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Sugawara-Mikami M, Tanigawa K, Kawashima A, Kiriya M, Nakamura Y, Fujiwara Y, Suzuki K. Pathogenicity and virulence of Mycobacterium leprae. Virulence 2022; 13:1985-2011. [PMID: 36326715 PMCID: PMC9635560 DOI: 10.1080/21505594.2022.2141987] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Leprosy is caused by Mycobacterium leprae (M. leprae) and M. lepromatosis, an obligate intracellular organism, and over 200,000 new cases occur every year. M. leprae parasitizes histiocytes (skin macrophages) and Schwann cells in the peripheral nerves. Although leprosy can be treated by multidrug therapy, some patients relapse or have a prolonged clinical course and/or experience leprosy reaction. These varying outcomes depend on host factors such as immune responses against bacterial components that determine a range of symptoms. To understand these host responses, knowledge of the mechanisms by which M. leprae parasitizes host cells is important. This article describes the characteristics of leprosy through bacteriology, genetics, epidemiology, immunology, animal models, routes of infection, and clinical findings. It also discusses recent diagnostic methods, treatment, and measures according to the World Health Organization (WHO), including prevention. Recently, the antibacterial activities of anti-hyperlipidaemia agents against other pathogens, such as M. tuberculosis and Staphylococcus aureus have been investigated. Our laboratory has been focused on the metabolism of lipids which constitute the cell wall of M. leprae. Our findings may be useful for the development of future treatments.
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Affiliation(s)
- Mariko Sugawara-Mikami
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan.,West Yokohama Sugawara Dermatology Clinic, Yokohama, Japan
| | - Kazunari Tanigawa
- Department of Molecular Pharmaceutics, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Akira Kawashima
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan
| | - Mitsuo Kiriya
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan
| | - Yasuhiro Nakamura
- Department of Molecular Pharmaceutics, Faculty of Pharma-Science, Teikyo University, Tokyo, Japan
| | - Yoko Fujiwara
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan
| | - Koichi Suzuki
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Tokyo, Japan
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Li Z, Wang Y, Fan W, Zhang C, Liu H, Zhang R, Cao L, Zhen Q, Chen W, Yu Y, Li B, Mao Y, Bai Y, Wang D, Luo S, Li Y, Qin Q, Ge H, Yong L, Hu X, Yu Y, Sun L. Human Leukocyte Antigen Fine-Mapping and Correlation Analysis of Han and Minority Leprosy Patients in Southern China. Front Genet 2022; 13:888361. [PMID: 35769990 PMCID: PMC9234480 DOI: 10.3389/fgene.2022.888361] [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: 03/05/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
Backround: Leprosy is very prevalent in many populations around the world, which is well known that both alleles for human leukocyte antigen (HLA) as well as single nucleotide polymorphisms (SNPs) in the HLA region are common in leprosy patients. Previous studies have identified leprosy-associated susceptibility genes that explain only part of disease risk and heritability. In view of the complicated characteristics of the major histocompatibility complex (MHC) region, this study aimed to explore the development and variation of HLA in leprosy and its possible mechanism.Methods: Previous genome-wide association data were extracted from Han and minority populations in southern China for HLA fine-mapping studies. Insertion and deletion (INDEL), SNP, and copy number variation (CNV) imputation were determined by using the Thousand People Database (1KGP Phase 3 Dataset) as a reference panel. The HAN-MHC database was used to input the HLA classical alleles and amino acids in the MHC region, and further step-regression analysis was performed to analyze independent variation signals associated with leprosy.Results: The most significant locus rs75324027 (the same locus as rs602875 in the HLA-DR region) [p = 7.49E-09, OR= 0.62, 95%,CI: 0.52–0.73] in the intergene region between HLA-DQA1 and HLA-DRB1 was related with leprosy in M-S(Han leprosy patients in south China)disease. In M-SM (Leprosy patients of ethnic minorities in south China)disease, one of the most significant loci of the HLA-DQB1 gene was 6-32626438-A-T (p = 4.49E-08, OR = 0.36, 95%,CI: 0.25–0.52). Therefore, rs75324027 is a locus in M-S disease, and 6-32626438-a-T may be a new locus in M-SM disease. The interaction between 6 and 32626438-A-T and RS75324027 was analyzed, and A significant interaction relationship was found. In the optimal model, the accuracy of prediction was 0.5974, cross-validation Consistency:10, p = 0.0107.Conclusion: In conclusion, this study is the first to assess the association between HLA and leprosy susceptibility in Han and other minority populations in southern China using the Thousand Population database and the Han MHC database. In addition, our analysis validated the previously reported locus rs602875 in the HLA-DR region and for the first time identified an unreported independent locus in leprosy among ethnic minorities in southern China.
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Affiliation(s)
- Zhuo Li
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Yirui Wang
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Wencheng Fan
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Chang Zhang
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Hao Liu
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Ruixue Zhang
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Lu Cao
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Qi Zhen
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Weiwei Chen
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Yafen Yu
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Bao Li
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Yiwen Mao
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Yuanming Bai
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Daiyue Wang
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Sihan Luo
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Yuanyuan Li
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Qin Qin
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Huiyao Ge
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Liang Yong
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Xia Hu
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Yanxia Yu
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
| | - Liangdan Sun
- Department of Dermatology, No. 1 Hospital, Anhui Medical University, Hefei, China
- Institute of Dermatology, Anhui Medical University, Hefei, China
- Key Laboratory of Dermatology, Anhui Medical University, Ministry of Education, Hefei, China
- Anhui Provincial Institute of Translational Medicine, Hefei, China
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, China
- *Correspondence: Liangdan Sun,
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Chokkakula S, Shui T, Jiang H, Yang J, Li X, He J, Shen L, Liu J, Wang D, Suryadevara NC, Pathakumari B, Wang L, Chen Y, Shi Y, Zhang W, Wang H, Chen H, Kuang Y, Li B, Yua M, Yan L, Vissa V, Tsang LSL, Li J, Wang H. Genotyping of Mycobacterium leprae for understanding the distribution and transmission of leprosy in endemic provinces of China. Int J Infect Dis 2020; 98:6-13. [PMID: 32553715 DOI: 10.1016/j.ijid.2020.06.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/08/2020] [Accepted: 06/10/2020] [Indexed: 11/26/2022] Open
Abstract
OBJECTIVES Understanding the nature of Mycobacterium leprae transmission is vital to implement better control strategies for leprosy elimination. The present study expands the knowledge of county-level strain diversity, distribution, and transmission patterns of leprosy in endemic provinces of China. METHODS We genetically characterized 290 clinical isolates of M. leprae from four endemic provinces using variable number tandem repeats (VNTR) and single nucleotide polymorphisms (SNPs). Attained genetic profiles and cluster consequences were contrasted with geographical and migration features of leprosy at county levels. RESULTS Considering the allelic variability of 17 VNTR loci by the discriminatory index, (GTA)9, (AT)17, (AT)15, (TA)18, (TTC)21, and (TA)10 are reported to be more highly polymorphic than other loci. The VNTR profile generated the low-density clustering pattern in the counties of Sichuan and Yunnan, whereas clusters have been observed from the isolates from Huayuan (N = 6), Yongding (N = 3), Zixing (N = 3), Chenxi (N = 2) and Zhongfang (N = 2) counties of Hunan, and Zhijin (N = 3), Anlong (N = 2), Zhenning (N = 2), and Xixiu (N = 2) counties of Guizhou. In some clusters, people's social relations have been observed between villages. From the 290 clinical isolates, the most predominantly reported SNP was 3K (278, 95.8%), followed by SNP 1D (10, 3.4%), which are typically observed to be predominant in China. We also detected the novel SNP 3J (2, 0.8%), which has not yet been reported in China. CONCLUSION The clustering pattern of M. leprae indicates the transmission of leprosy still persists at county levels, suggesting that there is a need to implement better approaches for tracing the close contacts of leprosy patients.
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Affiliation(s)
- Santosh Chokkakula
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; National Centre for STD and Leprosy Control, China CDC, Nanjing, China; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | | | - Haiqin Jiang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; National Centre for STD and Leprosy Control, China CDC, Nanjing, China; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Jun Yang
- Yunnan Provincial CDC, Kunming, China
| | - Xiong Li
- Yunnan Provincial CDC, Kunming, China
| | - Jun He
- Yunnan Provincial CDC, Kunming, China
| | | | - Jie Liu
- Guizhou Provincial CDC, Guiyang, China
| | - De Wang
- Guizhou Provincial CDC, Guiyang, China
| | | | - Balaji Pathakumari
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China
| | - Le Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; National Centre for STD and Leprosy Control, China CDC, Nanjing, China; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Yanqing Chen
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; National Centre for STD and Leprosy Control, China CDC, Nanjing, China; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Ying Shi
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; National Centre for STD and Leprosy Control, China CDC, Nanjing, China; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Wenyue Zhang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; National Centre for STD and Leprosy Control, China CDC, Nanjing, China; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Hao Wang
- Sichuan Provincial People's Hospital, Chengdu, China
| | - Huan Chen
- Hunan Provincial CDC, Changsha, China
| | | | - Bin Li
- Hunan Provincial CDC, Changsha, China
| | - Meiwen Yua
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China
| | - Liangbin Yan
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China
| | - Varalakshmi Vissa
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; National Centre for STD and Leprosy Control, China CDC, Nanjing, China; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Lemuel Shui Lun Tsang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; National Centre for STD and Leprosy Control, China CDC, Nanjing, China; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China
| | - Jinlan Li
- Guizhou Provincial CDC, Guiyang, China.
| | - Hongsheng Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, China; National Centre for STD and Leprosy Control, China CDC, Nanjing, China; Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, China; Centre for Global Health, School of Public Health, Nanjing Medical University, Nanjing, China.
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4
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Zhang X, Cheng Y, Zhang Q, Wang X, Lin Y, Yang C, Sun J, Huang H, Li Y, Sheng Y, Fan X, Sun Y, Zhang X, Zheng X, Zhang B, Yang S. Meta-Analysis Identifies Major Histocompatiblity Complex Loci in or Near HLA-DRB1, HLA-DQA1, HLA-C as Associated with Leprosy in Chinese Han Population. J Invest Dermatol 2018; 139:957-960. [PMID: 30389493 DOI: 10.1016/j.jid.2018.09.029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 09/05/2018] [Accepted: 09/24/2018] [Indexed: 11/16/2022]
Affiliation(s)
- Xuelei Zhang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Yuyan Cheng
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Qun Zhang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Xiaomeng Wang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Yan Lin
- Department of Dermatology, The Fourth Affiliated Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Chao Yang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Jingying Sun
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - He Huang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Yang Li
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Yujun Sheng
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Xing Fan
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China
| | - Yonghu Sun
- Shandong Provincial Key Laboratory for Dermatovenereology, Jinan, China
| | - Xuejun Zhang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China; Department of Dermatology, No. 2 Hospital, Anhui Medical University, Hefei, Anhui, China
| | - Xiaodong Zheng
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China.
| | - Bo Zhang
- Department of Dermatology, No. 2 Hospital, Anhui Medical University, Hefei, Anhui, China; School of Life Sciences, Anhui Medical University, Hefei, Anhui, China.
| | - Sen Yang
- Department of Dermatology, No. 1 Hospital and Key Laboratory of Dermatology, Ministry of Education, Anhui Medical University, Hefei, China.
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Lima LNC, Frota CC, Suffys PN, Fontes ANB, Mota RMS, Almeida RLF, de Andrade Pontes MA, Gonçalves HDS, Kendall C, Kerr LRS. Genotyping comparison of Mycobacterium leprae isolates by VNTR analysis from nasal samples in a Brazilian endemic region. Pathog Glob Health 2018; 112:79-85. [PMID: 29405082 PMCID: PMC6056818 DOI: 10.1080/20477724.2018.1427308] [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] [Indexed: 10/18/2022] Open
Abstract
This study analyzed the genetic diversity by MIRU-VNTR of Mycobacterium leprae isolates from nasal cavities and related to epidemiological and clinical data. The sample consisted of 48 newly diagnosed leprosy cases that tested positive for M. leprae PCR in nasal secretion (NS) attending to the National Reference Center of Dermatology Dona Libania (CDERM), Fortaleza, Brazil. Total DNA was extracted from NS of each patient and used for amplification of four M. leprae VNTR loci. Four clusters of M. leprae isolates were formed with identical genotypes. In the spatial analysis, 12 leprosy cases presented similar genotypes organized into 4 clusters. The most common genotypes in the current study was AC8b: 8, AC9: 7, AC8a: 8, GTA9: 10, which may represent a genotype of circulating strains most often in Ceará. A minimum set of four MIRU-VNTR loci was demonstrated to study the genetic diversity of M. leprae isolates from NS.
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Affiliation(s)
- Luana Nepomueceno Costa Lima
- Faculdade de Medicina, Departamento de Patologia e Medicina Legal, Federal University of Ceará, Fortaleza, Brazil
- Seção de Bacteriologia e Micologia, Instituto Evandro Chagas, Ananindeua, Brazil
| | - Cristiane Cunha Frota
- Faculdade de Medicina, Departamento de Patologia e Medicina Legal, Federal University of Ceará, Fortaleza, Brazil
| | - Phillip Noel Suffys
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, Brasil
| | - Amanda Nogueira Brum Fontes
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Instituto Oswaldo Cruz-Fiocruz, Rio de Janeiro, Brasil
| | - Rosa Maria Salani Mota
- Departamento de Estatística e Matemática Aplicada, Federal University of Ceará, Fortaleza, Brazil
| | | | | | - Heitor de Sá Gonçalves
- Department of the State of Ceará, Centro de Dermatologia Dona Libânia, Fortaleza, Brazil
| | - Carl Kendall
- Department of Global Community Health and Behavioral Sciences, School of Public Health and Tropical Medicine, Tulane University, New Orleans, LA, USA
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6
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Fontes ANB, Lima LNGC, Mota RMS, Almeida RLF, Pontes MA, Gonçalves HDS, Frota CC, Vissa VD, Brennan PJ, Guimaraes RJPS, Kendall C, Kerr LRFS, Suffys PN. Genotyping of Mycobacterium leprae for better understanding of leprosy transmission in Fortaleza, Northeastern Brazil. PLoS Negl Trop Dis 2017; 11:e0006117. [PMID: 29244821 PMCID: PMC5747459 DOI: 10.1371/journal.pntd.0006117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 12/29/2017] [Accepted: 11/17/2017] [Indexed: 11/19/2022] Open
Abstract
Leprosy is endemic in large part of Brazil with 28,761 new patients in 2015, the second largest number worldwide and reaches 9/10.000 in highly endemic regions and 2.7/10.000 in the city of Fortaleza, Ceará, Northeast Brazil. For better understanding of risk factors for leprosy transmission, we conducted an epidemiologic study supplemented by 17 locus VNTR and SNP 1-4 typing of Mycobacterium leprae in skin biopsy samples from new multibacillary (MB) patients diagnosed at a reference center in 2009 and 2010. Among the 1,519 new patients detected during the study period, 998 (65.7%) were MB and we performed DNA extraction and genotyping on 160 skin biopsy samples, resulting in 159 (16%) good multilocus VNTR types. Thirty-eight of these patients also provided VNTR types from M. leprae in nasal swabs. The SNP-Type was obtained for 157 patients and 87% were of type 4. Upon consideration all VNTR markers, 156 different genotypes and three pairs with identical genotypes were observed; no epidemiologic relation could be observed between individuals in these pairs. Considerable variability in differentiating index (DI) was observed between the different markers and the four with highest DI [(AT)15, (TA)18, (AT)17 and (GAA)21] frequently demonstrated differences in copy number when comparing genotypes from both type of samples. Excluding these markers from analysis resulted in 83 genotypes, 20 of which included 96 of the patients (60.3%). These clusters were composed of two (n = 8), three (n = 6), four (n = 1), five (n = 2), six (n = 1), 19 (n = 1) and 23 (n = 23) individuals and suggests that recent transmission is contributing to the maintenance of leprosy in Fortaleza. When comparing epidemiological and clinical variables among patients within clustered or with unique M. leprae genotypes, a positive bacterial index in skin biopsies and knowledge of working with someone with the disease were significantly associated with clustering. A tendency to belong to a cluster was observed with later notification of disease (mean value of 3.4 months) and having disability grade 2. A tendency for lack of clustering was observed for patients who reported to have lived with another leprosy case but this might be due to lack of inclusion of household contacts in the study. Although clusters were spread over the city, kernel analysis revealed that some of the patients belonging to the two major clusters were spatially related to some neighborhoods that report poverty and high disease incidence in children. Finally, inclusion of genotypes from nasal swabs might be warranted. A major limitation of the study is that sample size of 160 patients from a two year period represents only 15% of the new patients and this could have weakened statistical outcomes. This is the first molecular epidemiology study of leprosy in Brazil and although the high clustering level suggests that recent transmission is the major cause of disease in Fortaleza; the existence of two large clusters needs further investigation.
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Affiliation(s)
- Amanda N. B. Fontes
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
| | | | - Rosa M. S. Mota
- Department of Statistics and Applied Mathematics, Federal University of Ceará, Fortaleza, Brazil
| | - Rosa L. F. Almeida
- Post Graduation Program of Public Health, University of Fortaleza, Fortaleza, CE, Brazil
| | - Maria A. Pontes
- Reference Center on Dermatology Dona Libânia, State Health Office, Fortaleza, Brazil
| | | | | | - Varalakshmi D. Vissa
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States
| | - Patrick J. Brennan
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States
| | | | - Carl Kendall
- Department of Global Community Health and Behavioral Sciences, Tulane School of Public Health and Tropical Medicine, New Orleans, United States
- Department of Community Health, College of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Ligia R. F. S. Kerr
- Department of Community Health, College of Medicine, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Philip N. Suffys
- Laboratory of Molecular Biology Applied to Mycobacteria, Oswaldo Cruz Institute, Rio de Janeiro, Brazil
- Department of Biomedical Sciences, Mycobacteriology Unit, Tropical Institute of Medicine, Antwerp, Belgium
- * E-mail:
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7
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Positive Diagnosis of Ancient Leprosy and Tuberculosis Using Ancient DNA and Lipid Biomarkers. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9040046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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8
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Stefani MMA, Avanzi C, Bührer-Sékula S, Benjak A, Loiseau C, Singh P, Pontes MAA, Gonçalves HS, Hungria EM, Busso P, Piton J, Silveira MIS, Cruz R, Schetinni A, Costa MB, Virmond MCL, Diorio SM, Dias-Baptista IMF, Rosa PS, Matsuoka M, Penna MLF, Cole ST, Penna GO. Whole genome sequencing distinguishes between relapse and reinfection in recurrent leprosy cases. PLoS Negl Trop Dis 2017; 11:e0005598. [PMID: 28617800 PMCID: PMC5498066 DOI: 10.1371/journal.pntd.0005598] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 07/05/2017] [Accepted: 04/26/2017] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Since leprosy is both treated and controlled by multidrug therapy (MDT) it is important to monitor recurrent cases for drug resistance and to distinguish between relapse and reinfection as a means of assessing therapeutic efficacy. All three objectives can be reached with single nucleotide resolution using next generation sequencing and bioinformatics analysis of Mycobacterium leprae DNA present in human skin. METHODOLOGY DNA was isolated by means of optimized extraction and enrichment methods from samples from three recurrent cases in leprosy patients participating in an open-label, randomized, controlled clinical trial of uniform MDT in Brazil (U-MDT/CT-BR). Genome-wide sequencing of M. leprae was performed and the resultant sequence assemblies analyzed in silico. PRINCIPAL FINDINGS In all three cases, no mutations responsible for resistance to rifampicin, dapsone and ofloxacin were found, thus eliminating drug resistance as a possible cause of disease recurrence. However, sequence differences were detected between the strains from the first and second disease episodes in all three patients. In one case, clear evidence was obtained for reinfection with an unrelated strain whereas in the other two cases, relapse appeared more probable. CONCLUSIONS/SIGNIFICANCE This is the first report of using M. leprae whole genome sequencing to reveal that treated and cured leprosy patients who remain in endemic areas can be reinfected by another strain. Next generation sequencing can be applied reliably to M. leprae DNA extracted from biopsies to discriminate between cases of relapse and reinfection, thereby providing a powerful tool for evaluating different outcomes of therapeutic regimens and for following disease transmission.
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Affiliation(s)
- Mariane M. A. Stefani
- Tropical Pathology and Public Health Institute, Federal University of Goiás, Goiania, Goiás, Brazil
- * E-mail: (MMAS); (STC); (GOP)
| | - Charlotte Avanzi
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Switzerland
| | - Samira Bührer-Sékula
- Tropical Pathology and Public Health Institute, Federal University of Goiás, Goiania, Goiás, Brazil
- University of Amazonas State, Manaus, Amazonas, Brazil
- Tropical Medicine Foundation Dr. Heitor Vieira Dourado, Manaus, Amazonas, Brazil
| | - Andrej Benjak
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Switzerland
| | - Chloé Loiseau
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Switzerland
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Switzerland
| | - Pushpendra Singh
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Switzerland
- Department of Microbiology and Biotechnology Centre, Maharaja Sayajirao University of Baroda, Vadodara, India
| | | | | | - Emerith M. Hungria
- Tropical Pathology and Public Health Institute, Federal University of Goiás, Goiania, Goiás, Brazil
| | - Philippe Busso
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Switzerland
| | - Jérémie Piton
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Switzerland
| | | | - Rossilene Cruz
- University of Amazonas State, Manaus, Amazonas, Brazil
- Tropical Dermatology and Venerology, Alfredo da Matta Foundation, Manaus, Amazonas, Brazil
| | - Antônio Schetinni
- Tropical Dermatology and Venerology, Alfredo da Matta Foundation, Manaus, Amazonas, Brazil
| | - Maurício B. Costa
- Faculty of Medicine, Federal University of Goiás, Goiania, Goiás, Brazil
| | | | | | | | | | - Masanori Matsuoka
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
- Jyu-kanbo National Museum, Kusatsu, Gunma, Japan
| | - Maria L. F. Penna
- Epidemiology and Biostatistics Department, Universidade Federal Fluminense, Rio de Janeiro, Brazil
| | - Stewart T. Cole
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Switzerland
- * E-mail: (MMAS); (STC); (GOP)
| | - Gerson O. Penna
- Tropical Medicine Centre, University of Brasília, Brasília DF, Brazil
- Fiocruz, Brasilia, Brazil
- * E-mail: (MMAS); (STC); (GOP)
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9
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Avanzi C, Busso P, Benjak A, Loiseau C, Fomba A, Doumbia G, Camara I, Lamou A, Sock G, Drame T, Kodio M, Sakho F, Sow SO, Cole ST, Johnson RC. Transmission of Drug-Resistant Leprosy in Guinea-Conakry Detected Using Molecular Epidemiological Approaches. Clin Infect Dis 2016; 63:1482-1484. [PMID: 27558568 DOI: 10.1093/cid/ciw572] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/13/2016] [Indexed: 01/05/2023] Open
Abstract
Molecular drug susceptibility testing was performed on skin biopsies from 24 leprosy patients from Guinea-Conakry for the first time. We identified primary drug resistance in 4 cases and a dapsone-resistant cluster caused by the same strain. Primary transmission of drug-resistant Mycobacterium leprae, including a rifampicin-resistant strain, is reported.
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Affiliation(s)
- Charlotte Avanzi
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Switzerland
| | - Philippe Busso
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Switzerland
| | - Andrej Benjak
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Switzerland
| | - Chloé Loiseau
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Switzerland
| | - Abdoulaye Fomba
- Centre national d'Appui à la lutte contre la Maladie, Bamako, Mali
| | - Glodia Doumbia
- Centre national d'Appui à la lutte contre la Maladie, Bamako, Mali
| | | | - André Lamou
- Programme National Lèpre de Guinée, Conakry, Guinea
| | | | | | - Mamadou Kodio
- Centre national d'Appui à la lutte contre la Maladie, Bamako, Mali
| | | | - Samba O Sow
- Centre national d'Appui à la lutte contre la Maladie, Bamako, Mali
| | - Stewart T Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Switzerland
| | - Roch Christian Johnson
- Centre InterFacultaire de Formation et de Recherche en Environnement pour le Développement Durable University of Abomey-Calavi, Cotonou, Benin
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10
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Sun Z, Li W, Xu S, Huang H. The discovery, function and development of the variable number tandem repeats in different Mycobacterium species. Crit Rev Microbiol 2015; 42:738-58. [PMID: 26089025 DOI: 10.3109/1040841x.2015.1022506] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The method of genotyping by variable number tandem repeats (VNTRs) facilitates the epidemiological studies of different Mycobacterium species worldwide. Until now, the VNTR method is not fully understood, for example, its discovery, function and classification. The inconsistent nomenclature and terminology of VNTR is especially confusing. In this review, we first describe in detail the VNTRs in Mycobacterium tuberculosis (M. tuberculosis), as this pathogen resulted in more deaths than any other microbial pathogen as well as for which extensive studies of VNTRs were carried out, and then we outline the recent progress of the VNTR-related epidemiological research in several other Mycobacterium species, such as M. abscessus, M. africanum, M. avium, M. bovis, M. canettii, M. caprae, M. intracellulare, M. leprae, M. marinum, M. microti, M. pinnipedii and M. ulcerans from different countries and regions. This article is aimed mainly at the practical notes of VNTR to help the scientists in better understanding and performing this method.
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Affiliation(s)
- Zhaogang Sun
- a Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing Key Laboratory for Drug Resistance Tuberculosis Research , Beijing , China and
| | - Weimin Li
- b Beijing Chest Hospital, National Tuberculosis Clinical Laboratory, Capital Medical University , Beijing , China
| | - Shaofa Xu
- b Beijing Chest Hospital, National Tuberculosis Clinical Laboratory, Capital Medical University , Beijing , China
| | - Hairong Huang
- b Beijing Chest Hospital, National Tuberculosis Clinical Laboratory, Capital Medical University , Beijing , China
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11
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Chokkakula S, Dasari K, Attitalla IH, Aparna S, Ponnada P, Male MM. Strain Typing and Strain Differentiation of Mycobacterium leprae by TTC Repeats. INT J PHARMACOL 2014. [DOI: 10.3923/ijp.2014.168.174] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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12
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Turankar RP, Lavania M, Chaitanya VS, Sengupta U, Darlong J, Darlong F, Siva Sai KSR, Jadhav RS. Single nucleotide polymorphism-based molecular typing of M. leprae from multicase families of leprosy patients and their surroundings to understand the transmission of leprosy. Clin Microbiol Infect 2013; 20:O142-9. [PMID: 24520878 DOI: 10.1111/1469-0691.12365] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 07/21/2013] [Accepted: 08/02/2013] [Indexed: 11/29/2022]
Abstract
The exact mode of transmission of leprosy is not clearly understood; however, many studies have demonstrated active transmission of leprosy around a source case. Families of five active leprosy cases and their household contacts were chosen from a high endemic area in Purulia. Fifty-two soil samples were also collected from different areas of their houses. DNA was extracted from slit-skin smears (SSS) and soil samples and the Mycobacterium leprae-specific RLEP (129 bp) region was amplified using PCR. Molecular typing of M. leprae was performed for all RLEP PCR-positive samples by single nucleotide polymorphism (SNP) typing and confirmation by DNA sequencing. SSS of these five patients and six out of the total 28 contacts were PCR positive for RLEP whereas 17 soil samples out of 52 showed the presence of M. leprae DNA. SNP typing of M. leprae from all RLEP PCR-positive subjects (patients and smear-positive contacts) and 10 soil samples showed the SNP type 1 genotype. M. leprae DNA from the five leprosy patients and the six contacts was further subtyped and the D subtype was noted in all patients and contacts, except for one contact where the C subtype was identified. Typing followed by subtyping of M. leprae clearly revealed that either the contacts were infected by the patients or both patients and contacts had the same source of infection. It also revealed that the type of M. leprae in the soil in the inhabited areas where patients resided was also of the same type as that found in patients.
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Affiliation(s)
- R P Turankar
- Stanley Browne Laboratory, The Leprosy Mission, Community Hospital Nand Nagari, Delhi, India
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13
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Kai M, Nakata N, Matsuoka M, Sekizuka T, Kuroda M, Makino M. Characteristic mutations found in the ML0411 gene of Mycobacterium leprae isolated in Northeast Asian countries. INFECTION GENETICS AND EVOLUTION 2013; 19:200-4. [DOI: 10.1016/j.meegid.2013.07.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 07/12/2013] [Accepted: 07/12/2013] [Indexed: 10/26/2022]
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14
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Weng X, Xing Y, Liu J, Wang Y, Ning Y, Li M, Wu W, Zhang L, Li W, Heiden JV, Vissa V. Molecular, ethno-spatial epidemiology of leprosy in China: novel insights for tracing leprosy in endemic and non endemic provinces. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2013; 14:361-8. [PMID: 23291419 PMCID: PMC3668695 DOI: 10.1016/j.meegid.2012.12.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Revised: 12/04/2012] [Accepted: 12/10/2012] [Indexed: 10/27/2022]
Abstract
Leprosy continues to be detected at near stable rates in China even with established control programs, necessitating new knowledge and alternative methods to interrupt transmission. A molecular epidemiology investigation of 190 patients was undertaken to define Mycobacterium leprae strain types and discern genetic relationships and clusters in endemic and non-endemic regions spanning seventeen provinces and two autonomous regions. The findings support multiple locus variable number of tandem repeat (VNTR) analysis as a useful tool in uncovering characteristic patterns across the multiethnic and divergent geographic landscape of China. Several scenarios of clustering of leprosy from township to provincial to regional levels were recognized, while recent occupational or remote migration showed geographical separation of certain strains. First, prior studies indicated that of the four major M. leprae subtypes defined by single nucleotide polymorphisms (SNPs), only type 3 was present in China, purportedly entering from Europe/West/Central Asia via the Silk Road. However, this study revealed VNTR linked strains that are of type 1 in Guangdong, Fujian and Guangxi in southern China. Second, a subset of VNTR distinguishable strains of type 3, co-exist in these provinces. Third, type 3 strains with rpoT VNTR allele of 4, detected in Japan and Korea were discovered in Jiangsu and Anhui in the east and in western Sichuan bordering Tibet. Fourth, considering the overall genetic diversity, strains of endemic counties of Qiubei, Yunnan; Xing Yi, Guizhou; and across Sichuan in southwest were related. However, closer inspection showed distinct local strains and clusters. Altogether, these insights, primarily derived from VNTR typing, reveal multiple and overlooked paths for spread of leprosy into, within and out of China and invoke attention to historic maritime routes in the South and East China Sea. More importantly, new concepts and approaches for prospective case finding and tracking of leprosy from county to national level have been introduced.
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Affiliation(s)
- Xiaoman Weng
- Beijing Friendship Hospital - Affiliate of Capital University of Medical Sciences, Beijing Tropical Medicine Research Institute, 95 Yang An Road, Beijing, 100050
| | - Yan Xing
- Beijing Friendship Hospital - Affiliate of Capital University of Medical Sciences, Beijing Tropical Medicine Research Institute, 95 Yang An Road, Beijing, 100050
| | - Jian Liu
- Beijing Friendship Hospital - Affiliate of Capital University of Medical Sciences, Beijing Tropical Medicine Research Institute, 95 Yang An Road, Beijing, 100050
| | - Yonghong Wang
- Skin Diseases Control Station of XIngyi City, #54 Fuxingxi Road, Jishan New District, Xingyi, Guizhou Province, 562400
| | - Yong Ning
- Institute of Dermatology and Venereology, Sichuan Academy of Medical Sciences, #12 Sidao Street, Chengdu, Sichuan Province, 610031
| | - Ming Li
- Guangdong Provincial Center for Skin Disease and STI Control, Guangdong Provincial Dermatology Hospital, #2 Lujing Road, Guangzhou, Guangdong, 510095
| | - Wenbin Wu
- Fujian Provincial Center for Disease Prevention and Control, #76 Jintai Road, Fuzhou, Fujian, 350001
| | - Lianhua Zhang
- Jiangsu Provincial Center for Disease prevention and control, #172 Jiangsu Road, Nanjing, Jiangsu, 210009
| | - Wei Li
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA 80526
| | - Jason Vander Heiden
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA 80526
| | - Varalakshmi Vissa
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA 80526
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15
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Cardona-Castro N, Beltrán-Alzate JC, Romero-Montoya IM, Li W, Brennan PJ, Vissa V. Mycobacterium leprae in Colombia described by SNP7614 in gyrA, two minisatellites and geography. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2013; 14:375-82. [PMID: 23291420 PMCID: PMC3668693 DOI: 10.1016/j.meegid.2012.12.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Revised: 12/07/2012] [Accepted: 12/08/2012] [Indexed: 12/12/2022]
Abstract
New cases of leprosy are still being detected in Colombia after the country declared achievement of the WHO defined 'elimination' status. To study the ecology of leprosy in endemic regions, a combination of geographic and molecular tools were applied for a group of 201 multibacillary patients including six multi-case families from eleven departments. The location (latitude and longitude) of patient residences were mapped. Slit skin smears and/or skin biopsies were collected and DNA was extracted. Standard agarose gel electrophoresis following a multiplex PCR-was developed for rapid and inexpensive strain typing of Mycobacterium leprae based on copy numbers of two VNTR minisatellite loci 27-5 and 12-5. A SNP (C/T) in gyrA (SNP7614) was mapped by introducing a novel PCR-RFLP into an ongoing drug resistance surveillance effort. Multiple genotypes were detected combining the three molecular markers. The two frequent genotypes in Colombia were SNP7614(C)/27-5(5)/12-5(4) [C54] predominantly distributed in the Atlantic departments and SNP7614 (T)/27-5(4)/12-5(5) [T45] associated with the Andean departments. A novel genotype SNP7614 (C)/27-5(6)/12-5(4) [C64] was detected in cities along the Magdalena river which separates the Andean from Atlantic departments; a subset was further characterized showing association with a rare allele of minisatellite 23-3 and the SNP type 1 of M. leprae. The genotypes within intra-family cases were conserved. Overall, this is the first large scale study that utilized simple and rapid assay formats for identification of major strain types and their distribution in Colombia. It provides the framework for further strain type discrimination and geographic information systems as tools for tracing transmission of leprosy.
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Affiliation(s)
- Nora Cardona-Castro
- Instituto Colombiano de Medicina Tropical – Universidad CES, Sabaneta, Antioquia, Colombia
- Universidad de Antioquia, Facultad de Ciencias Exactas y Naturales, Medellín, Antioquia, Colombia
| | | | | | - Wei Li
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA. 80523
| | - Patrick J Brennan
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA. 80523
| | - Varalakshmi Vissa
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, USA. 80523
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16
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Lavania M, Jadhav RS, Turankar RP, Chaitanya VS, Singh M, Sengupta U. Single nucleotide polymorphisms typing of Mycobacterium leprae reveals focal transmission of leprosy in high endemic regions of India. Clin Microbiol Infect 2013; 19:1058-62. [PMID: 23331718 DOI: 10.1111/1469-0691.12125] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 12/05/2012] [Indexed: 11/27/2022]
Abstract
Earlier studies indicate that genotyping of Mycobaterium leprae based on single-nucleotide polymorphisms (SNPs) is useful for analysis of the global spread of leprosy. In the present study, we investigated the diversity of M. leprae at eight SNP loci using 180 clinical isolates obtained from patients with leprosy residing mainly in Delhi and Purulia (West Bengal) regions. It was observed that the frequency of SNP type 1 and subtype D was most predominant in the Indian population. Further, the SNP type 2 subtype E was noted only from East Delhi region and SNP type 2 subtype G was noted only from the nearby areas of Hoogly district of West Bengal. These results indicate the occurrence of focal transmission of M. leprae infection and demonstrate that analysis by SNP typing has great potential to help researchers in understanding the transmission of M. leprae infection in the community.
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Affiliation(s)
- M Lavania
- Stanley Browne Laboratory, TLM Community Hospital, Delhi, India
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17
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Aye KS, Oo YTN, Kyaw K, Win AA, Matsuoka M. Genotyping of Mycobacterium leprae in Myanmar and possible transmission modes. ACTA ACUST UNITED AC 2013; 81:191-8. [PMID: 23012847 DOI: 10.5025/hansen.81.191] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The polymorphism of TTC repeats in Mycobacterium leprae was examined using bacilli from slit skin samples of leprosy patients attending at Central Special Skin Clinic, Yangon General Hospital and nasal swabs of their contacts to elucidate the possible mode of leprosy transmission. It was found that bacilli with different TTC genotypes were distributed among same household contacts and also harbored bacilli in patients were different TTC genotype from that harbored on the nasal mucus of the healthy contacts. Genotypes of TTC repeats were found to differ between husband under treatment and his wife and also mother under treatment and her sons living in same house. This study revealed that TTC genotype of bacilli harbored by household contacts was different with the TTC genotype by index cases. These results indicate that the family members get transmission from outside the dwellings rather than from commonly supposed their MB index cases. There might have been some infectious sources to which the populace had been commonly exposed outside the dwellings.
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Affiliation(s)
- Khin Saw Aye
- Immunology Research Division, Department of Medical Research (Lower Myanmar), Yangon, Myanmar
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18
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Fontes ANB, Gomes HM, Araujo MID, Albuquerque ECAD, Baptista IMFD, Moura MMDF, Rezende DS, Pessolani MCV, Lara FA, Pontes MADA, Gonçalves HDS, Lucena-Silva N, Sarno EN, Vissa VD, Brennan PJ, Suffys PN. Genotyping of Mycobacterium leprae present on Ziehl-Neelsen-stained microscopic slides and in skin biopsy samples from leprosy patients in different geographic regions of Brazil. Mem Inst Oswaldo Cruz 2012; 107 Suppl 1:143-9. [DOI: 10.1590/s0074-02762012000900021] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 07/18/2012] [Indexed: 11/22/2022] Open
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Li W, Matsuoka M, Kai M, Thapa P, Khadge S, Hagge DA, Brennan PJ, Vissa V. Real-time PCR and high-resolution melt analysis for rapid detection of Mycobacterium leprae drug resistance mutations and strain types. J Clin Microbiol 2012; 50:742-53. [PMID: 22170923 PMCID: PMC3295127 DOI: 10.1128/jcm.05183-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2011] [Accepted: 11/30/2011] [Indexed: 12/25/2022] Open
Abstract
Drug resistance surveillance and strain typing of Mycobacterium leprae are necessary to investigate ongoing transmission of leprosy in regions of endemicity. To enable wider implementation of these molecular analyses, novel real-time PCR-high-resolution melt (RT-PCR-HRM) assays without allele-specific primers or probes and post-PCR sample handling were developed. For the detection of mutations within drug resistance-determining regions (DRDRs) of folP1, rpoB, and gyrA, targets for dapsone, rifampin, and fluoroquinolones, real-time PCR-HRM assays were developed. Wild-type and drug-resistant mouse footpad-derived strains that included three folP1, two rpoB, and one gyrA mutation types in a reference panel were tested. RT-PCR-HRM correctly distinguished the wild type from the mutant strains. In addition, RT-PCR-HRM analyses aided in recognizing samples with mixed or minor alleles and also a mislabeled sample. When tested in 121 sequence-characterized clinical strains, HRM identified all the folP1 mutants representing two mutation types, including one not within the reference panel. The false positives (<5%) could be attributed to low DNA concentration or PCR inhibition. A second set of RT-PCR-HRM assays for identification of three previously reported single nucleotide polymorphisms (SNPs) that have been used for strain typing were developed and validated in 22 reference and 25 clinical strains. Real-time PCR-HRM is a sensitive, simple, rapid, and high-throughput tool for routine screening known DRDR mutants in new and relapsed cases, SNP typing, and detection of minor mutant alleles in the wild-type background at lower costs than current methods and with the potential for quality control in leprosy investigations.
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Affiliation(s)
- Wei Li
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Masanori Matsuoka
- Leprosy Research Center, National Institute of Infection Diseases, Tokyo, Japan
| | - Masanori Kai
- Leprosy Research Center, National Institute of Infection Diseases, Tokyo, Japan
| | - Pratibha Thapa
- Mycobacterial Research Laboratory, Anandaban Hospital, Kathmandu, Nepal
| | - Saraswoti Khadge
- Mycobacterial Research Laboratory, Anandaban Hospital, Kathmandu, Nepal
| | - Deanna A. Hagge
- Mycobacterial Research Laboratory, Anandaban Hospital, Kathmandu, Nepal
| | - Patrick J. Brennan
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
| | - Varalakshmi Vissa
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
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Turankar RP, Lavania M, Singh M, Siva Sai KSR, Jadhav RS. Dynamics of Mycobacterium leprae transmission in environmental context: deciphering the role of environment as a potential reservoir. INFECTION GENETICS AND EVOLUTION 2011; 12:121-6. [PMID: 22101333 DOI: 10.1016/j.meegid.2011.10.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2011] [Revised: 10/20/2011] [Accepted: 10/24/2011] [Indexed: 11/26/2022]
Abstract
Leprosy is a disease caused by Mycobacterium leprae. Various modes of transmission have been suggested for this disease. Transmission and risk of the infection is perhaps related to presence of the infectious cases and is controlled by environmental factors. Evidence suggests that humidity may favor survival of M. leprae in the environment. Several reports show that non-human sources like 'naturally' infected armadillos or monkeys could act as reservoir for M. leprae. Inanimate objects or fomites like articles used by infectious patients may theoretically spread infection. However, it is only through detailed knowledge of the biodiversity and ecology that the importance of this mode of transmission can be fully assessed. Our study focuses here to decipher the role of environment in the transmission of the disease. Two hundred and seven soil samples were collected from a village in endemic area where active cases also resided at the time of sample collection. Slit skin smears were collected from 13 multibacillary (MB) leprosy patients and 12 household contacts of the patients suspected to be hidden cases. DNA and RNA of M. leprae were extracted and amplified using M. leprae specific primers. Seventy-one soil samples showed presence of M. leprae DNA whereas 16S rRNA could be detected in twenty-eight of these samples. Samples, both from the environment and the patients, exhibited the same genotype when tested by single nucleotide polymorphism (SNP) typing. Genotype of M. leprae found in the soil and the patients residing in the same area could help in understanding the transmission link in leprosy.
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Affiliation(s)
- Ravindra P Turankar
- Stanley Browne Laboratory, TLM Community Hospital, Nand Nagari, Delhi 110093, India
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Salipante SJ, Hall BG. Towards the molecular epidemiology of Mycobacterium leprae: Strategies, successes, and shortcomings. INFECTION GENETICS AND EVOLUTION 2011; 11:1505-13. [DOI: 10.1016/j.meegid.2011.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2011] [Revised: 06/03/2011] [Accepted: 06/07/2011] [Indexed: 12/23/2022]
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Singh P, Cole ST. Mycobacterium leprae: genes, pseudogenes and genetic diversity. Future Microbiol 2011; 6:57-71. [PMID: 21162636 DOI: 10.2217/fmb.10.153] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Leprosy, which has afflicted human populations for millenia, results from infection with Mycobacterium leprae, an unculturable pathogen with an exceptionally long generation time. Considerable insight into the biology and drug resistance of the leprosy bacillus has been obtained from genomics. M. leprae has undergone reductive evolution and pseudogenes now occupy half of its genome. Comparative genomics of four different strains revealed remarkable conservation of the genome (99.995% identity) yet uncovered 215 polymorphic sites, mainly single nucleotide polymorphisms, and a handful of new pseudogenes. Mapping these polymorphisms in a large panel of strains defined 16 single nucleotide polymorphism-subtypes that showed strong geographical associations and helped retrace the evolution of M. leprae.
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Affiliation(s)
- Pushpendra Singh
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, CH-1015 Lausanne, Switzerland
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Molecular typing of Mycobacterium leprae strains from northern India using short tandem repeats. Indian J Med Res 2011; 133:618-26. [PMID: 21727660 PMCID: PMC3135989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND & OBJECTIVES Due to the inability to cultivate Mycobacterium leprae in vitro and most cases being paucibacillary, it has been difficult to apply classical genotyping methods to this organism. The objective of this study was therefore, to analyze the diversity among M. leprae strains from Uttar Pradesh, north India, by targeting ten short tandem repeats (STRs) as molecular markers. METHODS Ninety specimens including 20 biopsies and 70 slit scrappings were collected in TE buffer from leprosy patients, who attended the OPD of National JALMA Institute for Leprosy and Other Mycobacterial Diseases, Tajganj, Agra, and from villages of Model Rural Health Research Unit (MRHRU) at Ghatampur, Kanpur, Uttar Pradesh. DNA was extracted from these specimens and ten STRs loci were amplified by using published and in-house designed primers. The copy numbers were determined by electrophoretic mobility as well as sequence analysis. Phylogenetic analysis was done on variable number of tandem repeats (VNTRs) data sets using start software. RESULTS Diversity was observed in the cross-sectional survey of isolates obtained from 90 patients. Allelic index for different loci was found to vary from 0.7 to 0.8 except for rpoT for which allelic index was 0.186. Similarity in fingerprinting profiles observed in specimens from the cases from same house or nearby locations indicated a possible common source of infection. Such analysis was also found to be useful in discriminating the relapse from possible reinfection. INTERPRETATION & CONCLUSIONS This study led to identification of STRs eliciting polymorphism in north Indian strains of M. leprae. The data suggest that these STRs can be used to study the sources and transmission chain in leprosy, which could be very important in monitoring of the disease dynamics in high endemic foci.
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Taylor GM, Donoghue HD. Multiple loci variable number tandem repeat (VNTR) analysis (MLVA) of Mycobacterium leprae isolates amplified from European archaeological human remains with lepromatous leprosy. Microbes Infect 2011; 13:923-9. [PMID: 21658464 DOI: 10.1016/j.micinf.2011.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 05/06/2011] [Accepted: 05/10/2011] [Indexed: 11/29/2022]
Abstract
Molecular typing methods based on polymorphisms in single nucleotides and short tandem repeat motifs have been developed as epidemiological typing tools for Mycobacterium leprae. We have used a variable number tandem repeat method based on three variable loci to identify strain variation in archaeological cases of lepromatous leprosy. The panel of polymorphic loci used revealed unique profiles in five cases of leprosy, including those with identical SNP type and subtype. These were also different from profiles of three previously studied lepromatous skeletons. Whilst examination with SNP typing provides evidence for disease origins, dissemination and phylogeny, tandem repeat typing may be useful for studying cases from within a defined area or community where SNP types may be identical due to geographical constraints. We envisage the technique may be useful in studying contemporaneous burials such as those associated with leprosaria and will prove invaluable in authentication of ancient DNA analyses.
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Affiliation(s)
- G Michael Taylor
- Department of Microbial Sciences, Faculty of Health and Medical Sciences, AW Building, University of Surrey, Guildford, Surrey GU27TE, UK.
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Weng X, Vander Heiden J, Xing Y, Liu J, Vissa V. Transmission of leprosy in Qiubei County, Yunnan, China: insights from an 8-year molecular epidemiology investigation. INFECTION GENETICS AND EVOLUTION 2010; 11:363-74. [PMID: 21129505 DOI: 10.1016/j.meegid.2010.11.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2010] [Revised: 11/19/2010] [Accepted: 11/22/2010] [Indexed: 11/25/2022]
Abstract
Leprosy continues to be endemic in parts of China. To track the occurrence of leprosy and determine at risk communities, molecular strain typing based on variable number of tandem repeats (VNTRs) was applied in Qiubei County, Wenshan Prefecture, Yunnan Province of the People's Republic of China, a multiethnic region that is home to four predominant ethnic minorities. A previous study, conducted between 2002 and 2005, provided the first descriptions of Mycobacterium leprae strains in the region. M. leprae strains in Qiubei are highly conserved, so only sufficiently polymorphic loci can distinguish strains. A balance between mutation rate and loci stability is needed, so that secondary transmissions can be identified as genotypic matches. The long incubation period of leprosy necessitated an extension of the study to assess the validity of VNTR typing and observe allelic shifts in the same multiethnic population. From 2006 to early 2010 the extension was performed to yield a cumulative total of 164 enrolled patients and 130 skin samples suitable for VNTR typing. Patient demographic information revealed that the case detection rate among certain minority populations in the county is considerably higher than the national rate. Cluster analysis of allele frequencies showed similar strain types within family groups and neighboring townships. Allele frequencies were not found to significantly differ between genders or clinical presentations. The percentage of cases showing near-matching genotypes varied with geography; showing a considerably higher rate in the northern townships. The northern townships continue to show strain types falling into the groups previously defined. Southern genotypes were distinct from those in the north, but clonal genetic relationships were indiscernible in the south. Social interactions and the physical, residential and occupational environments may be more conducive to transmission of community strains in the north.
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Affiliation(s)
- Xiaoman Weng
- Beijing Friendship Hospital--Affiliate of Capital University of Medicial Sciences, Beijing Tropical Medicine Research Institute, 95 Yong An Road, Beijing 100050, China
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MATSUOKA M. The history and characteristics of isolates maintained at the Leprosy Research Center. ACTA ACUST UNITED AC 2010; 79:247-56. [DOI: 10.5025/hansen.79.247] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Zhang F, Liu H, Chen S, Wang C, Zhu C, Zhang L, Chu T, Liu D, Yan X, Liu J. Evidence for an association of HLA-DRB1*15 and DRB1*09 with leprosy and the impact of DRB1*09 on disease onset in a Chinese Han population. BMC MEDICAL GENETICS 2009; 10:133. [PMID: 20003324 PMCID: PMC2797507 DOI: 10.1186/1471-2350-10-133] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/16/2009] [Accepted: 12/11/2009] [Indexed: 11/10/2022]
Abstract
Background Human leukocyte antigens (HLAs) have been proposed to modulate the immune response to Mycobacterium leprae. The association of HLA-DRB1 with leprosy has been reported in several populations, but not in a Chinese population. Methods The polymerase chain reaction-sequence-specific oligonucleotide probe with Luminex100 (PCR-SSOP-Luminex) method was used to genotype HLA-DRB1 alleles in 305 leprosy patients and 527 healthy control individuals. Results The HLA-DRB1*15 allele was significantly more prevalent among leprosy patients than healthy controls, whereas the frequency of the HLA-DRB1*09 allele was lower among leprosy patients, especially those with early-onset disease. Conclusion HLA-DRB1 alleles are associated with leprosy susceptibility in a Chinese population. The HLA-DRB1*09 allele was found to be protective exclusively in a subset of early-onset leprosy patients.
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Affiliation(s)
- Furen Zhang
- Shandong Provincial Institute of Dermatovenereology, Jinan, Shandong Province, PR China.
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Comparative genomic and phylogeographic analysis of Mycobacterium leprae. Nat Genet 2009; 41:1282-9. [PMID: 19881526 DOI: 10.1038/ng.477] [Citation(s) in RCA: 263] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2009] [Accepted: 09/01/2009] [Indexed: 11/08/2022]
Abstract
Reductive evolution and massive pseudogene formation have shaped the 3.31-Mb genome of Mycobacterium leprae, an unculturable obligate pathogen that causes leprosy in humans. The complete genome sequence of M. leprae strain Br4923 from Brazil was obtained by conventional methods (6x coverage), and Illumina resequencing technology was used to obtain the sequences of strains Thai53 (38x coverage) and NHDP63 (46x coverage) from Thailand and the United States, respectively. Whole-genome comparisons with the previously sequenced TN strain from India revealed that the four strains share 99.995% sequence identity and differ only in 215 polymorphic sites, mainly SNPs, and by 5 pseudogenes. Sixteen interrelated SNP subtypes were defined by genotyping both extant and extinct strains of M. leprae from around the world. The 16 SNP subtypes showed a strong geographical association that reflects the migration patterns of early humans and trade routes, with the Silk Road linking Europe to China having contributed to the spread of leprosy.
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Sakamuri RM, Kimura M, Li W, Kim HC, Lee H, Kiran MD, Black WC, Balagon M, Gelber R, Cho SN, Brennan PJ, Vissa V. Population-based molecular epidemiology of leprosy in Cebu, Philippines. J Clin Microbiol 2009; 47:2844-54. [PMID: 19571027 PMCID: PMC2738081 DOI: 10.1128/jcm.02021-08] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2008] [Revised: 05/22/2009] [Accepted: 06/08/2009] [Indexed: 11/20/2022] Open
Abstract
To address the persisting problem of leprosy in Cebu, Philippines, we compiled a database of more than 200 patients who attend an established referral skin clinic. We described the patient characteristics in conventional demographic parameters and also applied multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) and single nucleotide polymorphism (SNP) typing for Mycobacterium leprae in biopsied skin lesion samples. These combined approaches revealed that transmission is ongoing, with the affected including the young Cebuano population under 40 years of age in both crowded cities and rural areas of the island. The emergence of multicase families (MCF) is indicative of infection unconstrained by standard care measures. For the SNPs, we designed a low-cost PCR-restriction fragment length polymorphism typing method. MLVA in M. leprae was highly discriminatory in this population yet could retain broad groups, as defined by the more stable SNPs, implying temporal marker stability suitable for interpreting population structures and evolution. The majority of isolates belong to an Asian lineage (SNP type 1), and the rest belong to a putative postcolonial lineage (SNP type 3). Specific alleles at two VNTR loci, (GGT)5 and 21-3, were highly associated with SNP type 3 in this population. MLVA identified M. leprae genotype associations for patients with known epidemiological links such as in MCFs and in some villages. These methods provide a molecular database and a rational framework for targeted approaches to search and confirm leprosy transmission in various scenarios.
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Affiliation(s)
- Rama Murthy Sakamuri
- Department of Microbiology, Immunology, and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO 80523, USA
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Rapid variable-number tandem-repeat genotyping for Mycobacterium leprae clinical specimens. J Clin Microbiol 2009; 47:1757-66. [PMID: 19386839 DOI: 10.1128/jcm.02019-08] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium leprae is the noncultivable pathogen of leprosy. Since the genome sequence of an isolate of M. leprae has become available, multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) has been explored as a tool for strain typing and identification of chains of transmission of leprosy. In order to discover VNTRs and develop methods transferable to clinical samples, MLVA was applied to a global collection of M. leprae isolates derived from leprosy patients and propagated in armadillo hosts. PCR amplification, agarose gel electrophoresis, and sequencing methods were applied to DNA extracts from these infected armadillo tissues (n = 21). We identified polymorphisms in 15 out of 25 short-tandem-repeat (STR) loci previously selected by in silico analyses of the M. leprae genome. We then developed multiplex PCR for amplification of these 15 loci in four separate PCRs suitable for fluorescent fragment length analysis and demonstrated STR profiles highly concordant with those from the sequencing methods. Subsequently, we extended this method to DNA extracts from human clinical specimens, such as skin biopsy specimens (n = 30). With these techniques, mapping of multiple loci and differentiation of genotypes have been possible using total DNA extracts from limited amounts of clinical samples at a reduced cost and with less time. These practical methods are therefore available and applicable to answer focused epidemiological questions and to allow monitoring of the transmission of M. leprae in different countries where leprosy is endemic.
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Variable number tandem repeat loci providing discrimination within widespread genotypes of Acinetobacter baumannii. Eur J Clin Microbiol Infect Dis 2008; 28:499-507. [DOI: 10.1007/s10096-008-0659-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Accepted: 10/16/2008] [Indexed: 10/21/2022]
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Combined multilocus short-sequence-repeat and mycobacterial interspersed repetitive unit-variable-number tandem-repeat typing of Mycobacterium avium subsp. paratuberculosis isolates. J Clin Microbiol 2008; 46:4091-4. [PMID: 18923016 DOI: 10.1128/jcm.01349-08] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Short-sequence-repeat (SSR) sequencing was applied to 127 Mycobacterium avium subsp. paratuberculosis isolates typed by mycobacterial interspersed repetitive unit-variable-number tandem repeats (MIRU-VNTR) and IS900 restriction fragment length polymorphism (RFLP). Combined MIRU-VNTR and SSR typing followed by secondary IS900 RFLP typing is an improved approach to high-resolution genotyping of this pathogen.
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Oskam L, Dockrell HM, Brennan PJ, Gillis T, Vissa V, Richardus JH. Molecular methods for distinguishing between relapse and reinfection in leprosy. Trop Med Int Health 2008; 13:1325-6. [DOI: 10.1111/j.1365-3156.2008.02134_1.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Are variable-number tandem repeats appropriate for genotyping Mycobacterium leprae? J Clin Microbiol 2008; 46:2291-7. [PMID: 18495858 DOI: 10.1128/jcm.00239-08] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Comparative genomics analysis of the Tamil Nadu strain of Mycobacterium leprae has uncovered several polymorphic sites with potential as epidemiological tools. In this study we compared the stability of two different markers of genomic biodiversity of M. leprae in several biopsy samples isolated from the same leprosy patient. The first type comprises five different variable-number tandem repeats (VNTR), while the second is composed of three single nucleotide polymorphisms (SNP). Contrasting results were obtained, since no variation was seen in the SNP profiles of M. leprae from 42 patients from 7 different locations in Mali whereas the VNTR profiles varied considerably. Furthermore, since variation in the VNTR pattern was seen not only between different isolates of M. leprae but also between biopsy samples from the same patient, these VNTR may be too dynamic for use as epidemiological markers for leprosy.
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Leprosy: diagnostic and control challenges for a worldwide disease. Arch Dermatol Res 2008; 300:269-90. [DOI: 10.1007/s00403-008-0857-y] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2007] [Revised: 04/05/2008] [Accepted: 04/10/2008] [Indexed: 11/25/2022]
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Use of short tandem repeat sequences to study Mycobacterium leprae in leprosy patients in Malawi and India. PLoS Negl Trop Dis 2008; 2:e214. [PMID: 18398487 PMCID: PMC2271132 DOI: 10.1371/journal.pntd.0000214] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Accepted: 02/14/2008] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Inadequate understanding of the transmission of Mycobacterium leprae makes it difficult to predict the impact of leprosy control interventions. Genotypic tests that allow tracking of individual bacterial strains would strengthen epidemiological studies and contribute to our understanding of the disease. METHODOLOGY/PRINCIPAL FINDINGS Genotyping assays based on variation in the copy number of short tandem repeat sequences were applied to biopsies collected in population-based epidemiological studies of leprosy in northern Malawi, and from members of multi-case households in Hyderabad, India. In the Malawi series, considerable genotypic variability was observed between patients, and also within patients, when isolates were collected at different times or from different tissues. Less within-patient variability was observed when isolates were collected from similar tissues at the same time. Less genotypic variability was noted amongst the closely related Indian patients than in the Malawi series. CONCLUSIONS/SIGNIFICANCE Lineages of M. leprae undergo changes in their pattern of short tandem repeat sequences over time. Genetic divergence is particularly likely between bacilli inhabiting different (e.g., skin and nerve) tissues. Such variability makes short tandem repeat sequences unsuitable as a general tool for population-based strain typing of M. leprae, or for distinguishing relapse from reinfection. Careful use of these markers may provide insights into the development of disease within individuals and for tracking of short transmission chains.
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Blythe MJ, Zhang Q, Vaughan K, de Castro R, Salimi N, Bui HH, Lewinsohn DM, Ernst JD, Peters B, Sette A. An analysis of the epitope knowledge related to Mycobacteria. Immunome Res 2007; 3:10. [PMID: 18081934 PMCID: PMC2228276 DOI: 10.1186/1745-7580-3-10] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2007] [Accepted: 12/14/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tuberculosis, caused by the bacterium Mycobacterium tuberculosis, remains a leading cause of infectious disease morbidity and mortality, and is responsible for more than 2 million deaths a year. Reports about extremely drug resistant (XDR) strains have further heightened the sense of urgency for the development of novel strategies to prevent and treat TB. Detailed knowledge of the epitopes recognized by immune responses can aid in vaccine and diagnostics development, and provides important tools for basic research. The analysis of epitope data corresponding to M. tuberculosis can also identify gaps in our knowledge, and suggest potential areas for further research and discovery. The Immune Epitope Database (IEDB) is compiled mainly from literature sources, and describes a broad array of source organisms, including M. tuberculosis and other Mycobacterial species. DESCRIPTION A comprehensive analysis of IEDB data regarding the genus Mycobacteria was performed. The distribution of antibody/B cell and T cell epitopes was analyzed in terms of their associated recognition cell type effector function and chemical properties. The various species, strains and proteins which the epitope were derived, were also examined. Additional variables considered were the host in which the epitopes were defined, the specific TB disease state associated with epitope recognition, and the HLA associated with disease susceptibility and endemic regions were also scrutinized. Finally, based on these results, standardized reference datasets of mycobacterial epitopes were generated. CONCLUSION All current TB-related epitope data was cataloged for the first time from the published literature. The resulting inventory of more than a thousand different epitopes should prove a useful tool for the broad scientific community. Knowledge gaps specific to TB epitope data were also identified. In summary, few non-peptidic or post-translationally modified epitopes have been defined. Most importantly epitopes have apparently been defined from only 7% of all ORFs, and the top 30 most frequently studied protein antigens contain 65% of the epitopes, leaving the majority of M. tuberculosis genome unexplored. A lack of information related to the specific strains from which epitopes are derived is also evident. Finally, the generation of reference lists of mycobacterial epitopes should also facilitate future vaccine and diagnostic research.
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Affiliation(s)
- Martin J Blythe
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, California, 92037, USA
| | - Qing Zhang
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, California, 92037, USA
| | - Kerrie Vaughan
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, California, 92037, USA
| | - Romulo de Castro
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, California, 92037, USA
| | - Nima Salimi
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, California, 92037, USA
| | - Huynh-Hoa Bui
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, California, 92037, USA
| | - David M Lewinsohn
- Portland VA Medical Center/Oregon Heath and Science University, R&D 11, PVAMC, 3710 SW US Veterans Road, Portland, Oregon, 97239, USA
| | - Joel D Ernst
- Division of Infectious Diseases, New York University School of Medicine, 550 First Avenue, Smilow 901, New York, 10016, USA
| | - Bjoern Peters
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, California, 92037, USA
| | - Alessandro Sette
- Department of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, 9420 Athena Circle, La Jolla, California, 92037, USA
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Weng X, Wang Z, Liu J, Kimura M, Black WC, Brennan PJ, Li H, Vissa VD. Identification and distribution of Mycobacterium leprae genotypes in a region of high leprosy prevalence in China: a 3-year molecular epidemiological study. J Clin Microbiol 2007; 45:1728-34. [PMID: 17428944 PMCID: PMC1933063 DOI: 10.1128/jcm.00018-07] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Revised: 02/05/2007] [Accepted: 03/28/2007] [Indexed: 11/20/2022] Open
Abstract
Multiple-locus variable-number tandem-repeat (VNTR) analysis (MLVA) has been proposed as a means of strain typing for tracking the transmission of leprosy. However, empirical data for a defined population are lacking. To this end, a study was initiated to assess the diversity and distribution of prevalent Mycobacterium leprae strains in Qiubei County, Yunnan Province, People's Republic of China, where the annual detection rate of leprosy is 10-fold higher than the national average rate. Sixty-eight newly diagnosed leprosy patients were included in the study. MLVA at eight M. leprae loci was applied using DNA extracts from skin biopsies. The number of alleles per locus ranged from 4 to 24, providing adequate strain discrimination. MLVA strain typing identified several clusters of patients whose M. leprae specimens shared similar VNTR profiles. Two of these clusters were comprised of patients who resided predominantly in the north and northwest parts of Qiubei County. Furthermore, it was found that multicase families are common in this county: 23 of the 68 patients were from 11 families. Intrafamilial VNTR profiles closely matched within six families, although they were different between the families. Moreover, VNTR patterns related to those found in some multicase families were also detected in patients in the same or adjacent townships, indicating the utility of VNTR strain typing to identify and detect short-range transmission events. Social contact through village markets is proposed as a means of transmission.
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Affiliation(s)
- Xiaoman Weng
- Beijing Friendship Hospital-Affiliate of Capital University of Medical Sciences, Beijing Tropical Medicine Research Institute, 95 Yong An Road, Beijing 100050, People's Republic of China
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Ablordey A, Fonteyne PA, Stragier P, Vandamme P, Portaels F. Identification of a new variable number tandem repeat locus in Mycobacterium ulcerans for potential strain discrimination among African isolates. Clin Microbiol Infect 2007; 13:734-6. [PMID: 17403131 DOI: 10.1111/j.1469-0691.2007.01716.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Intra-species discrimination in the highly clonal pathogen Mycobacterium ulcerans was studied in a diverse collection of isolates by PCR amplification of a short sequence repeat locus containing heterogeneous arrays of tri-nucleotide repeats with an ACC consensus pattern. Post-amplification analysis indicated excellent typeability and identified five M. ulcerans alleles, including a unique Angolan type differentiated for the first time among a genetically conserved cluster of African isolates. These results are consistent with previously investigated independent markers, and provide an additional locus for variable number tandem repeat-based typing of M. ulcerans.
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Affiliation(s)
- A Ablordey
- Mycobacteriology Unit, Institute of Tropical Medicine Antwerp, Antwerp, Belgium
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Martinez AN, Britto CFPC, Nery JAC, Sampaio EP, Jardim MR, Sarno EN, Moraes MO. Evaluation of real-time and conventional PCR targeting complex 85 genes for detection of Mycobacterium leprae DNA in skin biopsy samples from patients diagnosed with leprosy. J Clin Microbiol 2006; 44:3154-9. [PMID: 16954241 PMCID: PMC1594745 DOI: 10.1128/jcm.02250-05] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In spite of the decrease in the number of registered leprosy patients, the number of new cases diagnosed each year (400,000) has remained essentially unchanged. Leprosy diagnosis is difficult due to the low sensitivity of current methodologies to identify new cases. In this study, conventional and TaqMan real-time PCR assays for detection of Mycobacterium leprae DNA were compared to current classification based on clinical, bacteriological, and histological evaluation. M. leprae DNA was extracted from frozen skin biopsy specimens from 69 leprosy patients enrolled in the study and was amplified using specific primers for either the antigen 85B-coding gene or the 85A-C intergenic region by using conventional and real-time PCR. The detection rate was 100% among multibacillary (MB) patients and ranged from 62.5% to 79.2% among paucibacillary (PB) patients according to the assay used. The TaqMan system for 85B gene amplification showed the highest sensitivity, although conventional PCR using the 85A-C gene as a target was also efficient. The cycle threshold (C(T)) values obtained using the TaqMan system were able to statistically (P < 0.0001) differentiate MB (mean C(T), 28.06; standard deviation [SD], 4.51) from PB (mean C(T), 33.06; SD, 2.24) patients. Also, there was a correlation between C(T) values and the bacteriological index for MB patients (Pearson's r, -0.444; P = 0.008). Within the PB patients' group, we tested normal skin from six patients exhibiting the pure neuritic form of leprosy (PNL). Five out of six PNL patients were positive for the presence of M. leprae DNA, even in the absence of skin lesions. In conclusion, the TaqMan real-time PCR developed here seems to be a useful tool for rapidly detecting and quantifying M. leprae DNA in clinical specimens in which bacilli were undetectable by conventional histological staining.
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Affiliation(s)
- Alejandra N Martinez
- Leprosy Laboratory, Mycobacterioses Department, Fiocruz, Av. Brasil 4365, Manguinhos, Rio de Janeiro, 21040-360, Brazil
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Matsuoka M, Roa RIL, Budiawan T, Kyaw K, Chae GT. Genotypic analysis of Mycobacterium leprae isolates from Japan and other Asian countries reveals a global transmission pattern of leprosy. FEMS Microbiol Lett 2006; 261:150-4. [PMID: 16842372 DOI: 10.1111/j.1574-6968.2006.00346.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The genotype of single-nucleotide polymorphism type 3, CTC, at positions 14676, 164275, and 2935685, along with four copies of 6 bp repeats in the rpoT gene, was predominant for isolates originating in the Japanese mainland. Type 1, CGA, type 2, CTA, and type 3 were detected from Korea, Indonesia, and Myanmar. No isolates with four copies of 6 bp were detected from Myanmar, Okinawa, and Japanese Brazilian patients. Type 4, TTC, with three copies of 6 bp, was detected only from Japanese Brazilians. The results indicate that infection occurred in Brazil and the disease developed later in Japan.
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Affiliation(s)
- Masanori Matsuoka
- Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan.
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