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Jäger HY, Atz Zanotelli D, Maixner F, Nicklisch N, Alt KW, Meller H, Pap I, Szikossy I, Pálfi G, Zink AR. Hit or miss - A metagenomic evaluation of intra-bone variability of host pathogen load in tuberculosis-infected human remains. Tuberculosis (Edinb) 2023; 143S:102392. [PMID: 38012935 DOI: 10.1016/j.tube.2023.102392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 07/11/2023] [Accepted: 07/26/2023] [Indexed: 11/29/2023]
Abstract
Many sampling protocols have been established to successfully retrieve human DNA from archaeological remains, however the systematic detection of ancient pathogens remains challenging. Here, we present a first assessment of the intra-bone variability of metagenomic composition in human skeletal remains and its effect on the sampling success for Mycobacterium tuberculosis (MTB) and human endogenous DNA. For this purpose, four bone samples from published peer-reviewed studies with PCR-based evidence for ancient MTB DNA were selected. Two bone samples of a Neolithic individual from Halberstadt, Germany and two ribs of two 18th-century Hungarian church mummies were sampled at multiple locations for equal amounts, followed by DNA extraction and library construction. Shotgun sequencing data was generated for taxonomic profiling as well as quantitative and qualitative evaluation of MTB and human endogenous DNA. Despite low variance in microbial diversity within and across samples, intra-bone variability of up to 36.45- and 62.88-fold for authentic ancient MTB and human reads, respectively, was detected. This study demonstrates the variable sampling success for MTB and human endogenous DNA within single skeletal samples despite relatively consistent microbial composition and highlights how a multisampling approach can facilitate the detection of hotspots with highly concentrated pathogen and human endogenous DNA.
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Affiliation(s)
- Heidi Y Jäger
- Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy.
| | - Daniel Atz Zanotelli
- Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy.
| | - Frank Maixner
- Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy.
| | - Nicole Nicklisch
- Center of Natural and Cultural Human History, Danube Private University, Krems-Stein, Austria; State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany.
| | - Kurt W Alt
- Center of Natural and Cultural Human History, Danube Private University, Krems-Stein, Austria; State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany.
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany.
| | - Ildikó Pap
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, 6726, Szeged, Közép Fasor 52, Hungary; Department of Anthropology, Hungarian Natural History Museum, 1083, Budapest, Ludovika Tér 2-6, Hungary; Department of Biological Anthropology, Eötvös Loránd University, Faculty of Science, 1117, Budapest, Pázmány Péter Sétány 1/c, Hungary.
| | - Ildikó Szikossy
- Department of Anthropology, Hungarian Natural History Museum, 1083, Budapest, Ludovika Tér 2-6, Hungary; Department of Biological Anthropology, Eötvös Loránd University, Faculty of Science, 1117, Budapest, Pázmány Péter Sétány 1/c, Hungary.
| | - György Pálfi
- Department of Biological Anthropology, Faculty of Science and Informatics, University of Szeged, 6726, Szeged, Közép Fasor 52, Hungary.
| | - Albert R Zink
- Institute for Mummy Studies, Eurac Research, Viale Druso, 1, 39100, Bolzano, Italy.
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Skuce R, Breadon E, Allen A, Milne G, McCormick C, Hughes C, Rutherford D, Smith G, Thompson S, Graham J, Harwood R, Byrne A. Longitudinal dynamics of herd-level Mycobacterium bovis MLVA type surveillance in cattle in Northern Ireland 2003-2016. INFECTION GENETICS AND EVOLUTION 2019; 79:104131. [PMID: 31786341 DOI: 10.1016/j.meegid.2019.104131] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/28/2019] [Accepted: 11/27/2019] [Indexed: 02/02/2023]
Abstract
Investigating genetically-structured diversity in pathogen populations over time is important to better understand disease maintenance and spread. Herd-level surveillance of Mycobacterium bovis genotypes (multi-locus VNTR analysis types, MLVA types) from all culture-confirmed bovine tuberculosis (TB) herd cases was undertaken in Northern Ireland (NI), generating an unparalleled, longitudinal, population-level 14-year survey for this pathogen. Across this population, 295 genetically-distinct M. bovis MLVA types were identified in the 19,717 M. bovis isolates surveyed. Of these, the most frequent was MLVA type 002 (23.0%); 151 MLVA types were represented more than once, in groups ranging from 2 to 4438 isolates. Only 23 MLVA types were isolated in all 14 years. Investigating inter-annual frequency of M. bovis MLVA types, examples of statistically-significant expansions (MLVA types 002, 004, 006, 009 and 027), contractions (MLVA types 001, 007 and 011) and maintenance (MLVA types 003 and 005) were disclosed, during a period of fluctuating bovine TB herd-level incidence at the NI scale. The fixed period frequency distribution of MLVA types remained highly right-skewed. Novel VNTR copy number variant MLVA types (N = 242; an average of 17 per annum) were identified throughout the survey. The MLVA type distribution in the landscape was not random; MLVA types showed statistically-significant geographical localization and strong spatial associations with Divisional Veterinary Office (DVO) regions. There was also evidence of differential risk of particular MLVA types across breeds (Holstein/Friesian vs. other), age-class, and sex and some evidence of an association between the number of animals testing positive for bovine TB during the disclosing test and particular MLVA types, although there was substantial variation.
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Affiliation(s)
- R Skuce
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK; School of Biological Sciences, Queen's University Belfast, Belfast BT7 1NN, UK.
| | - E Breadon
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - A Allen
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - G Milne
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - C McCormick
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK; Veterinary Service and Animal Health Group, Department of Agriculture, Environment and Rural Affairs, Dundonald House, Stormont, Belfast BT4 3SB, UK
| | - C Hughes
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - D Rutherford
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK; Faculty of Electrical Engineering, Czech Technical University, Prague, Czech Republic (⁎)current address
| | - G Smith
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - S Thompson
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - J Graham
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK
| | - R Harwood
- Veterinary Service and Animal Health Group, Department of Agriculture, Environment and Rural Affairs, Dundonald House, Stormont, Belfast BT4 3SB, UK
| | - A Byrne
- Veterinary Sciences Division, Agri-food and Biosciences Institute (AFBI), Stoney Road, Stormont, Belfast BT4 3SD, UK; School of Biological Sciences, Queen's University Belfast, Belfast BT7 1NN, UK; One-Health Unit, Surveillance, Animal By-Products and TSEs (SAT), Division Department of Agriculture, Food and Marine (DAFM), Agriculture House, Dublin 2, Ireland
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Abstract
Tuberculosis is a significant global disease today, so understanding its origins and history is important. It is primarily a lung infection and is transmitted by infectious aerosols from person to person, so a high population density encourages its spread. The causative organism is Mycobacterium tuberculosis, an obligate pathogen in the M. tuberculosis complex that also contains closely related species, such as Mycobacterium bovis, that primarily infect animals. Typical bone lesions occur in about 5% of untreated infections. These can be recognized in historical and archaeological material, along with nonspecific paleopathology such as new bone formation (periostitis), especially on ribs. Based on such lesions, tuberculosis has been found in ancient Egypt, pre-Columbian America, and Neolithic Europe. The detection of M. tuberculosis ancient DNA (aDNA) by using PCR led to the development of the new field of paleomicrobiology. As a result, a large number of tuberculosis cases were recognized in mummified tissue and bones with nonspecific or no lesions. In parallel with these developments, M. tuberculosis cell wall lipid biomarkers have detected tuberculosis suggested by paleopathology and confirmed aDNA findings. In well-preserved cases, molecular typing has identified M. tuberculosis lineages and genotypes. The current interest in targeted enrichment, shotgun sequencing, and metagenomic analysis reveals ancient mixed infections with different M. tuberculosis strains and other pathogens. Identification of M. tuberculosis lineages from samples of known age enables the date of the emergence of strains and lineages to be calculated directly rather than by making assumptions on the rate of evolutionary change.
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Klein EY, Smith DL, Cohen JM, Laxminarayan R. Bioeconomic analysis of child-targeted subsidies for artemisinin combination therapies: a cost-effectiveness analysis. J R Soc Interface 2016; 12:rsif.2014.1356. [PMID: 25994293 PMCID: PMC4590492 DOI: 10.1098/rsif.2014.1356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The Affordable Medicines Facility for malaria (AMFm) was conceived as a global market-based mechanism to increase access to effective malaria treatment and prolong effectiveness of artemisinin. Although results from a pilot implementation suggested that the subsidy was effective in increasing access to high-quality artemisinin combination therapies (ACTs), the Global Fund has converted AMFm into a country-driven mechanism whereby individual countries could choose to fund the subsidy from within their country envelopes. Because the initial costs of the subsidy in the pilot countries was higher than expected, countries are also exploring alternatives to a universal subsidy, such as subsidizing only child doses. We examined the incremental cost-effectiveness of a child-targeted policy using an age-structured bioeconomic model of malaria from the provider perspective. Because the vast majority of malaria deaths occur in children, targeting children could potentially improve the cost-effectiveness of the subsidy, though it would avert significantly fewer deaths. However, the benefits of a child-targeted subsidy (i.e. deaths averted) are eroded as leakage (i.e. older individuals taking young child-targeted doses) increases, with few of the benefits of a universal subsidy gained (i.e. reductions in overall prevalence). Although potentially more cost-effective, a child-targeted subsidy must contain measures to reduce the possibility of leakage.
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Affiliation(s)
- Eili Y Klein
- Center for Disease Dynamics, Economics and Policy, Washington, DC, USA Department of Emergency Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - David L Smith
- Department of Zoology, University of Oxford, Oxford, UK Sanaria Institute for Global Health & Tropical Medicine, Rockville, MD, USA
| | | | - Ramanan Laxminarayan
- Center for Disease Dynamics, Economics and Policy, Washington, DC, USA Princeton Environmental Institute, Princeton University, Princeton, NJ, USA Public Health Foundation of India, New Delhi, India
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Wu Y, Aandahl RZ, Tanaka MM. Dynamics of bacterial insertion sequences: can transposition bursts help the elements persist? BMC Evol Biol 2015; 15:288. [PMID: 26690348 PMCID: PMC4687120 DOI: 10.1186/s12862-015-0560-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 12/06/2015] [Indexed: 01/22/2023] Open
Abstract
Background Currently there is no satisfactory explanation for why bacterial insertion sequences (ISs) widely occur across prokaryotes despite being mostly harmful to their host genomes. Rates of horizontal gene transfer are likely to be too low to maintain ISs within a population. IS-induced beneficial mutations may be important for both prevalence of ISs and microbial adaptation to changing environments but may be too rare to sustain IS elements in the long run. Environmental stress can induce elevated rates of IS transposition activities; such episodes are known as ‘transposition bursts’. By examining how selective forces and transposition events interact to influence IS dynamics, this study asks whether transposition bursts can lead to IS persistence. Results We show through a simulation model that ISs are gradually eliminated from a population even if IS transpositions occasionally cause advantageous mutations. With beneficial mutations, transposition bursts create variation in IS copy numbers and improve cell fitness on average. However, these benefits are not usually sufficient to overcome the negative selection against the elements, and transposition bursts amplify the mean fitness effect which, if negative, simply accelerates the extinction of ISs. If down regulation of transposition occurs, IS extinctions are reduced while ISs still generate variation amongst bacterial genomes. Conclusions Transposition bursts do not help ISs persist in a bacterial population in the long run because most burst-induced mutations are deleterious and therefore not favoured by natural selection. However, bursts do create more genetic variation through which occasional advantageous mutations can help organisms adapt. Regulation of IS transposition bursts and stronger positive selection of the elements interact to slow down the burst-induced extinction of ISs. Electronic supplementary material The online version of this article (doi:10.1186/s12862-015-0560-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yue Wu
- School of Biotechnology & Biomolecular Sciences, University of New South Wales, Sydney, 2052, NSW, Australia. .,Evolution & Ecology Research Centre, University of New South Wales, Sydney, 2052, NSW, Australia. .,Present address: Telethon Kids Institute, University of Western Australia, Perth, 6008, WA, Australia.
| | - Richard Z Aandahl
- School of Biotechnology & Biomolecular Sciences, University of New South Wales, Sydney, 2052, NSW, Australia. .,Evolution & Ecology Research Centre, University of New South Wales, Sydney, 2052, NSW, Australia.
| | - Mark M Tanaka
- School of Biotechnology & Biomolecular Sciences, University of New South Wales, Sydney, 2052, NSW, Australia. .,Evolution & Ecology Research Centre, University of New South Wales, Sydney, 2052, NSW, Australia.
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Witas HW, Donoghue HD, Kubiak D, Lewandowska M, Gładykowska-Rzeczycka JJ. Molecular studies on ancient M. tuberculosis and M. leprae: methods of pathogen and host DNA analysis. Eur J Clin Microbiol Infect Dis 2015. [PMID: 26210385 PMCID: PMC4545183 DOI: 10.1007/s10096-015-2427-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Humans have evolved alongside infectious diseases for millennia. Despite the efforts to reduce their incidence, infectious diseases still pose a tremendous threat to the world population. Fast development of molecular techniques and increasing risk of new epidemics have resulted in several studies that look to the past in order to investigate the origin and evolution of infectious diseases. Tuberculosis and leprosy have become frequent targets of such studies, owing to the persistence of their molecular biomarkers in ancient material and the characteristic skeletal lesions each disease may cause. This review examines the molecular methods used to screen for the presence of M. tuberculosis and M. leprae ancient DNA (aDNA) and their differentiation in ancient human remains. Examples of recent studies, mainly from Europe, that employ the newest techniques of molecular analysis are also described. Moreover, we present a specific approach based on assessing the likely immunological profile of historic populations, in order to further elucidate the influence of M. tuberculosis and M. leprae on historical human populations.
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Affiliation(s)
- H W Witas
- Department of Molecular Biology, Medical University of Łódź, Łódź, Poland,
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8
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Abril C, Vilei EM, Brodard I, Burnens A, Frey J, Miserez R. Discovery of insertion element ISCfe1: a new tool for Campylobacter fetus subspecies differentiation. Clin Microbiol Infect 2007; 13:993-1000. [PMID: 17697006 DOI: 10.1111/j.1469-0691.2007.01787.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The species Campylobacter fetus is divided into the subspecies C. fetus subsp. venerealis (CFV) and C. fetus subsp. fetus (CFF). CFV is the causative agent of bovine genital campylobacteriosis, a highly contagious venereal disease that may lead to serious reproductive problems, including sterility and abortion. In contrast, CFF can be isolated from the gastrointestinal tract of a wide range of host species, is associated with abortion in sheep and cattle, and can also be isolated from local and systemic infections in humans. Despite differences in host and niche preferences, microbiological differentiation of the two subspecies of C. fetus is extremely difficult. This study describes the identification of a new insertion element, ISCfe1, which is present exclusively in CFV strains, with highly conserved specific ISCfe1 insertion sites. The results are useful for identification and differentiation of the two C. fetus subspecies and will help in understanding the evolution and pathogenesis of C. fetus.
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Affiliation(s)
- C Abril
- National Centre for Zoonoses, Bacterial Animal Diseases and Antimicrobial Resistance, Institute of Veterinary Bacteriology, Vetsuisse Faculty, Bern, Switzerland.
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Kinzer-Ursem TL, Linderman JJ. Both ligand- and cell-specific parameters control ligand agonism in a kinetic model of g protein-coupled receptor signaling. PLoS Comput Biol 2007; 3:e6. [PMID: 17222056 PMCID: PMC1769407 DOI: 10.1371/journal.pcbi.0030006] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2006] [Accepted: 11/30/2006] [Indexed: 12/17/2022] Open
Abstract
G protein–coupled receptors (GPCRs) exist in multiple dynamic states (e.g., ligand-bound, inactive, G protein–coupled) that influence G protein activation and ultimately response generation. In quantitative models of GPCR signaling that incorporate these varied states, parameter values are often uncharacterized or varied over large ranges, making identification of important parameters and signaling outcomes difficult to intuit. Here we identify the ligand- and cell-specific parameters that are important determinants of cell-response behavior in a dynamic model of GPCR signaling using parameter variation and sensitivity analysis. The character of response (i.e., positive/neutral/inverse agonism) is, not surprisingly, significantly influenced by a ligand's ability to bias the receptor into an active conformation. We also find that several cell-specific parameters, including the ratio of active to inactive receptor species, the rate constant for G protein activation, and expression levels of receptors and G proteins also dramatically influence agonism. Expressing either receptor or G protein in numbers several fold above or below endogenous levels may result in system behavior inconsistent with that measured in endogenous systems. Finally, small variations in cell-specific parameters identified by sensitivity analysis as significant determinants of response behavior are found to change ligand-induced responses from positive to negative, a phenomenon termed protean agonism. Our findings offer an explanation for protean agonism reported in β2--adrenergic and α2A-adrenergic receptor systems. G protein–coupled receptors (GPCRs) are transmembrane proteins involved in physiological functions ranging from vasodilation and immune response to memory. The binding of both endogenous ligands (e.g., hormones, neurotransmitters) and exogenous ligands (e.g., pharmaceuticals) to these receptors initiates intracellular events that ultimately lead to cell responses. We describe a dynamic model for G protein activation, an immediate outcome of GPCR signaling, and use it together with efficient parameter variation and sensitivity analysis techniques to identify the key cell- and ligand-specific parameters that influence G protein activation. Our results show that although ligand-specific parameters do strongly influence cell response (either causing increases or decreases in G protein activation), cellular parameters may also dictate the magnitude and direction of G protein activation. We apply our findings to describe how protean agonism, a phenomenon in which the same ligand may induce both positive and negative responses, may result from changes in cell-specific parameters. These findings may be used to understand the molecular basis of different responses of cell types and tissues to pharmacological treatment. In addition, these methods may be applied generally to models of cellular signaling and will help guide experimental resources toward further characterization of the key parameters in these networks.
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Affiliation(s)
- Tamara L Kinzer-Ursem
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Jennifer J Linderman
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, United States of America
- * To whom correspondence should be addressed. E-mail:
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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: 63] [Impact Index Per Article: 3.0] [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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11
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Visca P, De Mori P, Festa A, Montrone ML, Amicosante M, Pucillo LP. Evaluation of the BDProbeTec strand displacement amplification assay in comparison with the AMTD II direct test for rapid diagnosis of tuberculosis. Clin Microbiol Infect 2004; 10:332-4. [PMID: 15059123 DOI: 10.1111/j.1198-743x.2004.00818.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The BDProbeTec MTB assay for direct detection of Mycobacterium tuberculosis was evaluated in comparison with the AMTD-II assay on 94 samples from different patients with clinical suspicion of tuberculosis. Using a combination of culture on Lowenstein-Jensen medium (with or without preculture in BACTEC 9000) and clinical diagnosis as the standard, BDProbeTec MTB showed high sensitivity and specificity (96.1% and 100%, respectively), similar to AMTD-II (96.1% and 97.1%, respectively), with significantly higher sensitivity than the Ziehl-Neelsen stain for acid-fast bacilli (73%, p < 0.05).
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Affiliation(s)
- P Visca
- Molecular Microbiology Unit, National Institute for Infectious Disease "Lazzaro Spallanzani"-I.R.C.C.S., Rome, Italy.
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13
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Dale JW, Al-Ghusein H, Al-Hashmi S, Butcher P, Dickens AL, Drobniewski F, Forbes KJ, Gillespie SH, Lamprecht D, McHugh TD, Pitman R, Rastogi N, Smith AT, Sola C, Yesilkaya H. Evolutionary relationships among strains of Mycobacterium tuberculosis with few copies of IS6110. J Bacteriol 2003; 185:2555-62. [PMID: 12670980 PMCID: PMC152614 DOI: 10.1128/jb.185.8.2555-2562.2003] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Molecular typing of Mycobacterium tuberculosis by using IS6110 shows low discrimination when there are fewer than five copies of the insertion sequence. Using a collection of such isolates from a study of the epidemiology of tuberculosis in London, we have shown a substantial degree of congruence between IS6110 patterns and both spoligotype and PGRS type. This indicates that the IS6110 types mainly represent distinct families of strains rather than arising through the convergent insertion of IS6110 into favored positions. This is supported by identification of the genomic sites of the insertion of IS6110 in these strains. The combined data enable identification of the putative evolutionary relationships of these strains, comprising three lineages broadly associated with patients born in South Asia (India and Pakistan), Africa, and Europe, respectively. These lineages appear to be quite distinct from M. tuberculosis isolates with multiple copies of IS6110.
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Affiliation(s)
- Jeremy W Dale
- School of Biomedical and Life Sciences, University of Surrey, Guildford, Surrey GU2 7XH, United Kingdom.
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14
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Moström P, Gordon M, Sola C, Ridell M, Rastogi N. Methods used in the molecular epidemiology of tuberculosis. Clin Microbiol Infect 2002; 8:694-704. [PMID: 12445006 DOI: 10.1046/j.1469-0691.2002.00460.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- P Moström
- Department of Medical Microbiology and Immunology, Göteborg University, Gothenburg, Sweden
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15
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Tanaka MM, Rosenberg NA. Optimal estimation of transposition rates of insertion sequences for molecular epidemiology. Stat Med 2001; 20:2409-20. [PMID: 11512131 DOI: 10.1002/sim.910] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Outbreaks of infectious disease can be confirmed by identifying clusters of DNA fingerprints among bacterial isolates from infected individuals. This procedure makes assumptions about the underlying properties of the genetic marker used for fingerprinting. In particular, it requires that each fingerprint changes sufficiently slowly within an individual that isolates from separate individuals infected by the same strain will exhibit similar or identical fingerprints. We propose a model for the probability that an individual's fingerprint will change over a given period of time. We use this model together with published data in order to estimate the fingerprint change rate for IS6110 in human tuberculosis, obtaining a value of 0.0139 changes per copy per year. Although we focus on insertion sequences (IS), our method applies to other fingerprinting techniques such as pulsed-field gel electrophoresis (PFGE). We suggest sampling intervals that produce the least error in estimates of the fingerprint change rate, as well as sample sizes that achieve specified levels of error in the estimate.
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Affiliation(s)
- M M Tanaka
- Department of Biological Sciences, Stanford University, CA 94305, USA.
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Abstract
Despite the use of highly sensitive molecular tools, such as polymerase chain reaction, for the detection of Mycobacterium tuberculosis, ocular tuberculosis remains a subject of controversy. The diagnosis is often presumptive in the absence of ocular biopsies. Choroiditis is the most common ocular manifestation in patients with pulmonary and systemic tuberculosis. Indocyanine green angiography seems to be an interesting method to determine choroidal involvement. PCR technology is proposed to evaluate the presence of the tubercule bacillus DNA in ocular fluids and tissues when conventional microbiologic methods fail to confirm a bacterial etiology. Most of the presumed cases of ocular tuberculosis should be treated with associations of antituberculous drug, especially when a systemic steroid regimen is required.
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Affiliation(s)
- B Bodaghi
- Department of Ophthalmology, CHU Pitié-Salpêtrière, Paris, France.
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