCIPAL FINDINGS We retrospectively analyzed the clinical records of HIV-negative TB Patients with culture-proven MDR- or XDR-TB who were registered from July 2006 to June 2011 at five large-scale Tuberculosis Specialized Hospitals in China. Among 1662 HIV-seronegative TB cases which were culture-positive for M. tuberculosis complex and had positive sputum-smear microscopy results, 965 cases (58.1%) were DR-TB, and 586 cases (35.3%) were classified as having MDR-TB, accounting for 60.7% of DR-TB. 169 cases (10.2%) were XDR-TB, accounting for 17.5% of DR-TB, 28.8% of MDR-TB. The MDR-TB patients were divided into XDR-TB group (n=169) and other MDR-TB group (non-XDR MDR-TB) (n=417). In total, 240 patients (40.95%) had treatment success, and 346 (59.05%) had poor treatment outcomes. The treatment success rate in other MDR-TB group was 52.2%, significantly higher than that in the XDR-TB group (13%, P<0.001). In multivariate logistic regression analysis, poor outcomes were associated with duration of previous anti-TB treatment of more than one year (OR, 0.077; 95% CI, 0.011-0.499, P<0.001), a BMI less than 18.5 kg/m(2) (OR, 2.185; 95% CI, 1.372-3.478, P<0.001), XDR (OR, 13.368; 95% CI, 6.745-26.497, P<0.001), retreatment (OR, 0.171; 95% CI, 0.093-0.314, P<0.001), diabetes (OR, 0.305; 95% CI, 0.140-0.663, P=0.003), tumor (OR, 0.095; 95% CI, 0.011-0.795, P=0.03), decreased albumin (OR, 0.181; 95% CI, 0.118-0.295, P<0.001), cavitation (OR, 0.175; 95% CI, 0.108-0.286, P<0.001). CONCLUSIONS/SIGNIFICANCE The patients with MDR-TB and XDR-TB have poor treatment outcomes in China.The presence of extensive drug resistance, low BMI, hypoalbuminemia, comorbidity, cavitary disease and previous anti-TB treatment are independent prognostic factors for poor outcome in patients with MDR-TB.
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Affiliation(s)
- Shenjie Tang
- Department of Respiratory Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
- Tuberculosis Center for Diagnosis and Treatment, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shouyong Tan
- Department of Tuberculosis, Guangzhou Chest Hospital, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Lan Yao
- Tuberculosis Center for Diagnosis and Treatment, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Fujian Li
- Hangzhou Red Cross Hospital, Hangzhou, China
| | - Li Li
- Tianjin Haihe Hospital, Tianjin, China
| | - Xinzhi Guo
- Henan Infectious Hospital, Zhengzhou, China
| | - Yidian Liu
- Tuberculosis Center for Diagnosis and Treatment, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaohui Hao
- Tuberculosis Center for Diagnosis and Treatment, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yanqiong Li
- Department of Tuberculosis, Guangzhou Chest Hospital, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Xiuxiu Ding
- Department of Tuberculosis, Guangzhou Chest Hospital, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Zhanjun Zhang
- Tuberculosis Center for Diagnosis and Treatment, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, China
| | - Li Tong
- Department of Tuberculosis, Guangzhou Chest Hospital, State Key Laboratory of Respiratory Disease, Guangzhou, China
| | - Jianan Huang
- Department of Respiratory Medicine, The First Affiliated Hospital of Soochow University, Suzhou, China
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18
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Abstract
Unrecognized transmission is a major contributor to ongoing TB epidemics in high-burden, resource-constrained settings. Limitations in diagnosis, treatment, and infection control in health-care and community settings allow for continued transmission of drug-sensitive and drug-resistant TB, particularly in regions of high HIV prevalence. Health-care facilities are common sites of TB transmission. Improved implementation of infection control practices appropriate for the local setting and in combination, has been associated with reduced transmission. Community settings account for the majority of TB transmission and deserve increased focus. Strengthening and intensifying existing high-yield strategies, including household contact tracing, can reduce onward TB transmission. Recent studies documenting high transmission risk community sites and strategies for community-based intensive case finding hold promise for feasible, effective transmission reduction. Infection control in community settings has been neglected and requires urgent attention. Developing and implementing improved strategies for decreasing transmission to children, within prisons and of drug-resistant TB are needed.
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19
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Multidrug-resistant tuberculosis in panama is driven by clonal expansion of a multidrug-resistant Mycobacterium tuberculosis strain related to the KZN extensively drug-resistant M. tuberculosis strain from South Africa. J Clin Microbiol 2013; 51:3277-85. [PMID: 23884993 DOI: 10.1128/jcm.01122-13] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Multidrug-resistant tuberculosis (MDR-TB) is a significant health problem in Panama. The extent to which such cases are the result of primary or acquired resistance and the strain families involved are unknown. We performed whole-genome sequencing of a collection of 66 clinical MDR isolates, along with 31 drug-susceptible isolates, that were isolated in Panama between 2001 and 2010; 78% of the MDR isolates belong to the Latin American-Mediterranean (LAM) family. Drug resistance mutations correlated well with drug susceptibility profiles. To determine the relationships among these strains and to better understand the acquisition of resistance mutations, a phylogenetic tree was constructed based on a genome-wide single-nucleotide polymorphism analysis. The phylogenetic tree shows that the isolates are highly clustered, with a single strain (LAM9-c1) accounting for nearly one-half of the MDR isolates (29/66 isolates). The LAM9-c1 strain was most prevalent among male patients of working age and was associated with high mortality rates. Members of this cluster all share identical mutations conferring resistance to isoniazid (KatG S315T mutation), rifampin (RpoB S531L mutation), and streptomycin (rrs C517T mutation). This evidence of primary resistance supports a model in which MDR-TB in Panama is driven by clonal expansion and ongoing transmission of several strains in the LAM family, including the highly successful MDR strain LAM9-c1. The phylogenetic analysis also shows that the LAM9-c1 strain is closely related to the KwaZulu-Natal (KZN) extensively drug-resistant TB strain identified in KwaZulu-Natal, South Africa. The LAM9-c1 and KZN strains likely arose from a recent common ancestor that was transmitted between Panama and South Africa and had the capacity to tolerate an accumulation of multiple resistance mutations.
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20
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Chang KC, Yew WW. Management of difficult multidrug-resistant tuberculosis and extensively drug-resistant tuberculosis: update 2012. Respirology 2013; 18:8-21. [PMID: 22943408 DOI: 10.1111/j.1440-1843.2012.02257.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Multidrug-resistant (MDR) tuberculosis (TB) denotes bacillary resistance to at least isoniazid and rifampicin. Extensively drug-resistant (XDR) TB is MDR-TB with additional bacillary resistance to any fluoroquinolone and at least one second-line injectable drugs. Rooted in inadequate TB treatment and compounded by a vicious circle of diagnostic delay and improper treatment, MDR-TB/XDR-TB has become a global epidemic that is fuelled by poverty, human immunodeficiency virus (HIV) and neglect of airborne infection control. The majority of MDR-TB cases in some settings with high prevalence of MDR-TB are due to transmission of drug-resistant bacillary strains to previously untreated patients. Global efforts in controlling MDR-TB/XDR-TB can no longer focus solely on high-risk patients. It is difficult and costly to treat MDR-TB/XDR-TB. Without timely implementation of preventive and management strategies, difficult MDR-TB/XDR-TB can cripple global TB control efforts. Preventive strategies include prompt diagnosis with adequate TB treatment using the directly observed therapy, short-course (DOTS) strategy and drug-resistance programmes, airborne infection control, preventive treatment of TB/HIV, and optimal use of antiretroviral therapy. Management strategies for established cases of difficult MDR-TB/XDR-TB rely on harnessing existing drugs (notably newer generation fluoroquinolones, high-dose isoniazid, linezolid and pyrazinamide with in vitro activity) in the best combinations and dosing schedules, together with adjunctive surgery in carefully selected cases. Immunotherapy may also have a role in the future. New diagnostics, drugs and vaccines are required to meet the challenge, but science alone is insufficient. Difficult MDR-TB/XDR-TB cannot be tackled without achieving high cure rates with quality DOTS and beyond, and concurrently addressing poverty and HIV.
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Affiliation(s)
- Kwok-Chiu Chang
- Department of Health, Tuberculosis and Chest Service, the Chinese University of Hong Kong, Hong Kong, China.
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21
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Coffee M. Extensively drug-resistant tuberculosis: new strains, new challenges. Microb Drug Resist 2013. [DOI: 10.2217/ebo.12.500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Megan Coffee
- Megan Coffee was born in New York City (NY, USA), and was raised in New Jersey (NJ, USA). She completed her undergraduate degree at Harvard University (MA, USA) with high honors in chemistry. Her PhD from Oxford University (UK) is in mathematical modeling of infectious diseases, focusing on the epidemiology of HIV transmission with migration and other cofactors in South Africa and Zimbabwe. Her MD is from Harvard University, where she studied health sciences and technology, a joint program between
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22
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Shenoi SV, Brooks RP, Catterick K, Moll AP, Friedland GH. 'Cough officer' nurses in a general medical clinic successfully detect drug-susceptible and -resistant tuberculosis. Public Health Action 2013; 3:46-50. [PMID: 25392815 DOI: 10.5588/pha.12.0056] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
SETTING Intensive case finding (ICF) for tuberculosis (TB) is recommended by the World Health Organization among known human immunodeficiency virus (HIV) patients. However, ICF may also be appropriate in generalized patient populations. OBJECTIVE To evaluate the yield of ICF in a general medical clinic in a high HIV prevalence setting. METHODS A nurse designated as a 'cough officer' identified clinic attendees with cough of >2 weeks and collected sputum for evaluation at the hospital and provincial referral laboratories. We retrospectively evaluated the number and proportion of patients with microbiologically confirmed TB identified in 2007-2008. RESULTS Among 56 207 clinic attendees, 1442 (2.6%) TB suspects were identified and 122 (8.5%) were sputum Ziehl-Neelsen (ZN) positive. Of 389 available results, 72 (18.5%) were auramine-positive and 99 (25.4%) were culture-positive; multidrug-resistant and extensively drug-resistant TB were identified in 16 (16.2%). The number needed to screen was 11.8 patients to identify one ZN-positive case and 3.9 to identify one culture-positive case. CONCLUSIONS A nurse-facilitated cough officer program successfully identified TB suspects and drug-susceptible and drug-resistant TB. Culture was more sensitive for TB screening and critical for identifying drug resistance. ICF is operationally feasible, and should be expanded to general medical clinics in high HIV and TB prevalence, resource-limited settings.
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Affiliation(s)
- S V Shenoi
- Department of Medicine, Section of Infectious Diseases, AIDS Program, Yale University School of Medicine, New Haven, Connecticut, USA
| | - R P Brooks
- Philanjalo Care Centre, Tugela Ferry, South Africa
| | - K Catterick
- Church of Scotland Hospital, Tugela Ferry, South Africa
| | - A P Moll
- Church of Scotland Hospital, Tugela Ferry, South Africa
| | - G H Friedland
- Department of Medicine, Section of Infectious Diseases, AIDS Program, Yale University School of Medicine, New Haven, Connecticut, USA
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23
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Ilina EN, Shitikov EA, Ikryannikova LN, Alekseev DG, Kamashev DE, Malakhova MV, Parfenova TV, Afanas’ev MV, Ischenko DS, Bazaleev NA, Smirnova TG, Larionova EE, Chernousova LN, Beletsky AV, Mardanov AV, Ravin NV, Skryabin KG, Govorun VM. Comparative genomic analysis of Mycobacterium tuberculosis drug resistant strains from Russia. PLoS One 2013; 8:e56577. [PMID: 23437175 PMCID: PMC3577857 DOI: 10.1371/journal.pone.0056577] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 01/15/2013] [Indexed: 11/30/2022] Open
Abstract
Tuberculosis caused by multidrug-resistant (MDR) and extensively drug-resistant (XDR) Mycobacterium tuberculosis (MTB) strains is a growing problem in many countries. The availability of the complete nucleotide sequences of several MTB genomes allows to use the comparative genomics as a tool to study the relationships of strains and differences in their evolutionary history including acquisition of drug-resistance. In our work, we sequenced three genomes of Russian MTB strains of different phenotypes--drug susceptible, MDR and XDR. Of them, MDR and XDR strains were collected in Tomsk (Siberia, Russia) during the local TB outbreak in 1998-1999 and belonged to rare KQ and KY families in accordance with IS6110 typing, which are considered endemic for Russia. Based on phylogenetic analysis, our isolates belonged to different genetic families, Beijing, Ural and LAM, which made the direct comparison of their genomes impossible. For this reason we performed their comparison in the broader context of all M. tuberculosis genomes available in GenBank. The list of unique individual non-synonymous SNPs for each sequenced isolate was formed by comparison with all SNPs detected within the same phylogenetic group. For further functional analysis, all proteins with unique SNPs were ascribed to 20 different functional classes based on Clusters of Orthologous Groups (COG). We have confirmed drug resistant status of our isolates that harbored almost all known drug-resistance associated mutations. Unique SNPs of an XDR isolate CTRI-4(XDR), belonging to a Beijing family were compared in more detail with SNPs of additional 14 Russian XDR strains of the same family. Only type specific mutations in genes of repair, replication and recombination system (COG category L) were found common within this group. Probably the other unique SNPs discovered in CTRI-4(XDR) may have an important role in adaptation of this microorganism to its surrounding and in escape from antituberculosis drugs treatment.
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Affiliation(s)
- Elena N. Ilina
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Egor A. Shitikov
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
| | | | - Dmitry G. Alekseev
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | - Dmitri E. Kamashev
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Maja V. Malakhova
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
| | | | - Maxim V. Afanas’ev
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
| | - Dmitry S. Ischenko
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | - Nikolai A. Bazaleev
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
| | | | | | | | | | | | | | | | - Vadim M. Govorun
- Research Institute of Physical-Chemical Medicine, Moscow, Russian Federation
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24
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Gandhi NR, Weissman D, Moodley P, Ramathal M, Elson I, Kreiswirth BN, Mathema B, Shashkina E, Rothenberg R, Moll AP, Friedland G, Sturm AW, Shah NS. Nosocomial transmission of extensively drug-resistant tuberculosis in a rural hospital in South Africa. J Infect Dis 2013; 207:9-17. [PMID: 23166374 PMCID: PMC3523793 DOI: 10.1093/infdis/jis631] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Accepted: 07/20/2012] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Extensively drug-resistant tuberculosis (XDR-tuberculosis) is a global public health threat, but few data exist elucidating factors driving this epidemic. The initial XDR-tuberculosis report from South Africa suggested transmission is an important factor, but detailed epidemiologic and molecular analyses were not available for further characterization. METHODS We performed a retrospective, observational study among XDR-tuberculosis patients to identify hospital-associated epidemiologic links. We used spoligotyping, IS6110-based restriction fragment-length polymorphism analysis, and sequencing of resistance-determining regions to identify clusters. Social network analysis was used to construct transmission networks among genotypically clustered patients. RESULTS Among 148 XDR-tuberculosis patients, 98% were infected with human immunodeficiency virus (HIV), and 59% had smear-positive tuberculosis. Nearly all (93%) were hospitalized while infectious with XDR-tuberculosis (median duration, 15 days; interquartile range: 10-25 days). Genotyping identified a predominant cluster comprising 96% of isolates. Epidemiologic links were identified for 82% of patients; social network analysis demonstrated multiple generations of transmission across a highly interconnected network. CONCLUSIONS The XDR-tuberculosis epidemic in Tugela Ferry, South Africa, has been highly clonal. However, the epidemic is not the result of a point-source outbreak; rather, a high degree of interconnectedness allowed multiple generations of nosocomial transmission. Similar to the outbreaks of multidrug-resistant tuberculosis in the 1990s, poor infection control, delayed diagnosis, and a high HIV prevalence facilitated transmission. Important lessons from those outbreaks must be applied to stem further expansion of this epidemic.
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Affiliation(s)
- Neel R Gandhi
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, USA.
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25
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Viljoen S, Pienaar E, Viljoen HJ. A state-time epidemiology model of tuberculosis: importance of re-infection. Comput Biol Chem 2012; 36:15-22. [PMID: 22340441 DOI: 10.1016/j.compbiolchem.2011.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 11/17/2011] [Accepted: 11/20/2011] [Indexed: 10/14/2022]
Abstract
An epidemiological model is presented that considers five possible states of a population: susceptible (S), exposed (W), infectious (Y), in treatment (Z) and recovered (R). In certain instances transition rates (from one state to another) depend on the time spent in the state; therefore the states W, Y and Z depend on time and length of stay in that state - similar to age-structured models. The model is particularly amenable to describe delays of exposed persons to become infectious and re-infection of exposed persons. Other transitions that depend on state time include the case finding and diagnosis, increased death rate and treatment interruption. The mathematical model comprises of a set of partial differential and ordinary differential equations. Non-steady state solutions are first presented, followed by a bifurcation study of the stationary states.
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Affiliation(s)
- S Viljoen
- Department of Social Policy, London School of Economics, London WC2A 2AE, United Kingdom.
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