1
|
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: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.
| |
Collapse
|
2
|
Chokkakula S, Chen Z, Wang L, Jiang H, Chen Y, Shi Y, Zhang W, Gao W, Yang J, Li J, Li X, Shui T, He J, Shen L, Liu J, Wang D, Wang H, Chen H, Kuang Y, Li B, Chen Z, Wu A, Yu M, Yan L, Suryadevara NC, Vissa V, Liu W, Wang H. Molecular surveillance of antimicrobial resistance and transmission pattern of Mycobacterium leprae in Chinese leprosy patients. Emerg Microbes Infect 2020; 8:1479-1489. [PMID: 31621517 PMCID: PMC6818117 DOI: 10.1080/22221751.2019.1677177] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Reports on antimicrobial resistance (AMR) of Mycobacterium leprae, relationship with bacteriological index (BI), and transmission in China are limited. We investigated the emergence of AMR mutations, the relationship between BI and AMR in complete, moderate and lack of BI decline cases, and molecular epidemiological features of AMR cases by enrolling 290 leprosy cases from four endemic provinces. Seven (2.41%), one (0.34%), five (1.72%), one (0.34%), and one (0.34%) strains had single mutations in folP1, rpoC, gyrA, gyrB, and 23S rRNA, respectively. Double mutations in folP1 and gyrA, rpoB and gyrA, and gyrA and 23S rRNA were observed in one (0.34%) strain each. Mutated strains occurred in three out of 81 (95% CI-0.005-0.079, p = 0.083) cases with complete BI decline, in seven out of 103 (95% CI 0.018-0.117, p = 0.008) cases with moderate BI decline, and in four out of 34 (95% CI 0.003-0.231, p = 0.044) cases with lack of BI decline. Most of these mutated strains were geographically separated and diverged genotypically. AMR mutations may not be the main cause of the lack of BI decline. The low transmission of AMR strains at the county level indicates an ongoing transmission at close contact levels.
Collapse
Affiliation(s)
- Santosh Chokkakula
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , 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
| | - Zhiming Chen
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , 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
| | - Le Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , 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 , 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 , 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 , 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 , 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
| | - Wei Gao
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , 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
| | - Jinlan Li
- Guizhou Provincial CDC , Guiyang , China
| | - Xiong Li
- Yunnan Provincial CDC , Kunming , China
| | | | - Jun He
- Yunnan Provincial CDC , Kunming , China
| | - Limei Shen
- Guizhou Provincial CDC , Guiyang , China
| | - Jie Liu
- Guizhou Provincial CDC , Guiyang , China
| | - De Wang
- Guizhou Provincial CDC , Guiyang , China
| | - Hao Wang
- Sichuan Provincial People's Hospital , Chengdu , China
| | - Huan Chen
- Hunan Provincial CDC , Changsha , China
| | | | - Bin Li
- Hunan Provincial CDC , Changsha , China
| | - Ziyi Chen
- Suzhou Institute of Systems Medicine , Suzhou , China
| | - Aiping Wu
- Suzhou Institute of Systems Medicine , Suzhou , China
| | - Meiwen Yu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , China
| | - Liangbin Yan
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , China
| | | | - Varalakshmi Vissa
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , 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
| | - Weida Liu
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , China
| | - Hongsheng Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College , Nanjing , 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
| |
Collapse
|
3
|
Cambau E, Saunderson P, Matsuoka M, Cole ST, Kai M, Suffys P, Rosa PS, Williams D, Gupta UD, Lavania M, Cardona-Castro N, Miyamoto Y, Hagge D, Srikantam A, Hongseng W, Indropo A, Vissa V, Johnson RC, Cauchoix B, Pannikar VK, Cooreman EAWD, Pemmaraju VRR, Gillini L. Antimicrobial resistance in leprosy: results of the first prospective open survey conducted by a WHO surveillance network for the period 2009-15. Clin Microbiol Infect 2018; 24:1305-1310. [PMID: 29496597 PMCID: PMC6286419 DOI: 10.1016/j.cmi.2018.02.022] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/13/2018] [Accepted: 02/15/2018] [Indexed: 12/25/2022]
Abstract
OBJECTIVES Antimicrobial resistance (AMR) is a priority for surveillance in bacterial infections. For leprosy, AMR has not been assessed because Mycobacterium leprae does not grow in vitro. We aim to obtain AMR data using molecular detection of resistance genes and to conduct a prospective open survey of resistance to antileprosy drugs in countries where leprosy is endemic through a WHO surveillance network. METHODS From 2009 to 2015, multi-bacillary leprosy cases at sentinel sites of 19 countries were studied for resistance to rifampicin, dapsone and ofloxacin by PCR sequencing of the drug-resistance-determining regions of the genes rpoB, folP1 and gyrA. RESULTS Among 1932 (1143 relapse and 789 new) cases studied, 154 (8.0%) M. leprae strains were found with mutations conferring resistance showing 182 resistance traits (74 for rifampicin, 87 for dapsone and 21 for ofloxacin). Twenty cases showed rifampicin and dapsone resistance, four showed ofloxacin and dapsone resistance, but no cases were resistant to rifampicin and ofloxacin. Rifampicin resistance was observed among relapse (58/1143, 5.1%) and new (16/789, 2.0%) cases in 12 countries. India, Brazil and Colombia reported more than five rifampicin-resistant cases. CONCLUSIONS This is the first study reporting global data on AMR in leprosy. Rifampicin resistance emerged, stressing the need for expansion of surveillance. This is also a call for vigilance on the global use of antimicrobial agents, because ofloxacin resistance probably developed in relation to the general intake of antibiotics for other infections as it is not part of the multidrug combination used to treat leprosy.
Collapse
Affiliation(s)
- E Cambau
- Université Paris Diderot, UMR 1137 IAME Inserm, APHP-Lariboisière, APHP-Pitie-Salpêtrière, Centre de Référence des Mycobactéries et de la résistance des mycobactéries aux antituberculeux, Paris, France.
| | | | - M Matsuoka
- Leprosy Research Centre, National Institute of Infectious Diseases, Tokyo, Japan
| | - S T Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Switzerland; Fondation Raoul Follereau, Paris, France
| | - M Kai
- Leprosy Research Centre, National Institute of Infectious Diseases, Tokyo, Japan
| | - P Suffys
- Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - P S Rosa
- Instituto Lauro de Souza Lima, Sao Paulo, Brazil
| | - D Williams
- National Hansen's Disease Programs, Baton Rouge, USA
| | - U D Gupta
- National JALMA Institute of Leprosy & Other Mycobacterial Diseases, Agra, India
| | - M Lavania
- Stanley Browne Laboratory, TLM Community Hospital, Delhi, India
| | - N Cardona-Castro
- Institute Colombiano de Medicina Tropical, Sabaneta, Antioquia, Colombia
| | - Y Miyamoto
- Leprosy Research Centre, National Institute of Infectious Diseases, Tokyo, Japan
| | - D Hagge
- Mycobacterial Research Laboratories, Anandaban Hospital, Kathmandu, Nepal
| | - A Srikantam
- Lepra Blue Peter Public Health and Research Centre, Hyderabad, India
| | - W Hongseng
- Institute of Dermatology, Chinese Academy of Medical Sciences, National Center for STD and Leprosy Control, China CDC, China
| | - A Indropo
- Airlangga University, Surabaya, Indonesia
| | - V Vissa
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | | | - B Cauchoix
- Fondation Raoul Follereau, Paris, France
| | - V K Pannikar
- Global Leprosy Programme, WHO Regional Office for South-East Asia, New Delhi, India
| | - E A W D Cooreman
- Global Leprosy Programme, WHO Regional Office for South-East Asia, New Delhi, India
| | - V R R Pemmaraju
- Global Leprosy Programme, WHO Regional Office for South-East Asia, New Delhi, India
| | - L Gillini
- Global Leprosy Programme, WHO Regional Office for South-East Asia, New Delhi, India
| |
Collapse
|
4
|
Jiang H, Sun J, Chen Y, Chen Z, Wang L, Gao W, Shi Y, Zhang W, Mei Y, Chokkakula S, Vissa V, Jiang T, Wu A, Wang H. Landscape of the genome and host cell response of Mycobacterium shigaense reveals pathogenic features. Emerg Microbes Infect 2018; 7:112. [PMID: 29934568 PMCID: PMC6015043 DOI: 10.1038/s41426-018-0116-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 05/14/2018] [Accepted: 05/16/2018] [Indexed: 02/08/2023]
Abstract
A systems approach was used to explore the genome and transcriptome of Mycobacterium shigaense, a new opportunistic pathogen isolated from a patient with a skin infection, and the host response transcriptome was assessed using a macrophage infection model. The M. shigaense genome comprises 5,207,883 bp, with 67.2% G+C content and 5098 predicted coding genes. Evolutionarily, the bacterium belongs to a cluster in the phylogenetic tree along with three target opportunistic pathogenic strains, namely, M. avium, M. triplex and M. simiae. Potential virulence genes are indeed expressed by M. shigaense under culture conditions. Phenotypically, M. shigaense had similar infection and replication capacities in a macrophage model as the opportunistic species compared to M. tuberculosis. M. shigaense activated NF-κB, TNF, cytokines and chemokines in the host innate immune-related signaling pathways and elicited an early response shared with pathogenic bacilli except M. tuberculosis. M. shigaense upregulated specific host response genes such as TLR7, CCL4 and CXCL5. We performed an integrated and comparative analysis of M. shigaense. Multigroup comparison indicated certain differences with typical pathogenic bacilli in terms of gene features and the macrophage response.
Collapse
Affiliation(s)
- Haiqin Jiang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, 210042, China
| | - Jiya Sun
- Suzhou Institute of Systems Medicine, Center of Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, 215021, China
| | - Yanqing Chen
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, 210042, China
| | - Zhiming Chen
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, 210042, China
| | - Le Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, 210042, China
| | - Wei Gao
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, 210042, China
| | - Ying Shi
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, 210042, China
| | - Wenyue Zhang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, 210042, China
| | - Youming Mei
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, 210042, China
| | - Santosh Chokkakula
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, 210042, China
| | - Varalakshmi Vissa
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China.,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, 210042, China
| | - Taijiao Jiang
- Suzhou Institute of Systems Medicine, Center of Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, 215021, China.
| | - Aiping Wu
- Suzhou Institute of Systems Medicine, Center of Systems Medicine, Chinese Academy of Medical Sciences, Suzhou, 215021, China.
| | - Hongsheng Wang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, 210042, China. .,Jiangsu Key Laboratory of Molecular Biology for Skin Diseases and STIs, Nanjing, 210042, China.
| |
Collapse
|
5
|
Araujo S, Goulart LR, Truman RW, Goulart IMB, Vissa V, Li W, Matsuoka M, Suffys P, Fontes AB, Rosa PS, Scollard DM, Williams DL. qPCR-High resolution melt analysis for drug susceptibility testing of Mycobacterium leprae directly from clinical specimens of leprosy patients. PLoS Negl Trop Dis 2017; 11:e0005506. [PMID: 28570560 PMCID: PMC5453413 DOI: 10.1371/journal.pntd.0005506] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 03/20/2017] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Real-Time PCR-High Resolution Melting (qPCR-HRM) analysis has been recently described for rapid drug susceptibility testing (DST) of Mycobacterium leprae. The purpose of the current study was to further evaluate the validity, reliability, and accuracy of this assay for M. leprae DST in clinical specimens. METHODOLOGY/PRINCIPAL FINDINGS The specificity and sensitivity for determining the presence and susceptibility of M. leprae to dapsone based on the folP1 drug resistance determining region (DRDR), rifampin (rpoB DRDR) and ofloxacin (gyrA DRDR) was evaluated using 211 clinical specimens from leprosy patients, including 156 multibacillary (MB) and 55 paucibacillary (PB) cases. When comparing the results of qPCR-HRM DST and PCR/direct DNA sequencing, 100% concordance was obtained. The effects of in-house phenol/chloroform extraction versus column-based DNA purification protocols, and that of storage and fixation protocols of specimens for qPCR-HRM DST, were also evaluated. qPCR-HRM results for all DRDR gene assays (folP1, rpoB, and gyrA) were obtained from both MB (154/156; 98.7%) and PB (35/55; 63.3%) patients. All PCR negative specimens were from patients with low numbers of bacilli enumerated by an M. leprae-specific qPCR. We observed that frozen and formalin-fixed paraffin embedded (FFPE) tissues or archival Fite's stained slides were suitable for HRM analysis. Among 20 mycobacterial and other skin bacterial species tested, only M. lepromatosis, highly related to M. leprae, generated amplicons in the qPCR-HRM DST assay for folP1 and rpoB DRDR targets. Both DNA purification protocols tested were efficient in recovering DNA suitable for HRM analysis. However, 3% of clinical specimens purified using the phenol/chloroform DNA purification protocol gave false drug resistant data. DNA obtained from freshly frozen (n = 172), formalin-fixed paraffin embedded (FFPE) tissues (n = 36) or archival Fite's stained slides (n = 3) were suitable for qPCR-HRM DST analysis. The HRM-based assay was also able to identify mixed infections of susceptible and resistant M. leprae. However, to avoid false positives we recommend that clinical specimens be tested for the presence of the M. leprae using the qPCR-RLEP assay prior to being tested in the qPCR-HRM DST and that all specimens demonstrating drug resistant profiles in this assay be subjected to DNA sequencing. CONCLUSION/SIGNIFICANCE Taken together these results further demonstrate the utility of qPCR-HRM DST as an inexpensive screening tool for large-scale drug resistance surveillance in leprosy.
Collapse
Affiliation(s)
- Sergio Araujo
- National Reference Center for Sanitary Dermatology and Leprosy, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
- Post-Graduate Program in Health Sciences, School of Medicine, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
- Division National Hansen's Disease Programs (NHDP), Healthcare Systems Bureau (HSB), Health Resources and Services Administration (HRSA), U.S. Department of Health and Human Services (DHHS), Baton Rouge, Louisiana, United States of America
| | - Luiz Ricardo Goulart
- National Reference Center for Sanitary Dermatology and Leprosy, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
- Post-Graduate Program in Health Sciences, School of Medicine, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
- Institute of Genetics and Biochemistry, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
| | - Richard W. Truman
- Division National Hansen's Disease Programs (NHDP), Healthcare Systems Bureau (HSB), Health Resources and Services Administration (HRSA), U.S. Department of Health and Human Services (DHHS), Baton Rouge, Louisiana, United States of America
| | - Isabela Maria B. Goulart
- National Reference Center for Sanitary Dermatology and Leprosy, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
- Post-Graduate Program in Health Sciences, School of Medicine, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
| | - Varalakshmi Vissa
- Good Samaritan Society, Fort Collins, Colorado, United States of America
| | - Wei Li
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Masanori Matsuoka
- Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Philip Suffys
- Fundação Oswaldo Cruz, Laboratory of Molecular Biology applied to Mycobacteria, Rio de Janeiro, Rio de Janeiro, Brazil
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Amanda B. Fontes
- Fundação Oswaldo Cruz, Laboratory of Molecular Biology applied to Mycobacteria, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Patricia S. Rosa
- Instituto Lauro de Souza Lima, Department of Biology, Bauru, São Paulo, Brazil
| | - David M. Scollard
- Division National Hansen's Disease Programs (NHDP), Healthcare Systems Bureau (HSB), Health Resources and Services Administration (HRSA), U.S. Department of Health and Human Services (DHHS), Baton Rouge, Louisiana, United States of America
| | - Diana L. Williams
- Division National Hansen's Disease Programs (NHDP), Healthcare Systems Bureau (HSB), Health Resources and Services Administration (HRSA), U.S. Department of Health and Human Services (DHHS), Baton Rouge, Louisiana, United States of America
| |
Collapse
|
6
|
Jiang H, Jin Y, Vissa V, Zhang L, Liu W, Qin L, Wan K, Wu X, Wang H, Liu W, Wang B. Molecular Characteristics of Mycobacterium tuberculosis Strains Isolated from Cutaneous Tuberculosis Patients in China. Acta Derm Venereol 2017; 97:472-477. [PMID: 27840887 DOI: 10.2340/00015555-2577] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Cutaneous tuberculosis (CTB) is probably underreported due to difficulties in detection and diagnosis. To address this issue, genotypes of Mycobacterium tuberculosis strains isolated from 30 patients with CTB were mapped at multiple loci, namely, RD105 deletions, spacer oligonucleotides, and Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem Repeats (MIRU-VNTRs). Fifty-eight strains of pulmonary tuberculosis (PTB) were mapped as experimental controls. Drug resistance-associated gene mutations were determined by amplicon sequencing of target regions within 7 genes. Beijing family isolates were the most prevalent strains in CTB and PTB. MIRU-VNTR typing separated the Beijing strains from the non-Beijing strains, and the majority of CTB could be separated from PTB counterparts. Drug resistance determining regions showed only one CTB strain expressing isomazid resistance. Thus, while the CTB strains belonged to the same phylogenetic lineages and sub-lineages as the PTB strains, they differed at the level of several MIRU-VNTRs and in the proportion of drug resistance.
Collapse
Affiliation(s)
- Haiqin Jiang
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing, China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Cui P, Vissa V, Li W, Zhang X, Lin L, Wang H, Liu X, Wu Q, Zong W. Cutaneous Mycobacterium shigaense infection in immunocompetent Woman, China. Emerg Infect Dis 2013; 19:819-20. [PMID: 23697461 PMCID: PMC3647498 DOI: 10.3201/eid1905.121022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
MESH Headings
- China
- DNA, Bacterial/genetics
- DNA, Bacterial/isolation & purification
- DNA, Intergenic/genetics
- DNA, Intergenic/isolation & purification
- Female
- Humans
- Immunocompetence
- Middle Aged
- Mycobacterium/genetics
- Mycobacterium/isolation & purification
- Mycobacterium Infections/diagnosis
- Mycobacterium Infections/immunology
- Mycobacterium Infections/microbiology
- Mycobacterium Infections/pathology
- Polymerase Chain Reaction
- RNA, Ribosomal, 16S/genetics
- RNA, Ribosomal, 16S/isolation & purification
- Skin Diseases, Bacterial/diagnosis
- Skin Diseases, Bacterial/immunology
- Skin Diseases, Bacterial/microbiology
- Skin Diseases, Bacterial/pathology
Collapse
|
8
|
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. Infect Genet Evol 2013; 14:361-8. [PMID: 23291419 PMCID: PMC3668695 DOI: 10.1016/j.meegid.2012.12.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
9
|
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. Infect Genet Evol 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
10
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
11
|
Phetsuksiri B, Srisungngam S, Rudeeaneksin J, Bunchoo S, Lukebua A, Wongtrungkapun R, Paitoon S, Sakamuri RM, Brennan PJ, Vissa V. SNP Genotypes of <i>Mycobacterium leprae</i> Isolates in Thailand and Their Combination with <i>rpoT</i> and TTC Genotyping for Analysis of Leprosy Distribution and Transmission. Jpn J Infect Dis 2012. [DOI: 10.7883/yoken.65.52] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Benjawan Phetsuksiri
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Sopa Srisungngam
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Janisara Rudeeaneksin
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Supranee Bunchoo
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Atchariya Lukebua
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Thailand
| | - Ruch Wongtrungkapun
- Raj Pracha Samasai Institute, Department of Disease Control, Ministry of Public Health, Tailand
| | - Soontara Paitoon
- The Office of Disease Prevention and Control Regional Center 5, Thailand
| | | | | | | |
Collapse
|
12
|
Phetsuksiri B, Srisungngam S, Rudeeaneksin J, Bunchoo S, Lukebua A, Wongtrungkapun R, Paitoon S, Sakamuri RM, Brennan PJ, Vissa V. SNP genotypes of Mycobacterium leprae isolates in Thailand and their combination with rpoT and TTC genotyping for analysis of leprosy distribution and transmission. Jpn J Infect Dis 2012; 65:52-56. [PMID: 22274158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Based on the discovery of three single nucleotide polymorphisms (SNPs) in Mycobacterium leprae, it has been previously reported that there are four major SNP types associated with different geographic regions around the world. Another typing system for global differentiation of M. leprae is the analysis of the variable number of short tandem repeats within the rpoT gene. To expand the analysis of geographic distribution of M. leprae, classified by SNP and rpoT gene polymorphisms, we studied 85 clinical isolates from Thai patients and compared the findings with those reported from Asian isolates. SNP genotyping by PCR amplification and sequencing revealed that all strains like those in Myanmar were SNP type 1 and 3, with the former being predominant, while in Japan, Korea, and Indonesia, the SNP type 3 was found to be more frequent. The pattern of M. leprae distribution in Thailand and Myanmar is quite similar, except that SNP type 2 was not found in Thailand. In addition, the 3-copy hexamer genotype in the rpoT gene is shared among the isolates from these two neighboring countries. On the basis of these two markers, we postulate that M. leprae in leprosy patients from Myanmar and Thailand has a common historical origin. Further differentiation among Thai isolates was possible by assessing copy numbers of the TTC sequence, a more polymorphic microsatellite locus.
Collapse
Affiliation(s)
- Benjawan Phetsuksiri
- National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Tiwanond Road, Nonthaburi, Thailand. benjapsk@health.moph.go.th
| | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Li W, Sakamuri RM, Lyons DE, Orcullo FM, Shinde V, Pena ELD, Maghanoy AA, Mallari IB, Tan EV, Nath I, Brennan PJ, Balagon M, Vissa V. Transmission of dapsone-resistant leprosy detected by molecular epidemiological approaches. Antimicrob Agents Chemother 2011; 55:5384-7. [PMID: 21859943 PMCID: PMC3195063 DOI: 10.1128/aac.05236-11] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Accepted: 08/10/2011] [Indexed: 11/20/2022] Open
Abstract
Drug resistance surveillance identified six untreated leprosy patients in the Philippines with Mycobacterium leprae folP1 mutations which confer dapsone resistance. Five patients share a village of residence; four who carried the mutation, Thr53Val, were also linked by M. leprae variable-number tandem repeat (VNTR) strain types. In India, folP1 mutations were detected in two relapse patients with a history of dapsone treatment. Mutations were not found in the rifampin target gene rpoB. These findings indicate that dapsone resistance is being transmitted.
Collapse
Affiliation(s)
- Wei Li
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Rama M. Sakamuri
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Danielle E. Lyons
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Florenda M. Orcullo
- Leonard Wood Memorial Center for Leprosy Research, Cebu Skin Clinic, Cebu, Philippines
| | | | - Edred Lao Dela Pena
- Leonard Wood Memorial Center for Leprosy Research, Cebu Skin Clinic, Cebu, Philippines
| | - Armi A. Maghanoy
- Leonard Wood Memorial Center for Leprosy Research, Cebu Skin Clinic, Cebu, Philippines
| | - Irene B. Mallari
- Leonard Wood Memorial Center for Leprosy Research, Cebu Skin Clinic, Cebu, Philippines
| | - Esterlina V. Tan
- Leonard Wood Memorial Center for Leprosy Research, Cebu Skin Clinic, Cebu, Philippines
| | - Indira Nath
- Blue Peter Public Health and Research Centre, Hyderabad, India
| | - Patrick J. Brennan
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Marivic Balagon
- Leonard Wood Memorial Center for Leprosy Research, Cebu Skin Clinic, Cebu, Philippines
| | - Varalakshmi Vissa
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado 80523
| |
Collapse
|
14
|
Jensen RW, Rivest J, Li W, Vissa V. DNA fingerprinting of Mycobacterium leprae strains using variable number tandem repeat (VNTR) - fragment length analysis (FLA). J Vis Exp 2011:e3104. [PMID: 21775969 PMCID: PMC3196163 DOI: 10.3791/3104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The study of the transmission of leprosy is particularly difficult since the causative agent, Mycobacterium leprae, cannot be cultured in the laboratory. The only sources of the bacteria are leprosy patients, and experimentally infected armadillos and nude mice. Thus, many of the methods used in modern epidemiology are not available for the study of leprosy. Despite an extensive global drug treatment program for leprosy implemented by the WHO1, leprosy remains endemic in many countries with approximately 250,000 new cases each year.2 The entire M. leprae genome has been mapped3,4 and many loci have been identified that have repeated segments of 2 or more base pairs (called micro- and minisatellites).5 Clinical strains of M. leprae may vary in the number of tandem repeated segments (short tandem repeats, STR) at many of these loci.5,6,7 Variable number tandem repeat (VNTR)5 analysis has been used to distinguish different strains of the leprosy bacilli. Some of the loci appear to be more stable than others, showing less variation in repeat numbers, while others seem to change more rapidly, sometimes in the same patient. While the variability of certain VNTRs has brought up questions regarding their suitability for strain typing7,8,9, the emerging data suggest that analyzing multiple loci, which are diverse in their stability, can be used as a valuable epidemiological tool. Multiple locus VNTR analysis (MLVA)10 has been used to study leprosy evolution and transmission in several countries including China11,12, Malawi8, the Philippines10,13, and Brazil14. MLVA involves multiple steps. First, bacterial DNA is extracted along with host tissue DNA from clinical biopsies or slit skin smears (SSS).10 The desired loci are then amplified from the extracted DNA via polymerase chain reaction (PCR). Fluorescently-labeled primers for 4-5 different loci are used per reaction, with 18 loci being amplified in a total of four reactions.10 The PCR products may be subjected to agarose gel electrophoresis to verify the presence of the desired DNA segments, and then submitted for fluorescent fragment length analysis (FLA) using capillary electrophoresis. DNA from armadillo passaged bacteria with a known number of repeat copies for each locus is used as a positive control. The FLA chromatograms are then examined using Peak Scanner software and fragment length is converted to number of VNTR copies (allele). Finally, the VNTR haplotypes are analyzed for patterns, and when combined with patient clinical data can be used to track distribution of strain types.
Collapse
Affiliation(s)
- Ronald W Jensen
- Department of Microbiology, Immunology and Pathology, Colorado State University, USA
| | | | | | | |
Collapse
|
15
|
Weng XM, Li K, Wen Y, Xing Y, Liu J, Hong BH, Li HY, Vissa V. [Study on the factors influencing steady transmission of leprosy in Qiubei county, China]. Zhonghua Liu Xing Bing Xue Za Zhi 2011; 32:559-564. [PMID: 21781471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
OBJECTIVE To explore the factors influencing the steady transmission of leprosy as indicated by new case detection rate in Qiubei county, Yunnan province, China despite the implementation of MDT for the last 25 years. METHODS Information related to case-finding was collected. ELISA and PCR were applied to detect anti-PGL-1 antibody in sera and Mycobacterium leprae in nasal secretions respectively, in leprosy patients, their household contacts and the general population. M. leprae by PCR was also detected from water in the highly endemic villages. VNTR typing was performed to explore the mode and chain of transmission of M. leprae. RESULTS Prior to 2001, the proportion of new cases detected from the examination of household contacts of leprosy patients was low (number, compared to), while the proportion of patients whose identification was delayed by more than 2 years, was high (number, compared to). Qualities of these two indicators has been improved, along with the improvement of leprosy control program since 2001, but the detection rates has been steady at 4-5/100 000 during 1986 - 2010. The PGL-1 seropositivity rate was 20% - 30% in general population, with the peak rate (30%) detected in the teenage population in the endemic villages. In addition to the fact that M. leprae was detected in nasal secretion from patients, their contacts and from water, the M. leprae VNTR genotypes were found to be highly similar between skin biopsy and nasal secretion in untreated cases. Families with multi-cases were clustered and located in the Northern part of the County, and the genotypes of M. leprae were identical within those families. The percentage of clusters was considerably higher in Northern rather than Southern parts of the County. CONCLUSION Results from this molecular study demonstrated evidence that transmission of leprosy within the families and in the endemic-villages was severe. M. leprae were detected in waters from the endemic villages and others areas which might have a relation to the continued transmission of leprosy.
Collapse
Affiliation(s)
- Xiao-man Weng
- Beijing Tropical Medicine Research Institute, Beijing, China.
| | | | | | | | | | | | | | | |
Collapse
|
16
|
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. Infect Genet Evol 2010; 11:363-74. [PMID: 21129505 DOI: 10.1016/j.meegid.2010.11.014] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| | | | | | | | | |
Collapse
|
17
|
Cardona-castro N, Beltrán J, Ortiz-bernal A, Vissa V. Detection of Mycobacterium leprae DNA in nine-banded armadillos (Dasypus novemcinctus) from the Andean region of Colombia. LEPROSY REV 2009. [DOI: 10.47276/lr.80.4.424] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
18
|
Cardona-Castro N, Beltrán JC, Ortiz-Bernal A, Vissa V. Detection of Mycobacterium leprae DNA in nine-banded armadillos (Dasypus novemcinctus) from the Andean region of Colombia. LEPROSY REV 2009; 80:424-431. [PMID: 20306641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
OBJECTIVE To use DNA detection methodologies to test for M. leprae in nine-banded armadillos inhabiting forested regions located around the cities and towns where leprosy patients have been identified. DESIGN Ear lobe biopsies of 22 nine-banded armadillos were studied during a 2 year period. The biopsies were processed for DNA extraction and amplification by nested polymerase chain reaction (N-PCR) of a fragment of the high copy DNA locus of M. leprae known as R-LEP. RESULTS Nine of the 22 (40.9%) armadillos evaluated showed positive signals for M. leprae. Sequencing confirmed that PCR products were identical to the corresponding region of M. leprae DNA. CONCLUSIONS In Colombia, South America, the consumption of and contact with the nine-banded armadillo (Dasypus novemcinctus) are common, ignoring the fact that this animal can host and be a possible zoonotic reservoir of Mycobacterium leprae, the causal agent of leprosy. This is the first study demonstrating that M. leprae is present in nine-banded armadillos in a region of Colombia using specific DNA detection. The possibility of leprosy transmission due to contact and consumption of armadillo meat or use of blood for therapeutic purposes should be further investigated.
Collapse
Affiliation(s)
- N Cardona-Castro
- Instituto Colombiano de Medicina Tropical-Universidad CES, Cra. 43a No. 52 Sur 99 Sabaneta, Antioquia, Colombia.
| | | | | | | |
Collapse
|
19
|
Gillis T, Vissa V, Matsuoka M, Young S, Richardus JH, Truman R, Hall B, Brennan P, The Ideal Consortium Partners. Characterisation of Short tandem repeats for genotyping Mycobacterium leprae. LEPROSY REV 2009. [DOI: 10.47276/lr.80.3.250] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
20
|
Shinde V, Newton H, Sakamuri RM, Reddy V, Jain S, Joseph A, Gillis T, Nath I, Norman G, Vissa V. VNTR typing of Mycobacterium leprae in South Indian leprosy patients. LEPROSY REV 2009. [DOI: 10.47276/lr.80.3.290] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
21
|
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: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
Affiliation(s)
- Rama Murthy Sakamuri
- Department of Microbiology, Immunology, and Pathology, Colorado State University, 1682 Campus Delivery, Fort Collins, CO 80523, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Xing Y, Liu J, Sakamuri RM, Wang Z, Wen Y, Vissa V, Weng X. VNTR typing studies of Mycobacterium leprae in China: assessment of methods and stability of markers during treatment. LEPROSY REV 2009; 80:261-271. [PMID: 19961099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
OBJECTIVE To evaluate the reliability and feasibility of two methods of multilocus variable number of tandem repeat analysis (MLVA) for strain typing of M. leprae, and to study whether short tandem repeat loci are stable and suitable for epidemiological study of leprosy. METHODS Total DNA was extracted from skin biopsies of 20 new multibacillary (MB) patients from China diagnosed in 2006. To determine the copy numbers of short tandem repeats (STRs) for 13 loci, we amplified each locus individually by PCR, followed by sequence analysis of the amplicons. Separately, the same loci, plus four others were amplified by Multiplex PCRs (MP) using fluorescent primers and the copy number was identified by fragment length analysis (MP-FLA). MLVA was also performed at different times during treatment for a subset of the patients. RESULTS AND CONCLUSIONS Genetic variability of M. leprae in China can be assessed in microsatellite loci. (GTA)9 and (TTC)21 loci are hypervariable, with array sizes of 25 repeat units or more. The expansion of the (GTA)9 locus is a characteristic of some M. leprae isolates in China. A high level of allele concordance was observed between PCR-sequencing and MP-FLA methods. However, MP-FLA method was cost-effective, rapid, high throughput and suitable for strain typing. Five of the 20 isolates of M. leprae were from patients residing in the same township in Qiubei County, Yunnan, and matched closely by MLVA. Three of these patients are family contacts of previously diagnosed patients, with intra-familial strain types being similar, suggesting infections from common sources and transmission chain(s). The VNTR patterns were highly similar in biopsy and slit skin smears (SSS) before treatment, and in the SSS collected at various time points during treatment. Taken together, VNTR strain typing is a useful tool for study of short range transmission in leprosy.
Collapse
Affiliation(s)
- Yan Xing
- 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
| | | | | | | | | | | | | |
Collapse
|
23
|
Shinde V, Newton H, Sakamuri RM, Reddy V, Jain S, Joseph A, Gillis T, Nath I, Norman G, Vissa V. VNTR typing of Mycobacterium leprae in South Indian leprosy patients. LEPROSY REV 2009; 80:290-301. [PMID: 19961102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
OBJECTIVES To study the suitability, stability and diversity of short tandem repeat (STR) genomic markers to elicit strain variation in the Mycobacterium leprae isolates within leprosy patients from Andhra Pradesh and Tamil Nadu states in South India. MATERIALS AND METHODS Slit skin smear (SSS) samples were collected from lesions and various body sites of newly diagnosed leprosy patients. The SSSs from each patient were pooled, except in the case of five patients. Total DNA was extracted from SSS samples. M. leprae STRs were amplified from the DNA either by multiplex PCR (MP) or single PCR methods. The number of repeats for each STR locus (the STR allele) was obtained either by fragment length analysis (FLA) or by DNA sequencing of the PCR amplicons. RESULTS AND CONCLUSION Multiplex PCR minimised the use of DNA and reagents, and together with FLA, was time and cost effective for STR strain typing. After examination of the isolates of South Indian origin at 13 STR loci, it was determined that the alleles for (AC)8b, (GGT)5, 6-3a (rpoT), 21-3, 27-5, and 23-3 were conserved in two study populations. In a family from Andhra Pradesh, the M. leprae STR patterns in two patients were identical in 16 of 18 loci which indicate a common source of infection. Fourteen of 15 STR loci showed no intra-patient variation in the five patients tested in Tamil Nadu. Altogether, these studies indicate the suitability of STR strain typing for assessing short-range transmission chains.
Collapse
Affiliation(s)
- Vidyagouri Shinde
- Blue Peter Research Centre, LEPRA Society, Cherlapally, Hyderabad 501301, India
| | | | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Xing Y, Liu J, Sakamuri RM, Wang Z, Wen Y, Vissa V, Weng X. VNTR typing studies of Mycobacterium leprae in China: Assessment of methods and stability of markers during treatment. LEPROSY REV 2009. [DOI: 10.47276/lr.80.3.261] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
25
|
Srisungnam S, Rudeeaneksin J, Lukebua A, Wattanapokayakit S, Pasadorn S, Mahotarn K, Ajincholapan, Sakamuri RM, Kimura M, Brennan PJ, Phetsuksiri B, Vissa V. Molecular epidemiology of leprosy based on VNTR typing in Thailand. LEPROSY REV 2009. [DOI: 10.47276/lr.80.3.280] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
|
26
|
Cardona-Castro N, Beltrán-Alzate JC, Romero-Montoya IM, Meléndez E, Torres F, Sakamuri RM, Li W, Vissa V. Identification and comparison of Mycobacterium leprae genotypes in two geographical regions of Colombia. LEPROSY REV 2009; 80:316-321. [PMID: 19961104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
OBJECTIVE To evaluate and establish genomic strain typing markers suitable for the identification of transmission patterns of leprosy in different regions of Colombia. DESIGN Patients from Agua de Dios, Barranquilla and Cartagena cities and neighbouring towns were enrolled during 2006-2007. Slit skin smears or biopsies were obtained from newly detected untreated patients, and those undergoing multidrug therapy. DNA was extracted from the clinical samples and tested using 15 different short tandem repeat and three SNP polymorphic markers. RESULTS AND CONCLUSION Differences or similarities between strain types from the northeast (n = 20) and central regions of Colombia (n = 18) were noted. The alleles at two loci, 27-5 and 12-5 were different in the M. leprae in the two regions. The other microsatellite loci may be useful for further intra-population differentiation. There was strong association of 27-5 and 12-5 alleles with the SNP types. The 4-5 combination of alleles was associated with SNP type 3, while the 5-4 combination was mostly associated with SNP type 1, 2 or 4. The SNP type 4 m. leprae isolates were seen in patients in the northeast, but not in the central part.
Collapse
Affiliation(s)
- Nora Cardona-Castro
- Instituto Colombiano de Medicina Tropical (ICMT)--Universidad CES, Cra 43A No. 52 Sur 99. Sabaneta, Antioquia, Colombia.
| | | | | | | | | | | | | | | |
Collapse
|
27
|
Sakamuri RM, Harrison J, Gelber R, Saunderson P, Brennan PJ, Balagon M, Vissa V. A continuation: study and characterisation of Mycobacterium leprae short tandem repeat genotypes and transmission of leprosy in Cebu, Philippines. LEPROSY REV 2009; 80:272-279. [PMID: 19961100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
OBJECTIVE To study the stability and allelic diversity of tandem repeat loci in M. leprae in leprosy patients of Cebu, Philippines, and the suitability of multilocus variable number of tandem repeat (VNTR) analysis (MLVA) typing for detecting transmission. METHODS Seventy newly diagnosed leprosy patients consulting at the Leonard Wood Memorial, Cebu Skin Clinic Total DNA was extracted from slit skin smear (SSS) scrapings of each patient and used for amplification of 13 M. leprae VNTR loci by single locus or multiplex PCR. Number of repeats for each VNTR locus was obtained by DNA sequencing or fragment length analysis methods. Medical, social and geographic details were included in the molecular epidemiology database. RESULTS AND CONCLUSIONS Multiplex PCR (MP) and fragment length analysis (FLA) methods were found to be more efficient and accurate compared to single short tandem repeat (STR) amplification and DNA sequencing. Intra-patient MLVA patterns from four different samples were conserved in the minisatellites, while differences in one or more of the polymorphic and stutter prone microsatellites was observed, in four of five patients. The 13 loci could differentiate M. leprae strains in Cebu, however, MLVA patterns were stable enough during incubation and transmission between individuals within multi-case families. Thus M. leprae MLVA has potential for strain typing and transmission studies in Cebu.
Collapse
|
28
|
Srisungnam S, Rudeeaneksin J, Lukebua A, Wattanapokayakit S, Pasadorn S, Mahotarn K, Sakamuri RM, Kimura M, Brennan PJ, Phetsuksiri B, Vissa V. Molecular epidemiology of leprosy based on VNTR typing in Thailand. LEPROSY REV 2009; 80:280-289. [PMID: 19961101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Recently about 500 new cases of leprosy have been reported each year in Thailand. In addition to a steady rate of new case detection, Thailand is in Southeast Asia where leprosy is endemic in neighbouring countries; therefore, strain differentiation could be useful in tracing origins and routes of infection, and general leprosy surveillance. To identify suitable markers for differentiation of M. leprae strains in different global geographic regions and to determine the applicability of a systematic genotyping method for tracing leprosy transmission, variable nucleotide tandem repeats (VNTRs) of 14 loci were evaluated using DNA extracts from a total of 97 skin biopsies and slit skin smear samples. The alleles per locus ranged from 2-26 providing adequate strain differentiation. Microsatellite loci (GAA)21, (AT)17 are highly polymorphic followed by (GTA)9, (AC)8a, (AC)8b, and (AC)9. The minisatellites 6-7, 21-3 and 27-5 exhibited a limited number of alleles. The repeat of 23-3 showed no polymorphism. Overall, the strain types can be divided into two distinct Thai groups, according to the alleles at the (GGT)5 and 21-3 loci. However, there are no obvious geographical patterns of distribution of VNTR strain types. Closely matched VNTR profiles found in household members of two multi-case families suggested infection through a common source.
Collapse
Affiliation(s)
- Sopa Srisungnam
- Mycobacterial Laboratory, National Institute of Health, Ministry of Public Health, Thailand
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Gillis T, Vissa V, Matsuoka M, Young S, Richardus JH, Truman R, Hall B, Brennan P. Characterisation of short tandem repeats for genotyping Mycobacterium leprae. LEPROSY REV 2009; 80:250-260. [PMID: 19994470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
OBJECTIVE Establish a typing system for Mycobacterium leprae based on polymorphic DNA structures known as short tandem repeats (STR). DESIGN Assess 16 polymorphic STR for sensitivity, specificity and reproducibility in standard assays using reference strains of M. leprae. RESULTS Primers for 16 STR loci were selected based on PCR product size and for their ability to sequence each STR locus from both directions. All primer pairs produced a visible PCR amplicon of appropriate size from PCR reactions containing 10 M. leprae cells. DNA sequences for each STR locus, except (AT) 15, was correctly identified as M. leprae-specific in replicate samples containing 1000 M. leprae using either the forward or reverse PCR primers. Twelve of 13 M. leprae STR loci were stable during passage in heavily infected armadillo tissues over a 5 year and 7 month infection cycle. CONCLUSIONS Certain M. leprae STR provide suitable targets for strain typing with the potential for grouping M. leprae with shared genotypes that may prove useful for establishing linkages between leprosy cases within geographical regions.
Collapse
Affiliation(s)
- Thomas Gillis
- National Hansen's Disease Programs, Baton Rouge, LA 70803, USA.
| | | | | | | | | | | | | | | |
Collapse
|
30
|
Kaur D, Pham H, Larrouy-Maumus G, Rivière M, Vissa V, Guerin ME, Puzo G, Brennan PJ, Jackson M. Initiation of methylglucose lipopolysaccharide biosynthesis in mycobacteria. PLoS One 2009; 4:e5447. [PMID: 19421329 PMCID: PMC2674218 DOI: 10.1371/journal.pone.0005447] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2009] [Accepted: 04/10/2009] [Indexed: 11/19/2022] Open
Abstract
Background Mycobacteria produce two unique families of cytoplasmic polymethylated polysaccharides - the methylglucose lipopolysaccharides (MGLPs) and the methylmannose polysaccharides (MMPs) - the physiological functions of which are still poorly defined. Towards defining the roles of these polysaccharides in mycobacterial physiology, we generated knock-out mutations of genes in their putative biosynthetic pathways. Methodology/Principal Findings We report here on the characterization of the Rv1208 protein of Mycobacterium tuberculosis and its ortholog in Mycobacterium smegmatis (MSMEG_5084) as the enzymes responsible for the transfer of the first glucose residue of MGLPs. Disruption of MSMEG_5084 in M. smegmatis resulted in a dramatic decrease in MGLP synthesis directly attributable to the almost complete abolition of glucosyl-3-phosphoglycerate synthase activity in this strain. Synthesis of MGLPs in the mutant was restored upon complementation with wild-type copies of the Rv1208 gene from M. tuberculosis or MSMEG_5084 from M. smegmatis. Conclusions/Significance This is the first evidence linking Rv1208 to MGLP biosynthesis. Thus, the first step in the initiation of MGLP biosynthesis in mycobacteria has been defined, and subsequent steps can be inferred.
Collapse
Affiliation(s)
- Devinder Kaur
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Ha Pham
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Gérald Larrouy-Maumus
- Département «Mécanismes Moléculaires des Infections Mycobactériennes», Centre National de la Recherche Scientifique (CNRS), Institut de Pharmacologie et Biologie Structurale (UMR 5089), Université de Toulouse III, Toulouse, France
| | - Michel Rivière
- Département «Mécanismes Moléculaires des Infections Mycobactériennes», Centre National de la Recherche Scientifique (CNRS), Institut de Pharmacologie et Biologie Structurale (UMR 5089), Université de Toulouse III, Toulouse, France
| | - Varalakshmi Vissa
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Marcelo E. Guerin
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Germain Puzo
- Département «Mécanismes Moléculaires des Infections Mycobactériennes», Centre National de la Recherche Scientifique (CNRS), Institut de Pharmacologie et Biologie Structurale (UMR 5089), Université de Toulouse III, Toulouse, France
| | - Patrick J. Brennan
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Mary Jackson
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
| |
Collapse
|
31
|
Vissa V. New frontiers in tuberculosis research. Expert Rev Anti Infect Ther 2007; 5:173-5. [PMID: 17402832 DOI: 10.1586/14787210.5.2.173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Varalakshmi Vissa
- Colorado State University, Department of Microbiology, Immunology and Pathology, Fort Collins, CO 80523, USA.
| |
Collapse
|
32
|
Shi L, Berg S, Lee A, Spencer JS, Zhang J, Vissa V, McNeil MR, Khoo KH, Chatterjee D. The Carboxy Terminus of EmbC from Mycobacterium smegmatis Mediates Chain Length Extension of the Arabinan in Lipoarabinomannan. J Biol Chem 2006; 281:19512-26. [PMID: 16687411 DOI: 10.1074/jbc.m513846200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
D-Arabinofurans, attached to either a galactofuran or a lipomannan, are the primary constituents of mycobacterial cell wall, forming the unique arabinogalactan (AG) and lipoarabinomannan (LAM), respectively. Emerging data indicate that the arabinans of AG and LAM are distinguished by virtue of the additional presence of linear termini in LAM, which entails some unknown feature of the EmbC protein for proper synthesis. In common with the two paralogous EmbA and EmbB proteins functionally implicated for the arabinosylation of AG, EmbC is predicted to carry 13 transmembrane spanning helices in an integral N-terminal domain followed by a hydrophilic extracytoplasmic C-terminal domain. To delineate the function of this C-terminal domain, the embC knock-out mutant of Mycobacterium smegmatis was complemented with plasmids expressing truncated embC genes. The expression level of serially truncated EmbC protein thus induced was examined by EmbC-specific peptide antibody, and their functional implications were inferred from ensuing detailed structural analysis of the truncated LAM variants synthesized. Apart from critically showing that the smaller arabinans are mostly devoid of the linear terminal motif, beta-D-Araf(1-->2)-alpha-D-Araf(1-->5)-alpha-D-Araf(1-->5)-alpha-D-Araf, our studies clearly implicate the C-terminal domain of EmbC in the chain extension of LAM. For the first time a full range of arabinan chains as large as 18-22 Araf residues and beyond could be released intact by the use of an endogenous endo-D-arabinanase from M. smegmatis, profiled, and sequenced directly by tandem mass spectrometry. In conjunction with NMR studies, our results unequivocally show that the LAM-specific linear termini are an extension on a well defined inner branched Ara-(18-22) core. This hitherto unrecognized feature not only allows a significant revision of the structural model of LAM-arabinan since its first description a decade ago but also furnishes a probable molecular basis of selectivity in biosynthesis, as conferred by the EmbC protein.
Collapse
Affiliation(s)
- Libin Shi
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Ronning DR, Vissa V, Besra GS, Belisle JT, Sacchettini JC. Mycobacterium tuberculosis antigen 85A and 85C structures confirm binding orientation and conserved substrate specificity. J Biol Chem 2004; 279:36771-7. [PMID: 15192106 DOI: 10.1074/jbc.m400811200] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The maintenance of the highly hydrophobic cell wall is central to the survival of Mycobacterium tuberculosis within its host environment. The antigen 85 proteins (85A, 85B, and 85C) of M. tuberculosis help maintain the integrity of the cell wall 1) by catalyzing the transfer of mycolic acids to the cell wall arabinogalactan and 2) through the synthesis of trehalose dimycolate (cord factor). Additionally, these secreted proteins allow for rapid invasion of alveolar macrophages via direct interactions between the host immune system and the invading bacillus. Here we describe two crystal structures: the structure of antigen 85C co-crystallized with octylthioglucoside as substrate, resolved to 2.0 A, and the crystal structure of antigen 85A, which was solved at a resolution of 2.7 A. The structure of 85C with the substrate analog identifies residues directly involved in substrate binding. Elucidation of the antigen 85A structure, the last of the three antigen 85 homologs to be solved, shows that the active sites of the three antigen 85 proteins are virtually identical, indicating that these share the same substrate. However, in contrast to the high level of conservation within the substrate-binding site and the active site, surface residues disparate from the active site are quite variable, indicating that three antigen 85 enzymes are needed to evade the host immune system.
Collapse
Affiliation(s)
- Donald R Ronning
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA
| | | | | | | | | |
Collapse
|
34
|
Dhiman RK, Schulbach MC, Mahapatra S, Baulard AR, Vissa V, Brennan PJ, Crick DC. Identification of a novel class of omega,E,E-farnesyl diphosphate synthase from Mycobacterium tuberculosis. J Lipid Res 2004; 45:1140-7. [PMID: 15060088 DOI: 10.1194/jlr.m400047-jlr200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We have identified an omega,E,E-farnesyl diphosphate (omega,E,E-FPP) synthase, encoded by the open reading frame Rv3398c, from Mycobacterium tuberculosis that is unique among reported FPP synthases in that it does not contain the type I (eukaryotic) or the type II (eubacterial) omega,E,E-FPP synthase signature motif. Instead, it has a structural motif similar to that of the type I geranylgeranyl diphosphate synthase found in Archaea. Thus, the enzyme represents a novel class of omega,E,E-FPP synthase. Rv3398c was cloned from the M. tuberculosis H37Rv genome and expressed in Mycobacterium smegmatis using a new mycobacterial expression vector (pVV2) that encodes an in-frame N-terminal affinity tag fusion with the protein of interest. The fusion protein was well expressed and could be purified to near homogeneity, allowing facile kinetic analysis of recombinant Rv3398c. Of the potential allylic substrates tested, including dimethylallyl diphosphate, only geranyl diphosphate served as an acceptor for isopentenyl diphosphate. The enzyme has an absolute requirement for divalent cation and has a K(m) of 43 microM for isopentenyl diphosphate and 9.8 microM for geranyl diphosphate and is reported to be essential for the viability of M. tuberculosis.
Collapse
Affiliation(s)
- Rakesh K Dhiman
- Department of Microbiology, Colorado State University, Fort Collins, CO 80523-1677, USA
| | | | | | | | | | | | | |
Collapse
|