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Blevins KE, Crane AE, Lum C, Furuta K, Fox K, Stone AC. Evolutionary history of Mycobacterium leprae in the Pacific Islands. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190582. [PMID: 33012236 PMCID: PMC7702798 DOI: 10.1098/rstb.2019.0582] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
As one of the oldest known human diseases, leprosy or Hansen's disease remains a public health concern around the world with over 200 000 new cases in 2018. Most human leprosy cases are caused by Mycobacterium leprae, but a small number of cases are now known to be caused by Mycobacterium lepromatosis, a sister taxon of M. leprae. The global pattern of genomic variation in M. leprae is not well defined. Particularly, in the Pacific Islands, the origins of leprosy are disputed. Historically, it has been argued that leprosy arrived on the islands during nineteenth century colonialism, but some oral traditions and palaeopathological evidence suggest an older introduction. To address this, as well as investigate patterns of pathogen exchange across the Pacific Islands, we extracted DNA from 39 formalin-fixed paraffin-embedded biopsy blocks dating to 1992-2016. Using whole-genome enrichment and next-generation sequencing, we produced nine M. leprae genomes dating to 1998-2015 and ranging from 4-63× depth of coverage. Phylogenetic analyses indicate that these strains belong to basal lineages within the M. leprae phylogeny, specifically falling in branches 0 and 5. The phylogeographical patterning and evolutionary dating analysis of these strains support a pre-modern introduction of M. leprae into the Pacific Islands. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.
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Affiliation(s)
- Kelly E Blevins
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Center for Bioarchaeological Research, Arizona State University, Tempe, AZ, USA
| | - Adele E Crane
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Christopher Lum
- Department of Pathology, John A Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
| | - Kanako Furuta
- Hawaii Pathologists Laboratory, Honolulu, HI 96813, USA
| | - Keolu Fox
- Departments of Anthropology and Global Health, University of California, San Diego, CA, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Center for Bioarchaeological Research, Arizona State University, Tempe, AZ, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 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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Tió-Coma M, Avanzi C, Verhard EM, Pierneef L, van Hooij A, Benjak A, Roy JC, Khatun M, Alam K, Corstjens P, Cole ST, Richardus JH, Geluk A. Genomic Characterization of Mycobacterium leprae to Explore Transmission Patterns Identifies New Subtype in Bangladesh. Front Microbiol 2020; 11:1220. [PMID: 32612587 PMCID: PMC7308449 DOI: 10.3389/fmicb.2020.01220] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 05/13/2020] [Indexed: 01/06/2023] Open
Abstract
Mycobacterium leprae, the causative agent of leprosy, is an unculturable bacterium with a considerably reduced genome (3.27 Mb) compared to homologues mycobacteria from the same ancestry. In 2001, the genome of M. leprae was first described and subsequently four genotypes (1-4) and 16 subtypes (A-P) were identified providing means to study global transmission patterns for leprosy. In order to understand the role of asymptomatic carriers we investigated M. leprae carriage as well as infection in leprosy patients (n = 60) and healthy household contacts (HHC; n = 250) from Bangladesh using molecular detection of the bacterial element RLEP in nasal swabs (NS) and slit skin smears (SSS). In parallel, to study M. leprae genotype distribution in Bangladesh we explored strain diversity by whole genome sequencing (WGS) and Sanger sequencing. In the studied cohort in Bangladesh, M. leprae DNA was detected in 33.3% of NS and 22.2% of SSS of patients with bacillary index of 0 whilst in HHC 18.0% of NS and 12.3% of SSS were positive. The majority of the M. leprae strains detected in this study belonged to genotype 1D (55%), followed by 1A (31%). Importantly, WGS allowed the identification of a new M. leprae genotype, designated 1B-Bangladesh (14%), which clustered separately between the 1A and 1B strains. Moreover, we established that the genotype previously designated 1C, is not an independent subtype but clusters within the 1D genotype. Intraindividual differences were present between the M. leprae strains obtained including mutations in hypermutated genes, suggesting mixed colonization/infection or in-host evolution. In summary, we observed that M. leprae is present in asymptomatic contacts of leprosy patients fueling the concept that these individuals contribute to the current intensity of transmission. Our data therefore emphasize the importance of sensitive and specific tools allowing post-exposure prophylaxis targeted at M. leprae-infected or -colonized individuals.
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Affiliation(s)
- Maria Tió-Coma
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Charlotte Avanzi
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Els M. Verhard
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Louise Pierneef
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Anouk van Hooij
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Andrej Benjak
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Johan Chandra Roy
- Rural Health Program, The Leprosy Mission International Bangladesh, Nilphamari, Bangladesh
| | - Marufa Khatun
- Rural Health Program, The Leprosy Mission International Bangladesh, Nilphamari, Bangladesh
| | - Khorshed Alam
- Rural Health Program, The Leprosy Mission International Bangladesh, Nilphamari, Bangladesh
| | - Paul Corstjens
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Stewart T. Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institut Pasteur, Paris, France
| | - Jan Hendrik Richardus
- Department of Public Health, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Annemieke Geluk
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
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Krismawati H, Oktavian A, Maladan Y, Wahyuni T. Risk factor for <em>Mycobacterium leprae</em> detection in household contacts with leprosy patients: a study in Papua, East Indonesia. MEDICAL JOURNAL OF INDONESIA 2020. [DOI: 10.13181/mji.oa.192962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
BACKGROUND In the era of leprosy eradication, Jayapura is still one of the biggest leprosy pockets in Papua, Indonesia. The trend for leprosy case detection rate has remained relatively stable over recent years. This study was aimed to detect Mycobacterium leprae in household contacts and to evaluate the associated factors with the detection. METHODS This cross-sectional study recruited household contacts of leprosy patients who were diagnosed consecutively from March to August 2015 in Hamadi Point of Care, Jayapura. The leprosy patients were diagnosed using polymerase chain reaction (PCR). For each leprosy patient, up to four household contacts that had no symptom were included. Every household contact received screening through DNA detection of M. leprae extracted from nasal swab specimens and examined using PCR. Factors for bacteria detection included intensity, time duration and number of contacts living together in the same house, and random blood glucose levels were evaluated. Bivariate analysis was used to associate them with M. leprae detection in household contacts. RESULTS From 107 household contacts of 35 patients who had leprosy, M. leprae was detected in 19.6%. Household contacts with leprosy patients for >1 year was a risk factor for detection (OR = 12.45; 95% CI = 1.595–97.20; p = 0.002). Blood glucose (p = 0.444), ethnic (p = 0.456), sleeping proximity to leprosy case (p = 0.468) and relatives (p = 0.518) give no effect to M. leprae detection in household contacts. CONCLUSIONS Among the various risk factors studied, duration of living together with the patient significantly increased the risk of M. leprae transmission.
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WOO EUNJIN, KIM JAEHYUN, LEE WONJOON, CHO HELEN, PAK SUNYOUNG. Syphilitic infection in a pre-modern population from South Korea (19th century AD). ANTHROPOL SCI 2019. [DOI: 10.1537/ase.181122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- EUN JIN WOO
- Department of History, College of Liberal Art, Sejong University, Seoul
| | - JAE-HYUN KIM
- Department of Archaeology and Art History, College of Humanities, Dong-A University, Busan
| | - WON-JOON LEE
- National Forensic Service Seoul Institute, Seoul
| | - HELEN CHO
- Department of Anthropology, Davidson College, Davidson
| | - SUNYOUNG PAK
- Department of Anthropology, College of Social Sciences, Seoul National University, Seoul
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A Talip B, Snelling WJ, Sleator RD, Lowery C, Dooley JSG. A rapid and sensitive system for recovery of nucleic acids from Mycobacteria sp. on archived glass slides. BMC Microbiol 2018; 18:196. [PMID: 30477427 PMCID: PMC6260770 DOI: 10.1186/s12866-018-1335-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Accepted: 11/12/2018] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The field of diagnostics continues to advance rapidly with a variety of novel approaches, mainly dependent upon high technology platforms. Nonetheless much diagnosis, particularly in developing countries, still relies upon traditional methods such as microscopy. Biological material, particularly nucleic acids, on archived glass slides is a potential source of useful information both for diagnostic and epidemiological purposes. There are significant challenges faced when examining archived samples in order that an adequate amount of amplifiable DNA can be obtained. Herein, we describe a model system to detect low numbers of bacterial cells isolated from glass slides using (laser capture microscopy) LCM coupled with PCR amplification of a suitable target. RESULTS Mycobacterium smegmatis was used as a model organism to provide a proof of principle for a method to recover bacteria from a stained sample on a glass slide using a laser capture system. Ziehl-Neelsen (ZN) stained cells were excised and catapulted into tubes. Recovered cells were subjected to DNA extraction and pre-amplified with multiple displacement amplification (MDA). This system allowed a minimum of 30 catapulted cells to be detected following a nested real-time PCR assay, using rpoB specific primers. The combination of MDA and nested real-time PCR resulted in a 30-fold increase in sensitivity for the detection of low numbers of cells isolated using LCM. CONCLUSIONS This study highlights the potential of LCM coupled with MDA as a tool to improve the recovery of amplifiable nucleic acids from archived glass slides. The inclusion of the MDA step was essential to enable downstream amplification. This platform should be broadly applicable to a variety of diagnostic applications and we have used it as a proof of principle with a Mycobacterium sp. model system.
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Affiliation(s)
- Balkis A Talip
- School of Biomedical Sciences, Faculty of Life and Health Sciences, Ulster University, Cromore Road, BT52 1SA, Coleraine, County Londonderry, Northern Ireland.,Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, 84000 Pagoh, Muar, Johor, Malaysia
| | - William J Snelling
- School of Biomedical Sciences, Faculty of Life and Health Sciences, Ulster University, Cromore Road, BT52 1SA, Coleraine, County Londonderry, Northern Ireland
| | - Roy D Sleator
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Cork, Ireland
| | - Colm Lowery
- School of Biomedical Sciences, Faculty of Life and Health Sciences, Ulster University, Cromore Road, BT52 1SA, Coleraine, County Londonderry, Northern Ireland
| | - James S G Dooley
- School of Biomedical Sciences, Faculty of Life and Health Sciences, Ulster University, Cromore Road, BT52 1SA, Coleraine, County Londonderry, Northern Ireland.
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Kasai N, Kondo O, Suzuki K, Aoki Y, Ishii N, Goto M. Quantitative evaluation of maxillary bone deformation by computed tomography in patients with leprosy. PLoS Negl Trop Dis 2018. [PMID: 29522533 PMCID: PMC5862504 DOI: 10.1371/journal.pntd.0006341] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background Facial deformation as a sequela of leprosy is caused not only by a saddle nose but also by regression of the maxilla, as well documented in paleopathological observations of excavated skeletal remains of patients with leprosy. However, maxillary changes in living patients have been evaluated only by the subjective visual grading. Here, we attempted to evaluate maxillary bone deformation in patients with leprosy using three-dimensional computed tomography (3D-CT). Methods Three-dimensional images centered on the maxilla were reconstructed using multiplanar reconstruction methods in former patients with leprosy (n = 10) and control subjects (n = 5); the anterior-posterior length of the maxilla (MA-P) was then measured. The difference between the MA-P of the patients and those of controls was evaluated after compensating for individual skull size. These findings were also compared with those from previous paleopathological studies. Findings Three former patients with lepromatous leprosy showed marked atrophy of the maxilla at the prosthion (-8.6, -11.1 and -17.9 mm) which corresponded with the visual appearance of the maxillary deformity, and these results were consistent with paleopathological findings of excavated skeletal remains. Additionally, the precise bone defects of the maxilla could be individually calculated for accurate reconstructive surgery. Interpretation We have successfully illustrated maxillary bone deformities in living patients with leprosy. This study also confirmed the maxillary regression described in paleopathological studies. The sequelae of leprosy are diverse and include facial deformity. A characteristic facial deformity is saddle nose, and the common clinical approach to this facial deformity has been rhinoplasty. Paleopathological studies from excavated skeletal remains have revealed that leprosy also causes deformation of the maxillary bone, which supports the external nose; however, these changes have not been evaluated in living patients with leprosy. In this study, we reconstructed three-dimensional and stereoscopic images of the cranium from CT scan data and evaluated maxillary deformities both qualitatively and quantitatively. Out of the ten former patients with leprosy, three had severe deformity of the maxilla including: atrophy of the anterior nasal spine, resorption of the medial part of the alveolar process, loss of sharpness of the piriform aperture margins, and atrophy of the nasal turbinate and the septum. These changes were consistent with previous findings from paleopathological studies. We also developed a novel method for measuring the anterior-posterior length of the maxilla using 3D-CT images, with compensation for individual differences in cranial size. The calculated values are indicative of the severity of the maxillary defects as well as the thickness of bone that needs to be reconstructed to correct the deformed maxilla.
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Affiliation(s)
- Norio Kasai
- Department of Otolaryngology, National Sanatorium Oku-Komyoen, Setouchi City, Okayama, Japan
- Department of Otolaryngology, National Sanatorium Nagashima-Aiseien, Setouchi City, Okayama, Japan
| | - Osamu Kondo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Koichi Suzuki
- Department of Clinical Laboratory Science, Faculty of Medical Technology, Teikyo University, Itabashi-ku, Tokyo, Japan
- Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Yoshinori Aoki
- Department of Otolaryngology, National Sanatorium Oku-Komyoen, Setouchi City, Okayama, Japan
| | - Norihisa Ishii
- Leprosy Research Center, National Institute of Infectious Diseases, Higashimurayama, Tokyo, Japan
| | - Masamichi Goto
- National Sanatorium Hoshizuka-Keiaien, Kanoya, Kagoshima, Japan
- * E-mail:
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Positive Diagnosis of Ancient Leprosy and Tuberculosis Using Ancient DNA and Lipid Biomarkers. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9040046] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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9
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Staphylococcus aureus Sequences from Osteomyelitic Specimens of a Pathological Bone Collection from Pre-Antibiotic Times. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9040043] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Forst J, Brown TA. Inability of 'Whole Genome Amplification' to Improve Success Rates for the Biomolecular Detection of Tuberculosis in Archaeological Samples. PLoS One 2016; 11:e0163031. [PMID: 27654468 PMCID: PMC5031403 DOI: 10.1371/journal.pone.0163031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 09/01/2016] [Indexed: 11/30/2022] Open
Abstract
We assessed the ability of whole genome amplification (WGA) to improve the efficiency of downstream polymerase chain reactions (PCRs) directed at ancient DNA (aDNA) of members of the Mycobacterium tuberculosis complex (MTBC). Using extracts from a variety of bones and a tooth from human skeletons with or without lesions indicative of tuberculosis, from multiple time periods, we obtained inconsistent results. We conclude that WGA does not provide any advantage in studies of MTBC aDNA. The sporadic nature of our results are probably due to the fact that WGA is itself a PCR-based procedure which, although designed to deal with fragmented DNA, might be inefficient with the low concentration of templates in an aDNA extract. As such, WGA is subject to similar, if not the same, restrictions as PCR when applied to aDNA.
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Affiliation(s)
- Jannine Forst
- Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, Manchester, United Kingdom
| | - Terence A. Brown
- Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, Manchester, United Kingdom
- * E-mail:
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Luo Y, Degang Y, Ohtsuka M, Ishido Y, Ishii N, Suzuki K. Detection of Mycobacterium ulcerans subsp. shinshuense DNA from a water channel in familial Buruli ulcer cases in Japan. Future Microbiol 2016; 10:461-9. [PMID: 25865187 DOI: 10.2217/fmb.14.152] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To determine if Mycobacterium ulcerans subsp. shinshuense is present in the common living environment in a case of familial concurrent occurrence of Buruli ulcer in Japan. MATERIALS & METHODS Environmental samples were collected primarily from a water channel in the patient's residence. A combination of whole-genome amplification, touchdown PCR and DNA sequencing was used to detect M. ulcerans subsp. shinshuense DNA. RESULTS M. ulcerans subsp. shinshuense DNA was detected in a crayfish sampled in July, but not in other samples including a crayfish sampled in October. CONCLUSION These findings support an association between contaminated aquatic environments and Buruli ulcer in Japan. The data also suggest dynamic seasonal appearance of the pathogen in the environment may contribute to the seasonal variation of Buruli ulcer occurrence in Japan.
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Affiliation(s)
- Yuqian Luo
- Leprosy Research Center, National Institute of Infectious Diseases, 4-2-1 Aoba-cho, Higashimurayama-shi, Tokyo 189-0002, Japan
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Simón M, Montiel R, Smerling A, Solórzano E, Díaz N, Álvarez-Sandoval BA, Jiménez-Marín AR, Malgosa A. Molecular analysis of ancient caries. Proc Biol Sci 2015; 281:rspb.2014.0586. [PMID: 25056622 DOI: 10.1098/rspb.2014.0586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
An 84 base pair sequence of the Streptococcus mutans virulence factor, known as dextranase, has been obtained from 10 individuals from the Bronze Age to the Modern Era in Europe and from before and after the colonization in America. Modern samples show four polymorphic sites that have not been found in the ancient samples studied so far. The nucleotide and haplotype diversity of this region have increased over time, which could be reflecting the footprint of a population expansion. While this segment has apparently evolved according to neutral evolution, we have been able to detect one site that is under positive selection pressure both in present and past populations. This study is a first step to study the evolution of this microorganism, analysed using direct evidence obtained from ancient remains.
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Affiliation(s)
- Marc Simón
- Unitat d'Antropologia Biològica, Department of Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Spain
| | - Rafael Montiel
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, CINVESTAV-IPN. Km. 9.6 Libramiento Norte Carretera Irapuato - León, Irapuato, Guanajuato, Mexico
| | - Andrea Smerling
- Unitat d'Antropologia Biològica, Department of Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Spain
| | - Eduvigis Solórzano
- Unitat d'Antropologia Biològica, Department of Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Spain
| | - Nancy Díaz
- Unitat d'Antropologia Biològica, Department of Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Spain
| | - Brenda A Álvarez-Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, CINVESTAV-IPN. Km. 9.6 Libramiento Norte Carretera Irapuato - León, Irapuato, Guanajuato, Mexico
| | - Andrea R Jiménez-Marín
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, CINVESTAV-IPN. Km. 9.6 Libramiento Norte Carretera Irapuato - León, Irapuato, Guanajuato, Mexico
| | - Assumpció Malgosa
- Unitat d'Antropologia Biològica, Department of Biologia Animal, Biologia Vegetal i Ecologia, Universitat Autònoma de Barcelona, Spain
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Mendum TA, Schuenemann VJ, Roffey S, Taylor GM, Wu H, Singh P, Tucker K, Hinds J, Cole ST, Kierzek AM, Nieselt K, Krause J, Stewart GR. Mycobacterium leprae genomes from a British medieval leprosy hospital: towards understanding an ancient epidemic. BMC Genomics 2014; 15:270. [PMID: 24708363 PMCID: PMC4234520 DOI: 10.1186/1471-2164-15-270] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 04/03/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Leprosy has afflicted humankind throughout history leaving evidence in both early texts and the archaeological record. In Britain, leprosy was widespread throughout the Middle Ages until its gradual and unexplained decline between the 14th and 16th centuries. The nature of this ancient endemic leprosy and its relationship to modern strains is only partly understood. Modern leprosy strains are currently divided into 5 phylogenetic groups, types 0 to 4, each with strong geographical links. Until recently, European strains, both ancient and modern, were thought to be exclusively type 3 strains. However, evidence for type 2 strains, a group normally associated with Central Asia and the Middle East, has recently been found in archaeological samples in Scandinavia and from two skeletons from the medieval leprosy hospital (or leprosarium) of St Mary Magdalen, near Winchester, England. RESULTS Here we report the genotypic analysis and whole genome sequencing of two further ancient M. leprae genomes extracted from the remains of two individuals, Sk14 and Sk27, that were excavated from 10th-12th century burials at the leprosarium of St Mary Magdalen. DNA was extracted from the surfaces of bones showing osteological signs of leprosy. Known M. leprae polymorphisms were PCR amplified and Sanger sequenced, while draft genomes were generated by enriching for M. leprae DNA, and Illumina sequencing. SNP-typing and phylogenetic analysis of the draft genomes placed both of these ancient strains in the conserved type 2 group, with very few novel SNPs compared to other ancient or modern strains. CONCLUSIONS The genomes of the two newly sequenced M. leprae strains group firmly with other type 2F strains. Moreover, the M. leprae strain most closely related to one of the strains, Sk14, in the worldwide phylogeny is a contemporaneous ancient St Magdalen skeleton, vividly illustrating the epidemic and clonal nature of leprosy at this site. The prevalence of these type 2 strains indicates that type 2F strains, in contrast to later European and associated North American type 3 isolates, may have been the co-dominant or even the predominant genotype at this location during the 11th century.
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Affiliation(s)
- Tom A Mendum
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, GU2 7XH Guildford, UK
| | - Verena J Schuenemann
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstr 23, 72070 Tübingen, Germany
| | - Simon Roffey
- Department of Archaeology, University of Winchester, Winchester, UK
| | - G Michael Taylor
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, GU2 7XH Guildford, UK
| | - Huihai Wu
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, GU2 7XH Guildford, UK
| | - Pushpendra Singh
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Katie Tucker
- Department of Archaeology, University of Winchester, Winchester, UK
| | - Jason Hinds
- Bacterial Microarray Group, Division of Cellular and Molecular Medicine, St. George’s, University of London, Cranmer Terrace, London, UK
| | - Stewart T Cole
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Andrzej M Kierzek
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, GU2 7XH Guildford, UK
| | - Kay Nieselt
- Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany
| | - Johannes Krause
- Bacterial Microarray Group, Division of Cellular and Molecular Medicine, St. George’s, University of London, Cranmer Terrace, London, UK
| | - Graham R Stewart
- Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, GU2 7XH Guildford, UK
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14
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Suzuki K, Saso A, Hoshino K, Sakurai J, Tanigawa K, Luo Y, Ishido Y, Mori S, Hirata K, Ishii N. Paleopathological evidence and detection of Mycobacterium leprae DNA from archaeological skeletal remains of Nabe-kaburi (head-covered with iron pots) burials in Japan. PLoS One 2014; 9:e88356. [PMID: 24516638 PMCID: PMC3917912 DOI: 10.1371/journal.pone.0088356] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 01/11/2014] [Indexed: 11/18/2022] Open
Abstract
The Nabe-kaburi is a unique burial method, the purpose of which is shrouded in mystery. The burials were performed during the 15th to 18th centuries in eastern Japan, and involved covering the heads of the deceased with iron pots or mortars. The identification of leprosy-specific osteological lesions among some of the excavated remains has led to the suggestion that Nabe-kaburi burials were a reflection of the social stigma against certain infectious diseases, such as leprosy, tuberculosis or syphilis. However, molecular evidence for the presence of disease has been lacking. The goal of this study was to detect Mycobacterium leprae (M. leprae) DNA in archaeological human skeletal remains from Nabe-kaburi burials. The paleopathological data from three Nabe-kaburi burials were re-evaluated before small samples were taken from affected and control areas. DNA was extracted and used as a template to target the M. leprae-specific DNA using a combination of whole genome amplification, PCR analysis and DNA sequencing. M. leprae DNA fragments were detected in the two sets of skeletal remains that had also shown paleopathological evidence of leprosy. These findings provide definitive evidence that some of the Nabe-kaburi burials were performed for people affected by leprosy. Demonstration of the presence of M. leprae DNA, combined with archeological and anthropological examinations, will aid in solving the mystery of why Nabe-kaburi burials were performed in medieval Japan.
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Affiliation(s)
- Koichi Suzuki
- Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
- * E-mail:
| | - Aiko Saso
- The University Museum, The University of Tokyo, Tokyo, Japan
- Department of Biological Science, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Keigo Hoshino
- Department of Anatomy, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Junya Sakurai
- Faculty of Policy Management, Shobi University, Kawagoe, Japan
| | - Kazunari Tanigawa
- Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuqian Luo
- Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yuko Ishido
- Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Shuichi Mori
- Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Kazuaki Hirata
- Department of Anatomy, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Norihisa Ishii
- Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
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15
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Comprehensive analysis of prokaryotes in environmental water using DNA microarray analysis and whole genome amplification. Pathogens 2013; 2:591-605. [PMID: 25437334 PMCID: PMC4235703 DOI: 10.3390/pathogens2040591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 10/16/2013] [Accepted: 10/24/2013] [Indexed: 11/28/2022] Open
Abstract
The microflora in environmental water consists of a high density and diversity of bacterial species that form the foundation of the water ecosystem. Because the majority of these species cannot be cultured in vitro, a different approach is needed to identify prokaryotes in environmental water. A novel DNA microarray was developed as a simplified detection protocol. Multiple DNA probes were designed against each of the 97,927 sequences in the DNA Data Bank of Japan and mounted on a glass chip in duplicate. Evaluation of the microarray was performed using the DNA extracted from one liter of environmental water samples collected from seven sites in Japan. The extracted DNA was uniformly amplified using whole genome amplification (WGA), labeled with Cy3-conjugated 16S rRNA specific primers and hybridized to the microarray. The microarray successfully identified soil bacteria and environment-specific bacteria clusters. The DNA microarray described herein can be a useful tool in evaluating the diversity of prokaryotes and assessing environmental changes such as global warming.
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16
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Anastasiou E, Mitchell PD. Palaeopathology and genes: investigating the genetics of infectious diseases in excavated human skeletal remains and mummies from past populations. Gene 2013; 528:33-40. [PMID: 23792062 DOI: 10.1016/j.gene.2013.06.017] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 05/23/2013] [Accepted: 06/01/2013] [Indexed: 01/11/2023]
Abstract
The aim of this paper is to review the use of genetics in palaeomicrobiology, and to highlight the importance of understanding past diseases. Palaeomicrobiology is the study of disease pathogens in skeletal and mummified remains from archaeological contexts. It has revolutionarised our understanding of health in the past by enabling a deeper knowledge of the origins and evolution of many diseases that have shaped us as a species. Bacterial diseases explored include tuberculosis, leprosy, bubonic plague, typhoid, syphilis, endemic and epidemic typhus, trench fever, and Helicobacter pylori. Viral diseases discussed include influenza, hepatitis B, human papilloma virus (HPV), human T-cell lymphotrophic virus (HTLV-1) and human immunodeficiency virus (HIV). Parasitic diseases investigated include malaria, leishmaniasis, Chagas' disease, roundworm, whipworm, pinworm, Chinese liver fluke, fleas and lice. Through a better understanding of disease origins and their evolution, we can place into context how many infectious diseases are changing over time, and so help us estimate how they may change in the future.
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Affiliation(s)
- Evilena Anastasiou
- Division of Biological Anthropology, Department of Archaeology and Anthropology, University of Cambridge, The Henry Wellcome Building, Fitzwilliam Street, Cambridge CB2 1QH, UK
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17
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Taylor GM, Tucker K, Butler R, Pike AWG, Lewis J, Roffey S, Marter P, Lee OYC, Wu HHT, Minnikin DE, Besra GS, Singh P, Cole ST, Stewart GR. Detection and strain typing of ancient Mycobacterium leprae from a medieval leprosy hospital. PLoS One 2013; 8:e62406. [PMID: 23638071 PMCID: PMC3640063 DOI: 10.1371/journal.pone.0062406] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Accepted: 03/21/2013] [Indexed: 11/29/2022] Open
Abstract
Nine burials excavated from the Magdalen Hill Archaeological Research Project (MHARP) in Winchester, UK, showing skeletal signs of lepromatous leprosy (LL) have been studied using a multidisciplinary approach including osteological, geochemical and biomolecular techniques. DNA from Mycobacterium leprae was amplified from all nine skeletons but not from control skeletons devoid of indicative pathology. In several specimens we corroborated the identification of M. leprae with detection of mycolic acids specific to the cell wall of M. leprae and persistent in the skeletal samples. In five cases, the preservation of the material allowed detailed genotyping using single-nucleotide polymorphism (SNP) and multiple locus variable number tandem repeat analysis (MLVA). Three of the five cases proved to be infected with SNP type 3I-1, ancestral to contemporary M. leprae isolates found in southern states of America and likely carried by European migrants. From the remaining two burials we identified, for the first time in the British Isles, the occurrence of SNP type 2F. Stable isotope analysis conducted on tooth enamel taken from two of the type 3I-1 and one of the type 2F remains revealed that all three individuals had probably spent their formative years in the Winchester area. Previously, type 2F has been implicated as the precursor strain that migrated from the Middle East to India and South-East Asia, subsequently evolving to type 1 strains. Thus we show that type 2F had also spread westwards to Britain by the early medieval period.
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Affiliation(s)
- G Michael Taylor
- Department of Microbial and Cellular Science, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, United Kingdom.
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18
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Mori S, Yotsu RR, Suzuki K, Makino M, Ishii N. Present situation of leprosy in Japan, 2006–2010: Analysis of drug resistance in new registered and relapsed cases by molecular biological methods. J Dermatol Sci 2012; 67:192-4. [DOI: 10.1016/j.jdermsci.2012.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Revised: 04/25/2012] [Accepted: 05/08/2012] [Indexed: 11/30/2022]
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19
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Suzuki K, Akama T, Kawashima A, Yoshihara A, Yotsu RR, Ishii N. Current status of leprosy: epidemiology, basic science and clinical perspectives. J Dermatol 2011; 39:121-9. [PMID: 21973237 DOI: 10.1111/j.1346-8138.2011.01370.x] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Leprosy has affected humans for millennia and remains an important health problem worldwide, as evidenced by nearly 250 000 new cases detected every year. It is a chronic infectious disorder, caused by Mycobacterium leprae, that primarily affects the skin and peripheral nerves. Recent advances in basic science have improved our knowledge of the disease. Variation in the cellular immune response is the basis of a range of clinical manifestations. The introduction of multidrug therapy has significantly contributed to a decrease in the prevalence of the disease. However, leprosy control activities, including monitoring and prevention programs, must be maintained.
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Affiliation(s)
- Koichi Suzuki
- Leprosy Research Center, National Institute of Infectious Diseases Department of Dermatology, National Center for Global Health and Medicine, Tokyo, Japan.
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20
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Singh P, Cole ST. Mycobacterium leprae: genes, pseudogenes and genetic diversity. Future Microbiol 2011; 6:57-71. [PMID: 21162636 DOI: 10.2217/fmb.10.153] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Leprosy, which has afflicted human populations for millenia, results from infection with Mycobacterium leprae, an unculturable pathogen with an exceptionally long generation time. Considerable insight into the biology and drug resistance of the leprosy bacillus has been obtained from genomics. M. leprae has undergone reductive evolution and pseudogenes now occupy half of its genome. Comparative genomics of four different strains revealed remarkable conservation of the genome (99.995% identity) yet uncovered 215 polymorphic sites, mainly single nucleotide polymorphisms, and a handful of new pseudogenes. Mapping these polymorphisms in a large panel of strains defined 16 single nucleotide polymorphism-subtypes that showed strong geographical associations and helped retrace the evolution of M. leprae.
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Affiliation(s)
- Pushpendra Singh
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Station 19, CH-1015 Lausanne, Switzerland
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21
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Taylor GM, Donoghue HD. Multiple loci variable number tandem repeat (VNTR) analysis (MLVA) of Mycobacterium leprae isolates amplified from European archaeological human remains with lepromatous leprosy. Microbes Infect 2011; 13:923-9. [PMID: 21658464 DOI: 10.1016/j.micinf.2011.05.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 05/06/2011] [Accepted: 05/10/2011] [Indexed: 11/29/2022]
Abstract
Molecular typing methods based on polymorphisms in single nucleotides and short tandem repeat motifs have been developed as epidemiological typing tools for Mycobacterium leprae. We have used a variable number tandem repeat method based on three variable loci to identify strain variation in archaeological cases of lepromatous leprosy. The panel of polymorphic loci used revealed unique profiles in five cases of leprosy, including those with identical SNP type and subtype. These were also different from profiles of three previously studied lepromatous skeletons. Whilst examination with SNP typing provides evidence for disease origins, dissemination and phylogeny, tandem repeat typing may be useful for studying cases from within a defined area or community where SNP types may be identical due to geographical constraints. We envisage the technique may be useful in studying contemporaneous burials such as those associated with leprosaria and will prove invaluable in authentication of ancient DNA analyses.
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Affiliation(s)
- G Michael Taylor
- Department of Microbial Sciences, Faculty of Health and Medical Sciences, AW Building, University of Surrey, Guildford, Surrey GU27TE, UK.
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22
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Tsangaras K, Greenwood AD. Museums and disease: using tissue archive and museum samples to study pathogens. Ann Anat 2011; 194:58-73. [PMID: 21641784 DOI: 10.1016/j.aanat.2011.04.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Revised: 04/06/2011] [Accepted: 04/06/2011] [Indexed: 11/28/2022]
Abstract
Molecular studies of archival and fossil samples have traditionally focused on the nucleic acids derived from the host species. However, there has recently been an increase in ancient DNA research on the identification and characterization of infectious agents within the hosts. The study of pathogens from the past provides great opportunities for discovering the causes of historical infection events, characterizing host-microorganism co-evolution and directly investigating the evolution of specific pathogens. Several research teams have been able to isolate and characterize a variety of different bacterial, parasite and viral microorganisms. However, this emerging field is not without obstacles. The diagenetic processes that make ancient DNA research generally difficult are also impediments to ancient pathogen research and perhaps more so given that their DNA may represent an even rarer proportion of the remaining nucleic acids in a fossil sample than host DNA. However, studies performed under controlled conditions and following stringent ancient DNA protocols can and have yielded reliable and often surprising results. This article reviews the advantages, problems, and failures of ancient microbiological research.
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