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Kay GL, Sergeant MJ, Zhou Z, Chan JZM, Millard A, Quick J, Szikossy I, Pap I, Spigelman M, Loman NJ, Achtman M, Donoghue HD, Pallen MJ. Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe. Nat Commun 2015; 6:6717. [PMID: 25848958 PMCID: PMC4396363 DOI: 10.1038/ncomms7717] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 02/18/2015] [Indexed: 01/05/2023] Open
Abstract
Tuberculosis (TB) was once a major killer in Europe, but it is unclear how the strains and patterns of infection at ‘peak TB' relate to what we see today. Here we describe 14 genome sequences of M. tuberculosis, representing 12 distinct genotypes, obtained from human remains from eighteenth-century Hungary using metagenomics. All our historic genotypes belong to M. tuberculosis Lineage 4. Bayesian phylogenetic dating, based on samples with well-documented dates, places the most recent common ancestor of this lineage in the late Roman period. We find that most bodies yielded more than one M. tuberculosis genotype and we document an intimate epidemiological link between infections in two long-dead individuals. Our results suggest that metagenomic approaches usefully inform detection and characterization of historical and contemporary infections. Tuberculosis was once a major killer in Europe. Here the authors use metagenomics to obtain genomic sequences of Mycobacterium tuberculosis from human remains from eighteenth-century Hungary, revealing mixed infections within individuals as well as presence of the same strain in two individuals.
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Affiliation(s)
- Gemma L Kay
- Microbiology and Infection Unit, Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Martin J Sergeant
- Microbiology and Infection Unit, Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Zhemin Zhou
- Microbiology and Infection Unit, Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Jacqueline Z-M Chan
- Microbiology and Infection Unit, Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Andrew Millard
- Microbiology and Infection Unit, Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Joshua Quick
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Ildikó Szikossy
- Department of Anthropology, Hungarian Natural History Museum, Ludovika tér 2-6, 1083 Budapest, Hungary
| | - Ildikó Pap
- Department of Anthropology, Hungarian Natural History Museum, Ludovika tér 2-6, 1083 Budapest, Hungary
| | - Mark Spigelman
- 1] Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv 9112102, Israel [2] Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Nicholas J Loman
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Mark Achtman
- Microbiology and Infection Unit, Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - Helen D Donoghue
- Centre for Clinical Microbiology, Division of Infection and Immunity, University College London, London NW3 2PF, UK
| | - Mark J Pallen
- Microbiology and Infection Unit, Division of Translational and Systems Medicine, Warwick Medical School, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
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van Hest NA, Aldridge RW, de Vries G, Sandgren A, Hauer B, Hayward A, Arrazola de Oñate W, Haas W, Codecasa LR, Caylà JA, Story A, Antoine D, Gori A, Quabeck L, Jonsson J, Wanlin M, Orcau Å, Rodes A, Dedicoat M, Antoun F, van Deutekom H, Keizer S, Abubakar I. Tuberculosis control in big cities and urban risk groups in the European Union: a consensus statement. ACTA ACUST UNITED AC 2014; 19. [PMID: 24626210 DOI: 10.2807/1560-7917.es2014.19.9.20728] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In low-incidence countries in the European Union (EU), tuberculosis (TB) is concentrated in big cities, especially among certain urban high-risk groups including immigrants from TB high-incidence countries, homeless people, and those with a history of drug and alcohol misuse. Elimination of TB in European big cities requires control measures focused on multiple layers of the urban population. The particular complexities of major EU metropolises, for example high population density and social structure, create specific opportunities for transmission, but also enable targeted TB control interventions, not efficient in the general population, to be effective or cost effective. Lessons can be learnt from across the EU and this consensus statement on TB control in big cities and urban risk groups was prepared by a working group representing various EU big cities, brought together on the initiative of the European Centre for Disease Prevention and Control. The consensus statement describes general and specific social, educational, operational, organisational, legal and monitoring TB control interventions in EU big cities, as well as providing recommendations for big city TB control, based upon a conceptual TB transmission and control model.
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Affiliation(s)
- N A van Hest
- Municipal Public Health Service Rotterdam-Rijnmond, Rotterdam, the Netherlands
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Qualitative Analysis To Ascertain Genotypic Identity of or Differences between Mycobacterium tuberculosis Isolates in Laboratories with Limited Resources. J Clin Microbiol 2013; 51:4230-3. [PMID: 24088847 DOI: 10.1128/jcm.02183-13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis is currently genotyped using mycobacterial interspersed repetitive-unit-variable-number tandem-repeat (MIRU-VNTR) typing, although the high cost of this technique restricts its implementation in resource-limited settings. We designed a MIRU-VNTR format, MLP3 (MIRU-VNTR length polymorphism triplex), that is based on the qualitative comparison of 5 nonfluorescent 3-band fingerprints in conventional electrophoresis and minimizes costs and technical demands. MLP3 successfully resolved cross-contamination alerts, discriminated reinfections from reactivations, clarified suspected microepidemics, and tracked transmission events of high epidemiological interest.
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