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Li YF, Kong XL, Song WM, Li YM, Li YY, Fang WW, Yang JY, Yu CB, Li HC, Liu Y. Genomic analysis of lineage-specific transmission of multidrug resistance tuberculosis in China. Emerg Microbes Infect 2024; 13:2294858. [PMID: 38126135 PMCID: PMC10866052 DOI: 10.1080/22221751.2023.2294858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023]
Abstract
OBJECTIVES We investigated the genetic diversities and lineage-specific transmission dynamics of multidrug-resistant tuberculosis (MDR-TB), with the goal of determining the potential factors driving the MDR epidemics in China. METHODS We curated a large nationwide Mycobacterium tuberculosis (M. tuberculosis) whole genome sequence data set, including 1313 MDR strains. We reconstructed the phylogeny and mapped the transmission networks of MDR-TB across China using Bayesian inference. To identify drug-resistance variants linked to enhanced transmissibility, we employed ordinary least-squares (OLS) regression analysis. RESULT The majority of MDR-TB strains in China belong to lineage 2.2.1. Transmission chain analysis has indicated that the repeated and frequent transmission of L2.2.1 plays a central role in the establishment of MDR epidemic in China, but no occurrence of a large predominant MDR outbreak was detected. Using OLS regression, the most common single nucleotide polymorphisms (SNPs) associated with resistance to isoniazid (katG_p.Ser315Thr and katG_p.Ser315Asn) and rifampicin (rpoB_p.Ser450Leu, rpoB_p.His445Tyr, rpoB_p.His445Arg, rpoB_p.His445Asp, and rpoB_p.His445Asn) were more likely to be found in L2 clustered strains. Several putative compensatory mutations in rpoA, rpoC, and katG were significantly associated with clustering. The eastern, central, and southern regions of China had a high level of connectivity for the migration of L2 MDR strains throughout the country. The skyline plot showed distinct population size expansion dynamics for MDR-TB lineages in China. CONCLUSION MDR-TB epidemic in China is predominantly driven by the spread of highly transmissible Beijing strains. A range of drug-resistance mutations of L2 MDR-TB strains displayed minimal fitness costs and may facilitate their transmission.
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Affiliation(s)
- Yi-fan Li
- Department of Respiratory and Critical Care Medicine, The Third Affiliated Hospital of Shandong First Medical University, Jinan, People’s Republic of China
| | - Xiang-long Kong
- Shandong Artificial Intelligence Institute Qilu University of Technology (Shandong Academy of Sciences), Jinan, People’s Republic of China
| | - Wan-mei Song
- Department of Respiratory Medicine, Ruijin Hospital Affiliated to Shanghai Jiaotong University, Shanghai, People’s Republic of China
| | - Ya-meng Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
- Department of Respiratory and Critical Care Medicine, Shandong University of Traditional Chinese Medicine, Jinan, People’s Republic of China
| | - Ying-Ying Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
- Department of Respiratory and Critical Care Medicine, Shandong University of Traditional Chinese Medicine, Jinan, People’s Republic of China
| | - Wei-wei Fang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
| | - Jie-yu Yang
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
| | - Chun-Bao Yu
- Center for Integrative and Translational Medicine, Shandong Public Health Clinical Center, Jinan, People’s Republic of China
| | - Huai-chen Li
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
| | - Yao Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People’s Republic of China
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Lan Y, Crudu V, Ciobanu N, Codreanu A, Chitwood MH, Sobkowiak B, Warren JL, Cohen T. Identifying local foci of tuberculosis transmission in Moldova using a spatial multinomial logistic regression model. EBioMedicine 2024; 102:105085. [PMID: 38531172 PMCID: PMC10987885 DOI: 10.1016/j.ebiom.2024.105085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024] Open
Abstract
BACKGROUND Multidrug resistant tuberculosis (MDR-TB) represents a major public health concern in the Republic of Moldova, with an estimated 31% of new and 56% of previously treated TB cases having MDR disease in 2022. A recent genomic epidemiology study of incident TB occurring in 2018 and 2019 found that 92% of MDR-TB was the result of transmission. The MDR phenotype was concentrated among two M. tuberculosis (Mtb) lineages: L2.2.1 (Beijing) and L4.2.1 (Ural). METHODS We developed and applied a hierarchical Bayesian multinominal logistic regression model to Mtb genomic, spatial, and epidemiological data collected from all individuals with diagnosed TB in Moldova in 2018 and 2019 to identify locations in which specific Mtb strains are being transmitted. We then used a logistic regression model to estimate locality-level factors associated with local transmission. FINDINGS We found differences in the spatial distribution and degree of local concentration of disease due to specific strains of Beijing and Ural lineage Mtb. Foci of transmission for four strains of Beijing lineage Mtb, predominantly of the MDR-TB phenotype, were located in several regions, but largely concentrated in Transnistria. In contrast, transmission of Ural lineage Mtb had less marked patterns of spatial aggregation, with a single strain (also of the MDR phenotype) spatially clustered in southern Transnistria. We found a 30% (95% credible interval 2%-80%) increase in odds of a locality being a transmission cluster for each increase of 100 persons per square kilometer, while higher local tuberculosis incidence and poverty were not associated with a locality being a transmission focus. INTERPRETATION Our results identified localities where specific Mtb transmission networks were concentrated and quantified the association between locality-level factors and focal transmission. This analysis revealed Transnistria as the primary area where specific Mtb strains (predominantly of the MDR-TB phenotype) were locally transmitted and suggests that targeted intensified case finding in this region may be an attractive policy option. FUNDING Funding for this work was provided by the National Institute of Allergy and Infectious Diseases at the US National Institutes of Health.
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Affiliation(s)
- Yu Lan
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Valeriu Crudu
- Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Nelly Ciobanu
- Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | | | - Melanie H Chitwood
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Benjamin Sobkowiak
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Joshua L Warren
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
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Shavuka O, Iipumbu E, Boois L, Günther G, Hoddinott G, Lin HH, Nepolo E, Niemann S, Ruswa N, Seddon J, Claassens MM. Enhanced active case finding of drug-resistant tuberculosis in Namibia: a protocol for the hotspots, hospitals, and households (H3TB) study. BMJ Open 2024; 14:e082665. [PMID: 38341211 PMCID: PMC10862302 DOI: 10.1136/bmjopen-2023-082665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 01/17/2024] [Indexed: 02/12/2024] Open
Abstract
INTRODUCTION Namibia is a high tuberculosis (TB)-burden country with an estimated incidence of 460/100 000 (around 12 000 cases) per year. Approximately 4.5% of new cases and 7.9% of previously treated TB cases are multidrug resistant (MDR) and 47% of patients with MDR-TB are HIV coinfected. Published data suggest a clustering of MDR-TB transmission in specific areas. Identifying transmission clusters is key to implementing high-yield and cost-effective interventions. This includes knowing the yield of finding TB cases in high-transmission zones (eg, community hotspots, hospitals or households) to deliver community-based interventions. We aim to identify such transmission zones for enhanced case finding and evaluate the effectiveness of this approach. METHODS AND ANALYSIS H3TB is an observational cross-sectional study evaluating MDR-TB active case finding strategies. Sputum samples from MDR-TB cases in three regions of Namibia will be evaluated by whole genome sequencing (WGS) in addition to routine sputum investigations (Xpert MTB/RIF, culture and drug susceptibility testing). We will collect information on household contacts, use of community spaces and geographical map intersections between participants, synthesising these data to identify transmission hotspots. We will look at the feasibility, acceptability, yield and cost of case finding strategies in these hotspots, and in households of patients with MDR-TB and visitors of hospitalised patients with MDR-TB. A compartmental transmission dynamic model will be constructed to evaluate the impact and cost-effectiveness of the strategies if scaled. ETHICS AND DISSEMINATION Ethics approval was obtained. Participants will give informed consent. H3TB will capitalise on a partnership with the Ministry of Health and Social Services to follow up individuals diagnosed with MDR-TB and integrate WGS data with innovative contact network mapping, to allow enhanced case finding. Study data will contribute towards a systems approach to TB control. Equally important, it will serve as a role model for similar studies in other high-incidence settings.
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Affiliation(s)
- Olga Shavuka
- Department of Human Biological and Translational Medical Sciences, University of Namibia, Windhoek, Khomas, Namibia
| | - Etuhole Iipumbu
- Department of Human Biological and Translational Medical Sciences, University of Namibia, Windhoek, Khomas, Namibia
| | - Lorraine Boois
- Department of Human Biological and Translational Medical Sciences, University of Namibia, Windhoek, Khomas, Namibia
| | - Gunar Günther
- Department of Human Biological and Translational Medical Sciences, University of Namibia, Windhoek, Khomas, Namibia
- Inselspital, University of Bern, Bern, Switzerland
| | - Graeme Hoddinott
- Desmond Tutu TB Centre, Department of Pediatrics and Child Health, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, Western Cape, South Africa
| | | | - Emmanuel Nepolo
- Department of Human Biological and Translational Medical Sciences, University of Namibia, Windhoek, Khomas, Namibia
| | - Stefan Niemann
- Department of Human Biological and Translational Medical Sciences, University of Namibia, Windhoek, Khomas, Namibia
- Molecular and Experimental Mycobacteriology Group, Forschungszentrum Borstel, Borstel, Germany
| | - Nunurai Ruswa
- National Tuberculosis and Leprosy Programme (NTLP), Windhoek, Namibia
| | - James Seddon
- Desmond Tutu TB Centre, Department of Pediatrics and Child Health, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, Western Cape, South Africa
- Department of Infectious Disease, Imperial College London, London, UK
| | - Mareli M Claassens
- Department of Human Biological and Translational Medical Sciences, University of Namibia, Windhoek, Khomas, Namibia
- Desmond Tutu TB Centre, Department of Pediatrics and Child Health, Stellenbosch University Faculty of Medicine and Health Sciences, Cape Town, Western Cape, South Africa
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Amoori N, Cheraghian B, Amini P, Alavi SM. Identification of Risk Factors Associated with Tuberculosis in Southwest Iran: A Machine Learning Method. Med J Islam Repub Iran 2024; 38:5. [PMID: 38434222 PMCID: PMC10907055 DOI: 10.47176/mjiri.38.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Indexed: 03/05/2024] Open
Abstract
Background Tuberculosis is a principal public health issue. Reducing and controlling tuberculosis did not result in the expected success despite implementing effective preventive and therapeutic programs, one of the reasons for which is the delay in definitive diagnosis. Therefore, creating a diagnostic aid system for tuberculosis screening can help in the early diagnosis of this disease. This research aims to use machine learning techniques to identify economic, social, and environmental factors affecting tuberculosis. Methods This case-control study included 80 individuals with TB and 172 participants as controls. During January-October 2021, information was collected from thirty-six health centers in Ahvaz, southwest Iran. Five different machine learning approaches were used to identify factors associated with TB, including BMI, sex, age , marital status, education, employment status, size of the family, monthly income, cigarette smoking, hookah smoking, history of chronic illness, history of imprisonment, history of hospital admission, first-class family, second-class family, third-class family, friend, co-worker, neighbor, market, store, hospital, health center, workplace, restaurant, park, mosque, Basij base, Hairdressers and school. The data was analyzed using the statistical programming R software version 4.1.1. Results According to the calculated evaluation criteria, the accuracy level of 5 SVM, RF, LSSVM, KNN, and NB models is 0.99, 0.72, 0.97,0.99, and 0.95, respectively, and except for RF, the other models had the highest accuracy. Among the 39 investigated variables, 16 factors including First-class family (20.83%), friend (17.01%), health center (41.67%), hospital (24.74%), store (18.49%), market (14.32%), workplace (9.46%), history of hospital admission (51.82%), BMI (43.75%), sex (40.36%), age (22.83%), educational status (60.59%), employment status (43.58%), monthly income (63.80%), addiction (44.10%), history of imprisonment (38.19%) were of the highest importance on tuberculosis. Conclusion The obtained results demonstrated that machine-learning techniques are effective in identifying economic, social, and environmental factors associated with tuberculosis. Identifying these different factors plays a significant role in preventing and performing appropriate and timely interventions to control this disease.
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Affiliation(s)
- Neda Amoori
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Bahman Cheraghian
- Department of Biostatistics and Epidemiology, School of Public Health, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Payam Amini
- School of Medicine, Keele University, Staffordshire, UK
| | - Seyed Mohammad Alavi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Wang TT, Hu YL, Li YF, Kong XL, Li YM, Sun PY, Wang DX, Li YY, Zhang YZ, Han QL, Zhu XH, An QQ, Liu LL, Liu Y, Li HC. Polyketide synthases mutation in tuberculosis transmission revealed by whole genomic sequence, China, 2011-2019. Front Genet 2024; 14:1217255. [PMID: 38259610 PMCID: PMC10800454 DOI: 10.3389/fgene.2023.1217255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 11/30/2023] [Indexed: 01/24/2024] Open
Abstract
Introduction: Tuberculosis (TB) is an infectious disease caused by a bacterium called Mycobacterium tuberculosis (Mtb). Previous studies have primarily focused on the transmissibility of multidrug-resistant (MDR) or extensively drug-resistant (XDR) Mtb. However, variations in virulence across Mtb lineages may also account for differences in transmissibility. In Mtb, polyketide synthase (PKS) genes encode large multifunctional proteins which have been shown to be major mycobacterial virulence factors. Therefore, this study aimed to identify the role of PKS mutations in TB transmission and assess its risk and characteristics. Methods: Whole genome sequences (WGSs) data from 3,204 Mtb isolates was collected from 2011 to 2019 in China. Whole genome single nucleotide polymorphism (SNP) profiles were used for phylogenetic tree analysis. Putative transmission clusters (≤10 SNPs) were identified. To identify the role of PKS mutations in TB transmission, we compared SNPs in the PKS gene region between "clustered isolates" and "non-clustered isolates" in different lineages. Results: Cluster-associated mutations in ppsA, pks12, and pks13 were identified among different lineage isolates. They were statistically significant among clustered strains, indicating that they may enhance the transmissibility of Mtb. Conclusion: Overall, this study provides new insights into the function of PKS and its localization in M. tuberculosis. The study found that ppsA, pks12, and pks13 may contribute to disease progression and higher transmission of certain strains. We also discussed the prospective use of mutant ppsA, pks12, and pks13 genes as drug targets.
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Affiliation(s)
- Ting-Ting Wang
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yuan-Long Hu
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yi-Fan Li
- Department of Pulmonary and Critical Care Medicine, The Third Affiliated Hospital of Shandong First Medical University (Affiliated Hospital of Shandong Academy of Medical Sciences), Jinan, China
| | - Xiang-Long Kong
- Shandong Artificial Intelligence Institute Qilu University of Technology (Shandong Academy of Sciences), Jinan, China
| | - Ya-Meng Li
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | | | - Da-Xing Wang
- People’s Hospital of Huaiyin Jinan, Jinan, China
| | - Ying-Ying Li
- Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Yu-Zhen Zhang
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Qi-Lin Han
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Xue-Han Zhu
- Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Qi-Qi An
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to 11 Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Li-Li Liu
- People’s Hospital of Huaiyin Jinan, Jinan, China
| | - Yao Liu
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to 11 Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Huai-Chen Li
- Shandong University of Traditional Chinese Medicine, Jinan, China
- Department of Respiratory and Critical Care Medicine, Shandong Provincial Hospital Affiliated to 11 Shandong University, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
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Scott LE, Shapiro AN, Da Silva MP, Tsoka J, Jacobson KR, Emch M, Moultrie H, Jenkins HE, Moore D, Van Rie A, Stevens WS. Integrating Molecular Diagnostics and GIS Mapping: A Multidisciplinary Approach to Understanding Tuberculosis Disease Dynamics in South Africa Using Xpert MTB/RIF. Diagnostics (Basel) 2023; 13:3163. [PMID: 37891984 PMCID: PMC10606157 DOI: 10.3390/diagnostics13203163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/30/2023] [Accepted: 09/14/2023] [Indexed: 10/29/2023] Open
Abstract
An investigation was carried out to examine the use of national Xpert MTB/RIF data (2013-2017) and GIS technology for MTB/RIF surveillance in South Africa. The aim was to exhibit the potential of using molecular diagnostics for TB surveillance across the country. The variables analysed include Mycobacterium tuberculosis (Mtb) positivity, the mycobacterial proportion of rifampicin-resistant Mtb (RIF), and probe frequency. The summary statistics of these variables were generated and aggregated at the facility and municipal level. The spatial distribution patterns of the indicators across municipalities were determined using the Moran's I and Getis Ord (Gi) statistics. A case-control study was conducted to investigate factors associated with a high mycobacterial load. Logistic regression was used to analyse this study's results. There was striking spatial heterogeneity in the distribution of Mtb and RIF across South Africa. The median patient age, urban setting classification, and number of health care workers were found to be associated with the mycobacterial load. This study illustrates the potential of using data generated from molecular diagnostics in combination with GIS technology for Mtb surveillance in South Africa. Spatially targeted interventions can be implemented in areas where high-burden Mtb persists.
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Affiliation(s)
- Lesley Erica Scott
- Wits Diagnostic Innovation Hub, Faculty of Health Science, University of the Witwatersrand, Johannesburg 2093, South Africa; (M.P.D.S.); (J.T.); (W.S.S.)
| | - Anne Nicole Shapiro
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA; (A.N.S.); (H.E.J.)
| | - Manuel Pedro Da Silva
- Wits Diagnostic Innovation Hub, Faculty of Health Science, University of the Witwatersrand, Johannesburg 2093, South Africa; (M.P.D.S.); (J.T.); (W.S.S.)
- National Priority Program of the National Health Laboratory Services (NHLS), Johannesburg 2131, South Africa
| | - Jonathan Tsoka
- Wits Diagnostic Innovation Hub, Faculty of Health Science, University of the Witwatersrand, Johannesburg 2093, South Africa; (M.P.D.S.); (J.T.); (W.S.S.)
| | - Karen Rita Jacobson
- Division of Infectious Diseases, Boston Medical Center, Boston, MA 02118, USA;
| | - Michael Emch
- Department of Epidemiology, University of North Carolina School, Chapel Hill, NC 27127, USA;
- Department of Geography and Environment, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Harry Moultrie
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg 2192, South Africa;
| | - Helen Elizabeth Jenkins
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA; (A.N.S.); (H.E.J.)
| | - David Moore
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK;
| | - Annelies Van Rie
- Faculty of Medicine and Health Sciences, University of Antwerp, 2000 Antwerpen, Belgium;
| | - Wendy Susan Stevens
- Wits Diagnostic Innovation Hub, Faculty of Health Science, University of the Witwatersrand, Johannesburg 2093, South Africa; (M.P.D.S.); (J.T.); (W.S.S.)
- National Priority Program of the National Health Laboratory Services (NHLS), Johannesburg 2131, South Africa
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Li M, Lu L, Jiang Q, Jiang Y, Yang C, Li J, Zhang Y, Zou J, Li Y, Dai W, Hong J, Takiff H, Shen X, Guo X, Yuan Z, Gao Q. Genotypic and spatial analysis of transmission dynamics of tuberculosis in Shanghai, China: a 10-year prospective population-based surveillance study. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2023; 38:100833. [PMID: 37790084 PMCID: PMC10544272 DOI: 10.1016/j.lanwpc.2023.100833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/02/2023] [Accepted: 06/15/2023] [Indexed: 10/05/2023]
Abstract
Background With improved tuberculosis (TB) control programs, the incidence of TB in China declined dramatically over the past few decades, but recently the rate of decrease has slowed, especially in large cities such as Shanghai. To help formulate strategies to further reduce TB incidence, we performed a 10-year study in Songjiang, a district of Shanghai, to delineate the characteristics, transmission patterns, and dynamic changes of the local TB burden. Methods We conducted a population-based study of culture-positive pulmonary TB patients diagnosed in Songjiang during 2011-2020. Genomic clusters were defined with a threshold distance of 12-single-nucleotide-polymorphisms based on whole-genome sequencing, and risk factors for clustering were identified by logistic regression. Transmission inference was performed using phybreak. The distances between the residences of patients were compared to the genomic distances of their isolates. Spatial patient hotspots were defined with kernel density estimation. Findings Of 2212 enrolled patients, 74.7% (1652/2212) were internal migrants. The clustering rate (25.2%, 558/2212) and spatial concentrations of clustered and unclustered patients were unchanged over the study period. Migrants had significantly higher TB rates but less clustering than residents. Clustering was highest in male migrants, younger patients and both residents and migrants employed in physical labor. Only 22.1% of transmission events occurred between residents and migrants, with residents more likely to transmit to migrants. The clustering risk decreased rapidly with increasing distances between patient residences, but more than half of clustered patient pairs lived ≥5 km apart. Epidemiologic links were identified for only 15.6% of clustered patients, mostly in close contacts. Interpretation Although some of the TB in Songjiang's migrant population is caused by strains brought by infected migrants, local, recent transmission is an important driver of the TB burden. These results suggest that further reductions in TB incidence require novel strategies to detect TB early and interrupt urban transmission. Funding Shanghai Municipal Science and Technology Major Project (ZD2021CY001), National Natural Science Foundation of China (82272376), National Research Council of Science and Technology Major Project of China (2017ZX10201302-006).
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Affiliation(s)
- Meng Li
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Liping Lu
- Department of Tuberculosis Control, Songjiang District Center for Disease Control and Prevention, Shanghai, China
| | - Qi Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
- School of Public Health, Renmin Hospital Public Health Research Institute, Wuhan University, Wuhan, China
| | - Yuan Jiang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
- Shanghai Institute of Preventive Medicine, Shanghai, China
| | - Chongguang Yang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
- School of Public Health (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Shenzhen, China
| | - Jing Li
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
- Shanghai Institute of Preventive Medicine, Shanghai, China
| | - Yangyi Zhang
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
- Shanghai Institute of Preventive Medicine, Shanghai, China
| | - Jinyan Zou
- Department of Tuberculosis Control, Songjiang District Center for Disease Control and Prevention, Shanghai, China
| | - Yong Li
- Department of Tuberculosis Control, Songjiang District Center for Disease Control and Prevention, Shanghai, China
| | - Wenqi Dai
- Department of Clinical Laboratory, Songjiang District Central Hospital, Shanghai, China
| | - Jianjun Hong
- Department of Tuberculosis Control, Songjiang District Center for Disease Control and Prevention, Shanghai, China
| | - Howard Takiff
- Laboratorio de Genética Molecular, CMBC, Instituto Venezolano de Investigaciones Científicas, IVIC, Caracas, Venezuela
| | - Xin Shen
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
- Shanghai Institute of Preventive Medicine, Shanghai, China
| | - Xiaoqin Guo
- Department of Tuberculosis Control, Songjiang District Center for Disease Control and Prevention, Shanghai, China
| | - Zhengan Yuan
- Shanghai Municipal Center for Disease Control and Prevention, Shanghai, China
- Shanghai Institute of Preventive Medicine, Shanghai, China
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
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Amoori N, Amini P, Cheraghian B, Alavi SM. Investigating the intensity of social contacts associated with tuberculosis: a weighted networks model. BMC Pulm Med 2023; 23:226. [PMID: 37365556 DOI: 10.1186/s12890-023-02519-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 06/13/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Tuberculosis is known as one of the principal health problems, especially in developing countries. This study aimed to visualize, statistically model, and describe the weighted networks to investigate the intensity of social contacts associated with tuberculosis. METHODS In this case-control study, we applied weighted network analysis to assess the network of person-time spent in stores, workplaces, restaurants, mosques, Police bases, homes, hospitals, colleges, hairdressers, schools, contact homes, health centers, cinemas, parks, and markets. Modules will be determined based on the similarities between the variables in a topology overlap matrix. The most important variables will be found considering the association between each variable and module eigenvalues. RESULTS The result shows the extracted modules of locations based on the connectivity followed by the person-time at each place. The correlation (p-value) between TB and the turquoise, blue, and brown modules was 0.058 (0.351), 0.004 (0.943), and 0.117 (0.039), respectively. The brown module is the most important one, demonstrating a significant connection between homes, contact homes, health centers, and hospitals. Therefore, an association was found between person-time in four places and the occurrence of TB. CONCLUSION The finding of this study showed that most transmission of tuberculosis infection occurs in homes, contact homes, health centers, and hospitals. These place evaluations allow the identification of people with more contact and in need of screening, so critically leading to the identification of more patients with active TB.
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Affiliation(s)
- Neda Amoori
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Payam Amini
- Department of Biostatistics and Epidemiology, School of Public Health, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Bahman Cheraghian
- Department of Biostatistics and Epidemiology, School of Public Health, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Seyed Mohammad Alavi
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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9
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You S, Chitwood MH, Gunasekera KS, Crudu V, Codreanu A, Ciobanu N, Furin J, Cohen T, Warren JL, Yaesoubi R. Predicting resistance to fluoroquinolones among patients with rifampicin-resistant tuberculosis using machine learning methods. PLOS DIGITAL HEALTH 2022; 1:e0000059. [PMID: 36177394 PMCID: PMC9518704 DOI: 10.1371/journal.pdig.0000059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background Limited access to drug-susceptibility tests (DSTs) and delays in receiving DST results are challenges for timely and appropriate treatment of multi-drug resistant tuberculosis (TB) in many low-resource settings. We investigated whether data collected as part of routine, national TB surveillance could be used to develop predictive models to identify additional resistance to fluoroquinolones (FLQs), a critical second-line class of anti-TB agents, at the time of diagnosis with rifampin-resistant TB. Methods and findings We assessed three machine learning-based models (logistic regression, neural network, and random forest) using information from 540 patients with rifampicin-resistant TB, diagnosed using Xpert MTB/RIF and notified in the Republic of Moldova between January 2018 and December 2019. The models were trained to predict the resistance to FLQs based on demographic and TB clinical information of patients and the estimated district-level prevalence of resistance to FLQs. We compared these models based on the optimism-corrected area under the receiver operating characteristic curve (OC-AUC-ROC). The OC-AUC-ROC of all models were statistically greater than 0.5. The neural network model, which utilizes twelve features, performed best and had an estimated OC-AUC-ROC of 0.87 (0.83,0.91), which suggests reasonable discriminatory power. A limitation of our study is that our models are based only on data from the Republic of Moldova and since not externally validated, the generalizability of these models to other populations remains unknown. Conclusions Models trained on data from phenotypic surveillance of drug-resistant TB can predict resistance to FLQs based on patient characteristics at the time of diagnosis with rifampin-resistant TB using Xpert MTB/RIF, and information about the local prevalence of resistance to FLQs. These models may be useful for informing the selection of antibiotics while awaiting results of DSTs.
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Affiliation(s)
- Shiying You
- Department of Health Policy and Management, Yale School of Public Health, New Haven, Connecticut, United States of America
- Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Melanie H. Chitwood
- Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Kenneth S. Gunasekera
- Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Valeriu Crudu
- Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | | | - Nelly Ciobanu
- Phthisiopneumology Institute, Chisinau, Republic of Moldova
| | - Jennifer Furin
- Department of Medicine, Case Western Reserve University, Cleveland, Ohio, United States of America
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Ted Cohen
- Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Joshua L. Warren
- Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Reza Yaesoubi
- Department of Health Policy and Management, Yale School of Public Health, New Haven, Connecticut, United States of America
- Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America
- * E-mail:
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10
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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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11
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Van Deun A, Bola V, Lebeke R, Kaswa M, Hossain MA, Gumusboga M, Torrea G, De Jong BC, Rigouts L, Decroo T. OUP accepted manuscript. JAC Antimicrob Resist 2022; 4:dlac037. [PMID: 35415609 PMCID: PMC8994197 DOI: 10.1093/jacamr/dlac037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/13/2022] [Indexed: 11/14/2022] Open
Abstract
Background Objectives Methods Results Conclusions
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Affiliation(s)
| | - Valentin Bola
- Programme National de Lutte contre la Tuberculose, Direction Provinciale de Kinshasa, Kinshasa, République Démocratique du Congo
| | - Rossin Lebeke
- Programme National de Lutte contre la Tuberculose, Direction Provinciale de Kinshasa, Kinshasa, République Démocratique du Congo
| | - Michel Kaswa
- Programme National de Lutte contre la Tuberculose, Direction Nationale, Kinshasa, République Démocratique du Congo
| | | | - Mourad Gumusboga
- Institute of Tropical Medicine, Unit of Mycobacteriology, Department of Biomedical Sciences, 2000 Antwerp, Belgium
| | - Gabriela Torrea
- Institute of Tropical Medicine, Unit of Mycobacteriology, Department of Biomedical Sciences, 2000 Antwerp, Belgium
| | - Bouke Catharine De Jong
- Institute of Tropical Medicine, Unit of Mycobacteriology, Department of Biomedical Sciences, 2000 Antwerp, Belgium
| | - Leen Rigouts
- Institute of Tropical Medicine, Unit of Mycobacteriology, Department of Biomedical Sciences, 2000 Antwerp, Belgium
| | - Tom Decroo
- Institute of Tropical Medicine, Unit of HIV and TB, Department of Clinical Sciences, 2000 Antwerp, Belgium
- Corresponding author. E-mail:
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12
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Martínez-Lirola M, Jajou R, Mathys V, Martin A, Cabibbe AM, Valera A, Sola-Campoy PJ, Abascal E, Rodríguez-Maus S, Garrido-Cárdenas JA, Bonillo M, Chiner-Oms Á, López B, Vallejo-Godoy S, Comas I, Muñoz P, Cirillo DM, van Soolingen D, Pérez-Lago L, García de Viedma D. Integrative transnational analysis to dissect tuberculosis transmission events along the migratory route from Africa to Europe. J Travel Med 2021; 28:6211020. [PMID: 33822988 DOI: 10.1093/jtm/taab054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/26/2021] [Accepted: 03/24/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Growing international migration has increased the complexity of tuberculosis transmission patterns. Italy's decision to close its borders in 2018 made of Spain the new European porte entrée for migration from the Horn of Africa (HA). In one of the first rescues of migrants from this region at the end of 2018, tuberculosis was diagnosed in eight subjects, mainly unaccompanied minors. METHODS Mycobacterium tuberculosis isolates from these recently arrived migrants were analysed by Mycobacterial Interspersed Repetitive-Unit/Variable-Number of Tandem Repeat (MIRU-VNTR) and subsequent whole genome sequencing (WGS) analysis. Data were compared with those from collections from other European countries receiving migrants from the HA and a strain-specific PCR was applied for a fast searching of common strains. Infections in a cellular model were performed to assess strain virulence. RESULTS MIRU-VNTR analysis allowed identifying an epidemiological cluster involving three of the eight cases from Somalia (0 single-nucleotide polymorphisms between isolates, HA cluster). Following detailed interviews revealed that two of these cases had shared the same migratory route in most of the trip and had spent a long time at a detention camp in Libya. To confirm potential en route transmission for the three cases, we searched the same strain in collections from other European countries receiving migrants from the HA. MIRU-VNTR, WGS and a strain-specific PCR for the HA strain were applied. The same strain was identified in 12 cases from Eritrea diagnosed soon after their arrival in 2018 to the Netherlands, Belgium and Italy. Intracellular replication rate of the strain did not reveal abnormal virulence. CONCLUSIONS Our study suggests a potential en route transmission of a pan-susceptible strain, which caused at least 15 tuberculosis cases in Somalian and Eritrean migrants diagnosed in four different European countries.
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Affiliation(s)
| | - Rana Jajou
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Vanessa Mathys
- Unit Bacterial Diseases Service, Infectious Diseases in Humans, Sciensano, Brussels, Belgium
| | - Anandi Martin
- Université catholique de Louvain (UCLouvain) & Syngulon, 4102, Seraing, Belgium
| | - Andrea Maurizio Cabibbe
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Ana Valera
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Pedro J Sola-Campoy
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Estefanía Abascal
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Sandra Rodríguez-Maus
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | | | - Magdalena Bonillo
- Unidad de Prevención, Promoción y Vigilancia de la Salud del Área Sanitaria Norte de Almería. Consejería de Salud. Junta de Andalucia, Almería, Spain
| | - Álvaro Chiner-Oms
- Centro Superior de Investigación en Salud Pública (FISABIO)-Universitat de València, Valencia, Spain
| | - Begoña López
- UPPV Distrito Sanitario Granada metropolitano, Granada, Spain
| | | | - Iñaki Comas
- Instituto de Biomedicina de Valencia-CSIC, Valencia, Spain.,CIBER Salud Pública (CIBERESP), Madrid, Spain
| | - Patricia Muñoz
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain.,Departamento de Medicina, Universidad Complutense, Madrid, Spain
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Dick van Soolingen
- National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Laura Pérez-Lago
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | - Darío García de Viedma
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain.,Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades Respiratorias (CIBERES), Madrid, Spain
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13
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Shrestha S, Reja M, Gomes I, Baik Y, Pennington J, Islam S, Jamil Faisel A, Cordon O, Roy T, Suarez PG, Hussain H, Dowdy DW. Quantifying geographic heterogeneity in TB incidence and the potential impact of geographically targeted interventions in South and North City Corporations of Dhaka, Bangladesh: a model-based study. Epidemiol Infect 2021; 149:e106. [PMID: 33866998 PMCID: PMC8161375 DOI: 10.1017/s0950268821000832] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/16/2021] [Accepted: 03/30/2021] [Indexed: 11/22/2022] Open
Abstract
In rapidly growing and high-burden urban centres, identifying tuberculosis (TB) transmission hotspots and understanding the potential impact of interventions can inform future control and prevention strategies. Using data on local demography, TB reports and patient reporting patterns in Dhaka South City Corporation (DSCC) and Dhaka North City Corporation (DNCC), Bangladesh, between 2010 and 2017, we developed maps of TB reporting rates across wards in DSCC and DNCC and identified wards with high rates of reported TB (i.e. 'hotspots') in DSCC and DNCC. We developed ward-level transmission models and estimated the potential epidemiological impact of three TB interventions: active case finding (ACF), mass preventive therapy (PT) and a combination of ACF and PT, implemented either citywide or targeted to high-incidence hotspots. There was substantial geographic heterogeneity in the estimated TB incidence in both DSCC and DNCC: incidence in the highest-incidence wards was over ten times higher than in the lowest-incidence wards in each city corporation. ACF, PT and combined ACF plus PT delivered to 10% of the population reduced TB incidence by a projected 7%-9%, 13%-15% and 19%-23% over five years, respectively. Targeting TB hotspots increased the projected reduction in TB incidence achieved by each intervention 1.4- to 1.8-fold. The geographical pattern of TB notifications suggests high levels of ongoing TB transmission in DSCC and DNCC, with substantial heterogeneity at the ward level. Interventions that reduce transmission are likely to be highly effective and incorporating notification data at the local level can further improve intervention efficiency.
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Affiliation(s)
- Sourya Shrestha
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Mehdi Reja
- Challenge TB Project, Interactive Research & Development (IRD), Dhaka, Bangladesh
- Interactive Research & Development (IRD), Dhaka, Bangladesh
| | - Isabella Gomes
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Yeonsoo Baik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jeffrey Pennington
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Shamiul Islam
- National Tuberculosis Control Program (NTP), Dhaka, Bangladesh
| | - Abu Jamil Faisel
- Challenge TB Project, Interactive Research & Development (IRD), Dhaka, Bangladesh
- Interactive Research & Development (IRD), Dhaka, Bangladesh
| | - Oscar Cordon
- Challenge TB Project, Interactive Research & Development (IRD), Dhaka, Bangladesh
- Challenge TB Project, Management Sciences for Health, Dhaka, Bangladesh
| | - Tapash Roy
- Interactive Research & Development (IRD), Dhaka, Bangladesh
| | | | - Hamidah Hussain
- Interactive Research & Development (IRD) Global, Singapore, Singapore
| | - David W. Dowdy
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
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14
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Bui DP, Chandran SS, Oren E, Brown HE, Harris RB, Knight GM, Grandjean L. Community transmission of multidrug-resistant tuberculosis is associated with activity space overlap in Lima, Peru. BMC Infect Dis 2021; 21:275. [PMID: 33736597 PMCID: PMC7977184 DOI: 10.1186/s12879-021-05953-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/24/2021] [Indexed: 11/10/2022] Open
Abstract
Background Transmission of multidrug-resistant tuberculosis (MDRTB) requires spatial proximity between infectious cases and susceptible persons. We assess activity space overlap among MDRTB cases and community controls to identify potential areas of transmission. Methods We enrolled 35 MDRTB cases and 64 TB-free community controls in Lima, Peru. Cases were whole genome sequenced and strain clustering was used as a proxy for transmission. GPS data were gathered from participants over seven days. Kernel density estimation methods were used to construct activity spaces from GPS locations and the utilization distribution overlap index (UDOI) was used to quantify activity space overlap. Results Activity spaces of controls (median = 35.6 km2, IQR = 25.1–54) were larger than cases (median = 21.3 km2, IQR = 17.9–48.6) (P = 0.02). Activity space overlap was greatest among genetically clustered cases (mean UDOI = 0.63, sd = 0.67) and lowest between cases and controls (mean UDOI = 0.13, sd = 0.28). UDOI was positively associated with genetic similarity of MDRTB strains between case pairs (P < 0.001). The odds of two cases being genetically clustered increased by 22% per 0.10 increase in UDOI (OR = 1.22, CI = 1.09–1.36, P < 0.001). Conclusions Activity space overlap is associated with MDRTB clustering. MDRTB transmission may be occurring in small, overlapping activity spaces in community settings. GPS studies may be useful in identifying new areas of MDRTB transmission. Supplementary Information The online version contains supplementary material available at 10.1186/s12879-021-05953-8.
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Affiliation(s)
- David P Bui
- Department of Epidemiology and Biostatistics, The University of Arizona, Mel and Enid Zuckerman College of Public Health, 1295 N Martin Ave., Tucson, AZ, 85724, USA
| | - Shruthi S Chandran
- The London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - Eyal Oren
- San Diego State University, School of Public Health, 5500 Campanile Drive, San Diego, California, 92182, USA
| | - Heidi E Brown
- Department of Epidemiology and Biostatistics, The University of Arizona, Mel and Enid Zuckerman College of Public Health, 1295 N Martin Ave., Tucson, AZ, 85724, USA
| | - Robin B Harris
- Department of Epidemiology and Biostatistics, The University of Arizona, Mel and Enid Zuckerman College of Public Health, 1295 N Martin Ave., Tucson, AZ, 85724, USA
| | - Gwenan M Knight
- The London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - Louis Grandjean
- Universidad Peruana Cayetano Heredia, Lima, Peru. .,Institute of Child Health, University College London, 30 Guilford Street, London, UK.
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15
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Ault RC, Headley CA, Hare AE, Carruthers BJ, Mejias A, Turner J. Blood RNA signatures predict recent tuberculosis exposure in mice, macaques and humans. Sci Rep 2020; 10:16873. [PMID: 33037303 PMCID: PMC7547102 DOI: 10.1038/s41598-020-73942-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 09/18/2020] [Indexed: 11/18/2022] Open
Abstract
Tuberculosis (TB) is the leading cause of death due to a single infectious disease. Knowing when a person was infected with Mycobacterium tuberculosis (M.tb) is critical as recent infection is the strongest clinical risk factor for progression to TB disease in immunocompetent individuals. However, time since M.tb infection is challenging to determine in routine clinical practice. To define a biomarker for recent TB exposure, we determined whether gene expression patterns in blood RNA correlated with time since M.tb infection or exposure. First, we found RNA signatures that accurately discriminated early and late time periods after experimental infection in mice and cynomolgus macaques. Next, we found a 6-gene blood RNA signature that identified recently exposed individuals in two independent human cohorts, including adult household contacts of TB cases and adolescents who recently acquired M.tb infection. Our work supports the need for future longitudinal studies of recent TB contacts to determine whether biomarkers of recent infection can provide prognostic information of TB disease risk in individuals and help map recent transmission in communities.
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Affiliation(s)
- Russell C Ault
- Texas Biomedical Research Institute, San Antonio, TX, USA
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH, USA
- Biomedical Sciences Graduate Program, Ohio State University, Columbus, OH, USA
- Medical Scientist Training Program, Ohio State University, Columbus, OH, USA
| | - Colwyn A Headley
- Texas Biomedical Research Institute, San Antonio, TX, USA
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH, USA
- Biomedical Sciences Graduate Program, Ohio State University, Columbus, OH, USA
| | - Alexander E Hare
- Biomedical Sciences Graduate Program, Ohio State University, Columbus, OH, USA
- Medical Scientist Training Program, Ohio State University, Columbus, OH, USA
| | - Bridget J Carruthers
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH, USA
| | - Asuncion Mejias
- Center for Vaccines and Immunity, Abigail Wexner Research Institute at Nationwide Children's Hospital, Columbus, OH, USA
| | - Joanne Turner
- Texas Biomedical Research Institute, San Antonio, TX, USA.
- Department of Microbial Infection and Immunity, Ohio State University, Columbus, OH, USA.
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16
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Gunasekera KS, Zelner J, Becerra MC, Contreras C, Franke MF, Lecca L, Murray MB, Warren JL, Cohen T. Children as sentinels of tuberculosis transmission: disease mapping of programmatic data. BMC Med 2020; 18:234. [PMID: 32873309 PMCID: PMC7466499 DOI: 10.1186/s12916-020-01702-x] [Citation(s) in RCA: 1] [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: 04/01/2020] [Accepted: 07/09/2020] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Identifying hotspots of tuberculosis transmission can inform spatially targeted active case-finding interventions. While national tuberculosis programs maintain notification registers which represent a potential source of data to investigate transmission patterns, high local tuberculosis incidence may not provide a reliable signal for transmission because the population distribution of covariates affecting susceptibility and disease progression may confound the relationship between tuberculosis incidence and transmission. Child cases of tuberculosis and other endemic infectious disease have been observed to provide a signal of their transmission intensity. We assessed whether local overrepresentation of child cases in tuberculosis notification data corresponds to areas where recent transmission events are concentrated. METHODS We visualized spatial clustering of children < 5 years old notified to Peru's National Tuberculosis Program from two districts of Lima, Peru, from 2005 to 2007 using a log-Gaussian Cox process to model the intensity of the point-referenced child cases. To identify where clustering of child cases was more extreme than expected by chance alone, we mapped all cases from the notification data onto a grid and used a hierarchical Bayesian spatial model to identify grid cells where the proportion of cases among children < 5 years old is greater than expected. Modeling the proportion of child cases allowed us to use the spatial distribution of adult cases to control for unobserved factors that may explain the spatial variability in the distribution of child cases. We compare where young children are overrepresented in case notification data to areas identified as transmission hotspots using molecular epidemiological methods during a prospective study of tuberculosis transmission conducted from 2009 to 2012 in the same setting. RESULTS Areas in which childhood tuberculosis cases are overrepresented align with areas of spatial concentration of transmission revealed by molecular epidemiologic methods. CONCLUSIONS Age-disaggregated notification data can be used to identify hotspots of tuberculosis transmission and suggest local force of infection, providing an easily accessible source of data to target active case-finding intervention.
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Affiliation(s)
- Kenneth S Gunasekera
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA
| | - Jon Zelner
- Department of Epidemiology, University of Michigan School of Public Health, 267 SPH Tower, 1415 Washington Heights, Ann Arbor, MI, 48109, USA
| | - Mercedes C Becerra
- Department of Global Health and Social Medicine, Harvard Medical School, 641 Huntington Avenue, Boston, MA, 02115, USA
| | | | - Molly F Franke
- Department of Global Health and Social Medicine, Harvard Medical School, 641 Huntington Avenue, Boston, MA, 02115, USA
| | - Leonid Lecca
- Department of Global Health and Social Medicine, Harvard Medical School, 641 Huntington Avenue, Boston, MA, 02115, USA
- Socios En Salud, Lima, Peru
| | - Megan B Murray
- Department of Global Health and Social Medicine, Harvard Medical School, 641 Huntington Avenue, Boston, MA, 02115, USA
| | - Joshua L Warren
- Department of Biostatistics, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, 60 College Street, New Haven, CT, 06520, USA.
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17
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Trauer JM, Dodd PJ, Gomes MGM, Gomez GB, Houben RMGJ, McBryde ES, Melsew YA, Menzies NA, Arinaminpathy N, Shrestha S, Dowdy DW. The Importance of Heterogeneity to the Epidemiology of Tuberculosis. Clin Infect Dis 2020; 69:159-166. [PMID: 30383204 PMCID: PMC6579955 DOI: 10.1093/cid/ciy938] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/31/2018] [Indexed: 12/23/2022] Open
Abstract
Although less well-recognized than for other infectious diseases, heterogeneity is a defining feature of tuberculosis (TB) epidemiology. To advance toward TB elimination, this heterogeneity must be better understood and addressed. Drivers of heterogeneity in TB epidemiology act at the level of the infectious host, organism, susceptible host, environment, and distal determinants. These effects may be amplified by social mixing patterns, while the variable latent period between infection and disease may mask heterogeneity in transmission. Reliance on notified cases may lead to misidentification of the most affected groups, as case detection is often poorest where prevalence is highest. Assuming that average rates apply across diverse groups and ignoring the effects of cohort selection may result in misunderstanding of the epidemic and the anticipated effects of control measures. Given this substantial heterogeneity, interventions targeting high-risk groups based on location, social determinants, or comorbidities could improve efficiency, but raise ethical and equity considerations.
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Affiliation(s)
- James M Trauer
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Peter J Dodd
- Health Economic and Decision Science, University of Sheffield, United Kingdom
| | - M Gabriela M Gomes
- Liverpool School of Tropical Medicine, United Kingdom.,CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Portugal
| | - Gabriela B Gomez
- Department of Global Health and Development, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Rein M G J Houben
- Tuberculosis Centre, London School of Hygiene and Tropical Medicine, United Kingdom.,Infectious Disease Epidemiology Department, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Emma S McBryde
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland
| | - Yayehirad A Melsew
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Nicolas A Menzies
- Department of Global Health and Population, Harvard T. H. Chan School of Public Health, Boston, Massachusetts
| | - Nimalan Arinaminpathy
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, United Kingdom
| | - Sourya Shrestha
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - David W Dowdy
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
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18
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Kaguthi G, Nduba V, Rabuogi P, Okelloh D, Ouma SG, Blatner G, Gelderbloem S, Mitchell EMH, Scott CP, Verver S, Hawkridge T, de Steenwinkel JEM, Laserson KF, Richardus JH. Development of a TB vaccine trial site in Africa and lessons from the Ebola experience. BMC Public Health 2020; 20:999. [PMID: 32586316 PMCID: PMC7316575 DOI: 10.1186/s12889-020-09051-3] [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: 03/24/2020] [Accepted: 06/04/2020] [Indexed: 11/24/2022] Open
Abstract
Tuberculosis is the deadliest infection of our time. In contrast, about 11,000 people died of Ebola between 2014 and 2016. Despite this manifest difference in mortality, there is now a vaccine licensed in the United States and by the European Medicines Agency, with up to 100% efficacy against Ebola. The developments that led to the trialing of the Ebola vaccine were historic and unprecedented. The single licensed TB vaccine (BCG) has limited efficacy. There is a dire need for a more efficacious TB vaccine. To deploy such vaccines, trials are needed in sites that combine high disease incidence and research infrastructure. We describe our twelve-year experience building a TB vaccine trial site in contrast to the process in the recent Ebola outbreak. There are additional differences. Relative to the Ebola pipeline, TB vaccines have fewer trials and a paucity of government and industry led trials. While pathogens have varying levels of difficulty in the development of new vaccine candidates, there yet appears to be greater interest in funding and coordinating Ebola interventions. TB is a global threat that requires similar concerted effort for elimination.
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Affiliation(s)
- G Kaguthi
- Centre for Respiratory Diseases Research-Kenya Medical Research Institute (KEMRI-CRDR), Nairobi, Kenya. .,Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands. .,(at the time of the studies) KEMRI and Centers for Disease Control and Prevention Public Health Collaboration, Kisumu, Kenya.
| | - V Nduba
- Centre for Respiratory Diseases Research-Kenya Medical Research Institute (KEMRI-CRDR), Nairobi, Kenya.,(at the time of the studies) KEMRI and Centers for Disease Control and Prevention Public Health Collaboration, Kisumu, Kenya
| | - P Rabuogi
- Centre for Respiratory Diseases Research-Kenya Medical Research Institute (KEMRI-CRDR), Nairobi, Kenya.,(at the time of the studies) KEMRI and Centers for Disease Control and Prevention Public Health Collaboration, Kisumu, Kenya
| | - D Okelloh
- Centre for Respiratory Diseases Research-Kenya Medical Research Institute (KEMRI-CRDR), Nairobi, Kenya.,(at the time of the studies) KEMRI and Centers for Disease Control and Prevention Public Health Collaboration, Kisumu, Kenya
| | - S G Ouma
- Centre for Respiratory Diseases Research-Kenya Medical Research Institute (KEMRI-CRDR), Nairobi, Kenya.,(at the time of the studies) KEMRI and Centers for Disease Control and Prevention Public Health Collaboration, Kisumu, Kenya
| | - G Blatner
- AERAS (at the time of the studies), Cape Town, South Africa.,AERAS (at the time of the studies), Rockville, Maryland, USA
| | - S Gelderbloem
- AERAS (at the time of the studies), Cape Town, South Africa.,AERAS (at the time of the studies), Rockville, Maryland, USA
| | - Ellen M H Mitchell
- Institute of Tropical Medicine, Antwerp, Belgium.,(at the time of the studies) KNCV Tuberculosis Foundation, The Hague, The Netherlands
| | - Cherise P Scott
- AERAS (at the time of the studies), Cape Town, South Africa.,AERAS (at the time of the studies), Rockville, Maryland, USA
| | - S Verver
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,(at the time of the studies) KNCV Tuberculosis Foundation, The Hague, The Netherlands
| | - T Hawkridge
- AERAS (at the time of the studies), Cape Town, South Africa.,AERAS (at the time of the studies), Rockville, Maryland, USA
| | - J E M de Steenwinkel
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - K F Laserson
- (at the time of the studies) KEMRI and Centers for Disease Control and Prevention Public Health Collaboration, Kisumu, Kenya
| | - J H Richardus
- Department of Public Health, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
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19
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Jiang Q, Liu Q, Ji L, Li J, Zeng Y, Meng L, Luo G, Yang C, Takiff HE, Yang Z, Tan W, Yu W, Gao Q. Citywide Transmission of Multidrug-resistant Tuberculosis Under China's Rapid Urbanization: A Retrospective Population-based Genomic Spatial Epidemiological Study. Clin Infect Dis 2020; 71:142-151. [PMID: 31504306 PMCID: PMC8127054 DOI: 10.1093/cid/ciz790] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/26/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Population movement could extend multidrug-resistant tuberculosis (MDR-TB) transmission and complicate its global prevalence. We sought to identify the high-risk populations and geographic sites of MDR-TB transmission in Shenzhen, the most common destination for internal migrants in China. METHODS We performed a population-based, retrospective study in patients diagnosed with MDR-TB in Shenzhen during 2013-2017. By defining genomic clusters with a threshold of 12-single-nucleotide polymorphism distance based on whole-genome sequencing of their clinical strains, the clustering rate was calculated to evaluate the level of recent transmission. Risk factors were identified by multivariable logistic regression. To further delineate the epidemiological links, we invited the genomic-clustered patients to an in-depth social network investigation. RESULTS In total, 105 (25.2%) of the 417 enrolled patients with MDR-TB were grouped into 40 genome clusters, suggesting recent transmission of MDR strains. The adjusted risk for student to have a clustered strain was 4.05 (95% confidence interval, 1.06-17.0) times greater than other patients. The majority (70%, 28/40) of the genomic clusters involved patients who lived in different districts, with residences separated by an average of 8.76 kilometers. Other than household members, confirmed epidemiological links were also identified among classmates and workplace colleagues. CONCLUSIONS These findings demonstrate that local transmission of MDR-TB is a serious problem in Shenzhen. While most transmission occurred between people who lived distant from each other, there was clear evidence that transmission occurred in schools and workplaces, which should be included as targeted sites for active case finding.The average residential distance between genomic-clustered cases was more than 8 kilometers, while schools and workplaces, identified as sites of transmission in this study, deserve increased vigilance for targeted case finding of multidrug-resistant tuberculosis.
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Affiliation(s)
- Qi Jiang
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
- Key Laboratory of Medical Molecular Virology (Ministry of Education,National Health Commission, Chinese Academy of Medical Sciences), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shenzhen, China
| | - Qingyun Liu
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
- Key Laboratory of Medical Molecular Virology (Ministry of Education,National Health Commission, Chinese Academy of Medical Sciences), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shenzhen, China
| | - Lecai Ji
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Jinli Li
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Yaling Zeng
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Liangguang Meng
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Geyang Luo
- Key Laboratory of Medical Molecular Virology (Ministry of Education,National Health Commission, Chinese Academy of Medical Sciences), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shenzhen, China
| | - Chongguang Yang
- School of Public Health, Yale University, New Haven, Connecticut, USA
| | - Howard E Takiff
- Integrated Mycobacterial Pathogenomics Unit, Institut Pasteur, Paris, France
- Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Zheng Yang
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Weiguo Tan
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Weiye Yu
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Qian Gao
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
- Key Laboratory of Medical Molecular Virology (Ministry of Education,National Health Commission, Chinese Academy of Medical Sciences), School of Basic Medical Sciences, Shanghai Medical College and Shanghai Public Health Clinical Center, Fudan University, Shenzhen, China
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20
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Robsky KO, Kitonsa PJ, Mukiibi J, Nakasolya O, Isooba D, Nalutaaya A, Salvatore PP, Kendall EA, Katamba A, Dowdy D. Spatial distribution of people diagnosed with tuberculosis through routine and active case finding: a community-based study in Kampala, Uganda. Infect Dis Poverty 2020; 9:73. [PMID: 32571435 PMCID: PMC7310105 DOI: 10.1186/s40249-020-00687-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 06/01/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Routine tuberculosis (TB) notifications are geographically heterogeneous, but their utility in predicting the location of undiagnosed TB cases is unclear. We aimed to identify small-scale geographic areas with high TB notification rates based on routinely collected data and to evaluate whether these areas have a correspondingly high rate of undiagnosed prevalent TB. METHODS We used routinely collected data to identify geographic areas with high TB notification rates and evaluated the extent to which these areas correlated with the location of undiagnosed cases during a subsequent community-wide active case finding intervention in Kampala, Uganda. We first enrolled all adults who lived within 35 contiguous zones and were diagnosed through routine care at four local TB Diagnosis and Treatment Units. We calculated average monthly TB notification rates in each zone and defined geographic areas of "high risk" as zones that constituted the 20% of the population with highest notification rates. We compared the observed proportion of TB notifications among residents of these high-risk zones to the expected proportion, using simulated estimates based on population size and random variation alone. We then evaluated the extent to which these high-risk zones identified areas with high burdens of undiagnosed TB during a subsequent community-based active case finding campaign using a chi-square test. RESULTS We enrolled 45 adults diagnosed with TB through routine practices and who lived within the study area (estimated population of 49 527). Eighteen zones reported no TB cases in the 9-month period; among the remaining zones, monthly TB notification rates ranged from 3.9 to 39.4 per 100 000 population. The five zones with the highest notification rates constituted 62% (95% CI: 47-75%) of TB cases and 22% of the population-significantly higher than would be expected if population size and random chance were the only determinants of zone-to-zone variation (48%, 95% simulation interval: 40-59%). These five high-risk zones accounted for 42% (95% CI: 34-51%) of the 128 cases detected during the subsequent community-based case finding intervention, which was significantly higher than the 22% expected by chance (P < 0.001) but lower than the 62% of cases notified from those zones during the pre-intervention period (P = 0.02). CONCLUSIONS There is substantial heterogeneity in routine TB notification rates at the zone level. Using facility-based TB notification rates to prioritize high-yield areas for active case finding could double the yield of such case-finding interventions.
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Affiliation(s)
- Katherine O Robsky
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA. .,Uganda Tuberculosis Implementation Research Consortium, Makerere University, Kampala, Uganda.
| | - Peter J Kitonsa
- Uganda Tuberculosis Implementation Research Consortium, Makerere University, Kampala, Uganda
| | - James Mukiibi
- Uganda Tuberculosis Implementation Research Consortium, Makerere University, Kampala, Uganda
| | - Olga Nakasolya
- Uganda Tuberculosis Implementation Research Consortium, Makerere University, Kampala, Uganda
| | - David Isooba
- Uganda Tuberculosis Implementation Research Consortium, Makerere University, Kampala, Uganda
| | - Annet Nalutaaya
- Uganda Tuberculosis Implementation Research Consortium, Makerere University, Kampala, Uganda
| | - Phillip P Salvatore
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Emily A Kendall
- Uganda Tuberculosis Implementation Research Consortium, Makerere University, Kampala, Uganda.,Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Achilles Katamba
- Uganda Tuberculosis Implementation Research Consortium, Makerere University, Kampala, Uganda.,Department of Medicine, Clinical Epidemiology and Biostatistics Unit, Makerere University, College of Health Sciences, Kampala, Uganda
| | - David Dowdy
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.,Uganda Tuberculosis Implementation Research Consortium, Makerere University, Kampala, Uganda.,Johns Hopkins School of Medicine, Baltimore, MD, USA
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21
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A positively selected FBN1 missense variant reduces height in Peruvian individuals. Nature 2020; 582:234-239. [PMID: 32499652 PMCID: PMC7410362 DOI: 10.1038/s41586-020-2302-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 03/10/2020] [Indexed: 01/21/2023]
Abstract
On average, Peruvian individuals are among the shortest in the world1. Here we show that Native American ancestry is associated with reduced height in an ethnically diverse group of Peruvian individuals, and identify a population-specific, missense variant in the FBN1 gene (E1297G) that is significantly associated with lower height. Each copy of the minor allele (frequency of 4.7%) reduces height by 2.2 cm (4.4 cm in homozygous individuals). To our knowledge, this is the largest effect size known for a common height-associated variant. FBN1 encodes the extracellular matrix protein fibrillin 1, which is a major structural component of microfibrils. We observed less densely packed fibrillin-1-rich microfibrils with irregular edges in the skin of individuals who were homozygous for G1297 compared with individuals who were homozygous for E1297. Moreover, we show that the E1297G locus is under positive selection in non-African populations, and that the E1297 variant shows subtle evidence of positive selection specifically within the Peruvian population. This variant is also significantly more frequent in coastal Peruvian populations than in populations from the Andes or the Amazon, which suggests that short stature might be the result of adaptation to factors that are associated with the coastal environment in Peru.
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22
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Asare P, Otchere ID, Bedeley E, Brites D, Loiseau C, Baddoo NA, Asante-Poku A, Osei-Wusu S, Prah DA, Borrell S, Reinhard M, Forson A, Koram KA, Gagneux S, Yeboah-Manu D. Whole Genome Sequencing and Spatial Analysis Identifies Recent Tuberculosis Transmission Hotspots in Ghana. Front Med (Lausanne) 2020; 7:161. [PMID: 32509791 PMCID: PMC7248928 DOI: 10.3389/fmed.2020.00161] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/09/2020] [Indexed: 01/08/2023] Open
Abstract
Whole genome sequencing (WGS) is progressively being used to investigate the transmission dynamics of Mycobacterium tuberculosis complex (MTBC). We used WGS analysis to resolve traditional genotype clusters and explored the spatial distribution of confirmed recent transmission clusters. Bacterial genomes from a total of 452 MTBC isolates belonging to large traditional clusters from a population-based study spanning July 2012 and December 2015 were obtained through short read next-generation sequencing using the illumina HiSeq2500 platform. We performed clustering and spatial analysis using specified R packages and ArcGIS. Of the 452 traditional genotype clustered genomes, 314 (69.5%) were confirmed clusters with a median cluster size of 7.5 genomes and an interquartile range of 4–12. Recent tuberculosis (TB) transmission was estimated as 24.7%. We confirmed the wide spread of a Cameroon sub-lineage clone with a cluster size of 78 genomes predominantly from the Ablekuma sub-district of Accra metropolis. More importantly, we identified a recent transmission cluster associated with isoniazid resistance belonging to the Ghana sub-lineage of lineage 4. WGS was useful in detecting unsuspected outbreaks; hence, we recommend its use not only as a research tool but as a surveillance tool to aid in providing the necessary guided steps to track, monitor, and control TB.
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Affiliation(s)
- Prince Asare
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana.,West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana.,Department of Biochemistry, Cell and Molecular Biology, University of Ghana, Accra, Ghana
| | - Isaac Darko Otchere
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Edmund Bedeley
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Daniela Brites
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Chloé Loiseau
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | - Adwoa Asante-Poku
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Stephen Osei-Wusu
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Diana Ahu Prah
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Sonia Borrell
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Miriam Reinhard
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Audrey Forson
- Department of Chest Diseases, Korle-Bu Teaching Hospital, Korle-Bu, Accra, Ghana
| | - Kwadwo Ansah Koram
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana, Accra, Ghana.,West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
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23
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Siddiqui AR, Ali Nathwani A, Abidi SH, Mahmood SF, Azam I, Sawani S, Kazi AM, Hotwani A, Memon SA, Soomro J, Shaikh SA, Achakzai B, Saeed Q, Simms V, Khan P, Ferrand R, Mir F. Investigation of an extensive outbreak of HIV infection among children in Sindh, Pakistan: protocol for a matched case -control study. BMJ Open 2020; 10:e036723. [PMID: 32213527 PMCID: PMC7170612 DOI: 10.1136/bmjopen-2019-036723] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
INTRODUCTION In April 2019, 14 children were diagnosed with HIV infection by a private healthcare provider in Larkana district, Sindh province, Pakistan. Over the next 3 months, 930 individuals were diagnosed with HIV, >80% below 16 years, the largest ever outbreak of HIV in children in Pakistan. In this protocol paper, we describe research methods for assessing likely modes of HIV transmission in this outbreak and investigate spatial and molecular epidemiology. METHODS AND ANALYSIS A matched case-control study will be conducted with 406 cases recruited. Cases will be children aged below 16 years registered for care at the HIV treatment centre at Shaikh Zayed Children Hospital in Larkana City. Controls will be children who are HIV-uninfected (confirmed by a rapid HIV test) matched 1:1 by age (within 1 year), sex and neighbourhood. Following written informed consent from the guardian, a structured questionnaire will be administered to collect data on sociodemographic indices and exposure to risk factors for parenteral, vertical and sexual (only among those aged above 10 years) HIV transmission. A blood sample will be collected for hepatitis B and C serology (cases and controls) and HIV lineage studies (cases only). Mothers of participants will be tested for HIV to investigate the possibility of mother-to-child transmission. Conditional logistic regression will be used to investigate the association of a priori defined risk factors with HIV infection. Phylogenetic analyses will be conducted. Global positioning system coordinates of participants' addresses will be collected to investigate concordance between the genetic and spatial epidemiology. ETHICS AND DISSEMINATION Ethical approval was granted by the Ethics Review Committee of the Aga Khan University, Karachi. Study results will be shared with Sindh and National AIDS Control Programs, relevant governmental and non-governmental organisations, presented at national and international research conferences and published in international peer-reviewed scientific journals.
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Affiliation(s)
- Amna R Siddiqui
- Department of Community Health Sciences, Aga Khan University, Karachi, Sindh, Pakistan
| | - Apsara Ali Nathwani
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Syed H Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Sindh, Pakistan
| | - Syed Faisal Mahmood
- Section of Infectious Disease, Department of Internal Medicine, the Aga Khan University, Karachi, Sindh, Pakistan
| | - Iqbal Azam
- Department of Community Health Sciences, Aga Khan University, Karachi, Sindh, Pakistan
| | - Sobiya Sawani
- Department of Community Health Sciences, Aga Khan University, Karachi, Sindh, Pakistan
| | - Abdul M Kazi
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
| | - Aneeta Hotwani
- Infectious Disease Research Laboratory, Department of Pediatrics and Child Health, the Aga Khan University, Karachi, Sindh, Pakistan
| | - Sikander Ali Memon
- Sindh AIDS Control Program, Ministry of Health, Karachi, Sindh, Pakistan
| | - Jamila Soomro
- Public Health Wing, Ministry of Health, Karachi, Sindh, Pakistan
| | - Saqib Ali Shaikh
- Sindh AIDS Control Program, Ministry of Health, Karachi, Sindh, Pakistan
| | | | - Quaid Saeed
- National AIDS Control Program, Islamabad, Pakistan
| | - Victoria Simms
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Palwasha Khan
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK
| | - Rashida Ferrand
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
- Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK
| | - Fatima Mir
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, Pakistan
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24
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Carrasco-Escobar G, Schwalb A, Tello-Lizarraga K, Vega-Guerovich P, Ugarte-Gil C. Spatio-temporal co-occurrence of hotspots of tuberculosis, poverty and air pollution in Lima, Peru. Infect Dis Poverty 2020; 9:32. [PMID: 32204735 PMCID: PMC7092495 DOI: 10.1186/s40249-020-00647-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 03/05/2020] [Indexed: 12/03/2022] Open
Abstract
Growing evidence suggests pollution and other environmental factors have a role in the development of tuberculosis (TB), however, such studies have never been conducted in Peru. Considering the association between air pollution and specific geographic areas, our objective was to determine the spatial distribution and clustering of TB incident cases in Lima and their co-occurrence with clusters of fine particulate matter (PM2.5) and poverty. We found co-occurrences of clusters of elevated concentrations of air pollutants such as PM2.5, high poverty indexes, and high TB incidence in Lima. These findings suggest an interplay of socio-economic and environmental in driving TB incidence.
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Affiliation(s)
- Gabriel Carrasco-Escobar
- Health Innovation Lab, Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Alvaro Schwalb
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Kelly Tello-Lizarraga
- School of Public Health and Administration, Universidad Peruana Cayetano Heredia, Lima, Peru
| | | | - Cesar Ugarte-Gil
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru.
- School of Medicine, Universidad Peruana Cayetano Heredia, Lima, Peru.
- TB Centre, London School of Hygiene and Tropical Medicine, London, UK.
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25
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Cerezo-Cortés MI, Rodríguez-Castillo JG, Hernández-Pando R, Murcia MI. Circulation of M. tuberculosis Beijing genotype in Latin America and the Caribbean. Pathog Glob Health 2019; 113:336-351. [PMID: 31903874 PMCID: PMC7006823 DOI: 10.1080/20477724.2019.1710066] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Lineage 2 (East Asian), which includes the Beijing genotype, is one of the most prevalent lineages of Mycobacterium tuberculosis (Mtb) throughout the world. The Beijing family is associated to hypervirulence and drug-resistant tuberculosis. The study of this genotype's circulation in Latin America is crucial for achieving total control of TB, the goal established by the World Health Organization, for the American sub-continent, before 2035. In this sense, the present work presents an overview of the status of the Beijing genotype for this region, with a bibliographical review, and data analysis of MIRU-VNTRs for available Beijing isolates. Certain countries present a prevalent trend of <5%, suggesting low transmissibility for the region, with the exception of Cuba (17.2%), Perú (16%) and Colombia (5%). Minimum Spanning Tree analysis, obtained from MIRU-VNTR data, shows distribution of specific clonal complex strains in each country. From this data, in most countries, we found that molecular epidemiology has not been a tool used for the control of TB, suggesting that the Beijing genotype may be underestimated in Latin America. It is recommended that countries with the highest incidence of the Beijing genotype use effective control strategies and increased care, as a requirement for public health systems.
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Affiliation(s)
- MI Cerezo-Cortés
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - JG Rodríguez-Castillo
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
| | - R Hernández-Pando
- Experimental Pathology Section, Department of Pathology, National Institute of Medical Sciences and Nutrition, México D.F., Mexico
| | - MI Murcia
- Grupo MICOBAC-UN, Departamento de Microbiología, Facultad de Medicina, Universidad Nacional de Colombia, Bogotá, Colombia
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Rosenkrantz L, Amram O, Caudell MA, Schuurman N, Call DR. Spatial relationships between small-holder farms coupled with livestock management practices are correlated with the distribution of antibiotic resistant bacteria in northern Tanzania. One Health 2019; 8:100097. [PMID: 31249856 PMCID: PMC6584765 DOI: 10.1016/j.onehlt.2019.100097] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 05/21/2019] [Accepted: 06/10/2019] [Indexed: 11/24/2022] Open
Abstract
We examined the spatial distribution of antibiotic-resistant coliform bacteria amongst livestock from three distinct cultural groups, where group-level differences in practices (e.g., antibiotic use) may influence the magnitude of antibiotic resistance, while livestock interactions (e.g., mixing herds, shared markets) between these locations may reduce heterogeneity in the distribution of antibiotic resistant bacteria. Data was collected as part of a larger study of antibiotic-resistance in northern Tanzania. Simple regression and generalized linear regression were used to assess livestock management and care practices in relation to the prevalence of multidrug-resistant (MDR) coliform bacteria. Simple and multivariable logistic regression were then used to identify how different management practices affected the odds of households being found within MDR "hotspots." Households that had a higher median neighbourhood value within a 3000 m radius showed a significant positive correlation with livestock MDR prevalence (β = 4.33, 95% CI: 2.41-6.32). Households were more likely to be found within hotspots if they had taken measures to avoid disease (Adjusted Odds Ratio (AOR) 1.53, CI: 1.08-2.18), and if they reported traveling less than a day to reach the market (AOR 2.66, CI: 1.18-6.01). Hotspot membership was less likely when a greater number of livestock were kept at home (AOR 0.81, CI: 0.69-0.95), if livestock were vaccinated (AOR 0.32, CI: 0.21-0.51), or if distance to nearest village was greater (AOR 0.46, CI: 0.36-0.59). The probability of MDR increases when herds are mixed, consistent with evidence for passive transmission of resistant bacteria between animals. Reduced MDR with vaccination is consistent with many studies showing reduced antibiotic use with less disease burden. The neighbourhood effect has implications for design of intervention studies.
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Affiliation(s)
- Leah Rosenkrantz
- Department of Geography, Simon Fraser Univesity, Burnaby V5A 1S6, British Columbia, Canada
| | - Ofer Amram
- Elson S. Floyd College of Medicine, Washington State University, Spokane, PO Box 1495, WA, USA
| | - Mark A. Caudell
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, 99164 Washington, USA
| | - Nadine Schuurman
- Department of Geography, Simon Fraser Univesity, Burnaby V5A 1S6, British Columbia, Canada
| | - Douglas R. Call
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, 99164 Washington, USA
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Smith CM, Lessells R, Grant AD, Herbst K, Tanser F. Spatial clustering of drug-resistant tuberculosis in Hlabisa subdistrict, KwaZulu-Natal, 2011-2015. Int J Tuberc Lung Dis 2019; 22:287-293. [PMID: 29471906 PMCID: PMC7325217 DOI: 10.5588/ijtld.17.0457] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
SETTING: Incidence rates of tuberculosis (TB) in South Africa are among the highest in the world, and drug resistance is a major concern. Understanding geographic variations in disease may guide targeted interventions. OBJECTIVE: To characterise the spatial distribution of drug-resistant TB (DR-TB) in a rural area of KwaZulu-Natal, South Africa, and to test for clustering. DESIGN: This was a cross-sectional analysis of DR-TB patients managed at a rural district hospital from 2011 to 2015. We mapped all patients in hospital data to local areas, and then linked to a population-based demographic surveillance system to map the patients to individual homesteads. We used kernel density estimation to visualise the distribution of disease and tested for clustering using spatial scan statistics. RESULTS: There were 489 patients with DR-TB in the subdistrict; 111 lived in the smaller demographic surveillance area. Spatial clustering analysis identified a high-risk cluster (relative risk of DR-TB inside vs. outside cluster 3.0, P <0.001) in the south-east, a region characterised by high population density and a high prevalence of human immunodeficiency virus infection. CONCLUSION: We have demonstrated evidence of a geographic high-risk cluster of DR-TB. This suggests that targeting interventions to spatial areas of highest risk, where transmission may be ongoing, could be effective.
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Affiliation(s)
- C M Smith
- Centre for Public Health Data, Institute of Health Informatics, University College London, London
| | - R Lessells
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK, Africa Health Research Institute, School of Nursing and Public Health, University of KwaZulu-Natal, Somkhele
| | - A D Grant
- Department of Clinical Research, London School of Hygiene & Tropical Medicine, London, UK, Africa Health Research Institute, School of Nursing and Public Health, University of KwaZulu-Natal, Somkhele, School of Public Health, University of the Witwatersrand, Johannesburg
| | - K Herbst
- Africa Health Research Institute, School of Nursing and Public Health, University of KwaZulu-Natal, Somkhele
| | - F Tanser
- Africa Health Research Institute, School of Nursing and Public Health, University of KwaZulu-Natal, Somkhele, School of Nursing and Public Health, University of KwaZulu-Natal, Durban, Centre for the AIDS Programme of Research in South Africa, University of KwaZulu-Natal, Congella, South Africa
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28
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Bui DP, Oren E, Roe DJ, Brown HE, Harris RB, Knight GM, Gilman RH, Grandjean L. A Case-Control Study to Identify Community Venues Associated with Genetically-clustered, Multidrug-resistant Tuberculosis Disease in Lima, Peru. Clin Infect Dis 2019; 68:1547-1555. [PMID: 30239609 PMCID: PMC7181380 DOI: 10.1093/cid/ciy746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/24/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND The majority of tuberculosis transmission occurs in community settings. Our primary aim in this study was to assess the association between exposure to community venues and multidrug-resistant (MDR) tuberculosis. Our secondary aim was to describe the social networks of MDR tuberculosis cases and controls. METHODS We recruited laboratory-confirmed MDR tuberculosis cases and community controls that were matched on age and sex. Whole-genome sequencing was used to identify genetically clustered cases. Venue tracing interviews (nonblinded) were conducted to enumerate community venues frequented by participants. Logistic regression was used to assess the association between MDR tuberculosis and person-time spent in community venues. A location-based social network was constructed, with respondents connected if they reported frequenting the same venue, and an exponential random graph model (ERGM) was fitted to model the network. RESULTS We enrolled 59 cases and 65 controls. Participants reported 729 unique venues. The mean number of venues reported was similar in both groups (P = .92). Person-time in healthcare venues (adjusted odds ratio [aOR] = 1.67, P = .01), schools (aOR = 1.53, P < .01), and transportation venues (aOR = 1.25, P = .03) was associated with MDR tuberculosis. Healthcare venues, markets, cinemas, and transportation venues were commonly shared among clustered cases. The ERGM indicated significant community segregation between cases and controls. Case networks were more densely connected. CONCLUSIONS Exposure to healthcare venues, schools, and transportation venues was associated with MDR tuberculosis. Intervention across the segregated network of case venues may be necessary to effectively stem transmission.
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Affiliation(s)
- David P Bui
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, The University of Arizona, Tucson
| | - Eyal Oren
- School of Public Health, San Diego State University, California
| | - Denise J Roe
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, The University of Arizona, Tucson
| | - Heidi E Brown
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, The University of Arizona, Tucson
| | - Robin B Harris
- Department of Epidemiology and Biostatistics, Mel and Enid Zuckerman College of Public Health, The University of Arizona, Tucson
| | - Gwenan M Knight
- London School of Hygiene and Tropical Medicine, United Kingdom
| | - Robert H Gilman
- Universidad Peruana Cayetano Heredia, Lima, Peru
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - Louis Grandjean
- London School of Hygiene and Tropical Medicine, United Kingdom
- Universidad Peruana Cayetano Heredia, Lima, Peru
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29
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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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Cudahy PGT, Andrews JR, Bilinski A, Dowdy DW, Mathema B, Menzies NA, Salomon JA, Shrestha S, Cohen T. Spatially targeted screening to reduce tuberculosis transmission in high-incidence settings. THE LANCET. INFECTIOUS DISEASES 2019; 19:e89-e95. [PMID: 30554997 PMCID: PMC6401264 DOI: 10.1016/s1473-3099(18)30443-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 05/07/2018] [Accepted: 07/11/2018] [Indexed: 12/21/2022]
Abstract
As the leading infectious cause of death worldwide and the primary proximal cause of death in individuals living with HIV, tuberculosis remains a global concern. Existing tuberculosis control strategies that rely on passive case-finding appear insufficient to achieve targets for reductions in tuberculosis incidence and mortality. Active case-finding strategies aim to detect infectious individuals earlier in their infectious period to reduce onward transmission and improve treatment outcomes. Empirical studies of active case-finding have produced mixed results and determining how to direct active screening to those most at risk remains a topic of intense research. Our systematic review of literature evaluating the effects of geographically targeted tuberculosis screening interventions found three studies in low tuberculosis incidence settings, but none conducted in high tuberculosis incidence countries. We discuss open questions related to the use of spatially targeted approaches for active screening in countries where tuberculosis incidence is highest.
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Affiliation(s)
- Patrick G T Cudahy
- Section of Infectious Disease, Department of Medicine, Yale University School of Medicine, New Haven, CT, USA.
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Alyssa Bilinski
- Interfaculty Initiative in Health Policy, Harvard Graduate School of Arts and Sciences, Cambridge, MA, USA
| | - David W Dowdy
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Barun Mathema
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Nicolas A Menzies
- Department of Global Health and Population, Harvard T H Chan School of Public Health, Boston, MA, USA
| | - Joshua A Salomon
- Department of Global Health and Population, Harvard T H Chan School of Public Health, Boston, MA, USA; Center for Health Policy and Center for Primary Care and Outcomes Research, Stanford University, Stanford, CA, USA
| | - Sourya Shrestha
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Ted Cohen
- Department of Epidemiology (Microbial Diseases), Yale University School of Public Health, New Haven, CT, USA
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31
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Zelner J, Murray M, Becerra M, Galea J, Lecca L, Calderon R, Yataco R, Zhang Z, Cohen T. Protective effects of household-based TB interventions are robust to neighbourhood-level variation in exposure risk in Lima, Peru: a model-based analysis. Int J Epidemiol 2019; 47:185-192. [PMID: 29025111 DOI: 10.1093/ije/dyx171] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/07/2017] [Indexed: 11/14/2022] Open
Abstract
Background Untargeted active screening and treatment programmes for tuberculosis (TB) have not been shown to be more effective than passive screening and isoniazid preventive therapy (IPT) for reducing TB incidence. In this manuscript, we compare the efficacy of targeting screening and IPT on high-risk household contacts of diagnosed TB cases, with less-targeted active screening approaches in Lima, Peru. Methods We conducted a population-based prospective cohort study within households of TB cases in Lima. We identified all adults diagnosed with incident pulmonary TB from 2009 through 2012 at 106 participating public health centres (HC) within our catchment area of ∼3.3 million inhabitants. We estimated combined effects of community and household exposure on the risk of latent TB infection (LTBI) and incident TB disease. We used simulation modelling to assess the efficacy of TB screening programmes for reducing the risk of incident TB in these contacts. Results Individuals with household exposure to TB are more likely to present with LTBI and TB disease than those without this exposure, despite wide variation in community exposure. Simulations suggest that more cases are prevented by 1000 administrations of IPT to tuberculin skin test (TST)-positive household contacts of identified TB cases (30, 95% CI = 16,47) than from blanket screening and treatment in the community (7, 95% CI = 2,17). Conclusions Household exposure remains a major driver of incident TB risk among household contacts of identified TB cases. Targeting interventions on these individuals is likely to prevent more cases of TB than blanket screening of individuals in the community.
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Affiliation(s)
- Jon Zelner
- Department of Epidemiology.,Center for Social Epidemiology and Population Health, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Megan Murray
- Department of Epidemiology.,Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - Mercedes Becerra
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA.,Partners In Health/Socios En Salud, Boston, MA, USA/Lima, Peru.,Division of Global Health Equity, Brigham and Women's Hospital. Boston, MA, USA
| | - Jerome Galea
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA
| | - Leonid Lecca
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, MA, USA.,Partners In Health/Socios En Salud, Boston, MA, USA/Lima, Peru
| | - Roger Calderon
- Partners In Health/Socios En Salud, Boston, MA, USA/Lima, Peru
| | - Rosa Yataco
- Partners In Health/Socios En Salud, Boston, MA, USA/Lima, Peru
| | - Zibiao Zhang
- Division of Global Health Equity, Brigham and Women's Hospital. Boston, MA, USA
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
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32
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Vo LNQ, Vu TN, Nguyen HT, Truong TT, Khuu CM, Pham PQ, Nguyen LH, Le GT, Creswell J. Optimizing community screening for tuberculosis: Spatial analysis of localized case finding from door-to-door screening for TB in an urban district of Ho Chi Minh City, Viet Nam. PLoS One 2018; 13:e0209290. [PMID: 30562401 PMCID: PMC6298730 DOI: 10.1371/journal.pone.0209290] [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: 08/07/2018] [Accepted: 12/03/2018] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is the deadliest infectious disease globally. Current case finding approaches may miss many people with TB or detect them too late. DATA AND METHODS This study was a retrospective, spatial analysis of routine TB surveillance and cadastral data in Go Vap district, Ho Chi Minh City. We geocoded TB notifications from 2011 to 2015 and calculated theoretical yields of simulated door-to-door screening in three concentric catchment areas (50m, 100m, 200m) and three notification window scenarios (one, two and four quarters) for each index case. We calculated average yields, compared them to published reference values and fit a GEE (Generalized Estimating Equation) linear regression model onto the data. RESULTS The sample included 3,046 TB patients. Adjusted theoretical yields in 50m, 100m and 200m catchment areas were 0.32% (95%CI: 0.27,0.37), 0.21% (95%CI: 0.14,0.29) and 0.17% (95%CI: 0.09,0.25), respectively, in the baseline notification window scenario. Theoretical yields in the 50m-catchment area for all notification window scenarios were significantly higher than a reference yield from literature. Yield was positively associated with treatment failure index cases (beta = 0.12, p = 0.001) and short-term inter-province migrants (beta = 0.06, p = 0.022), while greater distance to the DTU (beta = -0.02, p<0.001) was associated with lower yield. CONCLUSIONS This study is an example of inter-departmental collaboration and application of repurposed cadastral data to progress towards the end TB objectives. The results from Go Vap showed that the use of spatial analysis may be able to identify areas where targeted active case finding in Vietnam can help improve TB case detection.
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Affiliation(s)
| | - Thanh Nguyen Vu
- Ho Chi Minh City Public Health Association, Ho Chi Minh City, Viet Nam
| | - Hoa Trung Nguyen
- Go Vap District Preventive Health Center, Ho Chi Minh City, Viet Nam
| | - Tung Thanh Truong
- Ho Chi Minh City Department of Science & Technology, Center for Applied Geographic Information Systems (HCMGIS), Ho Chi Minh City, Viet Nam
| | - Canh Minh Khuu
- Ho Chi Minh City Department of Science & Technology, Center for Applied Geographic Information Systems (HCMGIS), Ho Chi Minh City, Viet Nam
| | - Phuong Quoc Pham
- Ho Chi Minh City Department of Science & Technology, Center for Applied Geographic Information Systems (HCMGIS), Ho Chi Minh City, Viet Nam
| | | | - Giang Truong Le
- Ho Chi Minh City Public Health Association, Ho Chi Minh City, Viet Nam
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Nelson KN, Shah NS, Mathema B, Ismail N, Brust JCM, Brown TS, Auld SC, Omar SV, Morris N, Campbell A, Allana S, Moodley P, Mlisana K, Gandhi NR. Spatial Patterns of Extensively Drug-Resistant Tuberculosis Transmission in KwaZulu-Natal, South Africa. J Infect Dis 2018; 218:1964-1973. [PMID: 29961879 PMCID: PMC6217717 DOI: 10.1093/infdis/jiy394] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 06/26/2018] [Indexed: 12/29/2022] Open
Abstract
Background Transmission is driving the global drug-resistant tuberculosis (TB) epidemic; nearly three-quarters of drug-resistant TB cases are attributable to transmission. Geographic patterns of disease incidence, combined with information on probable transmission links, can define the spatial scale of transmission and generate hypotheses about factors driving transmission patterns. Methods We combined whole-genome sequencing data with home Global Positioning System coordinates from 344 participants with extensively drug-resistant (XDR) TB in KwaZulu-Natal, South Africa, diagnosed from 2011 to 2014. We aimed to determine if genomically linked (difference of ≤5 single-nucleotide polymorphisms) cases lived close to one another, which would suggest a role for local community settings in transmission. Results One hundred eighty-two study participants were genomically linked, comprising 1084 case-pairs. The median distance between case-pairs' homes was 108 km (interquartile range, 64-162 km). Between-district, as compared to within-district, links accounted for the majority (912/1084 [84%]) of genomic links. Half (526 [49%]) of genomic links involved a case from Durban, the urban center of KwaZulu-Natal. Conclusions The high proportions of between-district links with Durban provide insight into possible drivers of province-wide XDR-TB transmission, including urban-rural migration. Further research should focus on characterizing the contribution of these drivers to overall XDR-TB transmission in KwaZulu-Natal to inform design of targeted strategies to curb the drug-resistant TB epidemic.
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Affiliation(s)
- Kristin N Nelson
- Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - N Sarita Shah
- Rollins School of Public Health, Emory University, Atlanta, Georgia
- Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Barun Mathema
- Mailman School of Public Health, Columbia University, New York, New York
| | - Nazir Ismail
- National Institute for Communicable Diseases, Johannesburg
- University of Pretoria, South Africa
| | - James C M Brust
- Albert Einstein College of Medicine and Montefiore Medical Center, Bronx, New York
| | - Tyler S Brown
- Infectious Diseases Division, Massachusetts General Hospital, Boston
| | - Sara C Auld
- Rollins School of Public Health, Emory University, Atlanta, Georgia
- Emory University School of Medicine, Atlanta, Georgia
| | | | - Natashia Morris
- Environment and Health Research Unit, South African Medical Research Council, Johannesburg
| | - Angie Campbell
- Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Salim Allana
- Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Pravi Moodley
- National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Koleka Mlisana
- National Health Laboratory Service, University of KwaZulu-Natal, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Neel R Gandhi
- Rollins School of Public Health, Emory University, Atlanta, Georgia
- Emory University School of Medicine, Atlanta, Georgia
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Shaweno D, Karmakar M, Alene KA, Ragonnet R, Clements AC, Trauer JM, Denholm JT, McBryde ES. Methods used in the spatial analysis of tuberculosis epidemiology: a systematic review. BMC Med 2018; 16:193. [PMID: 30333043 PMCID: PMC6193308 DOI: 10.1186/s12916-018-1178-4] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Accepted: 09/20/2018] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) transmission often occurs within a household or community, leading to heterogeneous spatial patterns. However, apparent spatial clustering of TB could reflect ongoing transmission or co-location of risk factors and can vary considerably depending on the type of data available, the analysis methods employed and the dynamics of the underlying population. Thus, we aimed to review methodological approaches used in the spatial analysis of TB burden. METHODS We conducted a systematic literature search of spatial studies of TB published in English using Medline, Embase, PsycInfo, Scopus and Web of Science databases with no date restriction from inception to 15 February 2017. The protocol for this systematic review was prospectively registered with PROSPERO ( CRD42016036655 ). RESULTS We identified 168 eligible studies with spatial methods used to describe the spatial distribution (n = 154), spatial clusters (n = 73), predictors of spatial patterns (n = 64), the role of congregate settings (n = 3) and the household (n = 2) on TB transmission. Molecular techniques combined with geospatial methods were used by 25 studies to compare the role of transmission to reactivation as a driver of TB spatial distribution, finding that geospatial hotspots are not necessarily areas of recent transmission. Almost all studies used notification data for spatial analysis (161 of 168), although none accounted for undetected cases. The most common data visualisation technique was notification rate mapping, and the use of smoothing techniques was uncommon. Spatial clusters were identified using a range of methods, with the most commonly employed being Kulldorff's spatial scan statistic followed by local Moran's I and Getis and Ord's local Gi(d) tests. In the 11 papers that compared two such methods using a single dataset, the clustering patterns identified were often inconsistent. Classical regression models that did not account for spatial dependence were commonly used to predict spatial TB risk. In all included studies, TB showed a heterogeneous spatial pattern at each geographic resolution level examined. CONCLUSIONS A range of spatial analysis methodologies has been employed in divergent contexts, with all studies demonstrating significant heterogeneity in spatial TB distribution. Future studies are needed to define the optimal method for each context and should account for unreported cases when using notification data where possible. Future studies combining genotypic and geospatial techniques with epidemiologically linked cases have the potential to provide further insights and improve TB control.
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Affiliation(s)
- Debebe Shaweno
- Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia.
- Victorian Tuberculosis Program at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia.
| | - Malancha Karmakar
- Victorian Tuberculosis Program at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Kefyalew Addis Alene
- Research School of Population Health, College of Health and Medicine, The Australian National University, Canberra, Australia
- Institute of Public Health, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
| | - Romain Ragonnet
- Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
- Burnet Institute, Melbourne, Australia
| | | | - James M Trauer
- Victorian Tuberculosis Program at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Justin T Denholm
- Victorian Tuberculosis Program at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Victoria, Australia
| | - Emma S McBryde
- Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Queensland, Australia
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Warren JL, Grandjean L, Moore DAJ, Lithgow A, Coronel J, Sheen P, Zelner JL, Andrews JR, Cohen T. Investigating spillover of multidrug-resistant tuberculosis from a prison: a spatial and molecular epidemiological analysis. BMC Med 2018; 16:122. [PMID: 30071850 PMCID: PMC6091024 DOI: 10.1186/s12916-018-1111-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Accepted: 06/26/2018] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Congregate settings may serve as institutional amplifiers of tuberculosis (TB) and multidrug-resistant tuberculosis (MDR-TB). We analyze spatial, epidemiological, and pathogen genetic data prospectively collected from neighborhoods surrounding a prison in Lima, Peru, where inmates experience a high risk of MDR-TB, to investigate the risk of spillover into the surrounding community. METHODS Using hierarchical Bayesian statistical modeling, we address three questions regarding the MDR-TB risk: (i) Does the excess risk observed among prisoners also extend outside the prison? (ii) If so, what is the magnitude, shape, and spatial range of this spillover effect? (iii) Is there evidence of additional transmission across the region? RESULTS The region of spillover risk extends for 5.47 km outside of the prison (95% credible interval: 1.38, 9.63 km). Within this spillover region, we find that nine of the 467 non-inmate patients (35 with MDR-TB) have MDR-TB strains that are genetic matches to strains collected from current inmates with MDR-TB, compared to seven out of 1080 patients (89 with MDR-TB) outside the spillover region (p values: 0.022 and 0.008). We also identify eight spatially aggregated genetic clusters of MDR-TB, four within the spillover region, consistent with local transmission among individuals living close to the prison. CONCLUSIONS We demonstrate a clear prison spillover effect in this population, which suggests that interventions in the prison may have benefits that extend to the surrounding community.
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Affiliation(s)
- Joshua L Warren
- Department of Biostatistics, Yale University, New Haven, CT, 06510, USA.
| | - Louis Grandjean
- Paediatric Infectious Diseases, Section of Paediatrics, Department of Medicine, Imperial College, London, W2 1NY, UK.,Laboratorio de Investigacion y Desarrollo, Universidad Peruana Cayetano Heredia, San Martin de Porres, Lima, Peru
| | - David A J Moore
- Laboratorio de Investigacion y Desarrollo, Universidad Peruana Cayetano Heredia, San Martin de Porres, Lima, Peru.,TB Centre and Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK
| | - Anna Lithgow
- TB Centre and Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK
| | - Jorge Coronel
- Laboratorio de Investigacion y Desarrollo, Universidad Peruana Cayetano Heredia, San Martin de Porres, Lima, Peru
| | - Patricia Sheen
- Laboratorio de Investigacion y Desarrollo, Universidad Peruana Cayetano Heredia, San Martin de Porres, Lima, Peru
| | - Jonathan L Zelner
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Jason R Andrews
- Department of Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale University, New Haven, CT, 06510, USA
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McIntosh AI, Jenkins HE, White LF, Barnard M, Thomson DR, Dolby T, Simpson J, Streicher EM, Kleinman MB, Ragan EJ, van Helden PD, Murray MB, Warren RM, Jacobson KR. Using routinely collected laboratory data to identify high rifampicin-resistant tuberculosis burden communities in the Western Cape Province, South Africa: A retrospective spatiotemporal analysis. PLoS Med 2018; 15:e1002638. [PMID: 30130377 PMCID: PMC6103505 DOI: 10.1371/journal.pmed.1002638] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 07/13/2018] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND South Africa has the highest tuberculosis incidence globally (781/100,000), with an estimated 4.3% of cases being rifampicin resistant (RR). Control and elimination strategies will require detailed spatial information to understand where drug-resistant tuberculosis exists and why it persists in those communities. We demonstrate a method to enable drug-resistant tuberculosis monitoring by identifying high-burden communities in the Western Cape Province using routinely collected laboratory data. METHODS AND FINDINGS We retrospectively identified cases of microbiologically confirmed tuberculosis and RR-tuberculosis from all biological samples submitted for tuberculosis testing (n = 2,219,891) to the Western Cape National Health Laboratory Services (NHLS) between January 1, 2008, and June 30, 2013. Because the NHLS database lacks unique patient identifiers, we performed a series of record-linking processes to match specimen records to individual patients. We counted an individual as having a single disease episode if their positive samples came from within two years of each other. Cases were aggregated by clinic location (n = 302) to estimate the percentage of tuberculosis cases with rifampicin resistance per clinic. We used inverse distance weighting (IDW) to produce heatmaps of the RR-tuberculosis percentage across the province. Regression was used to estimate annual changes in the RR-tuberculosis percentage by clinic, and estimated average size and direction of change was mapped. We identified 799,779 individuals who had specimens submitted from mappable clinics for testing, of whom 222,735 (27.8%) had microbiologically confirmed tuberculosis. The study population was 43% female, the median age was 36 years (IQR 27-44), and 10,255 (4.6%, 95% CI: 4.6-4.7) cases had documented rifampicin resistance. Among individuals with microbiologically confirmed tuberculosis, 8,947 (4.0%) had more than one disease episode during the study period. The percentage of tuberculosis cases with rifampicin resistance documented among these individuals was 11.4% (95% CI: 10.7-12.0). Overall, the percentage of tuberculosis cases that were RR-tuberculosis was spatially heterogeneous, ranging from 0% to 25% across the province. Our maps reveal significant yearly fluctuations in RR-tuberculosis percentages at several locations. Additionally, the directions of change over time in RR-tuberculosis percentage were not uniform. The main limitation of this study is the lack of unique patient identifiers in the NHLS database, rendering findings to be estimates reliant on the accuracy of the person-matching algorithm. CONCLUSIONS Our maps reveal striking spatial and temporal heterogeneity in RR-tuberculosis percentages across this province. We demonstrate the potential to monitor RR-tuberculosis spatially and temporally with routinely collected laboratory data, enabling improved resource targeting and more rapid locally appropriate interventions.
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Affiliation(s)
- Avery I. McIntosh
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Helen E. Jenkins
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | - Laura F. White
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America
| | | | - Dana R. Thomson
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Tania Dolby
- National Health Laboratory Service, Cape Town, South Africa
| | - John Simpson
- National Health Laboratory Service, Cape Town, South Africa
| | - Elizabeth M. Streicher
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Mary B. Kleinman
- Section of Infectious Diseases, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts, United States of America
| | - Elizabeth J. Ragan
- Section of Infectious Diseases, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts, United States of America
| | - Paul D. van Helden
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Megan B. Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Robin M. Warren
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/SAMRC Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Karen R. Jacobson
- Section of Infectious Diseases, Boston University School of Medicine and Boston Medical Center, Boston, Massachusetts, United States of America
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Auld SC, Shah NS, Cohen T, Martinson NA, Gandhi NR. Where is tuberculosis transmission happening? Insights from the literature, new tools to study transmission and implications for the elimination of tuberculosis. Respirology 2018; 23:10.1111/resp.13333. [PMID: 29869818 PMCID: PMC6281783 DOI: 10.1111/resp.13333] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Revised: 05/14/2018] [Accepted: 05/20/2018] [Indexed: 12/12/2022]
Abstract
More than 10 million new cases of tuberculosis (TB) are diagnosed worldwide each year. The majority of these cases occur in low- and middle-income countries where the TB epidemic is predominantly driven by transmission. Efforts to 'end TB' will depend upon our ability to halt ongoing transmission. However, recent studies of new approaches to interrupt transmission have demonstrated inconsistent effects on reducing population-level TB incidence. TB transmission occurs across a wide range of settings, that include households and hospitals, but also community-based settings. While home-based contact investigations and infection control programmes in hospitals and clinics have a successful track record as TB control activities, there is a gap in our knowledge of where, and between whom, community-based transmission of TB occurs. Novel tools, including molecular epidemiology, geospatial analyses and ventilation studies, provide hope for improving our understanding of transmission in countries where the burden of TB is greatest. By integrating these diverse and innovative tools, we can enhance our ability to identify transmission events by documenting the opportunity for transmission-through either an epidemiologic or geospatial connection-alongside genomic evidence for transmission, based upon genetically similar TB strains. A greater understanding of locations and patterns of transmission will translate into meaningful improvements in our current TB control activities by informing targeted, evidence-based public health interventions.
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Affiliation(s)
- Sara C Auld
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - N Sarita Shah
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
- Division of Global HIV and TB, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Neil A Martinson
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Center for TB Research, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Neel R Gandhi
- Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
- Department of Global Health, Emory University Rollins School of Public Health, Atlanta, GA, USA
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Calderón RI, Velásquez GE, Becerra MC, Zhang Z, Contreras CC, Yataco RM, Galea JT, Lecca LW, Kritski AL, Murray MB, Mitnick CD. Prevalence of pyrazinamide resistance and Wayne assay performance analysis in a tuberculosis cohort in Lima, Peru. Int J Tuberc Lung Dis 2018; 21:894-901. [PMID: 28786798 DOI: 10.5588/ijtld.16.0850] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Multidrug-resistant tuberculosis (MDR-TB) regimens often contain pyrazinamide (PZA) even if susceptibility to the drug has not been confirmed. This gap is due to the limited availability and reliability of PZA susceptibility testing. OBJECTIVES To estimate the prevalence of PZA resistance using the Wayne assay among TB patients in Lima, Peru, to describe characteristics associated with PZA resistance and to compare the performance of Wayne with that of BACTEC™ MGIT™ 960. METHODS PZA susceptibility using the Wayne assay was tested in patients diagnosed with culture-positive pulmonary TB from September 2009 to August 2012. Factors associated with PZA resistance were evaluated. We compared the performance of the Wayne assay to that of MGIT 960 in a convenience sample. RESULTS The prevalence of PZA resistance was 6.6% (95%CI 5.8-7.5) among 3277 patients, and 47.7% (95%CI 42.7-52.6) among a subset of 405 MDR-TB patients. In multivariable analysis, MDR-TB (OR 86.0, 95%CI 54.0-136.9) and Latin American-Mediterranean lineage (OR 3.40, 95%CI 2.33-4.96) were associated with PZA resistance. The Wayne assay was in agreement with MGIT 960 in 83.9% of samples (κ 0.66, 95%CI 0.56-0.76). CONCLUSION PZA resistance was detected using the Wayne assay in nearly half of MDR-TB patients in Lima. This test can inform the selection and composition of regimens, especially those dependent on additional resistance.
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Affiliation(s)
- R I Calderón
- Socios En Salud Sucursal Peru, Lima, Peru; Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - G E Velásquez
- Division of Infectious Diseases, Brigham and Women's Hospital, Boston, Massachusetts, USA; Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - M C Becerra
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA; Division of Global Health Equity, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Z Zhang
- Division of Global Health Equity, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | | | - R M Yataco
- Socios En Salud Sucursal Peru, Lima, Peru
| | - J T Galea
- Socios En Salud Sucursal Peru, Lima, Peru
| | - L W Lecca
- Socios En Salud Sucursal Peru, Lima, Peru
| | - A L Kritski
- Faculdade de Medicina, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - M B Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA; Division of Global Health Equity, Brigham and Women's Hospital, Boston, Massachusetts, USA; Department of Epidemiology, Harvard T H Chan School of Public Health, Boston, Massachusetts, USA
| | - C D Mitnick
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA; Division of Global Health Equity, Brigham and Women's Hospital, Boston, Massachusetts, USA
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Internal migration and transmission dynamics of tuberculosis in Shanghai, China: an epidemiological, spatial, genomic analysis. THE LANCET. INFECTIOUS DISEASES 2018; 18:788-795. [PMID: 29681517 DOI: 10.1016/s1473-3099(18)30218-4] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 02/27/2018] [Accepted: 03/12/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Massive internal migration from rural to urban areas poses new challenges for tuberculosis control in China. We aimed to combine genomic, spatial, and epidemiological data to describe the dynamics of tuberculosis in an urban setting with large numbers of migrants. METHODS We did a population-based study of culture-positive Mycobacterium tuberculosis isolates in Songjiang, Shanghai. We used whole-genome sequencing to discriminate apparent genetic clusters of M tuberculosis sharing identical variable-number-tandem-repeat (VNTR) patterns, and analysed the relations between proximity of residence and the risk of genomically clustered M tuberculosis. Finally, we used genomic, spatial, and epidemiological data to estimate time of infection and transmission links among migrants and residents. FINDINGS Between Jan 1, 2009, and Dec 31, 2015, 1620 cases of culture-positive tuberculosis were recorded, 1211 (75%) of which occurred among internal migrants. 150 (69%) of 218 people sharing identical VNTR patterns had isolates within ten single-nucleotide polymorphisms (SNPs) of at least one other strain, consistent with recent transmission of M tuberculosis. Pairs of strains collected from individuals living in close proximity were more likely to be genetically similar than those from individuals who lived far away-for every additional km of distance between patients' homes, the odds that genotypically matched strains were within ten SNPs of each other decreased by about 10% (OR 0·89 [95% CI 0·87-0·91]; p<0·0001). We inferred that transmission from residents to migrants occurs as commonly as transmission from migrants to residents, and we estimated that more than two-thirds of migrants in genomic clusters were infected locally after migration. INTERPRETATION The primary mechanism driving local incidence of tuberculosis in urban centres is local transmission between both migrants and residents. Combined analysis of epidemiological, genomic, and spatial data contributes to a richer understanding of local transmission dynamics and should inform the design of more effective interventions. FUNDING National Natural Science Foundation of China, National Science and Technology Major Project of China, and US National Institutes of Health.
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Blanco-Guillot F, Castañeda-Cediel ML, Cruz-Hervert P, Ferreyra-Reyes L, Delgado-Sánchez G, Ferreira-Guerrero E, Montero-Campos R, Bobadilla-del-Valle M, Martínez-Gamboa RA, Torres-González P, Téllez-Vazquez N, Canizales-Quintero S, Yanes-Lane M, Mongua-Rodríguez N, Ponce-de-León A, Sifuentes-Osornio J, García-García L. Genotyping and spatial analysis of pulmonary tuberculosis and diabetes cases in the state of Veracruz, Mexico. PLoS One 2018. [PMID: 29534104 PMCID: PMC5849303 DOI: 10.1371/journal.pone.0193911] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background Genotyping and georeferencing in tuberculosis (TB) have been used to characterize the distribution of the disease and occurrence of transmission within specific groups and communities. Objective The objective of this study was to test the hypothesis that diabetes mellitus (DM) and pulmonary TB may occur in spatial and molecular aggregations. Material and methods Retrospective cohort study of patients with pulmonary TB. The study area included 12 municipalities in the Sanitary Jurisdiction of Orizaba, Veracruz, México. Patients with acid-fast bacilli in sputum smears and/or Mycobacterium tuberculosis in sputum cultures were recruited from 1995 to 2010. Clinical (standardized questionnaire, physical examination, chest X-ray, blood glucose test and HIV test), microbiological, epidemiological, and molecular evaluations were carried out. Patients were considered “genotype-clustered” if two or more isolates from different patients were identified within 12 months of each other and had six or more IS6110 bands in an identical pattern, or < 6 bands with identical IS6110 RFLP patterns and spoligotype with the same spacer oligonucleotides. Residential and health care centers addresses were georeferenced. We used a Jeep hand GPS. The coordinates were transferred from the GPS files to ArcGIS using ArcMap 9.3. We evaluated global spatial aggregation of patients in IS6110-RFLP/ spoligotype clusters using global Moran´s I. Since global distribution was not random, we evaluated “hotspots” using Getis-Ord Gi* statistic. Using bivariate and multivariate analysis we analyzed sociodemographic, behavioral, clinic and bacteriological conditions associated with “hotspots”. We used STATA® v13.1 for all statistical analysis. Results From 1995 to 2010, 1,370 patients >20 years were diagnosed with pulmonary TB; 33% had DM. The proportion of isolates that were genotyped was 80.7% (n = 1105), of which 31% (n = 342) were grouped in 91 genotype clusters with 2 to 23 patients each; 65.9% of total clusters were small (2 members) involving 35.08% of patients. Twenty three (22.7) percent of cases were classified as recent transmission. Moran`s I indicated that distribution of patients in IS6110-RFLP/spoligotype clusters was not random (Moran`s I = 0.035468, Z value = 7.0, p = 0.00). Local spatial analysis showed statistically significant spatial aggregation of patients in IS6110-RFLP/spoligotype clusters identifying “hotspots” and “coldspots”. GI* statistic showed that the hotspot for spatial clustering was located in Camerino Z. Mendoza municipality; 14.6% (50/342) of patients in genotype clusters were located in a hotspot; of these, 60% (30/50) lived with DM. Using logistic regression the statistically significant variables associated with hotspots were: DM [adjusted Odds Ratio (aOR) 7.04, 95% Confidence interval (CI) 3.03–16.38] and attending the health center in Camerino Z. Mendoza (aOR18.04, 95% CI 7.35–44.28). Conclusions The combination of molecular and epidemiological information with geospatial data allowed us to identify the concurrence of molecular clustering and spatial aggregation of patients with DM and TB. This information may be highly useful for TB control programs.
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Affiliation(s)
- Francles Blanco-Guillot
- Doctorado en Ciencias en Enfermedades Infecciosas, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | | | - Pablo Cruz-Hervert
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Leticia Ferreyra-Reyes
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Guadalupe Delgado-Sánchez
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Elizabeth Ferreira-Guerrero
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Rogelio Montero-Campos
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Miriam Bobadilla-del-Valle
- Laboratorio de Microbiología, Instituto Nacional de Ciencias Médicas y de Nutrición “Salvador Zubirán”, Ciudad de México, México
| | - Rosa Areli Martínez-Gamboa
- Laboratorio de Microbiología, Instituto Nacional de Ciencias Médicas y de Nutrición “Salvador Zubirán”, Ciudad de México, México
| | - Pedro Torres-González
- Laboratorio de Microbiología, Instituto Nacional de Ciencias Médicas y de Nutrición “Salvador Zubirán”, Ciudad de México, México
| | - Norma Téllez-Vazquez
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Sergio Canizales-Quintero
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
| | - Mercedes Yanes-Lane
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
- Facultad de Medicina, Universidad Autónoma de San Luis Potosí, San Luis Potosí, México
| | - Norma Mongua-Rodríguez
- Doctorado en Geografía, Universidad Nacional Autónoma de México, Ciudad de México, México
- Maestría en Ciencias Médicas con énfasis en Epidemiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, México
| | - Alfredo Ponce-de-León
- Laboratorio de Microbiología, Instituto Nacional de Ciencias Médicas y de Nutrición “Salvador Zubirán”, Ciudad de México, México
| | - José Sifuentes-Osornio
- Dirección Médica, Instituto Nacional de Ciencias Médicas y de Nutrición “Salvador Zubirán”, Ciudad de México, México
| | - Lourdes García-García
- Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, México
- * E-mail:
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Abstract
The DOTS strategy assisted global tuberculosis (TB) control, but was unable to prevent the emergence and spread of drug-resistant strains. Genomic evidence confirms the transmission of drug-resistant Mycobacterium tuberculosis strains in many different settings, indicative of epidemic spread. These findings emphasise the need for enhanced infection control measures in health care and congregate settings. Young children in TB endemic areas are particularly vulnerable. Although advances in TB drug and vaccine development are urgently needed, improved access to currently available preventive therapy and treatment for drug resistant TB could reduce the disease burden and adverse outcomes experienced by children. We review new insights into the transmission dynamics of drug resistant TB, the estimated disease burden in children and optimal management strategies to consider.
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Affiliation(s)
- Alexander C Outhred
- The Children's Hospital at Westmead and the Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia
| | - Philip N Britton
- The Children's Hospital at Westmead and the Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia
| | - Ben J Marais
- The Children's Hospital at Westmead and the Marie Bashir Institute for Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia.
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Auld SC, Kasmar AG, Dowdy DW, Mathema B, Gandhi NR, Churchyard GJ, Rustomjee R, Shah NS. Research Roadmap for Tuberculosis Transmission Science: Where Do We Go From Here and How Will We Know When We're There? J Infect Dis 2017; 216:S662-S668. [PMID: 29112744 PMCID: PMC5793854 DOI: 10.1093/infdis/jix353] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
High rates of tuberculosis transmission are driving the ongoing global tuberculosis epidemic, and there is a pressing need for research focused on understanding and, ultimately, halting transmission. The ongoing tuberculosis–human immunodeficiency virus (HIV) coepidemic and rising rates of drug-resistant tuberculosis in parts of the world add further urgency to this work. Success in this research will require a concerted, multidisciplinary effort on the part of tuberculosis scientists, clinicians, programs, and funders and must span the research spectrum from biomedical sciences to the social sciences, public health, epidemiology, cost-effectiveness analyses, and operations research. Heterogeneity of tuberculosis disease, both among individual patients and among communities, poses a substantial challenge to efforts to interrupt transmission. As such, it is likely that effective interventions to stop transmission will require a combination of approaches that will vary across different epidemiologic settings. This research roadmap summarizes key gaps in our current understanding of transmission, as laid out in the preceding articles in this series. We also hope that it will be a call to action for the global tuberculosis community to make a sustained commitment to tuberculosis transmission science. Halting transmission today is an essential step on the path to end tuberculosis tomorrow.
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Affiliation(s)
- Sara C Auld
- School of Medicine and Rollins School of Public Health, Emory University
| | - Anne G Kasmar
- Bill and Melinda Gates Foundation, Seattle, Washington
| | - David W Dowdy
- Bloomberg School of Public Health, Johns Hopkins University, Baltimore
| | - Barun Mathema
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Neel R Gandhi
- School of Medicine and Rollins School of Public Health, Emory University
| | - Gavin J Churchyard
- Aurum Institute and the School of Public Health, University of Witwatersrand.,Advancing Care for tuberculosis and HIV, South African Medical Research Council, Johannesburg, South Africa
| | - Roxana Rustomjee
- Division of AIDS, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland
| | - N Sarita Shah
- Division of Global HIV and Tuberculosis, Centers for Disease Control and Prevention, Atlanta, Georgia
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Churchyard G, Kim P, Shah NS, Rustomjee R, Gandhi N, Mathema B, Dowdy D, Kasmar A, Cardenas V. What We Know About Tuberculosis Transmission: An Overview. J Infect Dis 2017; 216:S629-S635. [PMID: 29112747 PMCID: PMC5791742 DOI: 10.1093/infdis/jix362] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Tuberculosis remains a global health problem with an enormous burden of disease, estimated at 10.4 million new cases in 2015. To stop the tuberculosis epidemic, it is critical that we interrupt tuberculosis transmission. Further, the interventions required to interrupt tuberculosis transmission must be targeted to high-risk groups and settings. A simple cascade for tuberculosis transmission has been proposed in which (1) a source case of tuberculosis (2) generates infectious particles (3) that survive in the air and (4) are inhaled by a susceptible individual (5) who may become infected and (6) then has the potential to develop tuberculosis. Interventions that target these events will interrupt tuberculosis transmission and accelerate the decline in tuberculosis incidence and mortality. The purpose of this article is to provide a high-level overview of what is known about tuberculosis transmission, using the tuberculosis transmission cascade as a framework, and to set the scene for the articles in this series, which address specific aspects of tuberculosis transmission.
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Affiliation(s)
- Gavin Churchyard
- Aurum Institute, Johannesburg, South Africa
- School of Public Health, University of the Witwatersrand, Johannesburg, South Africa,
- Advancing Care & Treatment for TB/HIV, Johannesburg, South Africa, and
- South African Medical Research Council, Johannesburg, South Africa
| | - Peter Kim
- Division of AIDS, National Institutes of Health, Bethesda, Maryland, and
| | - N Sarita Shah
- Division of Global HIV and Tuberculosis, Centers for Disease Control and Prevention, Atlanta, Georgia, and
| | - Roxana Rustomjee
- Division of AIDS, National Institutes of Health, Bethesda, Maryland, and
| | - Neel Gandhi
- Rollins School of Public Health, Emory University, Atlanta, Georgia, and
- Emory School of Medicine, Emory University, Atlanta, Georgia
| | - Barun Mathema
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York; and
| | - David Dowdy
- Johns Hopkins University, Baltimore, Maryland
| | - Anne Kasmar
- Bill and Melinda Gates Foundation, Seattle, Washington
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Chen YY, Chang JR, Wu CD, Yeh YP, Yang SJ, Hsu CH, Lin MC, Tsai CF, Lin MS, Su IJ, Dou HY. Combining molecular typing and spatial pattern analysis to identify areas of high tuberculosis transmission in a moderate-incidence county in Taiwan. Sci Rep 2017; 7:5394. [PMID: 28710410 PMCID: PMC5511213 DOI: 10.1038/s41598-017-05674-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 06/01/2017] [Indexed: 11/08/2022] Open
Abstract
In total, 303 randomly selected clinical Mycobacterium tuberculosis (MTB) isolates from 303 patients (collected January to December 2012) in central Taiwan were examined. The major lineages found were Beijing (N = 114, 37.62%), Haarlem (N = 76, 25.08%) and East African-Indian (EAI) (N = 42, 13.86%). Notably, younger persons (≤30 years old) were 6.58 times more likely to be infected with a Beijing genotype compared to older persons (>70 years) (p < 0.05). Combining molecular typing methods and geographical information system (GIS) analysis, we uncovered a twofold higher incidence of Beijing strains in a hotspot area (33%) compared to non-hotspot areas (17%). By 24 MIRU-VNTR typing, persons in clustered groups were 1.96 times more likely to be infected with a Beijing strain compared with non-clustered persons, suggesting recent spread and emergence of MTB. Finally, we observed a trend in which TB incidence increased as the density/concentration of analyzed environmental factors increased, suggesting that environmental factors are associated with TB transmission; however, only population density was found to be significantly associated with increased risk of TB (p < 0.05). Molecular typing methods combined with spatial analysis suggest possible TB transmission. Early intervention to interrupt transmission may be most effective if targeted to hot zones of TB.
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Affiliation(s)
- Yih-Yuan Chen
- Department of Biochemical Science and Technology, National Chiayi University, Chiai-Yi, Taiwan
| | - Jia-Ru Chang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Chih-Da Wu
- Department of Forestry and Natural Resources, National Chiayi University, Chia-Yi, Taiwan
- The Center for Health and the Global Environment, Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Yen-Po Yeh
- Chang-Hua County Public Health Bureau, Changhua City, Taiwan
| | - Shiu-Ju Yang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Chih-Hao Hsu
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Ming-Ching Lin
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Ching-Fang Tsai
- Department of Medical Research, Ditmanson Medical Foundation, Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Ming-Shian Lin
- Department of Internal Medicine, Ditmanson Medical Foundation, Chia-Yi Christian Hospital, Chia-Yi, Taiwan
| | - Ih-Jen Su
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Horng-Yunn Dou
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Zhunan, Miaoli, Taiwan.
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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: 382] [Impact Index Per Article: 54.6] [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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Spatial patterns of multidrug resistant tuberculosis and relationships to socio-economic, demographic and household factors in northwest Ethiopia. PLoS One 2017; 12:e0171800. [PMID: 28182726 PMCID: PMC5300134 DOI: 10.1371/journal.pone.0171800] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 01/26/2017] [Indexed: 11/19/2022] Open
Abstract
Background Understanding the geographical distribution of multidrug-resistant tuberculosis (MDR-TB) in high TB burden countries such as Ethiopia is crucial for effective control of TB epidemics in these countries, and thus globally. We present the first spatial analysis of multidrug resistant tuberculosis, and its relationship to socio-economic, demographic and household factors in northwest Ethiopia. Methods An ecological study was conducted using data on patients diagnosed with MDR-TB at the University of Gondar Hospital MDR-TB treatment centre, for the period 2010 to 2015. District level population data were extracted from the Ethiopia National and Regional Census Report. Spatial autocorrelation was explored using Moran’s I statistic, Local Indicators of Spatial Association (LISA), and the Getis-Ord statistics. A multivariate Poisson regression model was developed with a conditional autoregressive (CAR) prior structure, and with posterior parameters estimated using a Bayesian Markov chain Monte Carlo (MCMC) simulation approach with Gibbs sampling, in WinBUGS. Results A total of 264 MDR-TB patients were included in the analysis. The overall crude incidence rate of MDR-TB for the six-year period was 3.0 cases per 100,000 population. The highest incidence rate was observed in Metema (21 cases per 100,000 population) and Humera (18 cases per 100,000 population) districts; whereas nine districts had zero cases. Spatial clustering of MDR-TB was observed in districts located in the Ethiopia-Sudan and Ethiopia-Eritrea border regions, where large numbers of seasonal migrants live. Spatial clustering of MDR-TB was positively associated with urbanization (RR: 1.02; 95%CI: 1.01, 1.04) and the percentage of men (RR: 1.58; 95% CI: 1.26, 1.99) in the districts; after accounting for these factors there was no residual spatial clustering. Conclusion Spatial clustering of MDR-TB, fully explained by demographic factors (urbanization and percent male), was detected in the border regions of northwest Ethiopia, in locations where seasonal migrants live and work. Cross-border initiatives including options for mobile TB treatment and follow up are important for the effective control of MDR-TB in the region.
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47
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Smith CM, Maguire H, Anderson C, Macdonald N, Hayward AC. Multiple large clusters of tuberculosis in London: a cross-sectional analysis of molecular and spatial data. ERJ Open Res 2017; 3:00098-2016. [PMID: 28149918 PMCID: PMC5278261 DOI: 10.1183/23120541.00098-2016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 11/06/2016] [Indexed: 11/17/2022] Open
Abstract
Large outbreaks of tuberculosis (TB) represent a particular threat to disease control because they reflect multiple instances of active transmission. The extent to which long chains of transmission contribute to high TB incidence in London is unknown. We aimed to estimate the contribution of large clusters to the burden of TB in London and identify risk factors. We identified TB patients resident in London notified between 2010 and 2014, and used 24-locus mycobacterial interspersed repetitive units–variable number tandem repeat strain typing data to classify cases according to molecular cluster size. We used spatial scan statistics to test for spatial clustering and analysed risk factors through multinomial logistic regression. TB isolates from 7458 patients were included in the analysis. There were 20 large molecular clusters (with n>20 cases), comprising 795 (11%) of all cases; 18 (90%) large clusters exhibited significant spatial clustering. Cases in large clusters were more likely to be UK born (adjusted odds ratio 2.93, 95% CI 2.28–3.77), of black-Caribbean ethnicity (adjusted odds ratio 3.64, 95% CI 2.23–5.94) and have multiple social risk factors (adjusted odds ratio 3.75, 95% CI 1.96–7.16). Large clusters of cases contribute substantially to the burden of TB in London. Targeting interventions such as screening in deprived areas and social risk groups, including those of black ethnicities and born in the UK, should be a priority for reducing transmission. Large clusters contribute substantially to the burden of tuberculosis in London, indicating ongoing transmissionhttp://ow.ly/3xk23068P6w
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Affiliation(s)
- Catherine M Smith
- UCL Dept of Infectious Disease Informatics, Farr Institute of Health Informatics Research, University College London, London, UK
| | - Helen Maguire
- Field Epidemiology Service - South East and London, Public Health England, London, UK; Research Dept of Infection and Population Health, Centre for Infectious Disease Epidemiology, University College London, London, UK
| | - Charlotte Anderson
- Field Epidemiology Service - South East and London, Public Health England, London, UK
| | - Neil Macdonald
- Field Epidemiology Service - South East and London, Public Health England, London, UK
| | - Andrew C Hayward
- UCL Dept of Infectious Disease Informatics, Farr Institute of Health Informatics Research, University College London, London, UK
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48
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Ragonnet R, Trauer JM, Denholm JT, Marais BJ, McBryde ES. High rates of multidrug-resistant and rifampicin-resistant tuberculosis among re-treatment cases: where do they come from? BMC Infect Dis 2017; 17:36. [PMID: 28061832 PMCID: PMC5217596 DOI: 10.1186/s12879-016-2171-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 12/27/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Globally 3.9% of new and 21% of re-treatment tuberculosis (TB) cases are multidrug-resistant or rifampicin-resistant (MDR/RR), which is often interpreted as evidence that drug resistance results mainly from poor treatment adherence. This study aims to assess the respective contributions of the different causal pathways leading to MDR/RR-TB at re-treatment. METHODS We use a simple mathematical model to simulate progression between the different stages of disease and treatment for patients diagnosed with TB. The model is parameterised using region and country-specific TB disease burden data reported by the World Health Organization (WHO). The contributions of four separate causal pathways to MDR/RR-TB among re-treatment cases are estimated: I) initial drug-susceptible TB with resistance amplification during treatment; II) initial MDR/RR-TB inappropriately treated as drug-susceptible TB; III) MDR/RR-TB relapse despite appropriate treatment; and IV) re-infection with MDR/RR-TB. RESULTS At the global level, Pathways I, II, III and IV contribute 38% (28-49, 95% Simulation Interval), 44% (36-52, 95% SI), 6% (5-7, 95% SI) and 12% (7-19, 95% SI) respectively to the burden of MDR/RR-TB among re-treatment cases. Pathway II is dominant in the Western Pacific (74%; 67-80 95% SI), Eastern Mediterranean (68%; 60-74 95% SI) and European (53%; 48-59 95% SI) regions, while Pathway I makes the greatest contribution in the American (53%; 40-66 95% SI), African (43%; 28-61 95% SI) and South-East Asian (50%; 40-59 95% SI) regions. CONCLUSIONS Globally, failure to diagnose MDR/RR-TB at first presentation is the leading cause of the high proportion of MDR/RR-TB among re-treatment cases. These findings highlight the need for contextualised solutions to limit the impact and spread of MDR/RR-TB.
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Affiliation(s)
- Romain Ragonnet
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia. .,Centre for Population Health, Burnet Institute, 85 Commercial Road, Melbourne, 3141, VIC, Australia.
| | - James M Trauer
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia.,Centre for Population Health, Burnet Institute, 85 Commercial Road, Melbourne, 3141, VIC, Australia.,Victorian Tuberculosis Program, Melbourne Health, Melbourne, Australia.,School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Justin T Denholm
- Victorian Tuberculosis Program, Melbourne Health, Melbourne, Australia.,Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute, Melbourne, Australia.,Victorian Infectious Diseases Service, Royal Melbourne Hospital, Parkville, VIC, Australia
| | - Ben J Marais
- Marie Bashir Institute and the Centre for Research Excellence in Tuberculosis, University of Sydney, Sydney, Australia
| | - Emma S McBryde
- Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia.,Centre for Population Health, Burnet Institute, 85 Commercial Road, Melbourne, 3141, VIC, Australia.,Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Australia
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49
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Abstract
As we move into the era of the Sustainable Development Goals (SDGs), the World Health Organization (WHO) has developed the End TB strategy 2016-2035 with a goal to end the global epidemic of tuberculosis (TB) by 2035. Achieving the targets laid out in the Strategy will require strengthening of the whole TB diagnosis and treatment cascade, including improved case detection, the establishment of universal drug susceptibility testing and rapid treatment initiation. An estimated 3.9% of new TB cases and 21% of previously treated cases had rifampicin-resistant (RR) or multidrug-resistant (MDR) TB in 2015. These levels have remained stable over time, although limited data are available from major high burden settings. In addition to the emergence of drug resistance due to inadequate treatment, there is growing evidence that direct transmission is a large contributor to the RR/MDR-TB epidemic. Only 340,000 of the estimated 580,000 incident cases of RR/MDR-TB were notified to WHO in 2015. Among these, only 125,000 were initiated on second-line treatment. RR/MDR-TB epidemics are likely to be driven by direct transmission. The most important risk factor for MDR-TB is a history of previous treatment. Other risk factors vary according to setting but can include hospitalisation, incarceration and HIV infection. Children have the same risk of MDR-TB as adults and represent a diagnostic and treatment challenge. Rapid molecular technologies have revolutionized the diagnosis of drug-resistant TB. Until capacity can be established to test every TB patient for rifampicin resistance, countries should focus on gradually expanding their coverage of testing. DNA sequencing technologies are being increasingly incorporated into patient management and drug resistance surveillance. They offer additional benefits over conventional culture-based phenotypic testing, including a faster turn-around time for results, assessment of resistance patterns to a range of drugs, and investigation of strain clustering and transmission.
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Abstract
Tuberculosis (TB) is an airborne infectious disease caused by organisms of the Mycobacterium tuberculosis complex. Although primarily a pulmonary pathogen, M. tuberculosis can cause disease in almost any part of the body. Infection with M. tuberculosis can evolve from containment in the host, in which the bacteria are isolated within granulomas (latent TB infection), to a contagious state, in which the patient will show symptoms that can include cough, fever, night sweats and weight loss. Only active pulmonary TB is contagious. In many low-income and middle-income countries, TB continues to be a major cause of morbidity and mortality, and drug-resistant TB is a major concern in many settings. Although several new TB diagnostics have been developed, including rapid molecular tests, there is a need for simpler point-of-care tests. Treatment usually requires a prolonged course of multiple antimicrobials, stimulating efforts to develop shorter drug regimens. Although the Bacillus Calmette-Guérin (BCG) vaccine is used worldwide, mainly to prevent life-threatening TB in infants and young children, it has been ineffective in controlling the global TB epidemic. Thus, efforts are underway to develop newer vaccines with improved efficacy. New tools as well as improved programme implementation and financing are necessary to end the global TB epidemic by 2035.
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