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Sharma M, Dwivedi P, Joshi V, Singh P. Novel mutations found in Mycobacterium leprae DNA repair gene nth from central India. J Infect Chemother 2024; 30:531-535. [PMID: 38141720 DOI: 10.1016/j.jiac.2023.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/02/2023] [Accepted: 12/18/2023] [Indexed: 12/25/2023]
Abstract
INTRODUCTION The importance of DNA repair enzymes in maintaining genomic integrity is highlighted by the hypothesis that DNA damage by reactive oxygen/nitrogen species produced inside the host cell is essential for the mutagenesis process. Endonuclease III (Nth), formamidopyrimide (Fpg) and endonuclease VIII (Nei) DNA glycosylases are essential components of the bacterial base excision repair process. Mycobacterium leprae lost both fpg/nei genes during the reductive evolution event and only has the nth (ML2301) gene. This study aims to characterize the mutations in the nth gene of M. leprae strains and explore its correlation with drug-resistance. METHOD A total of 91 M. leprae positive DNA samples extracted from skin biopsy samples of newly diagnosed leprosy patients from NSCB Hospital Jabalpur were assessed for the nth gene as well as drug resistance-associated loci of the rpoB, gyrA and folP1 genes through PCR followed by Sanger sequencing. RESULTS Of these 91 patients, a total of two insertion frameshift mutations, two synonymous and seven nonsynonymous mutations were found in nth in seven samples. Sixteen samples were found to be resistant to ofloxacin and one was found to be dapsone resistant as per the known DRDR mutations. No mutations were found in the rpoB region. Interestingly, none of the nth mutations were identified in the drug-resistant associated samples. CONCLUSION The in-silico structural analysis of the non-synonymous mutations in the Nth predicted five of them were to be deleterious. Our results suggest that the mutations in the nth gene may be potential markers for phylogenetic and epidemiological studies.
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Affiliation(s)
- Mukul Sharma
- ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India
| | - Purna Dwivedi
- ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India; The Maharaja Sayajirao University of Baroda, Vadodara, Gujarat, India
| | - Vandana Joshi
- ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India; School of Biotechnology, Jawaharlal Nehru University, New Delhi, India
| | - Pushpendra Singh
- ICMR-National Institute of Research in Tribal Health, Jabalpur, Madhya Pradesh, India.
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de Souza FG, Silva CS, de Araújo GS, Santana-da-Silva MN, Gobbo AR, da Silva MB, Pinto P, da Costa PF, Salgado CG, Ribeiro-Dos-Santos Â, Cavalcante GC. Mitochondrial variants of complex I genes associated with leprosy clinical subtypes. Sci Rep 2024; 14:6365. [PMID: 38493220 PMCID: PMC10944465 DOI: 10.1038/s41598-024-57191-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 03/15/2024] [Indexed: 03/18/2024] Open
Abstract
Leprosy is a chronic bacterial infection mainly caused by Mycobacterium leprae that primarily affects skin and peripheral nerves. Due to its ability to absorb carbon from the host cell, the bacillus became dependent on energy production, mainly through oxidative phosphorylation. In fact, variations in genes of Complex I of oxidative phosphorylation encoded by mtDNA have been associated with several diseases in humans, including bacterial infections, which are possible influencers in the host response to leprosy. Here, we investigated the presence of variants in the mtDNA genes encoding Complex I regarding leprosy, as well as the analysis of their pathogenicity in the studied cohort. We found an association of 74 mitochondrial variants with either of the polar forms, Pole T (Borderline Tuberculoid) or Pole L (Borderline Lepromatous and Lepromatous) of leprosy. Notably, six variants were exclusively found in both clinical poles of leprosy, including m.4158A>G and m.4248T>C in MT-ND1, m.13650C>A, m.13674T>C, m.12705C>T and m.13263A>G in MT-ND5, of which there are no previous reports in the global literature. Our observations reveal a substantial number of mutations among different groups of leprosy, highlighting a diverse range of consequences associated with mutations in genes across these groups. Furthermore, we suggest that the six specific variants exclusively identified in the case group could potentially play a crucial role in leprosy susceptibility and its clinical differentiation. These variants are believed to contribute to the instability and dysregulation of oxidative phosphorylation during the infection, further emphasizing their significance.
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Affiliation(s)
- Felipe Gouvea de Souza
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Caio S Silva
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Gilderlanio S de Araújo
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Mayara N Santana-da-Silva
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Angélica Rita Gobbo
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Moisés Batista da Silva
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Pablo Pinto
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Patrícia Fagundes da Costa
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Claudio Guedes Salgado
- Laboratório de Dermato-Imunologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Marituba, PA, 67105-290, Brazil
| | - Ândrea Ribeiro-Dos-Santos
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil
| | - Giovanna C Cavalcante
- Laboratório de Genética Humana e Médica, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, PA, 66075-110, Brazil.
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Sisco MC, Brum Fontes AN, Lessmann LC, Rada E, Prado Palacios YY, Vasconcellos SEG, de Waard JH, Suffys PN. Antimicrobial resistance and genotyping of Mycobacterium leprae in Venezuela. FRONTIERS IN TROPICAL DISEASES 2023. [DOI: 10.3389/fitd.2023.1067439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2023] Open
Abstract
Leprosy is a neglected tropical disease that leads to physical disability and social discrimination. The active surveillance of new cases and vigilance for drug resistance can decrease the incidence, and improve the clinical outcomes of people affected by it. We analyzed, with molecular biology techniques, a set of skin biopsy samples from 25 Venezuelan patients. The patients had been diagnosed with leprosy in 2014 and early 2015, and 15 were relapse cases. The samples were tested for molecular drug resistance to dapsone, rifampicin, and fluoroquinolones. In addition, we performed molecular epidemiology analysis through multiple-locus variable-number tandem repeat analysis (MLVA) and single nucleotide polymorphism (SNP) typing. We did not find evidence of drug resistance and 76% of the samples (n = 16) had isolates belonging to SNP type 3. Genotype profiles allowed us to rule out the possibility of re-infection in a patient with persistent symptoms after treatment, as well as that of household transmission in two more patients. Although our sampling is relatively small, very similar or even identical Mycobacterium leprae genotypes were observed in Miranda State. The presence of this cluster is highly suggestive of high rates of local transmission and, in turn, the need to better control this disease. Finally, the copy number distribution of minisatellite 18–8 in a considerable number of SNP type 3 strains strongly suggests the presence of a sublineage of this disease that is particular to Venezuela.
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Nelson GC, Dodrill TN, Fitzpatrick SM. A probable case of leprosy from colonial period St. Vincent and the Grenadines, Southeastern Caribbean. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2022; 36:7-13. [PMID: 34785426 DOI: 10.1016/j.ijpp.2021.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/13/2021] [Accepted: 10/20/2021] [Indexed: 06/13/2023]
Abstract
OBJECTIVE To document and differentially diagnose facial pathology found in an isolated skull from St. Vincent and the Grenadines, southeastern Caribbean. To directly date this individual using radiocarbon dating. MATERIALS Isolated skull recovered from Petite Mustique Island. METHODS Describe facial pathology occurring in this individual and compare with known diseases or disease processes that impact the craniofacial complex. RESULTS Features of the rhinomaxillary syndrome are present, indicating a diagnosis of leprosy. Dating places the time of death to the late 18th or early 19th centuries. CONCLUSIONS Analysis of the rhinomaxillary syndrome produces a diagnosis of early-stage leprosy in an individual that correlates with the apparent attempt to locate a leprosarium on Petite Mustique Island in the first decade of the 19th century. SIGNIFICANCE Location and time corroborate historical records of at least one attempt to locate a leprosarium on Petite Mustique Island. Only directly dated individual with leprosy in the western hemisphere and possibly the earliest yet recorded. LIMITATIONS This is an isolated find that is archaeologically unprovenienced. SUGGESTIONS FOR FURTHER RESEARCH Professional archaeological survey of Petite Mustique.
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Affiliation(s)
- Greg C Nelson
- Department of Anthropology, University of Oregon, Eugene, OR 97403-1218, USA; Museum of Natural and Cultural History, University of Oregon, Eugene, OR, USA.
| | | | - Scott M Fitzpatrick
- Department of Anthropology, University of Oregon, Eugene, OR 97403-1218, USA; Museum of Natural and Cultural History, University of Oregon, Eugene, OR, USA.
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Avanzi C, Singh P, Truman RW, Suffys PN. Molecular epidemiology of leprosy: An update. INFECTION GENETICS AND EVOLUTION 2020; 86:104581. [PMID: 33022427 DOI: 10.1016/j.meegid.2020.104581] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/27/2020] [Accepted: 10/01/2020] [Indexed: 12/27/2022]
Abstract
Molecular epidemiology investigations are notoriously challenging in the leprosy field mainly because the inherent characteristics of the disease as well as its yet uncultivated causative agents, Mycobacterium leprae and M. lepromatosis. Despite significant developments in understanding the biology of leprosy bacilli through genomic approaches, the exact mechanisms of transmission is still unclear and the factors underlying pathological variation of the disease in different patients remain as major gaps in our knowledge about leprosy. Despite these difficulties, the last two decades have seen the development of genotyping procedures based on PCR-sequencing of target loci as well as by the genome-wide analysis of an increasing number of geographically diverse isolates of leprosy bacilli. This has provided a foundation for molecular epidemiology studies that are bringing a better understanding of strain evolution associated with ancient human migrations, and phylogeographical insights about the spread of disease globally. This review discusses the advantages and drawbacks of the main tools available for molecular epidemiological investigations of leprosy and summarizes various methods ranging from PCR-based genotyping to genome-typing techniques. We also describe their main applications in analyzing the short-range and long-range transmission of the disease. Finally, we summarise the current gaps and challenges that remain in the field of molecular epidemiology of leprosy.
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Affiliation(s)
- Charlotte Avanzi
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO, USA; Swiss Tropical and Public Health Institute, Basel, Switzerland; University of Basel, Basel, Switzerland
| | - Pushpendra Singh
- Indian Council of Medical Research - National Institute of Research in Tribal Health, Jabalpur, India
| | - Richard W Truman
- Department of Pathobiological Sciences, Louisiana State University, Baton Rouge, LO, USA
| | - Philip N Suffys
- Laboratory of Molecular Biology Applied to Mycobacteria - Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil.
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Ruiz-Fuentes JL, Rumbaut Castillo R, Hurtado Gascón LDLC, Pastrana F. Leprosy in children: a Cuban experience on leprosy control. BMJ Paediatr Open 2019; 3:e000500. [PMID: 31799450 PMCID: PMC6863670 DOI: 10.1136/bmjpo-2019-000500] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 10/07/2019] [Accepted: 10/09/2019] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Children are believed to be the most vulnerable group to leprosy. Childhood leprosy reflects disease transmission in the community as well as the efficiency of ongoing disease control programmes. In Cuba, leprosy is not a national health problem; however, new childhood leprosy cases are diagnosed every year. OBJECTIVE We summarise the experience of Cuba on childhood leprosy control over the past two decades. RESULTS Between 2000 and 2017, a total of 103 children in Cuba have been diagnosed with leprosy, showing that active transmission of cases remains in 13 of 15 provinces of Cuba. The majority of cases were multibacillary (66%), and 34% were paucibacillary cases. Clinically 60% of children have more than five lesions all over their body. Voluntary reporting was the principal method of case detection. The presence of familial and extrafamilial contact with leprosy cases may be a cause of concern, as it implies continuing transmission of the disease. Only four children had disabilities (one with grade 2 disabilities and three with grade 1 disabilities). A set of national investigations have been developed to intervene in a timely manner. Intervention strategies that combine clinical surveillance and laboratory test could be an option for early detection of childhood leprosy. CONCLUSIONS Early detection of cases due to effective health education campaigns, regular and complete treatment with MDT, and contact tracing may be important in reducing the burden of leprosy in the community.
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Guzmán-Castañeda SJ, Ortega-Vega EL, de la Cuesta-Zuluaga J, Velásquez-Mejía EP, Rojas W, Bedoya G, Escobar JS. Gut microbiota composition explains more variance in the host cardiometabolic risk than genetic ancestry. Gut Microbes 2019; 11:191-204. [PMID: 31311405 PMCID: PMC7053924 DOI: 10.1080/19490976.2019.1634416] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/10/2019] [Accepted: 06/16/2019] [Indexed: 02/03/2023] Open
Abstract
Cardiometabolic affections greatly contribute to the global burden of disease. The susceptibility to obesity, cardiovascular disease, and type-2 diabetes, conditions that add to the cardiometabolic syndrome (CMS), was associated with the ancestral genetic composition and gut microbiota. Studies explicitly testing associations between genetic ancestry and gut microbes are growing. We here examined whether the host genetic ancestry was associated with gut microbiota composition, and distinguished the effects of genetic ancestry and non-genetic factors on human cardiometabolic health. We performed a cross-sectional study with 441 community-dwelling Colombian mestizos from five cities spanning the Andes, Pacific, and Caribbean coasts. We characterized the host genetic ancestry by genotyping 40 ancestry informative markers; characterized gut microbiota through 16S rRNA gene sequencing; assessed diet intake, physical activity, cigarette, and medicament consumption; and measured cardiometabolic outcomes that allowed calculating a CMS risk scale. On average, each individual of our cohort was 67 ± 6% European, 21 ± 5% Native American and 12 ± 5% African. Multivariable-adjusted generalized linear models showed that individuals with higher Native American and African ancestries had increased fasting insulin, body mass index and CMS risk, as assessed by the CMS risk scale. Furthermore, we identified 21 OTUs associated to the host genetic ancestry and 20 to cardiometabolic health. While we highlight novel associations between genetic ancestry and gut microbiota, we found that the effect of intestinal microbes was more likely to explain the variance in CMS risk scale than the contributions of European, Native American and African genetic backgrounds.
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Affiliation(s)
- Sandra J. Guzmán-Castañeda
- Grupo de Investigación en Genética Molecular (GENMOL), Sede de Investigación Universitaria, Universidad de Antioquia, Medellin, Colombia
| | - Esteban L. Ortega-Vega
- Grupo de Investigación en Genética Molecular (GENMOL), Sede de Investigación Universitaria, Universidad de Antioquia, Medellin, Colombia
| | - Jacobo de la Cuesta-Zuluaga
- Vidarium–Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
- Department of Microbiome Science, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Eliana P. Velásquez-Mejía
- Vidarium–Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
| | - Winston Rojas
- Grupo de Investigación en Genética Molecular (GENMOL), Sede de Investigación Universitaria, Universidad de Antioquia, Medellin, Colombia
| | - Gabriel Bedoya
- Grupo de Investigación en Genética Molecular (GENMOL), Sede de Investigación Universitaria, Universidad de Antioquia, Medellin, Colombia
| | - Juan S. Escobar
- Vidarium–Nutrition, Health and Wellness Research Center, Grupo Empresarial Nutresa, Medellin, Colombia
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The arms race between man and Mycobacterium tuberculosis: Time to regroup. INFECTION GENETICS AND EVOLUTION 2018; 66:361-375. [DOI: 10.1016/j.meegid.2017.08.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 12/12/2022]
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Abstract
Humans encounter mycobacterial species due to their ubiquity in different environmental niches. In many individuals, pathogenic mycobacterial species may breach our first-line barrier defenses of the innate immune system and modulate the activation of phagocytes to cause disease of the respiratory tract or the skin and soft tissues, sometimes resulting in disseminated infection. Cutaneous mycobacterial infections may cause a wide range of clinical manifestations, which are divided into four main disease categories: (i) cutaneous manifestations of Mycobacterium tuberculosis infection, (ii) Buruli ulcer caused by Mycobacterium ulcerans and other related slowly growing mycobacteria, (iii) leprosy caused by Mycobacterium leprae and Mycobacterium lepromatosis, and (iv) cutaneous infections caused by rapidly growing mycobacteria. Clinically, cutaneous mycobacterial infections present with widely different clinical presentations, including cellulitis, nonhealing ulcers, subacute or chronic nodular lesions, abscesses, superficial lymphadenitis, verrucous lesions, and other types of findings. Mycobacterial infections of the skin and subcutaneous tissue are associated with important stigma, deformity, and disability. Geography-based environmental exposures influence the epidemiology of cutaneous mycobacterial infections. Cutaneous tuberculosis exhibits different clinical phenotypes acquired through different routes, including via extrinsic inoculation of the tuberculous bacilli and dissemination to the skin from other sites, or represents hypersensitivity reactions to M. tuberculosis infection. In many settings, leprosy remains an important cause of neurological impairment, deformity, limb loss, and stigma. Mycobacterium lepromatosis, a mycobacterial species related to M. leprae, is linked to diffuse lepromatous leprosy of Lucio and Latapí. Mycobacterium ulcerans produces a mycolactone toxin that leads to subcutaneous tissue destruction and immunosuppression, resulting in deep ulcerations that often produce substantial disfigurement and disability. Mycobacterium marinum, a close relative of M. ulcerans, is an important cause of cutaneous sporotrichoid nodular lymphangitic lesions. Among patients with advanced immunosuppression, Mycobacterium kansasii, the Mycobacterium avium-intracellulare complex, and Mycobacterium haemophilum may cause cutaneous or disseminated disease. Rapidly growing mycobacteria, including the Mycobacterium abscessus group, Mycobacterium chelonei, and Mycobacterium fortuitum, are increasingly recognized pathogens in cutaneous infections associated particularly with plastic surgery and cosmetic procedures. Skin biopsies of cutaneous lesions to identify acid-fast staining bacilli and cultures represent the cornerstone of diagnosis. Additionally, histopathological evaluation of skin biopsy specimens may be useful in identifying leprosy, Buruli ulcer, and cutaneous tuberculosis. Molecular assays are useful in some cases. The treatment for cutaneous mycobacterial infections depends on the specific pathogen and therefore requires a careful consideration of antimicrobial choices based on official treatment guidelines.
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Cardona-Pemberthy V, Rendón M, Beltrán JC, Soto-Ospina A, Muñoz-Gomez A, Araque-Marín P, Corredor M, Bedoya G, Cardona-Castro N. Genetic variants, structural, and functional changes of Myelin Protein Zero and Mannose-Binding Lectin 2 protein involved in immune response and its allelic transmission in families of patients with leprosy in Colombia. INFECTION GENETICS AND EVOLUTION 2018; 61:215-223. [DOI: 10.1016/j.meegid.2018.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 03/09/2018] [Accepted: 04/01/2018] [Indexed: 10/17/2022]
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Franco-Paredes C, Rodriguez-Morales AJ. Unsolved matters in leprosy: a descriptive review and call for further research. Ann Clin Microbiol Antimicrob 2016; 15:33. [PMID: 27209077 PMCID: PMC4875741 DOI: 10.1186/s12941-016-0149-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/11/2016] [Indexed: 10/25/2022] Open
Abstract
Leprosy, a chronic mycobacterial infection caused by Mycobacterium leprae, is an infectious disease that has ravaged human societies throughout millennia. This ancestral pathogen causes disfiguring cutaneous lesions, peripheral nerve injury, ostearticular deformity, limb loss and dysfunction, blindness and stigma. Despite ongoing efforts in interrupting leprosy transmission, large numbers of new cases are persistently identified in many endemic areas. Moreover, at the time of diagnosis, most newly identified cases have considerable neurologic disability. Many challenges remain in our understanding of the epidemiology of leprosy including: (a) the precise mode and route of transmission; (b) the socioeconomic, environmental, and behavioral factors that promote its transmission; and
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Affiliation(s)
- Carlos Franco-Paredes
- Infectious Diseases Clinic, Phoebe Putney Memorial Hospital, 507 3rd Avenue, Albany, GA, 31721, USA. .,Hospital Infantil de México, Federico Gómez, Mexico D.F., Mexico.
| | - Alfonso J Rodriguez-Morales
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Pereira, Risaralda, Colombia
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