1
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Refrégier G, Sola C, Guyeux C. Unexpected diversity of CRISPR unveils some evolutionary patterns of repeated sequences in Mycobacterium tuberculosis. BMC Genomics 2020; 21:841. [PMID: 33256602 PMCID: PMC7708916 DOI: 10.1186/s12864-020-07178-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 10/22/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Diversity of the CRISPR locus of Mycobacterium tuberculosis complex has been studied since 1997 for molecular epidemiology purposes. By targeting solely the 43 spacers present in the two first sequenced genomes (H37Rv and BCG), it gave a biased idea of CRISPR diversity and ignored diversity in the neighbouring cas-genes. RESULTS We set up tailored pipelines to explore the diversity of CRISPR-cas locus in Short Reads. We analyzed data from a representative set of 198 clinical isolates as evidenced by well-characterized SNPs. We found a relatively low diversity in terms of spacers: we recovered only the 68 spacers that had been described in 2000. We found no partial or global inversions in the sequences, letting always the Direct Variant Repeats (DVR) in the same order. In contrast, we found an unexpected diversity in the form of: SNPs in spacers and in Direct Repeats, duplications of various length, and insertions at various locations of the IS6110 insertion sequence, as well as blocks of DVR deletions. The diversity was in part specific to lineages. When reconstructing evolutionary steps of the locus, we found no evidence for SNP reversal. DVR deletions were linked to recombination between IS6110 insertions or between Direct Repeats. CONCLUSION This work definitively shows that CRISPR locus of M. tuberculosis did not evolve by classical CRISPR adaptation (incorporation of new spacers) since the last most recent common ancestor of virulent lineages. The evolutionary mechanisms that we discovered could be involved in bacterial adaptation but in a way that remains to be identified.
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Affiliation(s)
- Guislaine Refrégier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, cedex, 91198, Gif-sur-Yvette, France.
| | - Christophe Sola
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, cedex, 91198, Gif-sur-Yvette, France.
| | - Christophe Guyeux
- FEMTO-ST Institute, UMR 6174 CNRS, DISC Computer Science Department, Univ. Bourgogne Franche-Comté (UBFC), 16 Route de Gray, 25000, Besançon, France
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2
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Comin J, Chaure A, Cebollada A, Ibarz D, Viñuelas J, Vitoria MA, Iglesias MJ, Samper S. Investigation of a rapidly spreading tuberculosis outbreak using whole-genome sequencing. INFECTION GENETICS AND EVOLUTION 2020; 81:104184. [PMID: 31931260 DOI: 10.1016/j.meegid.2020.104184] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 12/17/2019] [Accepted: 01/06/2020] [Indexed: 12/01/2022]
Abstract
This paper describes the application of whole-genome sequencing (WGS) to investigate an outbreak of Mycobacterium tuberculosis occurring in Aragon, Spain, where strains have been submitted to genotyping since 2004. The responsible outbreak strain appeared in our region first in 2014 and it spread to 14 patients in the following three years. WGS found low variability between the isolates with none of the SNPs differences detected more than once, all of which were attributed to a recent transmission. Although two ambiguous bases linked two cases with those who presented the SNP in the same position, the establishment of a definitive transmission route was not possible. The epidemiological data supported the existence of a super-spreader, probably responsible for the majority of the cases involved since there was a two-year delay in diagnoses among cases. This fact would also help explaining the low variability found. The index case was not identified, possibly because it was not diagnosed in Aragon. In addition WGS characterised the strain as a Linage 4.3.3/LAM family and corroborated the susceptibility to anti-tuberculosis drugs observed by the clinical laboratories. This work shows the need to have epidemiological data to support the genomic data in order to clarify the evolution of tuberculosis outbreaks.
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Affiliation(s)
- Jessica Comin
- Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain
| | | | | | | | - Jesús Viñuelas
- Hospital Universitario Miguel Servet, Zaragoza, Spain; Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica, Madrid, Spain
| | - María Asunción Vitoria
- Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain; Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica, Madrid, Spain
| | - María José Iglesias
- Universidad de Zaragoza, Zaragoza, Spain; CIBER de enfermedades respiratorias, Madrid, Spain; Fundación IIS Aragón, Zaragoza, Spain
| | - Sofía Samper
- Instituto Aragonés de Ciencias de la Salud, Zaragoza, Spain; CIBER de enfermedades respiratorias, Madrid, Spain; Fundación IIS Aragón, Zaragoza, Spain.
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3
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Benítez-Guzmán A, Esquivel-Solís H, Romero-Torres C, Arriaga-Díaz C, Gutiérrez-Pabello JA. Genetically Related Mycobacterium bovis Strains Displayed Differential Intracellular Growth in Bovine Macrophages. Vet Sci 2019; 6:vetsci6040081. [PMID: 31635257 PMCID: PMC6958473 DOI: 10.3390/vetsci6040081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/14/2019] [Accepted: 10/17/2019] [Indexed: 01/30/2023] Open
Abstract
Molecular typing of bacterial isolates provides a powerful approach for distinguishing Mycobacterium bovis (M. bovis) genotypes. It is known that M. bovis strain virulence plays a role in prevalence and spread of the disease, suggesting that strain virulence and prevailing genotypes are associated. However, it is not well understood whether strain virulence correlates with particular genotypes. In this study, we assessed the in vitro intracellular growth of 18 M. bovis isolates in bovine macrophages as an indicator of bacterial virulence and sought a relationship with the genotype identified by spoligotyping. We found 14 different spoligotypes—11 were already known and three spoligotypes had never been reported before. We identified 2 clusters that were phylogenetically related, containing 10 and 6 strains, respectively, and 2 orphan strains. Intracellular growth and phagocytic rates of 18 M. bovis strains were heterogeneous. Our results suggest that M. bovis intracellular growth and phagocytosis are independent of the bacterial lineage identified by spoligotyping.
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Affiliation(s)
- Alejandro Benítez-Guzmán
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico.
| | - Hugo Esquivel-Solís
- Biotecnología Médica y Farmacéutica, Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco (CIATEJ), Guadalajara 44270, Mexico.
| | - Cecilia Romero-Torres
- Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, CENID Microbiología, Ciudad de México 05110, Mexico.
| | - Camila Arriaga-Díaz
- Instituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias, CENID Microbiología, Ciudad de México 05110, Mexico.
| | - José A Gutiérrez-Pabello
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad de México 04510, Mexico.
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4
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Transposition mechanism, molecular characterization and evolution of IS6110, the specific evolutionary marker of Mycobacterium tuberculosis complex. Mol Biol Rep 2016; 44:25-34. [DOI: 10.1007/s11033-016-4084-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 09/16/2016] [Indexed: 10/20/2022]
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5
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Akinola RO, Mazandu GK, Mulder NJ. A Quantitative Approach to Analyzing Genome Reductive Evolution Using Protein-Protein Interaction Networks: A Case Study of Mycobacterium leprae. Front Genet 2016; 7:39. [PMID: 27066064 PMCID: PMC4809885 DOI: 10.3389/fgene.2016.00039] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2015] [Accepted: 03/08/2016] [Indexed: 01/18/2023] Open
Abstract
The advance in high-throughput sequencing technologies has yielded complete genome sequences of several organisms, including complete bacterial genomes. The growing number of these available sequenced genomes has enabled analyses of their dynamics, as well as the molecular and evolutionary processes which these organisms are under. Comparative genomics of different bacterial genomes have highlighted their genome size and gene content in association with lifestyles and adaptation to various environments and have contributed to enhancing our understanding of the mechanisms of their evolution. Protein–protein functional interactions mediate many essential processes for maintaining the stability of the biological systems under changing environmental conditions. Thus, these interactions play crucial roles in the evolutionary processes of different organisms, especially for obligate intracellular bacteria, proven to generally have reduced genome sizes compared to their nearest free-living relatives. In this study, we used the approach based on the Renormalization Group (RG) analysis technique and the Maximum-Excluded-Mass-Burning (MEMB) model to investigate the evolutionary process of genome reduction in relation to the organization of functional networks of two organisms. Using a Mycobacterium leprae (MLP) network in comparison with a Mycobacterium tuberculosis (MTB) network as a case study, we show that reductive evolution in MLP was as a result of removal of important proteins from neighbors of corresponding orthologous MTB proteins. While each orthologous MTB protein had an increase in number of interacting partners in most instances, the corresponding MLP protein had lost some of them. This work provides a quantitative model for mapping reductive evolution and protein–protein functional interaction network organization in terms of roles played by different proteins in the network structure.
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Affiliation(s)
- Richard O Akinola
- Computational Biology Group, Department of Integrative Biomedical Sciences, Medical School, Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape Town, South Africa; Department of Mathematics, Faculty of Natural Sciences, University of JosJos, Nigeria
| | - Gaston K Mazandu
- Computational Biology Group, Department of Integrative Biomedical Sciences, Medical School, Institute of Infectious Disease and Molecular Medicine, University of Cape TownCape Town, South Africa; African Institute for Mathematical SciencesCape Town, South Africa; African Institute for Mathematical SciencesCape Coast, Ghana
| | - Nicola J Mulder
- Computational Biology Group, Department of Integrative Biomedical Sciences, Medical School, Institute of Infectious Disease and Molecular Medicine, University of Cape Town Cape Town, South Africa
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6
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Analysis of IS6110 insertion sites provide a glimpse into genome evolution of Mycobacterium tuberculosis. Sci Rep 2015. [PMID: 26215170 PMCID: PMC4517164 DOI: 10.1038/srep12567] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Insertion sequence (IS) 6110 is found at multiple sites in the Mycobacterium tuberculosis genome and displays a high degree of polymorphism with respect to copy number and insertion sites. Therefore, IS6110 is considered to be a useful molecular marker for diagnosis and strain typing of M. tuberculosis. Generally IS6110 elements are identified using experimental methods, useful for analysis of a limited number of isolates. Since short read genome sequences generated using next-generation sequencing (NGS) platforms are available for a large number of isolates, a computational pipeline for identification of IS6110 elements from these datasets was developed. This study shows results from analysis of NGS data of 1377 M. tuberculosis isolates. These isolates represent all seven major global lineages of M. tuberculosis. Lineage specific copy number patterns and preferential insertion regions were observed. Intra-lineage differences were further analyzed for identifying spoligotype specific variations. Copy number distribution and preferential locations of IS6110 in different lineages imply independent evolution of IS6110, governed mainly through ancestral insertion, fitness (gene truncation, promoter activity) and recombinational loss of some copies. A phylogenetic tree based on IS6110 insertion data of different isolates was constructed in order to understand genome level variations of different markers across different lineages.
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7
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In Vivo IS6110 Profile Changes in a Mycobacterium tuberculosis Strain as Determined by Tracking over 14 Years. J Clin Microbiol 2015; 53:2359-61. [PMID: 25948604 DOI: 10.1128/jcm.00607-15] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 04/28/2015] [Indexed: 11/20/2022] Open
Abstract
Transposition and homologous recombination of IS6110 appear in Mycobacterium tuberculosis along in vivo sequential infections. These events were checked in different clones of a successful strain, M. tuberculosis Zaragoza, with the focus on a variant in which integration of a copy of IS6110 in the origin of replication (oriC) region occurred.
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8
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Mehaffy C, Guthrie JL, Alexander DC, Stuart R, Rea E, Jamieson FB. Marked microevolution of a unique Mycobacterium tuberculosis strain in 17 years of ongoing transmission in a high risk population. PLoS One 2014; 9:e112928. [PMID: 25405861 PMCID: PMC4236100 DOI: 10.1371/journal.pone.0112928] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 08/22/2014] [Indexed: 11/18/2022] Open
Abstract
The transmission and persistence of Mycobacterium tuberculosis within high risk populations is a threat to tuberculosis (TB) control. In the current study, we used whole genome sequencing (WGS) to decipher the transmission dynamics and microevolution of M. tuberculosis ON-A, an endemic strain responsible for an ongoing outbreak of TB in an urban homeless/under-housed population. Sixty-one M. tuberculosis isolates representing 57 TB cases from 1997 to 2013 were subjected to WGS. Sequencing data was integrated with available epidemiological information and analyzed to determine how the M. tuberculosis ON-A strain has evolved during almost two decades of active transmission. WGS offers higher discriminatory power than traditional genotyping techniques, dividing the M. tuberculosis ON-A strain into 6 sub-clusters, each defined by unique single nucleotide polymorphism profiles. One sub-cluster, designated ON-ANM (Natural Mutant; 26 isolates from 24 cases) was also defined by a large, 15 kb genomic deletion. WGS analysis reveals the existence of multiple transmission chains within the same population/setting. Our results help validate the utility of WGS as a powerful tool for identifying genomic changes and adaptation of M. tuberculosis.
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Affiliation(s)
- Carolina Mehaffy
- Public Health Ontario, Toronto, Canada
- University of Toronto, Toronto, Canada
- * E-mail:
| | | | | | | | | | - Frances B. Jamieson
- Public Health Ontario, Toronto, Canada
- University of Toronto, Toronto, Canada
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9
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Shitikov EA, Bespyatykh JA, Ischenko DS, Alexeev DG, Karpova IY, Kostryukova ES, Isaeva YD, Nosova EY, Mokrousov IV, Vyazovaya AA, Narvskaya OV, Vishnevsky BI, Otten TF, Zhuravlev VY, Yablonsky PK, Ilina EN, Govorun VM. Unusual large-scale chromosomal rearrangements in Mycobacterium tuberculosis Beijing B0/W148 cluster isolates. PLoS One 2014; 9:e84971. [PMID: 24416324 PMCID: PMC3885621 DOI: 10.1371/journal.pone.0084971] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 11/28/2013] [Indexed: 11/18/2022] Open
Abstract
The Mycobacterium tuberculosis (MTB) Beijing family isolates are geographically widespread, and there are examples of Beijing isolates that are hypervirulent and associated with drug resistance. One-fourth of Beijing genotype isolates found in Russia belong to the B0/W148 group. The aim of the present study was to investigate features of these endemic strains on a genomic level. Four Russian clinical isolates of this group were sequenced, and the data obtained was compared with published sequences of various MTB strain genomes, including genome of strain W-148 of the same B0/W148 group. The comparison of the W-148 and H37Rv genomes revealed two independent inversions of large segments of the chromosome. The same inversions were found in one of the studied strains after deep sequencing using both the fragment and mate-paired libraries. Additionally, inversions were confirmed by RFLP hybridization analysis. The discovered rearrangements were verified by PCR in all four newly sequenced strains in the study and in four additional strains of the same Beijing B0/W148 group. The other 32 MTB strains from different phylogenetic lineages were tested and revealed no inversions. We suggest that the initial largest inversion changed the orientation of the three megabase (Mb) segment of the chromosome, and the second one occurred in the previously inverted region and partly restored the orientation of the 2.1 Mb inner segment of the region. This is another remarkable example of genomic rearrangements in the MTB in addition to the recently published of large-scale duplications. The described cases suggest that large-scale genomic rearrangements in the currently circulating MTB isolates may occur more frequently than previously considered, and we hope that further studies will help to determine the exact mechanism of such events.
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MESH Headings
- Antitubercular Agents/therapeutic use
- China/epidemiology
- Chromosome Inversion
- Chromosome Mapping
- Chromosomes, Bacterial
- DNA, Bacterial/classification
- DNA, Bacterial/genetics
- Drug Resistance, Multiple, Bacterial/drug effects
- Drug Resistance, Multiple, Bacterial/genetics
- Genome, Bacterial
- High-Throughput Nucleotide Sequencing
- Humans
- Mycobacterium tuberculosis/classification
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/isolation & purification
- Phylogeny
- Russia/epidemiology
- Tuberculosis, Pulmonary/drug therapy
- Tuberculosis, Pulmonary/epidemiology
- Tuberculosis, Pulmonary/microbiology
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Affiliation(s)
- Egor A. Shitikov
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
- * E-mail:
| | - Julia A. Bespyatykh
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
| | - Dmitry S. Ischenko
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | - Dmitry G. Alexeev
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
- Moscow Institute of Physics and Technology, Dolgoprudny, Russian Federation
| | - Irina Y. Karpova
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
| | | | - Yulia D. Isaeva
- Moscow Scientific-Practical Center of Treatment of Tuberculosis of Moscow Healthcare, Moscow, Russian Federation
| | - Elena Y. Nosova
- Moscow Scientific-Practical Center of Treatment of Tuberculosis of Moscow Healthcare, Moscow, Russian Federation
| | - Igor V. Mokrousov
- St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation
| | - Anna A. Vyazovaya
- St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation
| | - Olga V. Narvskaya
- St. Petersburg Pasteur Institute, St. Petersburg, Russian Federation
| | - Boris I. Vishnevsky
- Research Institute of Phthisiopulmonology, St. Petersburg, Russian Federation
| | - Tatiana F. Otten
- Research Institute of Phthisiopulmonology, St. Petersburg, Russian Federation
| | - Valery Y. Zhuravlev
- Research Institute of Phthisiopulmonology, St. Petersburg, Russian Federation
| | - Peter K. Yablonsky
- Research Institute of Phthisiopulmonology, St. Petersburg, Russian Federation
| | - Elena N. Ilina
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
| | - Vadim M. Govorun
- Research Institute of Physical - Chemical Medicine, Moscow, Russian Federation
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10
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Oakeson KF, Gil R, Clayton AL, Dunn DM, von Niederhausern AC, Hamil C, Aoyagi A, Duval B, Baca A, Silva FJ, Vallier A, Jackson DG, Latorre A, Weiss RB, Heddi A, Moya A, Dale C. Genome degeneration and adaptation in a nascent stage of symbiosis. Genome Biol Evol 2014; 6:76-93. [PMID: 24407854 PMCID: PMC3914690 DOI: 10.1093/gbe/evt210] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Symbiotic associations between animals and microbes are ubiquitous in nature, with an estimated 15% of all insect species harboring intracellular bacterial symbionts. Most bacterial symbionts share many genomic features including small genomes, nucleotide composition bias, high coding density, and a paucity of mobile DNA, consistent with long-term host association. In this study, we focus on the early stages of genome degeneration in a recently derived insect-bacterial mutualistic intracellular association. We present the complete genome sequence and annotation of Sitophilus oryzae primary endosymbiont (SOPE). We also present the finished genome sequence and annotation of strain HS, a close free-living relative of SOPE and other insect symbionts of the Sodalis-allied clade, whose gene inventory is expected to closely resemble the putative ancestor of this group. Structural, functional, and evolutionary analyses indicate that SOPE has undergone extensive adaptation toward an insect-associated lifestyle in a very short time period. The genome of SOPE is large in size when compared with many ancient bacterial symbionts; however, almost half of the protein-coding genes in SOPE are pseudogenes. There is also evidence for relaxed selection on the remaining intact protein-coding genes. Comparative analyses of the whole-genome sequence of strain HS and SOPE highlight numerous genomic rearrangements, duplications, and deletions facilitated by a recent expansion of insertions sequence elements, some of which appear to have catalyzed adaptive changes. Functional metabolic predictions suggest that SOPE has lost the ability to synthesize several essential amino acids and vitamins. Analyses of the bacterial cell envelope and genes encoding secretion systems suggest that these structures and elements have become simplified in the transition to a mutualistic association.
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Affiliation(s)
- Kelly F. Oakeson
- Department of Biology, University of Utah
- *Corresponding author: E-mail:
| | - Rosario Gil
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
| | | | | | | | - Cindy Hamil
- Department of Human Genetics, University of Utah
| | - Alex Aoyagi
- Department of Human Genetics, University of Utah
| | - Brett Duval
- Department of Human Genetics, University of Utah
| | | | - Francisco J. Silva
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
| | - Agnès Vallier
- INSA-Lyon, INRA, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Villeurbanne, France
| | | | - Amparo Latorre
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana FISABIO – Salud Pública, Valencia, Spain
| | | | - Abdelaziz Heddi
- INSA-Lyon, INRA, UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, Villeurbanne, France
| | - Andrés Moya
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain
- Área de Genómica y Salud, Fundación para el Fomento de la Investigación Sanitaria y Biomédica de la Comunitat Valenciana FISABIO – Salud Pública, Valencia, Spain
| | - Colin Dale
- Department of Biology, University of Utah
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11
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Alonso H, Samper S, Martín C, Otal I. Mapping IS6110 in high-copy number Mycobacterium tuberculosis strains shows specific insertion points in the Beijing genotype. BMC Genomics 2013; 14:422. [PMID: 23800083 PMCID: PMC3701491 DOI: 10.1186/1471-2164-14-422] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 06/19/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mycobacterium tuberculosis Beijing strains are characterized by a large number of IS6110 copies, suggesting the potential implication of this element in the virulence and capacity for rapid dissemination characteristic of this family. This work studies the insetion points of IS6110 in high-copy clinical isolates specifically focusing on the Beijing genotype. RESULTS In the present work we mapped the insertion points of IS6110 in all the Beijing strains available in the literature and in the DNA sequence databases. We generated a representative primer collection of the IS6110 locations, which was used to analyse 61 high-copy clinical isolates. A total of 440 points of insertion were identified and analysis of their flanking regions determined the exact location, the direct repeats (DRs), the orientation and the distance to neighboring genes of each copy of IS6110. We identified specific points of insertion in Beijing strains that enabled us to obtain a dendrogram that groups the Beijing genotype. CONCLUSIONS This work presents a detailed analysis of locations of IS6110 in high-copy clinical isolates, showing points of insertion present with high frequency in the Beijing family and absent in other strains.
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Affiliation(s)
- Henar Alonso
- Grupo de Genética de Micobacterias, Departamento de Microbiología, Medicina Preventiva y Salud Pública, Universidad de Zaragoza, C/ Domingo Miral sn, 50009, Zaragoza, Spain
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12
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Abstract
Tuberculosis globally results in almost 2 million human deaths annually, with 1 in 4 deaths from tuberculosis being human immunodeficiency virus/acquired immunodeficiency syndrome (HIV/AIDS)-related. Primarily a pathogen of the respiratory system, aerobic Mycobacterium tuberculosis complex (MTBC) infects the lungs via the inhalation of infected aerosol droplets generated by people with pulmonary disease through coughing. This review focuses on M. tuberculosis transmission, epidemiology, detection methods and technologies.
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Affiliation(s)
- Balkis A Talip
- Northern Ireland Centre for Food and Health (NICHE), School of Biomedical Sciences, University of Ulster, Coleraine
| | - Roy D Sleator
- Department of Biological Sciences, Cork Institute of Technology, Cork, Ireland
| | - Colm J Lowery
- Northern Ireland Centre for Food and Health (NICHE), School of Biomedical Sciences, University of Ulster, Coleraine
| | - James S G Dooley
- Northern Ireland Centre for Food and Health (NICHE), School of Biomedical Sciences, University of Ulster, Coleraine
| | - William J Snelling
- Northern Ireland Centre for Food and Health (NICHE), School of Biomedical Sciences, University of Ulster, Coleraine
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13
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Mancilla M, Marín CM, Blasco JM, Zárraga AM, López-Goñi I, Moriyón I. Spontaneous excision of the O-polysaccharide wbkA glycosyltranferase gene is a cause of dissociation of smooth to rough Brucella colonies. J Bacteriol 2012; 194:1860-7. [PMID: 22328663 PMCID: PMC3318470 DOI: 10.1128/jb.06561-11] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2011] [Accepted: 01/27/2012] [Indexed: 01/07/2023] Open
Abstract
The brucellae are Gram-negative pathogens that cause brucellosis, a zoonosis of worldwide importance. The genus Brucella includes smooth and rough species that differ in that they carry smooth and rough lipopolysaccharides, respectively. Brucella abortus, B. melitensis, and B. suis are typical smooth species. However, these smooth brucellae dissociate into rough mutants devoid of the lipopolysaccharide O-polysaccharide, a major antigen and a virulence determinant encoded in regions wbo (included in genomic island-2) and wbk. We demonstrate here the occurrence of spontaneous recombination events in those three Brucella species leading to the deletion of a 5.5-kb fragment carrying the wbkA glycosyltranferase gene and to the appearance of rough mutants. Analysis of the recombination intermediates suggested homologous recombination between the ISBm1 insertion sequences flanking wbkA as the mechanism generating the deletion. Excision of wbkA was reduced but not abrogated in a recA-deficient mutant, showing the existence of both RecA-dependent and -independent processes. Although the involvement of the ISBm1 copies flanking wbkA suggested a transpositional event, the predicted transpositional joint could not be detected. This absence of detectable transposition was consistent with the presence of polymorphism in the inverted repeats of one of the ISBm1 copies. The spontaneous excision of wbkA represents a novel dissociation mechanism of smooth brucellae that adds to the previously described excision of genomic island-2. This ISBm1-mediated wbkA excision and the different %GC levels of the excised fragment and of other wbk genes suggest that the Brucella wbk locus is the result of at least two horizontal acquisition events.
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Affiliation(s)
- Marcos Mancilla
- Instituto de Salud Tropical y Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Clara M. Marín
- Centro de Investigación y Tecnología Agroalimentaria, Unidad de Sanidad Animal, Gobierno de Aragón, Zaragoza, Spain
| | - José M. Blasco
- Centro de Investigación y Tecnología Agroalimentaria, Unidad de Sanidad Animal, Gobierno de Aragón, Zaragoza, Spain
| | - Ana María Zárraga
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Ignacio López-Goñi
- Instituto de Salud Tropical y Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
| | - Ignacio Moriyón
- Instituto de Salud Tropical y Departamento de Microbiología y Parasitología, Universidad de Navarra, Pamplona, Spain
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14
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Bentley SD, Comas I, Bryant JM, Walker D, Smith NH, Harris SR, Thurston S, Gagneux S, Wood J, Antonio M, Quail MA, Gehre F, Adegbola RA, Parkhill J, de Jong BC. The genome of Mycobacterium africanum West African 2 reveals a lineage-specific locus and genome erosion common to the M. tuberculosis complex. PLoS Negl Trop Dis 2012; 6:e1552. [PMID: 22389744 PMCID: PMC3289620 DOI: 10.1371/journal.pntd.0001552] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 01/17/2012] [Indexed: 01/16/2023] Open
Abstract
Background M. africanum West African 2 constitutes an ancient lineage of the M. tuberculosis complex that commonly causes human tuberculosis in West Africa and has an attenuated phenotype relative to M. tuberculosis. Methodology/Principal Findings In search of candidate genes underlying these differences, the genome of M. africanum West African 2 was sequenced using classical capillary sequencing techniques. Our findings reveal a unique sequence, RD900, that was independently lost during the evolution of two important lineages within the complex: the “modern” M. tuberculosis group and the lineage leading to M. bovis. Closely related to M. bovis and other animal strains within the M. tuberculosis complex, M. africanum West African 2 shares an abundance of pseudogenes with M. bovis but also with M. africanum West African clade 1. Comparison with other strains of the M. tuberculosis complex revealed pseudogenes events in all the known lineages pointing toward ongoing genome erosion likely due to increased genetic drift and relaxed selection linked to serial transmission-bottlenecks and an intracellular lifestyle. Conclusions/Significance The genomic differences identified between M. africanum West African 2 and the other strains of the Mycobacterium tuberculosis complex may explain its attenuated phenotype, and pave the way for targeted experiments to elucidate the phenotypic characteristic of M. africanum. Moreover, availability of the whole genome data allows for verification of conservation of targets used for the next generation of diagnostics and vaccines, in order to ensure similar efficacy in West Africa. Mycobacterium africanum, a close relative of M. tuberculosis, is studied for the following reasons: M. africanum is commonly isolated from West African patients with tuberculosis yet has not spread beyond this region, it is more common in HIV infected patients, and it is less likely to lead to tuberculosis after one is exposed to an infectious case. Understanding this organism's unique biology gets a boost from the decoding of its genome, reported in this issue. For example, genome analysis reveals that M. africanum contains a region shared with “ancient” lineages in the M. tuberculosis complex and other mycobacterial species, which was lost independently from both M. tuberculosis and M. bovis. This region encodes a protein involved in transmembrane transport. Furthermore, M. africanum has lost genes, including a known virulence gene and genes for vitamin synthesis, in addition to an intact copy of a gene that may increase its susceptibility to antibiotics that are insufficiently active against M. tuberculosis. Finally, the genome sequence and analysis reported here will aid in the development of new diagnostics and vaccines against tuberculosis, which need to take into account the differences between M. africanum and other species in order to be effective worldwide.
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Affiliation(s)
- Stephen D. Bentley
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Iñaki Comas
- Genomics and Health Unit, Centre for Public Health Research, Valencia, Spain
- Division of Mycobacterial Research, MRC National Institute for Medical Research, The Ridgeway, Mill Hill, London, United Kingdom
| | - Josephine M. Bryant
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Danielle Walker
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Noel H. Smith
- TB Research Group, Veterinary Laboratories Agency (VLA), Weybridge, New Haw, Addlestone, Surrey, United Kingdom and The Centre for the Study of Evolution, University of Sussex, Brighton, United Kingdom
| | - Simon R. Harris
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Scott Thurston
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Jonathan Wood
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | | | - Michael A. Quail
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Florian Gehre
- Vaccinology Theme, MRC Unit, Banjul, The Gambia
- Institute of Tropical Medicine, Antwerp, Belgium
| | | | - Julian Parkhill
- Wellcome Trust Genome Campus, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Bouke C. de Jong
- Vaccinology Theme, MRC Unit, Banjul, The Gambia
- Institute of Tropical Medicine, Antwerp, Belgium
- New York University, New York, New York, United States of America
- * E-mail:
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15
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Weiner B, Gomez J, Victor TC, Warren RM, Sloutsky A, Plikaytis BB, Posey JE, van Helden PD, Gey van Pittius NC, Koehrsen M, Sisk P, Stolte C, White J, Gagneux S, Birren B, Hung D, Murray M, Galagan J. Independent large scale duplications in multiple M. tuberculosis lineages overlapping the same genomic region. PLoS One 2012; 7:e26038. [PMID: 22347359 PMCID: PMC3274525 DOI: 10.1371/journal.pone.0026038] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Accepted: 09/16/2011] [Indexed: 11/19/2022] Open
Abstract
Mycobacterium tuberculosis, the causative agent of most human tuberculosis, infects one third of the world's population and kills an estimated 1.7 million people a year. With the world-wide emergence of drug resistance, and the finding of more functional genetic diversity than previously expected, there is a renewed interest in understanding the forces driving genome evolution of this important pathogen. Genetic diversity in M. tuberculosis is dominated by single nucleotide polymorphisms and small scale gene deletion, with little or no evidence for large scale genome rearrangements seen in other bacteria. Recently, a single report described a large scale genome duplication that was suggested to be specific to the Beijing lineage. We report here multiple independent large-scale duplications of the same genomic region of M. tuberculosis detected through whole-genome sequencing. The duplications occur in strains belonging to both M. tuberculosis lineage 2 and 4, and are thus not limited to Beijing strains. The duplications occur in both drug-resistant and drug susceptible strains. The duplicated regions also have substantially different boundaries in different strains, indicating different originating duplication events. We further identify a smaller segmental duplication of a different genomic region of a lab strain of H37Rv. The presence of multiple independent duplications of the same genomic region suggests either instability in this region, a selective advantage conferred by the duplication, or both. The identified duplications suggest that large-scale gene duplication may be more common in M. tuberculosis than previously considered.
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Affiliation(s)
- Brian Weiner
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - James Gomez
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Thomas C. Victor
- Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Health Sciences, National Research Foundation Centre of Excellence for Tuberculosis Research, Medical Research Council Centre for Molecular and Cellular Biology, Stellenbosch University, Tygerberg, South Africa
| | - Robert M. Warren
- Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Health Sciences, National Research Foundation Centre of Excellence for Tuberculosis Research, Medical Research Council Centre for Molecular and Cellular Biology, Stellenbosch University, Tygerberg, South Africa
| | - Alexander Sloutsky
- Massachusetts Supranational TB Reference Laboratory, Center for Health Policy and Research, University of Massachusetts Medical School, Shrewsbury, Massachusetts, United States of America
| | - Bonnie B. Plikaytis
- Mycobacteriology Laboratory Branch, Division of TB Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - James E. Posey
- Mycobacteriology Laboratory Branch, Division of TB Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Paul D. van Helden
- Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Health Sciences, National Research Foundation Centre of Excellence for Tuberculosis Research, Medical Research Council Centre for Molecular and Cellular Biology, Stellenbosch University, Tygerberg, South Africa
| | - Nicolass C. Gey van Pittius
- Division of Molecular Biology and Human Genetics, Department of Biomedical Science, Faculty of Health Sciences, National Research Foundation Centre of Excellence for Tuberculosis Research, Medical Research Council Centre for Molecular and Cellular Biology, Stellenbosch University, Tygerberg, South Africa
| | - Michael Koehrsen
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Peter Sisk
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Christian Stolte
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Jared White
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Sebastien Gagneux
- Medical Research Council, National Institute for Medical Research, London, United Kingdom
| | - Bruce Birren
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Deborah Hung
- The Broad Institute, Cambridge, Massachusetts, United States of America
| | - Megan Murray
- Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - James Galagan
- The Broad Institute, Cambridge, Massachusetts, United States of America
- Department of Biomedical Engineering and Microbiology, Boston University, Boston, Massachusetts, United States of America
- * E-mail:
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16
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Characterization of microevolution events in Mycobacterium tuberculosis strains involved in recent transmission clusters. J Clin Microbiol 2011; 49:3771-6. [PMID: 21940467 DOI: 10.1128/jcm.01285-11] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Under certain circumstances, it is possible to identify clonal variants of Mycobacterium tuberculosis infecting a single patient, probably as a result of subtle genetic rearrangements in part of the bacillary population. We systematically searched for these microevolution events in a different context, namely, recent transmission chains. We studied the clustered cases identified using a population-based universal molecular epidemiology strategy over a 5-year period. Clonal variants of the reference strain defining the cluster were found in 9 (12%) of the 74 clusters identified after the genotyping of 612 M. tuberculosis isolates by IS6110 restriction fragment length polymorphism analysis and mycobacterial interspersed repetitive units-variable-number tandem repeat typing. Clusters with microevolution events were epidemiologically supported and involved 4 to 9 cases diagnosed over a 1- to 5-year period. The IS6110 insertion sites from 16 representative isolates of reference and microevolved variants were mapped by ligation-mediated PCR in order to characterize the genetic background involved in microevolution. Both intragenic and intergenic IS6110 locations resulted from these microevolution events. Among those cases of IS6110 locations in intergenic regions which could have an effect on the regulation of adjacent genes, we identified the overexpression of cytochrome P450 in one microevolved variant using quantitative real-time reverse transcription-PCR. Our results help to define the frequency with which microevolution can be expected in M. tuberculosis transmission chains. They provide a snapshot of the genetic background of these subtle rearrangements and identify an event in which IS6110-mediated microevolution in an isogenic background has functional consequences.
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Alonso H, Aguilo JI, Samper S, Caminero JA, Campos-Herrero MI, Gicquel B, Brosch R, Martín C, Otal I. Deciphering the role of IS6110 in a highly transmissible Mycobacterium tuberculosis Beijing strain, GC1237. Tuberculosis (Edinb) 2011; 91:117-26. [DOI: 10.1016/j.tube.2010.12.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 12/20/2010] [Accepted: 12/28/2010] [Indexed: 10/18/2022]
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18
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A major subgroup of Beijing familyMycobacterium tuberculosisis associated with multidrug resistance and increased transmissibility. Epidemiol Infect 2010; 139:130-8. [DOI: 10.1017/s0950268810000890] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
SUMMARYThis study investigated further the association between the Beijing familyMycobacterium tuberculosiscirculating in rural China and anti-tuberculosis (TB) drug resistance. In total, 351M. tuberculosisisolates were collected through a population-based epidemiological study, 223 (63·5%) of which were resistant to at least one anti-TB drug, including 53 (15·1%) multidrug-resistant (MDR) isolates. Spoligotyping found 243 isolates (69·2%) that belonged to the Beijing family. A major subgroup of the Beijing family identified by mycobacterial interspersed repetitive unit (MIRU) genotyping (223325173533), showed significantly higher frequencies of MDR (44·7%vs. 13·7%, OR 6·18, 95% CI 2·68–14·23),katGandrpoBmutations (31·6%vs. 9·3%, OR 4·27, 95% CI 1·86–9·80), and being clustered by IS6110RFLP genotyping (60·5%vs. 21·0%, OR 6·14, 95% CI 2·82–13·37) in comparison with other Beijing family isolates. Our data suggest that MIRU genotype 223325173533 of the Beijing family is associated with MDR and increased transmissibility.
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19
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Freidlin PJ, Goldblatt D, Kaidar-Shwartz H, Rorman E. Polymorphic exact tandem repeat A (PETRA): a newly defined lineage of mycobacterium tuberculosis in israel originating predominantly in Sub-Saharan Africa. J Clin Microbiol 2009; 47:4006-20. [PMID: 19846636 PMCID: PMC2786624 DOI: 10.1128/jcm.01270-09] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2009] [Revised: 09/07/2009] [Accepted: 10/11/2009] [Indexed: 11/20/2022] Open
Abstract
As part of the Israel National Program for Prevention and Control of Tuberculosis, the molecular epidemiology of new tuberculosis cases is monitored. Prospective screening showed that about 20% of all new cases of culture-positive tuberculosis (43 of 222) in Israel in the year 2008 were caused by certain Mycobacterium tuberculosis strains of the central Asian (CAS) spoligotype lineage. The identity and similarity of these strains by mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing form a lineage we call PETRA for polymorphic at locus ETR A. The name PETRA was given to 79 strains we have found since the year 2000, because the largest number of strains with MIRU-VNTR profiles identical other than at locus A formed three groups, including 5 of 10 strains that had deleted the ETR A region from their genomes. No PETRA strain was found to be multiple drug resistant (resistant to both isoniazid and rifampin [rifampicin]). Most patients (75% [58 of 77 patients of known origin]) infected with PETRA were of sub-Saharan African origins. The genotypes associated with the 79 PETRA lineage strains presented in this paper suggest that the PETRA lineage is a large, major contributor to new tuberculosis cases in Israel.
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Affiliation(s)
- Paul J Freidlin
- National Public Health Laboratory, Ministry of Health, 69 Ben-Tzvi, Tel-Aviv, Israel.
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20
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EmbR2, a structural homologue of EmbR, inhibits the Mycobacterium tuberculosis kinase/substrate pair PknH/EmbR. Biochem J 2008; 410:309-17. [PMID: 17999640 DOI: 10.1042/bj20071384] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
EmbR is a transcriptional regulator that is phosphorylated by the cognate mycobacterial STPK (serine/threonine protein kinase) PknH. Recent studies demonstrated that PknH-dependent phosphorylation of EmbR enhances its DNA-binding activity and activates the transcription of the embCAB genes encoding arabinosyltransferases, which participate in arabinan biosynthesis. In the present study, we identified a genomic region of 4425 bp, which is present in Mycobacterium tuberculosis CDC1551, but absent from M. tuberculosis H37Rv, comprising the MT3428 gene, which is homologous with embR. Homology modelling of the MT3428 gene product illustrated its close relationship (56% identity) to EmbR, and it was hence termed EmbR2. In marked contrast with EmbR, EmbR2 was not phosphorylated by PknH, although it is a substrate of other M. tuberculosis kinases, including PknE and PknF. Tryptophan fluorescence emission of EmbR2 was monitored in the presence of three different PknH-derived phosphopeptides and demonstrated that EmbR2 binds to at least two of the threonine sites known to undergo autophosphorylation in PknH. We observed that the capacity of EmbR2 to interact physically with PknH without being phosphorylated was a result of EmbR2-mediated inhibition of kinase activity: incubation of PknH with increasing concentrations of EmbR2 led to a dose-response inhibition of the autokinase activity, similarly to O6-cyclohexylmethylguanine, a known inhibitor of eukaryotic cyclin-dependent kinases. Moreover, EmbR2 inhibited PknH-dependent phosphorylation of EmbR in a dose-dependent manner. Together, these results suggest that EmbR2 is a regulator of PknH activation, thus directly participating in the control of the PknH/EmbR pair and potentially in mycobacterial physiology/virulence of M. tuberculosis CDC1551.
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21
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Lazzarini LCO, Huard RC, Boechat NL, Gomes HM, Oelemann MC, Kurepina N, Shashkina E, Mello FCQ, Gibson AL, Virginio MJ, Marsico AG, Butler WR, Kreiswirth BN, Suffys PN, Lapa E Silva JR, Ho JL. Discovery of a novel Mycobacterium tuberculosis lineage that is a major cause of tuberculosis in Rio de Janeiro, Brazil. J Clin Microbiol 2007; 45:3891-902. [PMID: 17898156 PMCID: PMC2168543 DOI: 10.1128/jcm.01394-07] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The current study evaluated Mycobacterium tuberculosis isolates from Rio de Janeiro, Brazil, for genomic deletions. One locus in our panel of PCR targets failed to amplify in approximately 30% of strains. A single novel long sequence polymorphism (>26.3 kb) was characterized and designated RD(Rio). Homologous recombination between two similar protein-coding genes is proposed as the mechanism for deleting or modifying 10 genes, including two potentially immunogenic PPE proteins. The flanking regions of the RD(Rio) locus were identical in all strains bearing the deletion. Genetic testing by principal genetic group, spoligotyping, variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR), and IS6110-based restriction fragment length polymorphism analysis cumulatively support the idea that RD(Rio) strains are derived from a common ancestor belonging solely to the Latin American-Mediterranean spoligotype family. The RD(Rio) lineage is therefore the predominant clade causing tuberculosis (TB) in Rio de Janeiro and, as indicated by genotypic clustering in MIRU-VNTR analysis, the most significant source of recent transmission. Limited retrospective reviews of bacteriological and patient records showed a lack of association with multidrug resistance or specific risk factors for TB. However, trends in the data did suggest that RD(Rio) strains may cause a form of TB with a distinct clinical presentation. Overall, the high prevalence of this genotype may be related to enhanced virulence, transmissibility, and/or specific adaptation to a Euro-Latin American host population. The identification of RD(Rio) strains outside of Brazil points to the ongoing intercontinental dissemination of this important genotype. Further studies are needed to determine the differential strain-specific features, pathobiology, and worldwide prevalence of RD(Rio) M. tuberculosis.
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Affiliation(s)
- Luiz Claudio Oliveira Lazzarini
- Department of Medicine, Division of International Medicine and Infectious Diseases, Cornell University, Joan and Sanford I Weill Medical College, New York, NY 10021, USA
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22
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Ventura M, Canchaya C, Tauch A, Chandra G, Fitzgerald GF, Chater KF, van Sinderen D. Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol Mol Biol Rev 2007; 71:495-548. [PMID: 17804669 PMCID: PMC2168647 DOI: 10.1128/mmbr.00005-07] [Citation(s) in RCA: 597] [Impact Index Per Article: 35.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Actinobacteria constitute one of the largest phyla among bacteria and represent gram-positive bacteria with a high G+C content in their DNA. This bacterial group includes microorganisms exhibiting a wide spectrum of morphologies, from coccoid to fragmenting hyphal forms, as well as possessing highly variable physiological and metabolic properties. Furthermore, Actinobacteria members have adopted different lifestyles, and can be pathogens (e.g., Corynebacterium, Mycobacterium, Nocardia, Tropheryma, and Propionibacterium), soil inhabitants (Streptomyces), plant commensals (Leifsonia), or gastrointestinal commensals (Bifidobacterium). The divergence of Actinobacteria from other bacteria is ancient, making it impossible to identify the phylogenetically closest bacterial group to Actinobacteria. Genome sequence analysis has revolutionized every aspect of bacterial biology by enhancing the understanding of the genetics, physiology, and evolutionary development of bacteria. Various actinobacterial genomes have been sequenced, revealing a wide genomic heterogeneity probably as a reflection of their biodiversity. This review provides an account of the recent explosion of actinobacterial genomics data and an attempt to place this in a biological and evolutionary context.
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Affiliation(s)
- Marco Ventura
- Department of Genetics, Biology of Microorganisms, Anthropology and Evolution, University of Parma, parco Area delle Scienze 11a, 43100 Parma, Italy.
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23
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McEvoy CRE, Falmer AA, Gey van Pittius NC, Victor TC, van Helden PD, Warren RM. The role of IS6110 in the evolution of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2007; 87:393-404. [PMID: 17627889 DOI: 10.1016/j.tube.2007.05.010] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Revised: 05/15/2007] [Accepted: 05/22/2007] [Indexed: 10/23/2022]
Abstract
Members of the Mycobacterium tuberculosis complex contain the transposable element IS6110 which, due to its high numerical and positional polymorphism, has become a widely used marker in epidemiological studies. Here, we review the evidence that IS6110 is not simply a passive or 'junk' DNA sequence, but that, through its transposable activity, it is able to generate genotypic variation that translates into strain-specific phenotypic variation. We also speculate on the role that this variation has played in the evolution of M. tuberculosis and conclude that the presence of a moderate IS6110 copy number within the genome may provide the pathogen with a selective advantage that has aided its virulence.
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Affiliation(s)
- Christopher R E McEvoy
- DST/NRF Centre of Excellence in Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa.
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Asgharzade M, Shahbabian K, Samadi Kaf H, Rafi A. Use of DNA Fingerprinting in Identifying the Source Case of Tuberculosis in East Azarbaijan Province of Iran. JOURNAL OF MEDICAL SCIENCES 2007. [DOI: 10.3923/jms.2007.418.421] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Asgharzade M, Yousefee S, Kafil HS, Nahaei MR, Ansarin K, Akhi MT. Comparing Transmission of Mycobacterium tuberculosis in East Azarbaijan and West Azarbaijan Provinces of Iran by Using IS6110-RFLP Method. ACTA ACUST UNITED AC 2007. [DOI: 10.3923/biotech.2007.273.277] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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26
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Alland D, Lacher DW, Hazbón MH, Motiwala AS, Qi W, Fleischmann RD, Whittam TS. Role of large sequence polymorphisms (LSPs) in generating genomic diversity among clinical isolates of Mycobacterium tuberculosis and the utility of LSPs in phylogenetic analysis. J Clin Microbiol 2006; 45:39-46. [PMID: 17079498 PMCID: PMC1828963 DOI: 10.1128/jcm.02483-05] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis strains contain different genomic insertions or deletions called large sequence polymorphisms (LSPs). Distinguishing between LSPs that occur one time versus ones that occur repeatedly in a genomic region may provide insights into the biological roles of LSPs and identify useful phylogenetic markers. We analyzed 163 clinical M. tuberculosis isolates for 17 LSPs identified in a genomic comparison of M. tuberculosis strains H37Rv and CDC1551. LSPs were mapped onto a single-nucleotide polymorphism (SNP)-based phylogenetic tree created using nine novel SNP markers that were found to reproduce a 212-SNP-based phylogeny. Four LSPs (group A) mapped to a single SNP tree segment. Two LSPs (group B) and 11 LSPs (group C) were inferred to have arisen independently in the same genomic region either two or more than two times, respectively. None of the group A LSPs but one group B LSP and five group C LSPs were flanked by IS6110 sequences in the references strains. Genes encoding members of the proline-glutamic acid or proline-proline-glutamic acid protein families were present only in group B or C LSPs. SNP- versus LSP-based phylogenies were also compared. We classified each isolate into 58 LSP types by using a separate LSP-based phylogenetic analysis and mapped the LSP types onto the SNP tree. LSPs often assigned isolates to the correct phylogenetic lineage; however, significant mistakes occurred for 6/58 (10%) of the LSP types. In conclusion, most LSPs occur in genomic regions that are prone to repeated insertion/deletion events and were responsible for an unexpectedly high degree of genomic variation in clinical M. tuberculosis. Group B and C LSPs may represent polymorphisms that occur due to selective pressure and affect the phenotype of the organism, while group A LSPs are preferable phylogenetic markers.
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Affiliation(s)
- David Alland
- Division of Infectious Disease, Department of Medicine, University of Medicine and Dentistry of New Jersey, Newark, NJ 07103, USA.
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27
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Huard RC, Fabre M, de Haas P, Lazzarini LCO, van Soolingen D, Cousins D, Ho JL. Novel genetic polymorphisms that further delineate the phylogeny of the Mycobacterium tuberculosis complex. J Bacteriol 2006; 188:4271-87. [PMID: 16740934 PMCID: PMC1482959 DOI: 10.1128/jb.01783-05] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In a previous report, we described a PCR protocol for the differentiation of the various species of the Mycobacterium tuberculosis complex (MTC) on the basis of genomic deletions (R. C. Huard, L. C. de Oliveira Lazzarini, W. R. Butler, D. van Soolingen, and J. L. Ho, J. Clin. Microbiol. 41:1637-1650, 2003). That report also provided a broad cross-comparison of several previously identified, phylogenetically relevant, long-sequence and single-nucleotide polymorphisms (LSPs and SNPs, respectively). In the present companion report, we expand upon the previous work (i) by continuing the evaluation of known MTC phylogenetic markers in a larger collection of tubercle bacilli (n = 125), (ii) by evaluating additional recently reported MTC species-specific and interspecific polymorphisms, and (iii) by describing the identification and distribution of a number of novel LSPs and SNPs. Notably, new genomic deletions were found in various Mycobacterium tuberculosis strains, new species-specific SNPs were identified for "Mycobacterium canettii," Mycobacterium microti, and Mycobacterium pinnipedii, and, for the first time, intraspecific single-nucleotide DNA differences were discovered for the dassie bacillus, the oryx bacillus, and the two Mycobacterium africanum subtype I variants. Surprisingly, coincident polymorphisms linked one M. africanum subtype I genotype with the dassie bacillus and M. microti with M. pinnipedii, thereby suggesting closer evolutionary ties within each pair of species than had been previously thought. Overall, the presented data add to the genetic definitions of several MTC organisms as well as fine-tune current models for the evolutionary history of the MTC.
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Affiliation(s)
- Richard C Huard
- Division of International Medicine and Infectious Diseases, Department of Medicine, Joan and Sanford I. Weill Medical College, Cornell University, Room A-421, 525 East 68th St., New York, NY 10021, USA
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Namouchi A, Mardassi H. A genomic library-based amplification approach (GL-PCR) for the mapping of multiple IS6110 insertion sites and strain differentiation of Mycobacterium tuberculosis. J Microbiol Methods 2006; 67:202-11. [PMID: 16725220 DOI: 10.1016/j.mimet.2006.03.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2005] [Revised: 02/09/2006] [Accepted: 03/09/2006] [Indexed: 11/25/2022]
Abstract
Evidence suggests that insertion of the IS6110 element is not without consequence to the biology of Mycobacterium tuberculosis complex strains. Thus, mapping of multiple IS6110 insertion sites in the genome of biomedically relevant clinical isolates would result in a better understanding of the role of this mobile element, particularly with regard to transmission, adaptability and virulence. In the present paper, we describe a versatile strategy, referred to as GL-PCR, that amplifies IS6110-flanking sequences based on the construction of a genomic library. M. tuberculosis chromosomal DNA is fully digested with HincII and then ligated into a plasmid vector between T7 and T3 promoter sequences. The ligation reaction product is transformed into Escherichia coli and selective PCR amplification targeting both 5' and 3' IS6110-flanking sequences are performed on the plasmid library DNA. For this purpose, four separate PCR reactions are performed, each combining an outward primer specific for one IS6110 end with either T7 or T3 primer. Determination of the nucleotide sequence of the PCR products generated from a single ligation reaction allowed mapping of 21 out of the 24 IS6110 copies of two 12 banded M. tuberculosis strains, yielding an overall sensitivity of 87,5%. Furthermore, by simply comparing the migration pattern of GL-PCR-generated products, the strategy proved to be as valuable as IS6110 RFLP for molecular typing of M. tuberculosis complex strains. Importantly, GL-PCR was able to discriminate between strains differing by a single IS6110 band.
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Affiliation(s)
- Amine Namouchi
- Laboratory of Mycobacteria, Institut Pasteur de Tunis, 13, Place Pasteur, BP 74, 1002, Tunis-Belvedre, Tunisie, Tunisia
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Rao KR, Kauser F, Srinivas S, Zanetti S, Sechi LA, Ahmed N, Hasnain SE. Analysis of genomic downsizing on the basis of region-of-difference polymorphism profiling of Mycobacterium tuberculosis patient isolates reveals geographic partitioning. J Clin Microbiol 2006; 43:5978-82. [PMID: 16333085 PMCID: PMC1317167 DOI: 10.1128/jcm.43.12.5978-5982.2005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis, the etiological agent of tuberculosis, has lost many coding and noncoding regions in its genome during the course of evolution. We performed region-of-difference (RD) analysis using PCR-based genotyping of 131 M. tuberculosis clinical isolates obtained from four different countries, namely, India, Peru, Libya, and Angola. Our studies revealed that RD patterns are often distinct for strains circulating in specific geographical regions and can be used to trace the descent and spread of an isolate from its original reservoir. We describe our findings, which show that no single isolate from the four countries (n = 131) had all the 15 RDs either deleted or retained. Tuberculosis-specific deletion 1 (TbD1) was found to be conserved in 23% of the Indian isolates, indicating their possible ancient origin. RD9 was the most conserved region, RD11 was predominantly deleted, and RD6 was the most variable among the isolates in our collection irrespective of their geographic region. In contrast to earlier reports, our results demonstrate that the deletion of RD1 does not correlate with a decrease in the virulence potential of M. tuberculosis, as Indian isolates (n = 30) examined by us were from diseased individuals and yet had lost the RD1 region. Our results further illustrated that the intactness of the RD5 region may be associated with increased virulence of the organism. This study highlights that the RDs in M. tuberculosis genomes are geographically distributed and specific and may possibly be associated with virulence spectrum.
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Affiliation(s)
- K Rajender Rao
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500 076, India
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30
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Mostowy S, Inwald J, Gordon S, Martin C, Warren R, Kremer K, Cousins D, Behr MA. Revisiting the evolution of Mycobacterium bovis. J Bacteriol 2005; 187:6386-95. [PMID: 16159772 PMCID: PMC1236643 DOI: 10.1128/jb.187.18.6386-6395.2005] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Though careful consideration has been placed towards genetic characterization of tubercle bacillus isolates causing disease in humans, those causing disease predominantly among wild and domesticated mammals have received less attention. In contrast to Mycobacterium tuberculosis, whose host range is largely specific to humans, M. bovis and "M bovis-like" organisms infect a broad range of animal species beyond their most prominent host in cattle. To determine whether strains of variable genomic content are associated with distinct distributions of disease, the DNA contents of M. bovis or M. bovis-like isolates from a variety of hosts were investigated via Affymetrix GeneChip. Consistent with previous genomic analysis of the M. tuberculosis complex (MTC), large sequence polymorphisms of putative diagnostic and biological consequence were able to unambiguously distinguish interrogated isolates. The distribution of deleted regions indicates organisms genomically removed from M. bovis and also points to structured genomic variability within M. bovis. Certain genomic profiles spanned a variety of hosts but were clustered by geography, while others associated primarily with host type. In contrast to the prevailing assumption that M. bovis has broad host capacity, genomic profiles suggest that distinct MTC lineages differentially infect a variety of mammals. From this, a phylogenetic stratification of genotypes offers a predictive framework upon which to base future genetic and phenotypic studies of the MTC.
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Affiliation(s)
- Serge Mostowy
- McGill University Health Centre, Montreal, Quebec, Canada
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Kang J, Huang S, Blaser MJ. Structural and functional divergence of MutS2 from bacterial MutS1 and eukaryotic MSH4-MSH5 homologs. J Bacteriol 2005; 187:3528-37. [PMID: 15866941 PMCID: PMC1112012 DOI: 10.1128/jb.187.10.3528-3537.2005] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
MutS homologs, identified in nearly all bacteria and eukaryotes, include the bacterial proteins MutS1 and MutS2 and the eukaryotic MutS homologs 1 to 7, and they often are involved in recognition and repair of mismatched bases and small insertion/deletions, thereby limiting illegitimate recombination and spontaneous mutation. To explore the relationship of MutS2 to other MutS homologs, we examined conserved protein domains. Fundamental differences in structure between MutS2 and other MutS homologs suggest that MutS1 and MutS2 diverged early during evolution, with all eukaryotic homologs arising from a MutS1 ancestor. Data from MutS1 crystal structures, biochemical results from MutS2 analyses, and our phylogenetic studies suggest that MutS2 has functions distinct from other members of the MutS family. A mutS2 mutant was constructed in Helicobacter pylori, which lacks mutS1 and mismatch repair genes mutL and mutH. We show that MutS2 plays no role in mismatch or recombinational repair or deletion between direct DNA repeats. In contrast, MutS2 plays a significant role in limiting intergenomic recombination across a range of donor DNA tested. This phenotypic analysis is consistent with the phylogenetic and biochemical data suggesting that MutS1 and MutS2 have divergent functions.
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Affiliation(s)
- Josephine Kang
- Department of Microbiology, New York University School of Medicine, and VA Medical Center, New York, NY 10016, USA.
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32
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Niobe-Eyangoh SN, Kuaban C, Sorlin P, Thonnon J, Vincent V, Gutierrez MC. Molecular characteristics of strains of the cameroon family, the major group of Mycobacterium tuberculosis in a country with a high prevalence of tuberculosis. J Clin Microbiol 2005; 42:5029-35. [PMID: 15528691 PMCID: PMC525220 DOI: 10.1128/jcm.42.11.5029-5035.2004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A preliminary investigation of the genetic biodiversity of Mycobacterium tuberculosis complex strains in Cameroon, a country with a high prevalence of tuberculosis, described a group of closely related M. tuberculosis strains (the Cameroon family) currently responsible for more than 40% of smear-positive pulmonary tuberculosis cases. Here, we used various molecular methods to study the genetic characteristics of this family of strains. Cameroon family M. tuberculosis strains (i) are part of the major genetic group 2 and lack the TbD1 region like other families of epidemic strains, (ii) lack spacers 23, 24, and 25 in their direct repeat (DR) region, (iii) have an identical number of repeats in 8 of 12 variable-number tandem repeats of mycobacterial interspersed repetitive unit (MIRU-VNTR) loci, (iv) have similar IS6110-restriction fragment length polymorphism (RFLP) multiband patterns (10 to 15 copies) with seven common IS6110 bands, (v) do not have an IS6110 element in their DR locus, and (vi) have four IS6110 elements in open reading frames (adenylate cyclase, phospholipase C, moeY, and ATP binding genes). Analysis by spoligotyping, MIRU-VNTR, and IS6110-RFLP typing methods revealed differences not observed in previous studies; polymorphism as assessed by MIRU-VNTR typing was lower than suggested by spoligotyping, and in rare cases, strains with identical IS6110-RFLP patterns had spoligotypes differing by as much as 15 spacers. Our findings confirm the recent expansion of this family in Cameroon and indicate that the interpretation of molecular typing results has to be adapted to the characteristics of the strain population within each setting. The knowledge of this particular genotype, with its large involvement in tuberculosis in Cameroon, allows greater refinement of tuberculosis transmission studies by interpreting data in the context of this geographic area.
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Affiliation(s)
- Sara Ngo Niobe-Eyangoh
- Centre National de Référence des Mycobactéries, Institut Pasteur, 25 rue du Dr Roux, 75724 Cedex 15, Paris, France
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Rajakumar K, Shafi J, Smith RJ, Stabler RA, Andrew PW, Modha D, Bryant G, Monk P, Hinds J, Butcher PD, Barer MR. Use of genome level-informed PCR as a new investigational approach for analysis of outbreak-associated Mycobacterium tuberculosis isolates. J Clin Microbiol 2004; 42:1890-6. [PMID: 15131145 PMCID: PMC404642 DOI: 10.1128/jcm.42.5.1890-1896.2004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis strain CH, the index isolate linked to a major tuberculosis outbreak associated with high levels of transmissibility and virulence, was characterized by microarray analysis by use of a PCR product array representative of the genome of M. tuberculosis strain H37Rv. Seven potential genomic deletions were identified in CH, five of which were confirmed by PCR analysis across the predicted deletion points. The panel of five PCRs required to individually interrogate these loci was collectively referred to as the genome level-informed PCR (GLIP) assay. GLIP analysis was performed with CH, 12 other epidemiologically linked isolates, and 43 recent, non-outbreak-associated isolates derived from patients within the local area. All 13 outbreak-linked isolates showed a profile corresponding to the presence of all five deletions. These 13 isolates were also found to share common variable-number tandem repeat and mycobacterial interspersed repetitive unit profiles. None of the 43 non-outbreak-associated isolates exhibited the five-deletion profile. Although three individual deletions were present in upwards of 44% of the non-outbreak-associated isolates, no single-deletion isolates were detected. Interestingly, none of these deletions had been previously recognized, and sequence analysis of the immediate flanking regions in CH failed to identify a likely mechanism of deletion for four of the five loci. The GLIP assay also proved valuable in ongoing surveillance of the outbreak, rapidly identifying a further two outbreak-associated cases months after the initial cluster and, importantly, dismissing a further 12 epidemiologically suspect cases, which allowed the optimum deployment of public health resources.
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Affiliation(s)
- Kumar Rajakumar
- Department of Infection, Immunity and Inflammation, Leicester Medical School, University of Leicester, and Department of Clinical Microbiology, University Hospitals of Leicester NHS Trust, Leicester LE1 5WW, United Kingdom
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Springer B, Sander P, Sedlacek L, Hardt WD, Mizrahi V, Schär P, Böttger EC. Lack of mismatch correction facilitates genome evolution in mycobacteria. Mol Microbiol 2004; 53:1601-9. [PMID: 15341642 DOI: 10.1111/j.1365-2958.2004.04231.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In silico genome sequence analyses suggested that mycobacteria are devoid of the highly conserved mutLS-based post-replicative mismatch repair system. Here, we present the first biological evidence for the lack of a classical mismatch repair function in mycobacteria. We found that frameshifts, but not general mutation rates are unusually high in Mycobacterium smegmatis. However, despite the absence of mismatch correction, M. smegmatis establishes a strong barrier to recombination between homeologous DNA sequences. We show that 10-12% of DNA sequence heterology restricts initiation of recombination but not extension of heteroduplex DNA intermediates. Together, the lack of mismatch correction and a high stringency of initiation of homologous recombination provide an adequate strategy for mycobacterial genome evolution, which occurs by gene duplication and divergent evolution.
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Affiliation(s)
- Burkhard Springer
- Institut für Medizinische Mikrobiologie, Universität Zürich, Gloriastrasse 30/32, CH-3028 Zürich, Switzerland
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35
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Mostowy S, Onipede A, Gagneux S, Niemann S, Kremer K, Desmond EP, Kato-Maeda M, Behr M. Genomic analysis distinguishes Mycobacterium africanum. J Clin Microbiol 2004; 42:3594-9. [PMID: 15297503 PMCID: PMC497617 DOI: 10.1128/jcm.42.8.3594-3599.2004] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2004] [Revised: 04/28/2004] [Accepted: 05/07/2004] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium africanum is thought to comprise a unique species within the Mycobacterium tuberculosis complex. M. africanum has traditionally been identified by phenotypic criteria, occupying an intermediate position between M. tuberculosis and M. bovis according to biochemical characteristics. Although M. africanum isolates present near-identical sequence homology to other species of the M. tuberculosis complex, several studies have uncovered large genomic regions variably deleted from certain M. africanum isolates. To further investigate the genomic characteristics of organisms characterized as M. africanum, the DNA content of 12 isolates was interrogated by using Affymetrix GeneChip. Analysis revealed genomic regions of M. tuberculosis deleted from all isolates of putative diagnostic and biological consequence. The distribution of deleted sequences suggests that M. africanum subtype II isolates are situated among strains of "modern" M. tuberculosis. In contrast, other M. africanum isolates (subtype I) constitute two distinct evolutionary branches within the M. tuberculosis complex. To test for an association between deleted sequences and biochemical attributes used for speciation, a phenotypically diverse panel of "M. africanum-like" isolates from Guinea-Bissau was tested for these deletions. These isolates clustered together within one of the M. africanum subtype I branches, irrespective of phenotype. These results indicate that convergent biochemical profiles can be independently obtained for M. tuberculosis complex members, challenging the traditional approach to M. tuberculosis complex speciation. Furthermore, the genomic results suggest a rational framework for defining M. africanum and provide tools to accurately assess its prevalence in clinical specimens.
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36
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Safi H, Barnes PF, Lakey DL, Shams H, Samten B, Vankayalapati R, Howard ST. IS6110 functions as a mobile, monocyte-activated promoter in Mycobacterium tuberculosis. Mol Microbiol 2004; 52:999-1012. [PMID: 15130120 DOI: 10.1111/j.1365-2958.2004.04037.x] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The mobile insertion sequence, IS6110, is an important marker in tracking of Mycobacterium tuberculosis strains. Here, we demonstrate that IS6110 can upregulate downstream genes through an outward-directed promoter in its 3' end, thus adding to the significance of this element. Promoter activity was orientation dependent and was localized within a 110 bp fragment adjacent to the right terminal inverted repeat. Transcripts from this promoter, named OP6110, begin approximately 85 bp upstream of the 3' end of IS6110. Use of green fluorescent protein (GFP) expression constructs showed that OP6110 was upregulated in M. tuberculosis during growth in human monocytes and in late growth phases in broth. Analysis of natural insertion sites in M. tuberculosis showed that IS6110 upregulated expression of several downstream genes during growth in human monocytes, including Rv2280 in H37Rv and the PE-PGRS gene, Rv1468c, in the clinical strain 210, which is a member of the Beijing family. Transcription between IS6110 and downstream genes was confirmed by reverse transcription polymerase chain reaction. The ability to activate genes during infection suggests that IS6110 has the potential to influence growth characteristics of different strains, and indicates another mechanism by which IS6110 can impact M. tuberculosis evolution.
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Affiliation(s)
- Hassan Safi
- Department of Microbiology, Center for Pulmonary and Infectious Disease Control, University of Texas Health Center at Tyler, 11937 US Highway 271, Tyler, TX 75708-3154, USA
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37
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Sampson SL, Richardson M, Van Helden PD, Warren RM. IS6110-mediated deletion polymorphism in isogenic strains of Mycobacterium tuberculosis. J Clin Microbiol 2004; 42:895-8. [PMID: 14766883 PMCID: PMC344511 DOI: 10.1128/jcm.42.2.895-898.2004] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Previous studies have described IS6110-mediated polymorphism as an important driving force in Mycobacterium tuberculosis genome evolution and have provided indirect evidence for IS6110-driven deletion events. This study provides the first description of an IS6110-mediated deletion event in truly isogenic strains. We also provide further support for the hypothesis that the region from Rv1754 to Rv1765 is a hot spot for IS6110 insertion and deletion events.
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Affiliation(s)
- S L Sampson
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts 02115, USA
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38
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Hirsh AE, Tsolaki AG, DeRiemer K, Feldman MW, Small PM. Stable association between strains of Mycobacterium tuberculosis and their human host populations. Proc Natl Acad Sci U S A 2004; 101:4871-6. [PMID: 15041743 PMCID: PMC387341 DOI: 10.1073/pnas.0305627101] [Citation(s) in RCA: 268] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2003] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium tuberculosis is an important human pathogen in virtually every part of the world. Here we investigate whether distinct strains of M. tuberculosis infect different human populations and whether associations between host and pathogen populations are stable despite global traffic and the convergence of diverse strains of the pathogen in cosmopolitan urban centers. The recent global movement and transmission history of 100 M. tuberculosis isolates was inferred from a molecular epidemiologic study of tuberculosis that spans 12 years. Genetic relationships among these isolates were deduced from the distribution of large genomic deletions, which were identified by DNA microarray and confirmed by PCR and sequence analysis. Phylogenetic analysis of these deletions indicates that they are unique event polymorphisms and that horizontal gene transfer is extremely rare in M. tuberculosis. In conjunction with the epidemiological data, phylogenies reveal three large phylogeographic regions. A host's region of origin is predictive of the strain of tuberculosis he or she carries, and this association remains strong even when transmission takes place in a cosmopolitan urban center outside of the region of origin. Approximate dating of the time since divergence of East Asian and Philippine clades of M. tuberculosis suggests that these lineages diverged centuries ago. Thus, associations between host and pathogen populations appear to be highly stable.
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Affiliation(s)
- Aaron E Hirsh
- Department of Biological Sciences, Stanford University, Stanford, CA 94305, USA.
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39
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Viana-Niero C, de Haas PE, van Soolingen D, Leão SC. Analysis of genetic polymorphisms affecting the four phospholipase C (plc) genes in Mycobacterium tuberculosis complex clinical isolates. Microbiology (Reading) 2004; 150:967-978. [PMID: 15073306 DOI: 10.1099/mic.0.26778-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Mycobacterium tuberculosis genome contains four highly related genes which present significant similarity to Pseudomonas aeruginosa genes encoding phospholipase C enzymes. Three of these genes, plcA, plcB and plcC, are organized in tandem (locus plcABC). The fourth gene, plcD, is located in a different region. This study investigates variations in plcABC and plcD genes in clinical isolates of M. tuberculosis, Mycobacterium africanum and ‘Mycobacterium canettii’. Genetic polymorphisms were examined by PCR, Southern blot hybridization, sequence analysis and RT-PCR. Seven M. tuberculosis isolates contain insertions of IS6110 elements within plcA, plcC or plcD. In 19 of 25 M. tuberculosis isolates examined, genomic deletions were identified, resulting in loss of parts of genes or complete genes from the plcABC and/or plcD loci. Partial plcD deletion was observed in one M. africanum isolate. In each case, deletions were associated with the presence of a copy of the IS6110 element and in all occurrences IS6110 was transposed in the same orientation. A mechanism of deletion resulting from homologous recombination of two copies of IS6110 was recognized in a group of genetically related M. tuberculosis isolates. Five M. tuberculosis isolates presented major polymorphisms in the plcABC and plcD regions, along with loss of expression competence that affected all four plc genes. Phospholipase C is a well-known bacterial virulence factor. The precise role of phospholipase C in the pathogenicity of M. tuberculosis is unknown, but considering the potential importance that the plc genes may have in the virulence of the tubercle bacillus, the study of isolates cultured from patients with active tuberculosis bearing genetic variations affecting these genes may provide insights into the significance of phospholipase C enzymes for tuberculosis pathogenicity.
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Affiliation(s)
- C Viana-Niero
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo - Escola Paulista de Medicina (UNIFESP-EPM), Rua Botucatu, 862 3° andar, 04023-062, São Paulo, Brazil
| | - P E de Haas
- Diagnostic Laboratory of Infectious Diseases and Perinatal Screening, National Institute of Public Health and the Environment (RIVM), PO Box 1, 3720 BA, The Netherlands
| | - D van Soolingen
- Diagnostic Laboratory of Infectious Diseases and Perinatal Screening, National Institute of Public Health and the Environment (RIVM), PO Box 1, 3720 BA, The Netherlands
| | - S C Leão
- Departamento de Microbiologia, Imunologia e Parasitologia, Universidade Federal de São Paulo - Escola Paulista de Medicina (UNIFESP-EPM), Rua Botucatu, 862 3° andar, 04023-062, São Paulo, Brazil
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40
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Tsolaki AG, Hirsh AE, DeRiemer K, Enciso JA, Wong MZ, Hannan M, Goguet de la Salmoniere YOL, Aman K, Kato-Maeda M, Small PM. Functional and evolutionary genomics of Mycobacterium tuberculosis: insights from genomic deletions in 100 strains. Proc Natl Acad Sci U S A 2004; 101:4865-70. [PMID: 15024109 PMCID: PMC387340 DOI: 10.1073/pnas.0305634101] [Citation(s) in RCA: 275] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To better understand genome function and evolution in Mycobacterium tuberculosis, the genomes of 100 epidemiologically well characterized clinical isolates were interrogated by DNA microarrays and sequencing. We identified 68 different large-sequence polymorphisms (comprising 186,137 bp, or 4.2% of the genome) that are present in H37Rv, but absent from one or more clinical isolates. A total of 224 genes (5.5%), including genes in all major functional categories, were found to be partially or completely deleted. Deletions are not distributed randomly throughout the genome but instead tend to be aggregated. The distinct deletions in some aggregations appear in closely related isolates, suggesting a genomically disruptive process specific to an individual mycobacterial lineage. Other genomic aggregations include distinct deletions that appear in phylogenetically unrelated isolates, suggesting that a genomic region is vulnerable throughout the species. Although the deletions identified here are evidently inessential to the causation of disease (they are found in active clinical cases), their frequency spectrum suggests that most are weakly deleterious to the pathogen. For some deletions, short-term evolutionary pressure due to the host immune system or antibiotics may favor the elimination of genes, whereas longer-term physiological requirements maintain the genes in the population.
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Affiliation(s)
- Anthony G Tsolaki
- Division of Infectious Diseases and Geographic Medicine, Stanford University Medical Center, Stanford, CA 94305, USA
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Warren RM, Victor TC, Streicher EM, Richardson M, Beyers N, Gey van Pittius NC, van Helden PD. Patients with active tuberculosis often have different strains in the same sputum specimen. Am J Respir Crit Care Med 2003; 169:610-4. [PMID: 14701710 DOI: 10.1164/rccm.200305-714oc] [Citation(s) in RCA: 208] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
It is generally accepted that tuberculosis results from a single infection with a single Mycobacterium tuberculosis strain. Such infections are thought to confer protective immunity against exogenous reinfection. In this study, a novel polymerase chain reaction method was developed to specifically identify M. tuberculosis strains belonging to the Beijing and non-Beijing evolutionary lineages in sputum specimens collected from tuberculosis patients resident in an epidemiologic field site in Cape Town, South Africa. The sensitivity and specificity of the polymerase chain reaction-based strain classification method were 100% (95% confidence interval, 85-100%) when compared with DNA fingerprinting and spacer oligotyping (spoligotyping). Application of this method showed that 19% of all patients were simultaneously infected with Beijing and non-Beijing strains, and 57% of patients infected with a Beijing strain were also infected with a non-Beijing strain. Multiple infections were more frequent in retreatment cases (23%) as compared with new cases (17%), but were not associated with sex, age, or smear grading. These results suggest that multiple infections are frequent, implying high reinfection rates and the absence of efficient protective immunity conferred by the initial infection. This finding could influence our understanding of the epidemiology of disease in high-incidence regions and our understanding for vaccine development.
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Affiliation(s)
- Robin M Warren
- Medical Research Council Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, Stellenbosch University, Tygerberg, South Africa.
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42
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Alland D, Whittam TS, Murray MB, Cave MD, Hazbon MH, Dix K, Kokoris M, Duesterhoeft A, Eisen JA, Fraser CM, Fleischmann RD. Modeling bacterial evolution with comparative-genome-based marker systems: application to Mycobacterium tuberculosis evolution and pathogenesis. J Bacteriol 2003; 185:3392-9. [PMID: 12754238 PMCID: PMC155390 DOI: 10.1128/jb.185.11.3392-3399.2003] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The comparative-genomic sequencing of two Mycobacterium tuberculosis strains enabled us to identify single nucleotide polymorphism (SNP) markers for studies of evolution, pathogenesis, and epidemiology in clinical M. tuberculosis. Phylogenetic analysis using these "comparative-genome markers" (CGMs) produced a highly unusual phylogeny with a complete absence of secondary branches. To investigate CGM-based phylogenies, we devised computer models to simulate sequence evolution and calculate new phylogenies based on an SNP format. We found that CGMs represent a distinct class of phylogenetic markers that depend critically on the genetic distances between compared "reference strains." Properly distanced reference strains generate CGMs that accurately depict evolutionary relationships, distorted only by branch collapse. Improperly distanced reference strains generate CGMs that distort and reroot outgroups. Applying this understanding to the CGM-based phylogeny of M. tuberculosis, we found evidence to suggest that this species is highly clonal without detectable lateral gene exchange. We noted indications of evolutionary bottlenecks, including one at the level of the PHRI "C" strain previously associated with particular virulence characteristics. Our evidence also suggests that loss of IS6110 to fewer than seven elements per genome is uncommon. Finally, we present population-based evidence that KasA, an important component of mycolic acid biosynthesis, develops G312S polymorphisms under selective pressure.
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Affiliation(s)
- David Alland
- Department of Medicine, Center for Emerging Pathogens, New Jersey Medical School, Newark, New Jersey 07103, USA.
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Sampson SL, Warren RM, Richardson M, Victor TC, Jordaan AM, van der Spuy GD, van Helden PD. IS6110-mediated deletion polymorphism in the direct repeat region of clinical isolates of Mycobacterium tuberculosis. J Bacteriol 2003; 185:2856-66. [PMID: 12700265 PMCID: PMC154393 DOI: 10.1128/jb.185.9.2856-2866.2003] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
This study investigates the phenomenon of IS6110-mediated deletion polymorphism in the direct repeat (DR) region of the genome of Mycobacterium tuberculosis. Clinical isolates and their putative predecessors were compared using a combination of DR region restriction fragment length polymorphism, IS6110 DNA fingerprinting, spoligotyping, and DNA sequencing, which allowed the mapping of chromosome structure and deletion junctions. The data suggest that adjacently situated IS6110 elements mediate genome deletion. However, in contrast to previous reports, deletions appear to be mediated by inversely oriented IS6110 elements. This suggests that these events may occur via mechanisms other than RecA-mediated homologous recombination. The results underscore the important role of IS6110-associated deletion hypervariability in driving M. tuberculosis genome evolution.
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Affiliation(s)
- S L Sampson
- MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, Faculty of Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa
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44
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Puustinen K, Marjamäki M, Rastogi N, Sola C, Filliol I, Ruutu P, Holmström P, Viljanen MK, Soini H. Characterization of Finnish Mycobacterium tuberculosis isolates by spoligotyping. J Clin Microbiol 2003; 41:1525-8. [PMID: 12682140 PMCID: PMC153930 DOI: 10.1128/jcm.41.4.1525-1528.2003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The molecular epidemiology of tuberculosis (TB) in Finland was studied by spoligotyping 380 Mycobacterium tuberculosis isolates. The isolates were obtained during a 1-year study period from July 2000 to June 2001 and represented 90% of new M. tuberculosis findings by culture in the whole country during the study period. The spoligotyping results were compared to the World Spoligotyping Database of the Institut Pasteur de Guadeloupe, which contains data from >14,000 M. tuberculosis isolates obtained worldwide. A total of 138 different spoligotypes were identified among the 380 M. tuberculosis isolates. Thirty-eight (10%) isolates had unique spoligotypes, while 342 (90%) isolates belonged to 100 shared types. The four most common spoligotypes caused approximately one-third of the Finnish TB cases. Forty-seven of the 138 (34.1%) spoligotypes and 61 (16.1%) of the 380 M. tuberculosis isolates had spoligotypes that had not been previously reported. Only four (1.1%) patients were infected with an isolate belonging to the Beijing genotype. The characterization of Finnish M. tuberculosis isolates by spoligotyping shows that ubiquitous spoligotypes were common, but many spoligotypes specific to Finland were also found. However, Beijing family isolates were rarely encountered, although this spoligotype is predominant in our eastern and southern neighbors.
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Affiliation(s)
- Kirsi Puustinen
- Mycobacterial Reference Laboratory, National Public Health Institute, Turku, Finland
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45
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Warren RM, Streicher EM, Sampson SL, van der Spuy GD, Richardson M, Nguyen D, Behr MA, Victor TC, van Helden PD. Microevolution of the direct repeat region of Mycobacterium tuberculosis: implications for interpretation of spoligotyping data. J Clin Microbiol 2002; 40:4457-65. [PMID: 12454136 PMCID: PMC154636 DOI: 10.1128/jcm.40.12.4457-4465.2002] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The direct repeat (DR) region has been determined to be an important chromosomal domain for studying the evolution of Mycobacterium tuberculosis. Despite this, very little is known about microevolutionary events associated with clonal expansion and how such events influence the interpretation of both restriction fragment length polymorphism (RFLP) and spoligotype data. This study examined the structure of the DR region in three independently evolving lineages of M. tuberculosis with a combination of DR-RFLP, spoligotyping, and partial DNA sequencing. The results show that the duplication of direct variable repeat (DVR) sequences and single-nucleotide polymorphisms is rare; conversely, the deletion of DVR sequences and IS6110-mediated mutation is observed frequently. Deletion of either single or contiguous DVR sequences was observed. The deletion of adjacent DVR sequences occurred in a dependent manner rather than as an accumulation of independent events. Insertion of IS6110 into either the direct repeat or spacer sequences influenced the spoligotype pattern, resulting in apparent deletion of DVR sequences. Homologous recombination between adjacent IS6110 elements led to extensive deletion in the DR region, again demonstrating a dependent evolutionary mechanism. Different isolates from the same strain family and isolates from different strain families were observed to converge to the same spoligotype pattern. In conclusion, the binary data of the spoligotype are unable to provide sufficient information to accurately establish genotypic relationships between certain clinical isolates of M. tuberculosis. This has important implications for molecular epidemiologic strain tracking and for the application of spoligotype data to phylogenetic analysis of M. tuberculosis isolates.
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Affiliation(s)
- R. M. Warren
- MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, Faculty of Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa, Department of Medicine, McGill University Health Centre, Montreal H3G 1A4, Canada
| | - E. M. Streicher
- MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, Faculty of Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa, Department of Medicine, McGill University Health Centre, Montreal H3G 1A4, Canada
| | - S. L. Sampson
- MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, Faculty of Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa, Department of Medicine, McGill University Health Centre, Montreal H3G 1A4, Canada
| | - G. D. van der Spuy
- MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, Faculty of Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa, Department of Medicine, McGill University Health Centre, Montreal H3G 1A4, Canada
| | - M. Richardson
- MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, Faculty of Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa, Department of Medicine, McGill University Health Centre, Montreal H3G 1A4, Canada
| | - D. Nguyen
- MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, Faculty of Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa, Department of Medicine, McGill University Health Centre, Montreal H3G 1A4, Canada
| | - M. A. Behr
- MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, Faculty of Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa, Department of Medicine, McGill University Health Centre, Montreal H3G 1A4, Canada
| | - T. C. Victor
- MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, Faculty of Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa, Department of Medicine, McGill University Health Centre, Montreal H3G 1A4, Canada
| | - P. D. van Helden
- MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, Faculty of Health Sciences, Stellenbosch University, Tygerberg 7505, South Africa, Department of Medicine, McGill University Health Centre, Montreal H3G 1A4, Canada
- Corresponding author. Mailing address: MRC Centre for Molecular and Cellular Biology, Department of Medical Biochemistry, Stellenbosch University, P.O. Box 19063, Tygerberg 7505, South Africa. Phone: 27 21 9389401. Fax: 27 21 9389467. E-mail:
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46
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Mokrousov I, Narvskaya O, Otten T, Vyazovaya A, Limeschenko E, Steklova L, Vyshnevskyi B. Phylogenetic reconstruction within Mycobacterium tuberculosis Beijing genotype in northwestern Russia. Res Microbiol 2002; 153:629-37. [PMID: 12558181 DOI: 10.1016/s0923-2508(02)01374-8] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A selection of genetic markers was used to study the evolution of Mycobacterium tuberculosis Beijing family strains in northwestern Russia. A total of 221 of 434 epidemiologically unlinked isolates studied in 1996-2001 belonged to the Beijing family as determined by standard spoligotyping (signals 35-43). Ninety-six percent of these Beijing isolates ("typical") were closely related in IS6110-RFLP (D > 0.85) while 9 remaining isolates (2 different profiles, "atypical") were more distant from the rest (D = 0.6-0.7). Further analysis was performed on a selection of 12 typical and both atypical Beijing strains with different IS6110-RFLP profiles (2 isolates each). All 28 Beijing isolates studied had the KatG 463Leu allele, an intact mtp40 fragment of the mpcA gene, and an identical structure of the DR locus (15 DVRs) with an upstream IS6110 copy in opposite orientation. The IS6110-RFLP based neighbor-joining (distance) and quartet-puzzling (maximum-likelihood) trees showed that the branch lengths were considerably longer for atypical Beijing strains. Typical Beijing strains had the 1.02 kb Rv3135 PPE-family gene and two IS1547 copies (iplA and iplB) one of them (iplB) disrupted by IS6110 insertion. Atypical Beijing strains had the 1.97 kb Rv3135 gene and a single intact IS1547/iplA copy. We suggest that the M. tuberculosis Beijing family strains currently circulating in the northwest of Russia are relatively ancient and thus appear to be endemic in this region since evolutionarily distant time. The prevalent typical Beijing strains (96%) are likely to be of monophyletic origin and their ongoing dissemination has started recently: these strains differ in rapidly evolving IS6110-RFLP but have identical structure of other polymorphic genome regions studied. The atypical Beijing strains (4%) are evolutionary older; they probably had a common (unknown) ancestor with typical Beijing strains.
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Affiliation(s)
- Igor Mokrousov
- Laboratory of Molecular Microbiology Pasteur Institute, St. Petersburg, 197101, Russia.
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47
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Fleischmann RD, Alland D, Eisen JA, Carpenter L, White O, Peterson J, DeBoy R, Dodson R, Gwinn M, Haft D, Hickey E, Kolonay JF, Nelson WC, Umayam LA, Ermolaeva M, Salzberg SL, Delcher A, Utterback T, Weidman J, Khouri H, Gill J, Mikula A, Bishai W, Jacobs WR, Venter JC, Fraser CM. Whole-genome comparison of Mycobacterium tuberculosis clinical and laboratory strains. J Bacteriol 2002; 184:5479-90. [PMID: 12218036 PMCID: PMC135346 DOI: 10.1128/jb.184.19.5479-5490.2002] [Citation(s) in RCA: 492] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Virulence and immunity are poorly understood in Mycobacterium tuberculosis. We sequenced the complete genome of the M. tuberculosis clinical strain CDC1551 and performed a whole-genome comparison with the laboratory strain H37Rv in order to identify polymorphic sequences with potential relevance to disease pathogenesis, immunity, and evolution. We found large-sequence and single-nucleotide polymorphisms in numerous genes. Polymorphic loci included a phospholipase C, a membrane lipoprotein, members of an adenylate cyclase gene family, and members of the PE/PPE gene family, some of which have been implicated in virulence or the host immune response. Several gene families, including the PE/PPE gene family, also had significantly higher synonymous and nonsynonymous substitution frequencies compared to the genome as a whole. We tested a large sample of M. tuberculosis clinical isolates for a subset of the large-sequence and single-nucleotide polymorphisms and found widespread genetic variability at many of these loci. We performed phylogenetic and epidemiological analysis to investigate the evolutionary relationships among isolates and the origins of specific polymorphic loci. A number of these polymorphisms appear to have occurred multiple times as independent events, suggesting that these changes may be under selective pressure. Together, these results demonstrate that polymorphisms among M. tuberculosis strains are more extensive than initially anticipated, and genetic variation may have an important role in disease pathogenesis and immunity.
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Affiliation(s)
- R D Fleischmann
- The Institute for Genomic Research, Rockville, Maryland 20850, USA.
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48
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Laurent JP, Faske S, Cangelosi GA. Characterization of IS999, an unstable genetic element in Mycobacterium avium. Gene 2002; 294:249-57. [PMID: 12234687 DOI: 10.1016/s0378-1119(02)00797-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
An IS3-family insertion element, IS999, was identified in the opportunistic pathogen Mycobacterium avium. The 1347 bp element has 29 bp inverted repeats and two overlapping open reading frames coding for putative transposases. It was detected in the genomes of ten of 12 M. avium isolates examined. Copy numbers ranged from four to 16. IS999 is less stable than IS1245, the most commonly-used marker for typing M. avium isolates. Among 60 colonies picked from a single patient isolate, there were two distinct IS1245 restriction fragment length polymorphism banding patterns compared to eight distinct IS999 patterns (five in one IS1245 group and three in the other). In view of its instability, we asked whether transposition of IS999 might have phenotypic consequences. Nucleotide sequence analysis of insertion sites in four isolates revealed 16 putative structural genes that were variably disrupted by IS999. Insertions into hdhA, a gene that codes for a putative short chain alcohol dehydrogenase, were distributed non-randomly between colony type variants, consistent with phenotypic consequences that exert selective pressure. These observations illustrate the genetic heterogeneity that can exist within populations of M. avium that appear to be homogeneous by IS1245 analysis. IS999 may be a useful marker for tracking, at the sub-strain level, the rapid genetic drift that M. avium isolates undergo in nature and in the laboratory.
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Affiliation(s)
- Jean-Pierre Laurent
- Seattle Biomedical Research Institute, 4 Nickerson Street, Seattle, WA 98109, USA
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49
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Parsons LM, Brosch R, Cole ST, Somoskövi A, Loder A, Bretzel G, Van Soolingen D, Hale YM, Salfinger M. Rapid and simple approach for identification of Mycobacterium tuberculosis complex isolates by PCR-based genomic deletion analysis. J Clin Microbiol 2002; 40:2339-45. [PMID: 12089245 PMCID: PMC120548 DOI: 10.1128/jcm.40.7.2339-2345.2002] [Citation(s) in RCA: 177] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although the virulences and host ranges differ among members of the Mycobacterium tuberculosis complex (TBC; M. tuberculosis, M. africanum, M. canettii, M. microti, M. bovis, and M. bovis BCG), commercially available molecular assays cannot differentiate these organisms because of the genetic identities of their 16S rRNA gene sequences. Comparative genomic analyses with the complete DNA sequence of M. tuberculosis H37Rv has provided information on regions of difference (RD 1 to RD 16) deleted in members of the TBC other than M. tuberculosis. To determine whether deletion analysis could accurately differentiate members of TBC, we used PCR to assess the presence or absence of specific regions of the genome in 88 well-characterized isolates of M. tuberculosis, M. africanum, M. microti, M. bovis, and M. bovis BCG. The identifications obtained by use of the specific deletion profiles correlated 100% with the original identifications for all TBC members except M. africanum, but further characterization resulted in profiles specific for all members. Although six RD regions were used in the analyses with the original 88 isolates, it was found that the use of RD 1, RD 9, and RD 10 was sufficient for initial screenings, followed by the use of RD 3, RD 5, and RD 11 if the results for any of the first three regions were negative. When 605 sequential clinical isolates were screened, 578 (96%) were identified as M. tuberculosis, 6 (1%) were identified as M. africanum, 8 (1%) were identified as M. bovis, and 13 (2%) were identified as M. bovis BCG. Since PCR-based assays can be implemented in most clinical mycobacteriology laboratories, this approach provides a rapid and simple means for the differentiation of members of TBC, especially M. bovis and M. tuberculosis, when it is important to distinguish between zoonotic sources (i.e., cattle and unpasteurized dairy products) and human sources of tuberculosis disease.
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Affiliation(s)
- Linda M Parsons
- Wadsworth Center, New York State Department of Health, Albany, NY 12208, USA.
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50
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Kivi M, Liu X, Raychaudhuri S, Altman RB, Small PM. Determining the genomic locations of repetitive DNA sequences with a whole-genome microarray: IS6110 in Mycobacterium tuberculosis. J Clin Microbiol 2002; 40:2192-8. [PMID: 12037086 PMCID: PMC130717 DOI: 10.1128/jcm.40.6.2192-2198.2002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The mycobacterial insertion sequence IS6110 has been exploited extensively as a clonal marker in molecular epidemiologic studies of tuberculosis. In addition, it has been hypothesized that this element is an important driving force behind genotypic variability that may have phenotypic consequences. We present here a novel, DNA microarray-based methodology, designated SiteMapping, that simultaneously maps the locations and orientations of multiple copies of IS6110 within the genome. To investigate the sensitivity, accuracy, and limitations of the technique, it was applied to eight Mycobacterium tuberculosis strains for which complete or partial IS6110 insertion site information had been determined previously. SiteMapping correctly located 64% (38 of 59) of the IS6110 copies predicted by restriction fragment length polymorphism analysis. The technique is highly specific; 97% of the predicted insertion sites were true insertions. Eight previously unknown insertions were identified and confirmed by PCR or sequencing. The performance could be improved by modifications in the experimental protocol and in the approach to data analysis. SiteMapping has general applicability and demonstrates an expansion in the applications of microarrays that complements conventional approaches in the study of genome architecture.
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Affiliation(s)
- Mårten Kivi
- Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University, Stanford, California 94305, USA
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