1
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L'Hôte L, Light I, Mattiangeli V, Teasdale MD, Halpin Á, Gourichon L, Key FM, Daly KG. An 8000 years old genome reveals the Neolithic origin of the zoonosis Brucella melitensis. Nat Commun 2024; 15:6132. [PMID: 39033187 PMCID: PMC11271283 DOI: 10.1038/s41467-024-50536-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Accepted: 07/15/2024] [Indexed: 07/23/2024] Open
Abstract
Brucella melitensis is a major livestock bacterial pathogen and zoonosis, causing disease and infection-related abortions in small ruminants and humans. A considerable burden to animal-based economies today, the presence of Brucella in Neolithic pastoral communities has been hypothesised but we lack direct genomic evidence thus far. We report a 3.45X B. melitensis genome preserved in an ~8000 year old sheep specimen from Menteşe Höyük, Northwest Türkiye, demonstrating that the pathogen had evolved and was circulating in Neolithic livestock. The genome is basal with respect to all known B. melitensis and allows the calibration of the B. melitensis speciation time from the primarily cattle-infecting B. abortus to approximately 9800 years Before Present (BP), coinciding with a period of consolidation and dispersal of livestock economies. We use the basal genome to timestamp evolutionary events in B. melitensis, including pseudogenization events linked to erythritol response, the supposed determinant of the pathogen's placental tropism in goats and sheep. Our data suggest that the development of herd management and multi-species livestock economies in the 11th-9th millennium BP drove speciation and host adaptation of this zoonotic pathogen.
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Affiliation(s)
- Louis L'Hôte
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Ian Light
- Max Planck Institute for Infection Biology, Evolutionary Pathogenomics, 10117, Berlin, Germany
| | | | - Matthew D Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
- Bioinformatics Support Unit, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Áine Halpin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Felix M Key
- Max Planck Institute for Infection Biology, Evolutionary Pathogenomics, 10117, Berlin, Germany
| | - Kevin G Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
- School of Agriculture and Food Science, University College Dublin, Dublin 4, Ireland.
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2
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Akar K, Holzer K, Hoelzle LE, Yıldız Öz G, Abdelmegid S, Baklan EA, Eroğlu B, Atıl E, Moustafa SA, Wareth G, Elkhayat M. An Evaluation of the Lineage of Brucella Isolates in Turkey by a Whole-Genome Single-Nucleotide Polymorphism Analysis. Vet Sci 2024; 11:316. [PMID: 39058000 PMCID: PMC11281417 DOI: 10.3390/vetsci11070316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2024] [Revised: 07/11/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Brucellosis is a disease caused by the Brucella (B.) species. It is a zoonotic disease that affects farm animals and causes economic losses in many countries worldwide. Brucella has the ability to persist in the environment and infect the host at low doses. Thus, it is more important to trace brucellosis outbreaks, identify their sources of infection, and interrupt their transmission. Some countries already have initial data, but most of these data are based on a Multiple-Locus Variable-Number Tandem-Repeat Analysis (MLVA), which is completely unsuitable for studying the Brucella genome. Since brucellosis is an endemic disease in Turkey, this study aimed to examine the genome of Turkish Brucella isolates collected between 2018 and 2020, except for one isolate, which was from 2012. A total of 28 strains of B. melitensis (n = 15) and B. abortus (n = 13) were analyzed using a core-genome single-nucleotide polymorphism (cgSNP) analysis. A potential connection between the Turkish isolates and entries from Sweden, Israel, Syria, Austria, and India for B. melitensis was detected. For B. abortus, there may be potential associations with entries from China. This explains the tight ties found between Brucella strains from neighboring countries and isolates from Turkey. Therefore, it is recommended that strict measures be taken and the possible effects of uncontrolled animal introduction are emphasized.
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Affiliation(s)
- Kadir Akar
- Faculty of Veterinary Medicine, Van Yuzuncu Yıl University, 65090 Van, Turkey
| | - Katharina Holzer
- Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, 70599 Stuttgart, Germany;
| | - Ludwig E. Hoelzle
- Department of Livestock Infectiology and Environmental Hygiene, Institute of Animal Science, University of Hohenheim, 70599 Stuttgart, Germany;
| | - Gülseren Yıldız Öz
- NRL for Brucellosis, Pendik Veterinary Control Institute, 34890 Istanbul, Turkey; (G.Y.Ö.); (E.A.B.); (B.E.); (E.A.)
| | | | - Emin Ayhan Baklan
- NRL for Brucellosis, Pendik Veterinary Control Institute, 34890 Istanbul, Turkey; (G.Y.Ö.); (E.A.B.); (B.E.); (E.A.)
| | - Buket Eroğlu
- NRL for Brucellosis, Pendik Veterinary Control Institute, 34890 Istanbul, Turkey; (G.Y.Ö.); (E.A.B.); (B.E.); (E.A.)
| | - Eray Atıl
- NRL for Brucellosis, Pendik Veterinary Control Institute, 34890 Istanbul, Turkey; (G.Y.Ö.); (E.A.B.); (B.E.); (E.A.)
| | - Shawky A. Moustafa
- Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt; (S.A.M.); (M.E.)
| | - Gamal Wareth
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institute, 07743 Jena, Germany;
- Institute of Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany
| | - Manar Elkhayat
- Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt; (S.A.M.); (M.E.)
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3
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Pochon Z, Bergfeldt N, Kırdök E, Vicente M, Naidoo T, van der Valk T, Altınışık NE, Krzewińska M, Dalén L, Götherström A, Mirabello C, Unneberg P, Oskolkov N. aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow. Genome Biol 2023; 24:242. [PMID: 37872569 PMCID: PMC10591440 DOI: 10.1186/s13059-023-03083-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 10/06/2023] [Indexed: 10/25/2023] Open
Abstract
Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been a challenge in ancient metagenomics, and the availability of computational frameworks that meet the demands of the field is limited. Here, we propose aMeta, an accurate metagenomic profiling workflow for ancient DNA designed to minimize the amount of false discoveries and computer memory requirements. Using simulated data, we benchmark aMeta against a current state-of-the-art workflow and demonstrate its superiority in microbial detection and authentication, as well as substantially lower usage of computer memory.
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Affiliation(s)
- Zoé Pochon
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Nora Bergfeldt
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Emrah Kırdök
- Department of Biotechnology, Faculty of Science, Mersin University, Mersin, Turkey
| | - Mário Vicente
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Thijessen Naidoo
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Ancient DNA Unit, Science for Life Laboratory, Stockholm, Sweden
- Ancient DNA Unit, Science for Life Laboratory, Uppsala, Sweden
| | - Tom van der Valk
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - N Ezgi Altınışık
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800, Beytepe, Ankara, Turkey
| | - Maja Krzewińska
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Love Dalén
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Claudio Mirabello
- Department of Physics, Chemistry and Biology, Science for Life Laboratory, National Bioinformatics Infrastructure Sweden, Linköping University, Linköping, Sweden
| | - Per Unneberg
- Department of Cell and Molecular Biology, Science for Life Laboratory, National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden
| | - Nikolay Oskolkov
- Department of Biology, Science for Life Laboratory, National Bioinformatics Infrastructure Sweden, Lund University, Lund, Sweden.
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4
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Rifkin RF, Vikram S, Alcorta J, Ramond JB, Cowan DA, Jakobsson M, Schlebusch CM, Lombard M. Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago. Commun Biol 2023; 6:240. [PMID: 36869137 PMCID: PMC9984395 DOI: 10.1038/s42003-023-04582-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 02/13/2023] [Indexed: 03/05/2023] Open
Abstract
The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, e.g., the sickle cell trait which provides protection against malaria, there is inadequate direct human genomic evidence for ancient human-pathogen infection in the region. Here, we analysed shotgun metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, c. 2000 years ago. This resulted in the identification of ancient DNA sequence reads homologous to Rickettsia felis, the causative agent of typhus-like flea-borne rickettsioses, and the reconstruction of an ancient R. felis genome.
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Affiliation(s)
- Riaan F Rifkin
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa.
- Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK.
| | - Surendra Vikram
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Jaime Alcorta
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Jean-Baptiste Ramond
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
- Department of Anthropology and Geography, Human Origins and Palaeoenvironmental Research Group, Oxford Brookes University, Oxford, UK
- Department of Molecular Genetics and Microbiology, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Don A Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hatfield, South Africa
| | - Mattias Jakobsson
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen, Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa
- SciLifeLab, Uppsala, Sweden
| | - Carina M Schlebusch
- Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen, Uppsala, Sweden
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa
- SciLifeLab, Uppsala, Sweden
| | - Marlize Lombard
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa.
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5
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Shevtsov A, Cloeckaert A, Berdimuratova K, Shevtsova E, Shustov AV, Amirgazin A, Karibayev T, Kamalova D, Zygmunt MS, Ramanculov Y, Vergnaud G. Brucella abortus in Kazakhstan, population structure and comparison with worldwide genetic diversity. Front Microbiol 2023; 14:1106994. [PMID: 37032899 PMCID: PMC10073595 DOI: 10.3389/fmicb.2023.1106994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 03/01/2023] [Indexed: 04/11/2023] Open
Abstract
Brucella abortus is the main causative agent of brucellosis in cattle, leading to severe economic consequences in agriculture and affecting public health. The zoonotic nature of the infection increases the need to control the spread and dynamics of outbreaks in animals with the incorporation of high resolution genotyping techniques. Based on such methods, B. abortus is currently divided into three clades, A, B, and C. The latter includes subclades C1 and C2. This study presents the results of whole-genome sequencing of 49 B. abortus strains isolated in Kazakhstan between 1947 and 2015 and of 36 B. abortus strains of various geographic origins isolated from 1940 to 2004. In silico Multiple Locus Sequence Typing (MLST) allowed to assign strains from Kazakhstan to subclades C1 and to a much lower extend C2. Whole-genome Single-Nucleotide Polymorphism (wgSNP) analysis of the 46 strains of subclade C1 with strains of worldwide origins showed clustering with strains from neighboring countries, mostly North Caucasia, Western Russia, but also Siberia, China, and Mongolia. One of the three Kazakhstan strains assigned to subclade C2 matched the B. abortus S19 vaccine strain used in cattle, the other two were genetically close to the 104 M vaccine strain. Bayesian phylodynamic analysis dated the introduction of B. abortus subclade C1 into Kazakhstan to the 19th and early 20th centuries. We discuss this observation in view of the history of population migrations from Russia to the Kazakhstan steppes.
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Affiliation(s)
- Alexandr Shevtsov
- National Center for Biotechnology, Astana, Kazakhstan
- *Correspondence: Alexandr Shevtsov,
| | | | | | | | | | | | | | | | | | - Yerlan Ramanculov
- National Center for Biotechnology, Astana, Kazakhstan
- School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
| | - Gilles Vergnaud
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
- Gilles Vergnaud,
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6
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van der Kuyl AC. Historic and Prehistoric Epidemics: An Overview of Sources Available for the Study of Ancient Pathogens. EPIDEMIOLOGIA (BASEL, SWITZERLAND) 2022; 3:443-464. [PMID: 36547255 PMCID: PMC9778136 DOI: 10.3390/epidemiologia3040034] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022]
Abstract
Since life on earth developed, parasitic microbes have thrived. Increases in host numbers, or the conquest of a new species, provide an opportunity for such a pathogen to enjoy, before host defense systems kick in, a similar upsurge in reproduction. Outbreaks, caused by "endemic" pathogens, and epidemics, caused by "novel" pathogens, have thus been creating chaos and destruction since prehistorical times. To study such (pre)historic epidemics, recent advances in the ancient DNA field, applied to both archeological and historical remains, have helped tremendously to elucidate the evolutionary trajectory of pathogens. These studies have offered new and unexpected insights into the evolution of, for instance, smallpox virus, hepatitis B virus, and the plague-causing bacterium Yersinia pestis. Furthermore, burial patterns and historical publications can help in tracking down ancient pathogens. Another source of information is our genome, where selective sweeps in immune-related genes relate to past pathogen attacks, while multiple viruses have left their genomes behind for us to study. This review will discuss the sources available to investigate (pre)historic diseases, as molecular knowledge of historic and prehistoric pathogens may help us understand the past and the present, and prepare us for future epidemics.
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Affiliation(s)
- Antoinette C. van der Kuyl
- Laboratory of Experimental Virology, Department of Medical Microbiology and Infection Prevention, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, 1105 AZ Amsterdam, The Netherlands; ; Tel.: +31-205-666-778
- Amsterdam Institute for Infection and Immunity, 1100 DD Amsterdam, The Netherlands
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7
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Moreno E. The one hundred year journey of the genus Brucella (Meyer and Shaw 1920). FEMS Microbiol Rev 2021; 45:5917985. [PMID: 33016322 DOI: 10.1093/femsre/fuaa045] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 09/08/2020] [Indexed: 12/18/2022] Open
Abstract
The genus Brucella, described by Meyer and Shaw in 1920, comprises bacterial pathogens of veterinary and public health relevance. For 36 years, the genus came to include three species that caused brucellosis in livestock and humans. In the second half of the 20th century, bacteriologists discovered five new species and several 'atypical' strains in domestic animals and wildlife. In 1990, the Brucella species were recognized as part of the Class Alphaproteobacteria, clustering with pathogens and endosymbionts of animals and plants such as Bartonella, Agrobacterium and Ochrobactrum; all bacteria that live in close association with eukaryotic cells. Comparisons with Alphaproteobacteria contributed to identify virulence factors and to establish evolutionary relationships. Brucella members have two circular chromosomes, are devoid of plasmids, and display close genetic relatedness. A proposal, asserting that all brucellae belong to a single species with several subspecies debated for over 70 years, was ultimately rejected in 2006 by the subcommittee of taxonomy, based on scientific, practical, and biosafety considerations. Following this, the nomenclature of having multiples Brucella species prevailed and defined according to their molecular characteristics, host preference, and virulence. The 100-year history of the genus corresponds to the chronicle of scientific efforts and the struggle for understanding brucellosis.
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Affiliation(s)
- Edgardo Moreno
- Programa de Investigación en Enfermedades Tropicales, Escuela de Medicina Veterinaria, Campues Benjamín Nuñez, Universidad Nacional, Heredia 40104, Costa Rica
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8
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Whatmore AM, Foster JT. Emerging diversity and ongoing expansion of the genus Brucella. INFECTION GENETICS AND EVOLUTION 2021; 92:104865. [PMID: 33872784 DOI: 10.1016/j.meegid.2021.104865] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 12/15/2022]
Abstract
Remarkable genetic diversity and breadth of host species has been uncovered in the Brucella genus over the past decade, fundamentally changing our concept of what it means to be a Brucella. From ocean fishes and marine mammals, to pond dwelling amphibians, forest foxes, desert rodents, and cave-dwelling bats, Brucella have revealed a variety of previously unknown niches. Classical microbiological techniques have been able to help us classify many of these new strains but at times have limited our ability to see the true relationships among or within species. The closest relatives of Brucella are soil bacteria and the adaptations of Brucella spp. to live intracellularly suggest that the genus has evolved to live in vertebrate hosts. Several recently discovered species appear to have phenotypes that are intermediate between soil bacteria and core Brucella, suggesting that they may represent ancestral traits that were subsequently lost in the traditional species. Remarkably, the broad relationships among Brucella species using a variety of sequence and fragment-based approaches have been upheld when using comparative genomics with whole genomes. Nonetheless, genomes are required for fine-scale resolution of many of the relationships and for understanding the evolutionary history of the genus. We expect that the coming decades will reveal many more hosts and previously unknown diversity in a wide range of environments.
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Affiliation(s)
- Adrian M Whatmore
- OIE and FAO Brucellosis Reference Laboratory, Department of Bacteriology, Animal and Plant Health Agency (APHA), Woodham Lane, Addlestone, Surrey, United Kingdom.
| | - Jeffrey T Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
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9
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Janowicz A, De Massis F, Zilli K, Ancora M, Tittarelli M, Sacchini F, Di Giannatale E, Sahl JW, Foster JT, Garofolo G. Evolutionary history and current distribution of the West Mediterranean lineage of Brucella melitensis in Italy. Microb Genom 2020; 6. [PMID: 33030422 PMCID: PMC7725330 DOI: 10.1099/mgen.0.000446] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Ovine and caprine brucellosis, caused by Brucella melitensis, is one of the world’s most widespread zoonoses and is a major cause of economic losses in domestic ruminant production. In Italy, the disease remains endemic in several southern provinces, despite an ongoing brucellosis eradication programme. In this study, we used whole-genome sequencing to detail the genetic diversity of circulating strains, and to examine the origins of the predominant sub-lineages of B. melitensis in Italy. We reconstructed a global phylogeny of B. melitensis, strengthened by 339 new whole-genome sequences, from Italian isolates collected from 2011 to 2018 as part of a national livestock surveillance programme. All Italian strains belonged to the West Mediterranean lineage, which further divided into two major clades that diverged roughly between the 5th and 7th centuries. We observed that Sicily serves as a brucellosis burden hotspot, giving rise to several distinct sub-lineages. More than 20 putative outbreak clusters of ovine and caprine brucellosis were identified, several of which persisted over the 8 year survey period despite an aggressive brucellosis eradication campaign. While the outbreaks in Central and Northern Italy were generally associated with introductions of single clones of B. melitensis and their subsequent dissemination within neighbouring territories, we observed weak geographical segregation of genotypes in the southern regions. Biovar determination, recommended in routine analysis of all Brucella strains by the World Organisation for Animal Health (OIE), could not discriminate among the four main global clades. This demonstrates a need for updating the guidelines used for monitoring B. melitensis transmission and spread, both at the national and international level, and to include whole-genome-based typing as the principal method for identification and tracing of brucellosis outbreaks.
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Affiliation(s)
- Anna Janowicz
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", via Campo Boario, 64100 Teramo, Italy
| | - Fabrizio De Massis
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", via Campo Boario, 64100 Teramo, Italy
| | - Katiuscia Zilli
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", via Campo Boario, 64100 Teramo, Italy
| | - Massimo Ancora
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", via Campo Boario, 64100 Teramo, Italy
| | - Manuela Tittarelli
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", via Campo Boario, 64100 Teramo, Italy
| | - Flavio Sacchini
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", via Campo Boario, 64100 Teramo, Italy
| | - Elisabetta Di Giannatale
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", via Campo Boario, 64100 Teramo, Italy
| | - Jason W Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Jeffrey T Foster
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Giuliano Garofolo
- National and OIE Reference Laboratory for Brucellosis, Istituto Zooprofilattico Sperimentale dell'Abruzzo e del Molise "G. Caporale", via Campo Boario, 64100 Teramo, Italy
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10
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Duchêne S, Ho SYW, Carmichael AG, Holmes EC, Poinar H. The Recovery, Interpretation and Use of Ancient Pathogen Genomes. Curr Biol 2020; 30:R1215-R1231. [PMID: 33022266 PMCID: PMC7534838 DOI: 10.1016/j.cub.2020.08.081] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The ability to sequence genomes from ancient biological material has provided a rich source of information for evolutionary biology and engaged considerable public interest. Although most studies of ancient genomes have focused on vertebrates, particularly archaic humans, newer technologies allow the capture of microbial pathogens and microbiomes from ancient and historical human and non-human remains. This coming of age has been made possible by techniques that allow the preferential capture and amplification of discrete genomes from a background of predominantly host and environmental DNA. There are now near-complete ancient genome sequences for three pathogens of considerable historical interest - pre-modern bubonic plague (Yersinia pestis), smallpox (Variola virus) and cholera (Vibrio cholerae) - and for three equally important endemic human disease agents - Mycobacterium tuberculosis (tuberculosis), Mycobacterium leprae (leprosy) and Treponema pallidum pallidum (syphilis). Genomic data from these pathogens have extended earlier work by paleopathologists. There have been efforts to sequence the genomes of additional ancient pathogens, with the potential to broaden our understanding of the infectious disease burden common to past populations from the Bronze Age to the early 20th century. In this review we describe the state-of-the-art of this rapidly developing field, highlight the contributions of ancient pathogen genomics to multidisciplinary endeavors and describe some of the limitations in resolving questions about the emergence and long-term evolution of pathogens.
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Affiliation(s)
- Sebastián Duchêne
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia.
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia
| | | | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Hendrik Poinar
- McMaster Ancient DNA Centre, Departments of Anthropology and Biochemistry, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4L9, Canada; Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, 1280 Main St. W., Hamilton, ON L8S 4L8, Canada; Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, Canada.
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11
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Host Diversity and Origin of Zoonoses: The Ancient and the New. Animals (Basel) 2020; 10:ani10091672. [PMID: 32957467 PMCID: PMC7552289 DOI: 10.3390/ani10091672] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/08/2020] [Accepted: 09/14/2020] [Indexed: 02/06/2023] Open
Abstract
Simple Summary There is a wide variety of diseases caused by bacteria, viruses, and parasites that are transmitted to humans by different routes from other animals. These diseases, known as zoonoses, represent 75% of new or reemerging infectious diseases. There is a considerable impact of these diseases on the economy and health at local and global levels, including zoonotic diseases caused by the ingestion of food and products derived from animals. The wide range of animal species that host these disease-causing organisms include all groups of mammals. Birds are the second significant animal group to act as hosts for zoonoses. Much progress has been made in understanding disease evolution and animal origin, with important contributions from fields such as paleopathology and analysis of DNA, applied to ancient human bone remains. The study of ancient diseases such as brucellosis and tuberculosis benefits from these approaches. More research is needed as new diseases emerge causing pandemics and some previously eradicated reemerge in some regions. Global efforts are focused, based on evidence generated by research, on the prevention of new pandemics. Abstract Bacterial, viral, and parasitic zoonotic diseases are transmitted to humans from a wide variety of animal species that act as reservoir hosts for the causative organisms. Zoonoses contribute an estimated 75% of new or reemerging infectious diseases in humans. All groups of mammals have been shown to act as hosts for transmission of different organisms that cause zoonoses, followed in importance by birds; with both wild and domestic species identified as hosts in specific cases. There has been considerable research progress leading to a better understanding of the host range, animal origin, evolution, and transmission of important zoonoses, including those caused by the ingestion of food and products derived from animals. Paleopathology studies of ancient human bone lesions, in combination with ancient DNA analysis of the causative pathogen, have contributed to our understanding of the origin of zoonotic diseases, including brucellosis and mycobacterial zoonoses. However, there are still knowledge gaps and new confirmed and potential hosts are reported locally with some frequency. Both the economic cost and burden of disease of zoonoses are substantial at local and global levels, as reflected by recent coronavirus pandemics that spread rapidly around the world. Evidence-based prevention strategies are currently a global priority increasingly recognized, especially in zoonoses-affected regions.
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Sabin S, Herbig A, Vågene ÅJ, Ahlström T, Bozovic G, Arcini C, Kühnert D, Bos KI. A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex. Genome Biol 2020; 21:201. [PMID: 32778135 PMCID: PMC7418204 DOI: 10.1186/s13059-020-02112-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 07/17/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Although tuberculosis accounts for the highest mortality from a bacterial infection on a global scale, questions persist regarding its origin. One hypothesis based on modern Mycobacterium tuberculosis complex (MTBC) genomes suggests their most recent common ancestor followed human migrations out of Africa approximately 70,000 years before present. However, studies using ancient genomes as calibration points have yielded much younger dates of less than 6000 years. Here, we aim to address this discrepancy through the analysis of the highest-coverage and highest-quality ancient MTBC genome available to date, reconstructed from a calcified lung nodule of Bishop Peder Winstrup of Lund (b. 1605-d. 1679). RESULTS A metagenomic approach for taxonomic classification of whole DNA content permitted the identification of abundant DNA belonging to the human host and the MTBC, with few non-TB bacterial taxa comprising the background. Genomic enrichment enabled the reconstruction of a 141-fold coverage M. tuberculosis genome. In utilizing this high-quality, high-coverage seventeenth-century genome as a calibration point for dating the MTBC, we employed multiple Bayesian tree models, including birth-death models, which allowed us to model pathogen population dynamics and data sampling strategies more realistically than those based on the coalescent. CONCLUSIONS The results of our metagenomic analysis demonstrate the unique preservation environment calcified nodules provide for DNA. Importantly, we estimate a most recent common ancestor date for the MTBC of between 2190 and 4501 before present and for Lineage 4 of between 929 and 2084 before present using multiple models, confirming a Neolithic emergence for the MTBC.
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Affiliation(s)
- Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Åshild J. Vågene
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
- Present address: Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Torbjörn Ahlström
- Department of Archaeology and Ancient History, Lund University, 221 00 Lund, Sweden
| | - Gracijela Bozovic
- Department of Medical Imaging and Clinical Physiology, Skåne University Hospital Lund and Lund University, 221 00 Lund, Sweden
| | - Caroline Arcini
- Arkeologerna, National Historical Museum, 226 60 Lund, Sweden
| | - Denise Kühnert
- Transmission, Infection, Diversification & Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Kirsten I. Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
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Arning N, Wilson DJ. The past, present and future of ancient bacterial DNA. Microb Genom 2020; 6:mgen000384. [PMID: 32598277 PMCID: PMC7478633 DOI: 10.1099/mgen.0.000384] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/18/2020] [Indexed: 12/12/2022] Open
Abstract
Groundbreaking studies conducted in the mid-1980s demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. Microbiologists were thus given a powerful tool to glimpse directly into inscrutable bacterial history, hitherto inaccessible due to a poor fossil record. Initially plagued by concerns regarding contamination, the field has grown alongside technical progress, with the advent of high-throughput sequencing being a breakthrough in sequence output and authentication. Albeit burdened with challenges unique to the analysis of bacteria, a growing number of viable sources for aDNA has opened multiple avenues of microbial research. Ancient pathogens have been extracted from bones, dental pulp, mummies and historical medical specimens and have answered focal historical questions such as identifying the aetiological agent of the black death as Yersinia pestis. Furthermore, ancient human microbiomes from fossilized faeces, mummies and dental plaque have shown shifts in human commensals through the Neolithic demographic transition and industrial revolution, whereas environmental isolates stemming from permafrost samples have revealed signs of ancient antimicrobial resistance. Culminating in an ever-growing repertoire of ancient genomes, the quickly expanding body of bacterial aDNA studies has also enabled comparisons of ancient genomes to their extant counterparts, illuminating the evolutionary history of bacteria. In this review we summarize the present avenues of research and contextualize them in the past of the field whilst also pointing towards questions still to be answered.
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Affiliation(s)
- Nicolas Arning
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF, UK
| | - Daniel J. Wilson
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford, OX3 7LF, UK
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Wareth G, El-Diasty M, Melzer F, Schmoock G, Moustafa SA, El-Beskawy M, Khater DF, Hamdy ME, Zaki HM, Ferreira AC, Ekateriniadou LV, Boukouvala E, Abdel-Glil MY, Menshawy AM, Sancho MP, Sakhria S, Pletz MW, Neubauer H. MLVA-16 Genotyping of Brucella abortus and Brucella melitensis Isolates from Different Animal Species in Egypt: Geographical Relatedness and the Mediterranean Lineage. Pathogens 2020; 9:pathogens9060498. [PMID: 32580472 PMCID: PMC7350383 DOI: 10.3390/pathogens9060498] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 01/16/2023] Open
Abstract
Brucellosis is a common zoonotic disease in Egypt. However, there are limited data available on the genetic diversity of brucellae circulating in Egypt and other Mediterranean areas. One hundred and nine Brucella (B.) strains were isolated from different animal species in thirteen Egyptian governorates. Multi-locus variable number tandem repeats (VNTRs) analysis (MLVA-16) was employed to determine the geographical relatedness and the genetic diversity of a panel of selected Egyptian strains (n = 69), with strains originating from Italy (n = 49), Portugal (n = 52), Greece (n = 63), and Tunisia (n = 4). Egyptian B. melitensis strains clustered into two main clusters containing 21 genotypes. Egyptian B. abortus strains clustered into three main clusters containing nine genotypes. The genotypes were irregularly distributed over time and space in the study area. Egyptian strains of B. melitensis showed MLVA-16 patterns closer to that of Italian strains. Egyptian B. abortus strains isolated from cattle share the same genotype with strains from Portugal and similar to strains from Italy with low genetic diversity. Strains with similar MLVA patterns isolated from different governorates highlight the movement of the pathogen among governorates. Hence, it may also reflect the long endemicity of brucellosis in Egypt with earlier dispersal of types and great local genetic diversity. Open markets may contribute to cross-species transmission and dissemination of the new types nationwide. The presence of West Mediterranean lineages of B. melitensis and relatedness of B. abortus strains from the studied countries is a result of the socio-historical connections among the Mediterranean countries. Transnational eradication of brucellosis in the Mediterranean basin is highly demanded.
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Affiliation(s)
- Gamal Wareth
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07743 Jena, Germany; (F.M.); (G.S.); (M.Y.A.-G.); (H.N.)
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany;
- Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh 13736, Egypt;
- Correspondence: ; Tel.: +4936418042296
| | - Mohamed El-Diasty
- Department of Brucellosis, Animal Health Research Institute, P.O. Box 264-Giza, Cairo 12618, Egypt; (M.E.-D.); (D.F.K.); (H.M.Z.)
| | - Falk Melzer
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07743 Jena, Germany; (F.M.); (G.S.); (M.Y.A.-G.); (H.N.)
| | - Gernot Schmoock
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07743 Jena, Germany; (F.M.); (G.S.); (M.Y.A.-G.); (H.N.)
| | - Shawky A. Moustafa
- Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh 13736, Egypt;
| | - Mohamed El-Beskawy
- Department of Animal Medicine, Faculty of Veterinary Medicine, Matrouh University, Matrouh 51744, Egypt;
| | - Dali F. Khater
- Department of Brucellosis, Animal Health Research Institute, P.O. Box 264-Giza, Cairo 12618, Egypt; (M.E.-D.); (D.F.K.); (H.M.Z.)
| | - Mahmoud E.R. Hamdy
- Department of Brucellosis, Animal Health Research Institute, P.O. Box 264-Giza, Cairo 12618, Egypt; (M.E.-D.); (D.F.K.); (H.M.Z.)
| | - Hoda M. Zaki
- Department of Brucellosis, Animal Health Research Institute, P.O. Box 264-Giza, Cairo 12618, Egypt; (M.E.-D.); (D.F.K.); (H.M.Z.)
| | - Ana Cristina Ferreira
- National Reference Laboratory for Brucellosis, National Institute of Agrarian and Veterinary Research (INIAV, IP), 157 Oeiras, Portugal;
- Faculdade de Ciências, Universidade de Lisboa, Biosystems and Integrative Sciences Institute (BioISI), Edificio TecLabs, Campus da FCUL, Campo Grande, 1749-016 Lisbon, Portugal
| | - Loukia V. Ekateriniadou
- Veterinary Research Institute, Hellenic Agricultural Organization- DEMETER, 54124 Thessaloniki, Greece; (L.V.E.); (E.B.)
| | - Evridiki Boukouvala
- Veterinary Research Institute, Hellenic Agricultural Organization- DEMETER, 54124 Thessaloniki, Greece; (L.V.E.); (E.B.)
| | - Mostafa Y. Abdel-Glil
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07743 Jena, Germany; (F.M.); (G.S.); (M.Y.A.-G.); (H.N.)
| | - Ahmed M.S. Menshawy
- Faculty of Veterinary Medicine, Beni-Suef University, Shamlaa Street, Beni-Suef 62511, Egypt;
| | - Marta Pérez Sancho
- Centro VISAVET, Universidad Complutense de Madrid, Avenida Puerta de Hierro, s/n, PC 28040 Madrid, Spain;
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Sonia Sakhria
- Institute of Veterinary Research of Tunisia, University of Tunis El Manar, Tunis 1006, Tunisia;
| | - Mathias W. Pletz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany;
| | - Heinrich Neubauer
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07743 Jena, Germany; (F.M.); (G.S.); (M.Y.A.-G.); (H.N.)
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Zoonotic brucellosis from the long view: Can the past contribute to the present? Infect Control Hosp Epidemiol 2020; 42:505-506. [PMID: 32618528 DOI: 10.1017/ice.2020.270] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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16
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Arriola LA, Cooper A, Weyrich LS. Palaeomicrobiology: Application of Ancient DNA Sequencing to Better Understand Bacterial Genome Evolution and Adaptation. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00040] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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" Bridging the Gap" Everything that Could Have Been Avoided If We Had Applied Gender Medicine, Pharmacogenetics and Personalized Medicine in the Gender-Omics and Sex-Omics Era. Int J Mol Sci 2019; 21:ijms21010296. [PMID: 31906252 PMCID: PMC6982247 DOI: 10.3390/ijms21010296] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/21/2019] [Accepted: 12/30/2019] [Indexed: 02/06/2023] Open
Abstract
Gender medicine is the first step of personalized medicine and patient-centred care, an essential development to achieve the standard goal of a holistic approach to patients and diseases. By addressing the interrelation and integration of biological markers (i.e., sex) with indicators of psychological/cultural behaviour (i.e., gender), gender medicine represents the crucial assumption for achieving the personalized health-care required in the third millennium. However, ‘sex’ and ‘gender’ are often misused as synonyms, leading to frequent misunderstandings in those who are not deeply involved in the field. Overall, we have to face the evidence that biological, genetic, epigenetic, psycho-social, cultural, and environmental factors mutually interact in defining sex/gender differences, and at the same time in establishing potential unwanted sex/gender disparities. Prioritizing the role of sex/gender in physiological and pathological processes is crucial in terms of efficient prevention, clinical signs’ identification, prognosis definition, and therapy optimization. In this regard, the omics-approach has become a powerful tool to identify sex/gender-specific disease markers, with potential benefits also in terms of socio-psychological wellbeing for each individual, and cost-effectiveness for National Healthcare systems. “Being a male or being a female” is indeed important from a health point of view and it is no longer possible to avoid “sex and gender lens” when approaching patients. Accordingly, personalized healthcare must be based on evidence from targeted research studies aimed at understanding how sex and gender influence health across the entire life span. The rapid development of genetic tools in the molecular medicine approaches and their impact in healthcare is an example of highly specialized applications that have moved from specialists to primary care providers (e.g., pharmacogenetic and pharmacogenomic applications in routine medical practice). Gender medicine needs to follow the same path and become an established medical approach. To face the genetic, molecular and pharmacological bases of the existing sex/gender gap by means of omics approaches will pave the way to the discovery and identification of novel drug-targets/therapeutic protocols, personalized laboratory tests and diagnostic procedures (sex/gender-omics). In this scenario, the aim of the present review is not to simply resume the state-of-the-art in the field, rather an opportunity to gain insights into gender medicine, spanning from molecular up to social and psychological stances. The description and critical discussion of some key selected multidisciplinary topics considered as paradigmatic of sex/gender differences and sex/gender inequalities will allow to draft and design strategies useful to fill the existing gap and move forward.
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Hübler R, Key FM, Warinner C, Bos KI, Krause J, Herbig A. HOPS: automated detection and authentication of pathogen DNA in archaeological remains. Genome Biol 2019; 20:280. [PMID: 31842945 PMCID: PMC6913047 DOI: 10.1186/s13059-019-1903-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 11/27/2019] [Indexed: 01/28/2023] Open
Abstract
High-throughput DNA sequencing enables large-scale metagenomic analyses of complex biological systems. Such analyses are not restricted to present-day samples and can also be applied to molecular data from archaeological remains. Investigations of ancient microbes can provide valuable information on past bacterial commensals and pathogens, but their molecular detection remains a challenge. Here, we present HOPS (Heuristic Operations for Pathogen Screening), an automated bacterial screening pipeline for ancient DNA sequences that provides detailed information on species identification and authenticity. HOPS is a versatile tool for high-throughput screening of DNA from archaeological material to identify candidates for genome-level analyses.
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Affiliation(s)
- Ron Hübler
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Felix M Key
- Max Planck Institute for the Science of Human History, Jena, Germany. .,Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. .,Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
| | | | - Kirsten I Bos
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Jena, Germany.
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19
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Wright GD. Environmental and clinical antibiotic resistomes, same only different. Curr Opin Microbiol 2019; 51:57-63. [DOI: 10.1016/j.mib.2019.06.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 06/10/2019] [Accepted: 06/20/2019] [Indexed: 10/26/2022]
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Abstract
Over the past decade, a genomics revolution, made possible through the development of high-throughput sequencing, has triggered considerable progress in the study of ancient DNA, enabling complete genomes of past organisms to be reconstructed. A newly established branch of this field, ancient pathogen genomics, affords an in-depth view of microbial evolution by providing a molecular fossil record for a number of human-associated pathogens. Recent accomplishments include the confident identification of causative agents from past pandemics, the discovery of microbial lineages that are now extinct, the extrapolation of past emergence events on a chronological scale and the characterization of long-term evolutionary history of microorganisms that remain relevant to public health today. In this Review, we discuss methodological advancements, persistent challenges and novel revelations gained through the study of ancient pathogen genomes.
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Bos KI, Kühnert D, Herbig A, Esquivel-Gomez LR, Andrades Valtueña A, Barquera R, Giffin K, Kumar Lankapalli A, Nelson EA, Sabin S, Spyrou MA, Krause J. Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens. Annu Rev Microbiol 2019; 73:639-666. [PMID: 31283430 DOI: 10.1146/annurev-micro-090817-062436] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The last century has witnessed progress in the study of ancient infectious disease from purely medical descriptions of past ailments to dynamic interpretations of past population health that draw upon multiple perspectives. The recent adoption of high-throughput DNA sequencing has led to an expanded understanding of pathogen presence, evolution, and ecology across the globe. This genomic revolution has led to the identification of disease-causing microbes in both expected and unexpected contexts, while also providing for the genomic characterization of ancient pathogens previously believed to be unattainable by available methods. In this review we explore the development of DNA-based ancient pathogen research, the specialized methods and tools that have emerged to authenticate and explore infectious disease of the past, and the unique challenges that persist in molecular paleopathology. We offer guidelines to mitigate the impact of these challenges, which will allow for more reliable interpretations of data in this rapidly evolving field of investigation.
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Affiliation(s)
- Kirsten I Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Luis Roger Esquivel-Gomez
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Aida Andrades Valtueña
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Karen Giffin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Aditya Kumar Lankapalli
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Elizabeth A Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany;
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany; .,Faculty of Biological Sciences, Friedrich Schiller University, 07737 Jena, Germany
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Rodríguez AM, Delpino MV, Miraglia MC, Giambartolomei GH. Immune Mediators of Pathology in Neurobrucellosis: From Blood to Central Nervous System. Neuroscience 2019; 410:264-273. [PMID: 31128159 DOI: 10.1016/j.neuroscience.2019.05.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 01/18/2023]
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Guellil M, Kersten O, Namouchi A, Bauer EL, Derrick M, Jensen AØ, Stenseth NC, Bramanti B. Genomic blueprint of a relapsing fever pathogen in 15th century Scandinavia. Proc Natl Acad Sci U S A 2018; 115:10422-10427. [PMID: 30249639 PMCID: PMC6187149 DOI: 10.1073/pnas.1807266115] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Louse-borne relapsing fever (LBRF) is known to have killed millions of people over the course of European history and remains a major cause of mortality in parts of the world. Its pathogen, Borrelia recurrentis, shares a common vector with global killers such as typhus and plague and is known for its involvement in devastating historical epidemics such as the Irish potato famine. Here, we describe a European and historical genome of Brecurrentis, recovered from a 15th century skeleton from Oslo. Our distinct European lineage has a discrete genomic makeup, displaying an ancestral oppA-1 gene and gene loss in antigenic variation sites. Our results illustrate the potential of ancient DNA research to elucidate dynamics of reductive evolution in a specialized human pathogen and to uncover aspects of human health usually invisible to the archaeological record.
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Affiliation(s)
- Meriam Guellil
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway;
| | - Oliver Kersten
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway
| | - Amine Namouchi
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway
| | - Egil L Bauer
- Norwegian Institute for Cultural Heritage Research, N-0155 Oslo, Norway
| | - Michael Derrick
- Norwegian Institute for Cultural Heritage Research, N-0155 Oslo, Norway
| | - Anne Ø Jensen
- Norwegian Institute for Cultural Heritage Research, N-0155 Oslo, Norway
| | - Nils C Stenseth
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway;
| | - Barbara Bramanti
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, N-0316 Oslo, Norway;
- Department of Biomedical and Specialty Surgical Sciences, Faculty of Medicine, Pharmacy and Prevention, University of Ferrara, 35-441221 Ferrara, Italy
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Hull NC, Schumaker BA. Comparisons of brucellosis between human and veterinary medicine. Infect Ecol Epidemiol 2018; 8:1500846. [PMID: 30083304 PMCID: PMC6063340 DOI: 10.1080/20008686.2018.1500846] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 07/04/2018] [Indexed: 11/16/2022] Open
Abstract
Brucellosis is the world's most widespread zoonosis, but also ranks as one of the seven most neglected diseases, according to the World Health Organization. Additionally, it is recognized as the world's most common laboratory-acquired infection. There are a reported 500,000 incident cases of human brucellosis per year. However, true incidence is estimated to be 5,000,000 to 12,500,000 cases annually. Once diagnosed, focus is directed at treating individual patients with antibiotic regimes, yet overall neglecting the animal reservoir of disease. Countries with the highest incidence of human brucellosis are Syria (1,603.4 cases per 1,000,000 individuals), Mongolia (391.0), and Tajikistan (211.9). Surveillance on animal populations is lacking in many developed and developing countries. According to the World Animal Health Information Database, Mexico had the largest number of reported outbreaks, 5,514 in 2014. Mexico is followed by China (2,138), Greece (1,268), and Brazil (1,142). The majority of these outbreaks is Brucella abortus, the etiologic agent of bovine brucellosis. Brucellosis is an ancient disease that still plagues the world. There are still knowledge gaps and a need for better diagnostics and vaccines to make inroads towards control and eradication.
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Affiliation(s)
- Noah C. Hull
- Department of Veterinary Sciences, University of Wyoming, Laramie, Wyoming, USA
| | - Brant A. Schumaker
- Department of Veterinary Sciences, University of Wyoming, Laramie, Wyoming, USA
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The Role of aDNA in Understanding the Coevolutionary Patterns of Human Sexually Transmitted Infections. Genes (Basel) 2018; 9:genes9070317. [PMID: 29941858 PMCID: PMC6070984 DOI: 10.3390/genes9070317] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 06/18/2018] [Accepted: 06/20/2018] [Indexed: 12/18/2022] Open
Abstract
Analysis of pathogen genome data sequenced from clinical and historical samples has made it possible to perform phylogenetic analyses of sexually transmitted infections on a global scale, and to estimate the diversity, distribution, and coevolutionary host relationships of these pathogens, providing insights into pathogen emergence and disease prevention. Deep-sequenced pathogen genomes from clinical studies and ancient samples yield estimates of within-host and between-host evolutionary rates and provide data on changes in pathogen genomic stability and evolutionary responses. Here we examine three groups of pathogens transmitted mainly through sexual contact between modern humans to provide insight into ancient human behavior and history with their pathogens. Exploring ancient pathogen genomic divergence and the ancient viral-host parallel evolutionary histories will help us to reconstruct the origin of present-day geographical distribution and diversity of clinical pathogen infections, and will hopefully allow us to foresee possible environmentally induced pathogen evolutionary responses. Lastly, we emphasize that ancient pathogen DNA research should be combined with modern clinical pathogen data, and be equitable and provide advantages for all researchers worldwide, e.g., through shared data.
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Abou Zaki N, Salloum T, Osman M, Rafei R, Hamze M, Tokajian S. Typing and comparative genome analysis of Brucella melitensis isolated from Lebanon. FEMS Microbiol Lett 2018; 364:4157788. [PMID: 28961704 DOI: 10.1093/femsle/fnx199] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 09/12/2017] [Indexed: 01/20/2023] Open
Abstract
Brucella melitensis is the main causative agent of the zoonotic disease brucellosis. This study aimed at typing and characterizing genetic variation in 33 Brucella isolates recovered from patients in Lebanon. Bruce-ladder multiplex PCR and PCR-RFLP of omp31, omp2a and omp2b were performed. Sixteen representative isolates were chosen for draft-genome sequencing and analyzed to determine variations in virulence, resistance, genomic islands, prophages and insertion sequences. Comparative whole-genome single nucleotide polymorphism analysis was also performed. The isolates were confirmed to be B. melitensis. Genome analysis revealed multiple virulence determinants and efflux pumps. Genome comparisons and single nucleotide polymorphisms divided the isolates based on geographical distribution but revealed high levels of similarity between the strains. Sequence divergence in B. melitensis was mainly due to lateral gene transfer of mobile elements. This is the first report of an in-depth genomic characterization of B. melitensis in Lebanon.
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Affiliation(s)
- Natalia Abou Zaki
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos 36, Lebanon
| | - Tamara Salloum
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos 36, Lebanon
| | - Marwan Osman
- Health and Environmental Microbiology Laboratory, Doctoral School for Sciences and Technology and Faculty of Public Health-Lebanese University, Tripoli 1300, Lebanon
| | - Rayane Rafei
- Health and Environmental Microbiology Laboratory, Doctoral School for Sciences and Technology and Faculty of Public Health-Lebanese University, Tripoli 1300, Lebanon
| | - Monzer Hamze
- Health and Environmental Microbiology Laboratory, Doctoral School for Sciences and Technology and Faculty of Public Health-Lebanese University, Tripoli 1300, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos 36, Lebanon
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Genotyping of Brucella melitensis and Brucella abortus strains in Kazakhstan using MLVA-15. INFECTION GENETICS AND EVOLUTION 2017; 58:135-144. [PMID: 29278754 DOI: 10.1016/j.meegid.2017.12.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 12/06/2017] [Accepted: 12/21/2017] [Indexed: 11/27/2022]
Abstract
Currently, although the prevalence of brucellosis in Kazakhstan remains high, there are limited data available on the genetic diversity of circulating Brucella strains. Here, MLVA was employed to genotype a panel of 102 Brucella isolates collected from eight Kazakh regions and neighboring countries (Russia, Kyrgyzstan) during the period 1935-2017. MLVA-11 analysis classified 64 B. abortus strains into genotypes 72, 82, 331, 71, 341 and 69, while one genotype was novel, having no correspondence within the MLVA international database. MLVA-11 analysis of 37 B. melitensis strains showed 100% identity with genotypes 116, 114 and 11. One B. suis strain was classified into genotype 33. Phylogeography based on MLVA-15 demonstrated that all B. abortus and B. melitensis strains belonged to "Abortus C" and "East Mediterranean" lineages, respectively. B. abortus strains from Kazakhstan and Russia resulted genetically related to Portuguese, Brazilian and US isolates, suggesting ancient spread of these lineages from Europe westwards to South America and eastwards to Turkey, Russia and Asia. Most of Kazakh B. melitensis isolates were related to strains circulating in China, likely due to long-term trading partnerships between the two countries. In fine-scale MLVA-15 analysis, 17 B. abortus and 12 B. melitensis genotypes were identified; among them 12 are novel. Interestingly, epidemiological information supporting molecular data were retrieved for two clusters within the B. abortus group, thus proving that MLVA is an appropriate tool for effective traceback analyses. Our findings suggest that molecular genotyping should be applied systematically to support control plans for eradication of brucellosis in Kazakhstan.
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Rifkin RF, Potgieter M, Ramond J, Cowan DA. Ancient oncogenesis, infection and human evolution. Evol Appl 2017; 10:949-964. [PMID: 29151852 PMCID: PMC5680625 DOI: 10.1111/eva.12497] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 05/22/2017] [Indexed: 12/27/2022] Open
Abstract
The recent discovery that malignant neoplastic lesions date back nearly 2 million years ago not only highlights the antiquity of cancer in the human lineage, but also provides remarkable insight into ancestral hominin disease pathology. Using these Early Pleistocene examples as a point of departure, we emphasize the prominent role of viral and bacterial pathogens in oncogenesis and evaluate the impact of pathogens on human evolutionary processes in Africa. In the Shakespearean vernacular "what's past is prologue," we highlight the significance of novel information derived from ancient pathogenic DNA. In particular, and given the temporal depth of human occupation in sub-Saharan Africa, it is emphasized that the region is ideally positioned to play a strategic role in the discovery of ancient pathogenic drivers of not only human mortality, but also human evolution. Ancient African pathogen genome data can provide novel revelations concerning human-pathogen coevolutionary processes, and such knowledge is essential for forecasting the ways in which emerging zoonotic and increasingly transmissible diseases might influence human demography and longevity in the future.
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Affiliation(s)
- Riaan F. Rifkin
- Center for Microbial Ecology and Genomics (CMEG)Department of GeneticsUniversity of PretoriaHatfieldSouth Africa
| | - Marnie Potgieter
- Center for Microbial Ecology and Genomics (CMEG)Department of GeneticsUniversity of PretoriaHatfieldSouth Africa
| | - Jean‐Baptiste Ramond
- Center for Microbial Ecology and Genomics (CMEG)Department of GeneticsUniversity of PretoriaHatfieldSouth Africa
| | - Don A. Cowan
- Center for Microbial Ecology and Genomics (CMEG)Department of GeneticsUniversity of PretoriaHatfieldSouth Africa
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Identification of genetic variants of Brucella spp. through genome-wide association studies. INFECTION GENETICS AND EVOLUTION 2017; 56:92-98. [PMID: 29154929 DOI: 10.1016/j.meegid.2017.11.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/08/2017] [Accepted: 11/14/2017] [Indexed: 12/25/2022]
Abstract
Brucellosis is an important zoonotic disease caused by Brucella spp. We present a phylogeny of 552 strains based on genome-wide single nucleotide polymorphisms (SNPs) determined by an alignment-free k-mer approach. A total of 138,029 SNPs were identified from 552 Brucella genomes. Of these, 31,152 and 106,877 were core and non-core SNPs, respectively. Based on pan-genome analysis 11,937 and 972 genes were identified as pan and core genome, respectively. The pan-genome-wide analysis studies (Pan-GWAS) could not identify the group-specific variants in Brucella spp. Therefore, we focused on SNP based genome-wide association studies (SNP-GWAS) to identify the species-specific genetic determinants in Brucella spp. Phylogenetic tree representing eleven recognized Brucella spp. showed 16 major lineages. We identified 143 species-specific SNPs in Brucella abortus that are conserved in 311 B. abortus genomes. Of these, 141 species-specific SNPs were confined in the positively significant SNPs of B. abortus using SNP-GWAS. Since conserved in all the B. abortus genomes studied, these SNPs might have originated very early during the evolution of B. abortus and might be responsible for the evolution of B. abortus with cattle as the preferred host. Similarly, we identified 383 species-specific SNPs conserved in 132 Brucella melitensis genomes. Of these 379 species-specific SNPs were identified as positively associated using GWAS. Interestingly, >98% of the SNPs that are significantly, positively associated with the traits showed 100% sensitivity and 100% specificity. These identified species-specific core-SNPs identified in Brucella genomes could be responsible for the speciation and their respective host adaptation.
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Luhmann N, Doerr D, Chauve C. Comparative scaffolding and gap filling of ancient bacterial genomes applied to two ancient Yersinia pestis genomes. Microb Genom 2017; 3:e000123. [PMID: 29114402 PMCID: PMC5643016 DOI: 10.1099/mgen.0.000123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Accepted: 06/07/2017] [Indexed: 12/12/2022] Open
Abstract
Yersinia pestis is the causative agent of the bubonic plague, a disease responsible for several dramatic historical pandemics. Progress in ancient DNA (aDNA) sequencing rendered possible the sequencing of whole genomes of important human pathogens, including the ancient Y. pestis strains responsible for outbreaks of the bubonic plague in London in the 14th century and in Marseille in the 18th century, among others. However, aDNA sequencing data are still characterized by short reads and non-uniform coverage, so assembling ancient pathogen genomes remains challenging and often prevents a detailed study of genome rearrangements. It has recently been shown that comparative scaffolding approaches can improve the assembly of ancient Y. pestis genomes at a chromosome level. In the present work, we address the last step of genome assembly, the gap-filling stage. We describe an optimization-based method AGapEs (ancestral gap estimation) to fill in inter-contig gaps using a combination of a template obtained from related extant genomes and aDNA reads. We show how this approach can be used to refine comparative scaffolding by selecting contig adjacencies supported by a mix of unassembled aDNA reads and comparative signal. We applied our method to two Y. pestis data sets from the London and Marseilles outbreaks, for which we obtained highly improved genome assemblies for both genomes, comprised of, respectively, five and six scaffolds with 95 % of the assemblies supported by ancient reads. We analysed the genome evolution between both ancient genomes in terms of genome rearrangements, and observed a high level of synteny conservation between these strains.
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Affiliation(s)
- Nina Luhmann
- 2Genome Informatics, Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany.,1International Research Training Group "Computational Methods for the Analysis of the Diversity and Dynamics of Genomes", Bielefeld University, Bielefeld, Germany
| | - Daniel Doerr
- 2Genome Informatics, Faculty of Technology and Center for Biotechnology, Bielefeld University, Bielefeld, Germany.,3School of Computer and Communication Sciences, EPFL, 1015 Lausanne, Switzerland
| | - Cedric Chauve
- 4Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada
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Tadepalli G, Konduru B, Murali HS, Batra HV. Intraperitoneal administration of a novel chimeric immunogen (rOP) elicits IFN-γ and IL-12p70 protective immune response in BALB/c mice against virulent Brucella. Immunol Lett 2017; 192:79-87. [PMID: 29106986 DOI: 10.1016/j.imlet.2017.10.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2017] [Revised: 10/03/2017] [Accepted: 10/24/2017] [Indexed: 02/02/2023]
Abstract
Recombinant engineering of immunologically active chimeric protein consisting of Omp19 and P39 domains of B. abortus (rOP), was purified under denaturing conditions upon expression in E. coli BL21 (DE3) and refolded to dynamic form. The immuno-protective efficacy of rOP was evaluated by challenging the BALB/c mice intraperitoneally (I.P) with the infective species of Brucella in the absence or presence of adjuvants, such as Aluminum hydroxide gel (Al), or Freund's Complete Adjuvant (FCA)/Incomplete Freund's Adjuvant (IFA). Surprisingly, after second boosting, mice received rOP per se were found to be immunogenic in terms of IgG response with the dominant expression of IgG2a and significant IFN-γ by splenic T cells, suggesting that rOP is a strong inducer of anti-Brucella immunity. The resulted anti-rOP antibodies recognized native Omp19 and P39 among species of Brucella with distinct double bands and single band against chimera in immunoblotting. An enhanced and comparable antibody response with varied IgG isotype combinations were noticed in the mice primed and boosted with rOP in adjuvants. However, rOP+FCA/IFA formulation was found to be the most effective in lymphocyte recall assays at inducing significant (P<0.001) proliferation index (P.I.) as well as increased Th1-coupled cytokines (IFN-γ, IL-2 and IL-12p70) than rOP+Al in response to rOP re-stimulation. Furthermore, in vitro defensive assay revealed that compared to anti-rOP antisera, the polyclonal anti-sera from rOP+adjuvants exhibited enhanced protection of RAW264.7 cells against virulent challenge by B. melitensis 16M and B. abortus 544. In addition, compared to sham group, enumeration of Brucella CFU after challenge with the above species showed a significant (P<0.01) reduction of bacteria (log CFU) in the macrophage cell lines and organs of vaccinated mice. On the whole, a relatively higher and faster reduction was noticed in the mice vaccinated with similar amount of purified antigen in Freund's adjuvant. Ability of inducing Th1 directed immune protection in the absence of adjuvant support, postulated rOP as a plausible entrant for developing a chimeric based subunit vaccine against Brucella.
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Affiliation(s)
- Ganesh Tadepalli
- Department of Microbiology, Defence Food Research Laboratory, Siddarthanagar, Mysore, Karnataka, India.
| | - Balakrishna Konduru
- Department of Microbiology, Defence Food Research Laboratory, Siddarthanagar, Mysore, Karnataka, India
| | | | - Harsh Vardhan Batra
- Department of Microbiology, Defence Food Research Laboratory, Siddarthanagar, Mysore, Karnataka, India
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Warinner C, Herbig A, Mann A, Fellows Yates JA, Weiß CL, Burbano HA, Orlando L, Krause J. A Robust Framework for Microbial Archaeology. Annu Rev Genomics Hum Genet 2017; 18:321-356. [PMID: 28460196 PMCID: PMC5581243 DOI: 10.1146/annurev-genom-091416-035526] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Microbial archaeology is flourishing in the era of high-throughput sequencing, revealing the agents behind devastating historical plagues, identifying the cryptic movements of pathogens in prehistory, and reconstructing the ancestral microbiota of humans. Here, we introduce the fundamental concepts and theoretical framework of the discipline, then discuss applied methodologies for pathogen identification and microbiome characterization from archaeological samples. We give special attention to the process of identifying, validating, and authenticating ancient microbes using high-throughput DNA sequencing data. Finally, we outline standards and precautions to guide future research in the field.
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Affiliation(s)
- Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany;
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma 73019
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany;
| | - Allison Mann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany;
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma 73019
| | - James A Fellows Yates
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany;
| | - Clemens L Weiß
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Hernán A Burbano
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, 1350 Copenhagen K, Denmark
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université Toulouse III - Paul Sabatier, Toulouse 31000, France
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany;
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Green EJ, Speller CF. Novel Substrates as Sources of Ancient DNA: Prospects and Hurdles. Genes (Basel) 2017; 8:E180. [PMID: 28703741 PMCID: PMC5541313 DOI: 10.3390/genes8070180] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 06/22/2017] [Accepted: 07/10/2017] [Indexed: 12/17/2022] Open
Abstract
Following the discovery in the late 1980s that hard tissues such as bones and teeth preserve genetic information, the field of ancient DNA analysis has typically concentrated upon these substrates. The onset of high-throughput sequencing, combined with optimized DNA recovery methods, has enabled the analysis of a myriad of ancient species and specimens worldwide, dating back to the Middle Pleistocene. Despite the growing sophistication of analytical techniques, the genetic analysis of substrates other than bone and dentine remain comparatively "novel". Here, we review analyses of other biological substrates which offer great potential for elucidating phylogenetic relationships, paleoenvironments, and microbial ecosystems including (1) archaeological artifacts and ecofacts; (2) calcified and/or mineralized biological deposits; and (3) biological and cultural archives. We conclude that there is a pressing need for more refined models of DNA preservation and bespoke tools for DNA extraction and analysis to authenticate and maximize the utility of the data obtained. With such tools in place the potential for neglected or underexploited substrates to provide a unique insight into phylogenetics, microbial evolution and evolutionary processes will be realized.
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Affiliation(s)
- Eleanor Joan Green
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
| | - Camilla F Speller
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York YO10 5DD, UK.
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Pathogens of Food Animals: Sources, Characteristics, Human Risk, and Methods of Detection. ADVANCES IN FOOD AND NUTRITION RESEARCH 2017; 82:277-365. [PMID: 28427535 DOI: 10.1016/bs.afnr.2016.12.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Pathogens associated with food production (livestock) animals come in many forms causing a multitude of disease for humans. For the purpose of this review, these infectious agents can be divided into three broad categories: those that are associated with bacterial disease, those that are associated with viruses, and those that are parasitic in nature. The goal of this chapter is to provide the reader with an overview of the most common pathogens that cause disease in humans through exposure via the food chain and the consequence of this exposure as well as risk and detection methods. We have also included a collection of unusual pathogens that although rare have still caused disease, and their recognition is warranted in light of emerging and reemerging diseases. These provide the reader an understanding of where the next big outbreak could occur. The influence of the global economy, the movement of people, and food makes understanding production animal-associated disease paramount to being able to address new diseases as they arise.
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35
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Fournié G, Pfeiffer DU, Bendrey R. Early animal farming and zoonotic disease dynamics: modelling brucellosis transmission in Neolithic goat populations. ROYAL SOCIETY OPEN SCIENCE 2017; 4:160943. [PMID: 28386446 PMCID: PMC5367282 DOI: 10.1098/rsos.160943] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 01/11/2017] [Indexed: 05/30/2023]
Abstract
Zoonotic pathogens are frequently hypothesized as emerging with the origins of farming, but evidence of this is elusive in the archaeological records. To explore the potential impact of animal domestication on zoonotic disease dynamics and human infection risk, we developed a model simulating the transmission of Brucella melitensis within early domestic goat populations. The model was informed by archaeological data describing goat populations in Neolithic settlements in the Fertile Crescent, and used to assess the potential of these populations to sustain the circulation of Brucella. Results show that the pathogen could have been sustained even at low levels of transmission within these domestic goat populations. This resulted from the creation of dense populations and major changes in demographic characteristics. The selective harvesting of young male goats, likely aimed at improving the efficiency of food production, modified the age and sex structure of these populations, increasing the transmission potential of the pathogen within these populations. Probable interactions between Neolithic settlements would have further promoted pathogen maintenance. By fostering conditions suitable for allowing domestic goats to become reservoirs of Brucella melitensis, the early stages of agricultural development were likely to promote the exposure of humans to this pathogen.
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Affiliation(s)
- Guillaume Fournié
- Veterinary Epidemiology, Economics and Public Health group, Department of Production and Population Health, Royal Veterinary College, University of London, Hawkshead Lane, North Mymms, Hatfield AL9 7TA, UK
| | - Dirk U. Pfeiffer
- Veterinary Epidemiology, Economics and Public Health group, Department of Production and Population Health, Royal Veterinary College, University of London, Hawkshead Lane, North Mymms, Hatfield AL9 7TA, UK
- School of Veterinary Medicine, City University of Hong Kong, Kowloon, Hong Kong
| | - Robin Bendrey
- Department of Archaeology, University of Reading, Whiteknights Box 226, Reading RG6 6AB, UK
- School of History, Classics and Archaeology, University of Edinburgh, William Robertson Wing, Old Medical School, Teviot Place, Edinburgh EH8 9AG, UK
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36
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Rascovan N, Telke A, Raoult D, Rolain JM, Desnues C. Exploring divergent antibiotic resistance genes in ancient metagenomes and discovery of a novel beta-lactamase family. ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:886-895. [PMID: 27518706 DOI: 10.1111/1758-2229.12453] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 08/04/2016] [Indexed: 05/28/2023]
Abstract
Antibiotic resistance in pathogenic bacteria is a major problem for human health. We analyzed metagenomic datasets from ancient and remote samples from diverse environmental sources and observed the presence of all the eleven antibiotic resistance genes (ARG) groups evaluated. Since ancient samples are not subjected to modern effects of antibiotic misuse, they represent a clean model to explore the natural diversity of ARG in the environment. Most sequences showed high divergence compared with known ARG, representing a much larger universe than the currently known and characterized ARGs. We explored whether proteins within the "divergent resistome" may correspond to functional ARG by characterizing a beta-lactamase hit with very low similarity to any known sequence (<45% to best BLAST hit in NCBI). By starting from purely in-silico data, we revived a new family of class B beta-lactamases from ancient medieval samples, which exhibited a very high penicillinase activity. In this work, we explored ancient resistomes and added novel support to previous works showing that the universe of ARG is naturally vast and diverse in microbial communities. Our results bring a new perspective to the exploration of environmental ARG and indicate that this gigantic reservoir represents a natural endless source of emerging resistances.
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Affiliation(s)
- Nicolás Rascovan
- Aix Marseille University, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Amar Telke
- Aix Marseille University, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
| | - Didier Raoult
- Aix Marseille University, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
- Fédération de Microbiologie Clinique, Hôpital de la Timone, Marseille, France
| | - Jean Marc Rolain
- Aix Marseille University, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
- Fédération de Microbiologie Clinique, Hôpital de la Timone, Marseille, France
| | - Christelle Desnues
- Aix Marseille University, URMITE, UM63, CNRS 7278, IRD 198, INSERM 1095, Marseille, France
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37
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Sun MJ, Di DD, Li Y, Zhang ZC, Yan H, Tian LL, Jing ZG, Li JP, Jiang H, Fan WX. Genotyping of Brucella melitensis and Brucella abortus strains currently circulating in Xinjiang, China. INFECTION GENETICS AND EVOLUTION 2016; 44:522-529. [DOI: 10.1016/j.meegid.2016.07.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 06/16/2016] [Accepted: 07/20/2016] [Indexed: 11/29/2022]
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38
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Andam CP, Worby CJ, Chang Q, Campana MG. Microbial Genomics of Ancient Plagues and Outbreaks. Trends Microbiol 2016; 24:978-990. [PMID: 27618404 DOI: 10.1016/j.tim.2016.08.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2016] [Revised: 07/29/2016] [Accepted: 08/16/2016] [Indexed: 01/22/2023]
Abstract
The recent use of next-generation sequencing methods to investigate historical disease outbreaks has provided us with an unprecedented ability to address important and long-standing questions in epidemiology, pathogen evolution, and human history. In this review, we present major findings that illustrate how microbial genomics has provided new insights into the nature and etiology of infectious diseases of historical importance, such as plague, tuberculosis, and leprosy. Sequenced isolates collected from archaeological remains also provide evidence for the timing of historical evolutionary events as well as geographic spread of these pathogens. Elucidating the genomic basis of virulence in historical diseases can provide relevant information on how we can effectively understand the emergence and re-emergence of infectious diseases today and in the future.
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Affiliation(s)
- Cheryl P Andam
- Harvard T. H. Chan School of Public Health, Department of Epidemiology, Boston, MA 02115, USA; University of New Hampshire, Department of Molecular, Cellular and Biomedical Sciences, Durham, NH 03824, USA.
| | - Colin J Worby
- Harvard T. H. Chan School of Public Health, Department of Epidemiology, Boston, MA 02115, USA
| | - Qiuzhi Chang
- Harvard T. H. Chan School of Public Health, Department of Epidemiology, Boston, MA 02115, USA
| | - Michael G Campana
- Smithsonian Conservation Biology Institute, Center for Conservation Genomics, 3001 Connecticut Avenue NW, Washington, DC 20008, USA.
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39
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Bianucci R, Loynes RD, Sutherland ML, Lallo R, Kay GL, Froesch P, Pallen MJ, Charlier P, Nerlich AG. Forensic Analysis Reveals Acute Decompensation of Chronic Heart Failure in a 3500-Year-Old Egyptian Dignitary. J Forensic Sci 2016; 61:1378-81. [DOI: 10.1111/1556-4029.13138] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 12/19/2015] [Accepted: 01/02/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Raffaella Bianucci
- Legal Medicine Section; Department of Public Health and Paediatric Sciences; University of Turin; Corso Galileo Galilei 22, 10126 Turin Italy
- UMR 7268; Laboratoire d'Anthropologie bio-culturelle; Droit, Etique & Santé (Adés); Faculté de Médecine de Marseille; Bd Pierre Dramard, BAT A CS, 80011 13444 Marseilles- Cedex 15- France
| | - Robert D. Loynes
- KNH Centre for Biomedical Egyptology; University of Manchester; 3.5 Stopford Building, Oxford Road Manchester, M13 9PT U.K
| | | | - Rudy Lallo
- Clinica Pinna Pintor; Via Amerigo Vespucci 61 10129 Turin Italy
| | - Gemma L. Kay
- Microbiology and Infection Unit; Warwick Medical School; University of Warwick; Medical School Building Coventry, West Midlands CV4 United Kingdom
| | - Philippe Froesch
- Section of Medical and Forensic Anthropology (UVSQ & Paris 5 University EA 4569); 2 Avenue de la source de la Bièvre, Montigny-le-Bretonneux 78180 France
| | - Mark J. Pallen
- Microbiology and Infection Unit; Warwick Medical School; University of Warwick; Medical School Building Coventry, West Midlands CV4 United Kingdom
| | - Philippe Charlier
- Section of Medical and Forensic Anthropology (UVSQ & Paris 5 University EA 4569); 2 Avenue de la source de la Bièvre, Montigny-le-Bretonneux 78180 France
| | - Andreas G. Nerlich
- Institute of Pathology; Klinikum München-Bogenhausen; Englschalkinger Str. 77 81925 Munich Germany
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Bianucci R, Araujo A, Pusch CM, Nerlich AG. The identification of malaria in paleopathology-An in-depth assessment of the strategies to detect malaria in ancient remains. Acta Trop 2015; 152:176-180. [PMID: 26366472 DOI: 10.1016/j.actatropica.2015.09.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 07/19/2015] [Accepted: 09/01/2015] [Indexed: 01/07/2023]
Abstract
The comprehensive analyses of human remains from various places and time periods, either by immunological or molecular approaches, provide circumstantial evidence that malaria tropica haunted humankind at least since dynastic ancient Egypt. Here we summarize the "actual state-of-the-art" of these bio-molecular investigations and offer a solid basis for the discussion of the paleopathology of malaria in human history.
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Affiliation(s)
- Raffaella Bianucci
- Department of Public Health and Paediatric Sciences, Laboratory of Physical Anthropology, University of Turin, Italy; Centre for Ecological and Evolutionary Synthesis (CEES), Department Biosciences, University of Oslo, Norway; UMR 7568, Laboratoire d'Anthropologie bio-culturelle, Droit, Etique & Santé (Adés), Faculté de Médecine de Marseille, France
| | - Adauto Araujo
- Laboratório de Paleoparasitologia, Escola Nacional de Saúde Pública Sérgio Arouca, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Carsten M Pusch
- Institute of Anthropology and Human Genetics, Division of Molecular Genetics, University of Tübingen, Germany
| | - Andreas G Nerlich
- Institute of Pathology, Klinikum München-Bogenhausen, Munich, Germany.
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Chen L, Zheng D, Liu B, Yang J, Jin Q. VFDB 2016: hierarchical and refined dataset for big data analysis--10 years on. Nucleic Acids Res 2015; 44:D694-7. [PMID: 26578559 PMCID: PMC4702877 DOI: 10.1093/nar/gkv1239] [Citation(s) in RCA: 913] [Impact Index Per Article: 101.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 11/02/2015] [Indexed: 12/21/2022] Open
Abstract
The virulence factor database (VFDB, http://www.mgc.ac.cn/VFs/) is dedicated to providing up-to-date knowledge of virulence factors (VFs) of various bacterial pathogens. Since its inception the VFDB has served as a comprehensive repository of bacterial VFs for over a decade. The exponential growth in the amount of biological data is challenging to the current database in regard to big data analysis. We recently improved two aspects of the infrastructural dataset of VFDB: (i) removed the redundancy introduced by previous releases and generated two hierarchical datasets--one core dataset of experimentally verified VFs only and another full dataset including all known and predicted VFs and (ii) refined the gene annotation of the core dataset with controlled vocabularies. Our efforts enhanced the data quality of the VFDB and promoted the usability of the database in the big data era for the bioinformatic mining of the explosively growing data regarding bacterial VFs.
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Affiliation(s)
- Lihong Chen
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100176, China
| | - Dandan Zheng
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100176, China
| | - Bo Liu
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100176, China
| | - Jian Yang
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100176, China
| | - Qi Jin
- MOH Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100176, China
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Abstract
Twenty years ago, the publication of the first bacterial genome sequence, from Haemophilus influenzae, shook the world of bacteriology. In this Timeline, we review the first two decades of bacterial genome sequencing, which have been marked by three revolutions: whole-genome shotgun sequencing, high-throughput sequencing and single-molecule long-read sequencing. We summarize the social history of sequencing and its impact on our understanding of the biology, diversity and evolution of bacteria, while also highlighting spin-offs and translational impact in the clinic. We look forward to a 'sequencing singularity', where sequencing becomes the method of choice for as-yet unthinkable applications in bacteriology and beyond.
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Affiliation(s)
- Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham B15 2TT, UK
| | - Mark J Pallen
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
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Coughlan LM, Cotter PD, Hill C, Alvarez-Ordóñez A. Biotechnological applications of functional metagenomics in the food and pharmaceutical industries. Front Microbiol 2015; 6:672. [PMID: 26175729 PMCID: PMC4485178 DOI: 10.3389/fmicb.2015.00672] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2015] [Accepted: 06/19/2015] [Indexed: 12/31/2022] Open
Abstract
Microorganisms are found throughout nature, thriving in a vast range of environmental conditions. The majority of them are unculturable or difficult to culture by traditional methods. Metagenomics enables the study of all microorganisms, regardless of whether they can be cultured or not, through the analysis of genomic data obtained directly from an environmental sample, providing knowledge of the species present, and allowing the extraction of information regarding the functionality of microbial communities in their natural habitat. Function-based screenings, following the cloning and expression of metagenomic DNA in a heterologous host, can be applied to the discovery of novel proteins of industrial interest encoded by the genes of previously inaccessible microorganisms. Functional metagenomics has considerable potential in the food and pharmaceutical industries, where it can, for instance, aid (i) the identification of enzymes with desirable technological properties, capable of catalyzing novel reactions or replacing existing chemically synthesized catalysts which may be difficult or expensive to produce, and able to work under a wide range of environmental conditions encountered in food and pharmaceutical processing cycles including extreme conditions of temperature, pH, osmolarity, etc; (ii) the discovery of novel bioactives including antimicrobials active against microorganisms of concern both in food and medical settings; (iii) the investigation of industrial and societal issues such as antibiotic resistance development. This review article summarizes the state-of-the-art functional metagenomic methods available and discusses the potential of functional metagenomic approaches to mine as yet unexplored environments to discover novel genes with biotechnological application in the food and pharmaceutical industries.
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Affiliation(s)
| | - Paul D Cotter
- Teagasc Food Research Centre Cork, Ireland ; Alimentary Pharmabiotic Centre Cork, Ireland
| | - Colin Hill
- Alimentary Pharmabiotic Centre Cork, Ireland ; School of Microbiology, University College Cork Cork, Ireland
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Quick J, Ashton P, Calus S, Chatt C, Gossain S, Hawker J, Nair S, Neal K, Nye K, Peters T, De Pinna E, Robinson E, Struthers K, Webber M, Catto A, Dallman TJ, Hawkey P, Loman NJ. Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella. Genome Biol 2015; 16:114. [PMID: 26025440 PMCID: PMC4702336 DOI: 10.1186/s13059-015-0677-2] [Citation(s) in RCA: 201] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Accepted: 05/14/2015] [Indexed: 12/30/2022] Open
Abstract
Background Foodborne outbreaks of Salmonella remain a pressing public health concern. We recently detected a large outbreak of Salmonella enterica serovar Enteritidis phage type 14b affecting more than 30 patients in our hospital. This outbreak was linked to community, national and European-wide cases. Hospital patients with Salmonella are at high risk, and require a rapid response. We initially investigated this outbreak by whole-genome sequencing using a novel rapid protocol on the Illumina MiSeq; we then integrated these data with whole-genome data from surveillance sequencing, thereby placing the outbreak in a national context. Additionally, we investigated the potential of a newly released sequencing technology, the MinION from Oxford Nanopore Technologies, in the management of a hospital outbreak of Salmonella. Results We demonstrate that rapid MiSeq sequencing can reduce the time to answer compared to the standard sequencing protocol with no impact on the results. We show, for the first time, that the MinION can acquire clinically relevant information in real time and within minutes of a DNA library being loaded. MinION sequencing permits confident assignment to species level within 20 min. Using a novel streaming phylogenetic placement method samples can be assigned to a serotype in 40 min and determined to be part of the outbreak in less than 2 h. Conclusions Both approaches yielded reliable and actionable clinical information on the Salmonella outbreak in less than half a day. The rapid availability of such information may facilitate more informed epidemiological investigations and influence infection control practices. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0677-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Joshua Quick
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK. .,NIHR Surgical Reconstruction and Microbiology Research Centre, University of Birmingham, Birmingham, B15 2TT, UK.
| | | | - Szymon Calus
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK. .,NIHR Surgical Reconstruction and Microbiology Research Centre, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Carole Chatt
- Public Health England, Field Epidemiology Service (Birmingham Office), Birmingham, UK.
| | - Savita Gossain
- Public Health England Birmingham Public Health Laboratory, Heart of England NHS Trust, Birmingham, UK.
| | - Jeremy Hawker
- Public Health England, Field Epidemiology Service (Birmingham Office), Birmingham, UK.
| | | | - Keith Neal
- Public Health England, Field Epidemiology Service (Birmingham Office), Birmingham, UK.
| | - Kathy Nye
- Public Health England Birmingham Public Health Laboratory, Heart of England NHS Trust, Birmingham, UK.
| | | | | | - Esther Robinson
- Department of Microbiology, University of Warwick, Warwick, UK.
| | - Keith Struthers
- Public Health England Birmingham Public Health Laboratory, Heart of England NHS Trust, Birmingham, UK.
| | - Mark Webber
- NIHR Surgical Reconstruction and Microbiology Research Centre, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Andrew Catto
- Medical Directorate, Heart of England NHS Trust, Birmingham, UK.
| | | | - Peter Hawkey
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK. .,Public Health England Birmingham Public Health Laboratory, Heart of England NHS Trust, Birmingham, UK.
| | - Nicholas J Loman
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, B15 2TT, UK.
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Abstract
Parasite finds in ancient material launched a new field of science: palaeoparasitology. Ever since the pioneering studies, parasites were identified in archaeological and palaeontological remains, some preserved for millions of years by fossilization. However, the palaeoparasitological record consists mainly of parasites found specifically in human archaeological material, preserved in ancient occupation sites, from prehistory until closer to 2015. The results include some helminth intestinal parasites still commonly found in 2015, such as Ascaris lumbricoides, Trichuris trichiura and hookworms, besides others such as Amoebidae and Giardia intestinalis, as well as viruses, bacteria, fungi and arthropods. These parasites as a whole provide important data on health, diet, climate and living conditions among ancient populations. This chapter describes the principal findings and their importance for knowledge on the origin and dispersal of infectious diseases.
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Tan KK, Tan YC, Chang LY, Lee KW, Nore SS, Yee WY, Mat Isa MN, Jafar FL, Hoh CC, AbuBakar S. Full genome SNP-based phylogenetic analysis reveals the origin and global spread of Brucella melitensis. BMC Genomics 2015; 16:93. [PMID: 25888205 PMCID: PMC4409723 DOI: 10.1186/s12864-015-1294-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 01/29/2015] [Indexed: 11/17/2022] Open
Abstract
Background Brucellosis is an important zoonotic disease that affects both humans and animals. We sequenced the full genome and characterised the genetic diversity of two Brucella melitensis isolates from Malaysia and the Philippines. In addition, we performed a comparative whole-genome single nucleotide polymorphism (SNP) analysis of B. melitensis strains collected from around the world, to investigate the potential origin and the history of the global spread of B. melitensis. Results Single sequencing runs of each genome resulted in draft genome sequences of MY1483/09 and Phil1136/12, which covered 99.85% and 99.92% of the complete genome sequences, respectively. The B. melitensis genome sequences, and two B. abortus strains used as the outgroup strains, yielded a total of 13,728 SNP sites. Phylogenetic analysis using whole-genome SNPs and geographical distribution of the isolates revealed spatial clustering of the B. melitensis isolates into five genotypes, I, II, III, IV and V. The Mediterranean strains, identified as genotype I, occupied the basal node of the phylogenetic tree, suggesting that B. melitensis may have originated from the Mediterranean regions. All of the Asian B. melitensis strains clustered into genotype II with the SEA strains, including the two isolates sequenced in this study, forming a distinct clade denoted here as genotype IId. Genotypes III, IV and V of B. melitensis demonstrated a restricted geographical distribution, with genotype III representing the African lineage, genotype IV representing the European lineage and genotype V representing the American lineage. Conclusion We showed that SNPs retrieved from the B. melitensis draft full genomes were sufficient to resolve the interspecies relationships between B. melitensis strains and to discriminate between the vaccine and endemic strains. Phylogeographic reconstruction of the history of B. melitensis global spread at a finer scale by using whole-genome SNP analyses supported the origin of all B. melitensis strains from the Mediterranean region. The possible global distribution of B. melitensis following the ancient trade routes was also consistent with whole-genome SNP phylogeny. The whole genome SNP phylogenetics analysis, hence is a powerful tool for intraspecies discrimination of closely related species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1294-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kim-Kee Tan
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia. .,Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Yung-Chie Tan
- Codon Genomics S/B, No 26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200, Seri Kembangan, Selangor, Malaysia.
| | - Li-Yen Chang
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia. .,Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Kok Wei Lee
- Codon Genomics S/B, No 26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200, Seri Kembangan, Selangor, Malaysia.
| | - Siti Sarah Nore
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Wai-Yan Yee
- Codon Genomics S/B, No 26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200, Seri Kembangan, Selangor, Malaysia.
| | - Mohd Noor Mat Isa
- Malaysia Genome Institute, Ministry of Science, Technology and Innovation, Jalan Bangi, 43000, Kajang, Selangor, Malaysia.
| | - Faizatul Lela Jafar
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Chee-Choong Hoh
- Codon Genomics S/B, No 26, Jalan Dutamas 7, Taman Dutamas, Balakong, 43200, Seri Kembangan, Selangor, Malaysia.
| | - Sazaly AbuBakar
- Tropical Infectious Diseases Research and Education Centre (TIDREC), University of Malaya, 50603, Kuala Lumpur, Malaysia. .,Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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Ancient pathogen genomics: insights into timing and adaptation. J Hum Evol 2014; 79:137-49. [PMID: 25532802 DOI: 10.1016/j.jhevol.2014.11.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 09/08/2014] [Accepted: 11/05/2014] [Indexed: 12/15/2022]
Abstract
Disease is a major cause of natural selection affecting human evolution, whether through a sudden pandemic or persistent morbidity and mortality. Recent contributions in the field of ancient pathogen genomics have advanced our understanding of the antiquity and nature of human-pathogen interactions through time. Technical advancements have facilitated the recovery, enrichment, and high-throughput sequencing of pathogen and parasite DNA from archived and archaeological remains. These time-stamped genomes are crucial for calibrating molecular clocks to infer the timing of evolutionary events, while providing finer-grain resolution to phylogenetic reconstructions and complex biogeographical patterns. Additionally, genome scale data allow better identification of substitutions linked to adaptations of the pathogen to their human hosts. As methodology continues to improve, ancient genomes of humans and their diverse microbiomes from a range of eras and archaeological contexts will enable population-level ancient analyses in the near future and a better understanding of their co-evolutionary history.
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Doughty EL, Sergeant MJ, Adetifa I, Antonio M, Pallen MJ. Culture-independent detection and characterisation of Mycobacterium tuberculosis and M. africanum in sputum samples using shotgun metagenomics on a benchtop sequencer. PeerJ 2014; 2:e585. [PMID: 25279265 PMCID: PMC4179564 DOI: 10.7717/peerj.585] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 08/28/2014] [Indexed: 01/27/2023] Open
Abstract
Tuberculosis remains a major global health problem. Laboratory diagnostic methods that allow effective, early detection of cases are central to management of tuberculosis in the individual patient and in the community. Since the 1880s, laboratory diagnosis of tuberculosis has relied primarily on microscopy and culture. However, microscopy fails to provide species- or lineage-level identification and culture-based workflows for diagnosis of tuberculosis remain complex, expensive, slow, technically demanding and poorly able to handle mixed infections. We therefore explored the potential of shotgun metagenomics, sequencing of DNA from samples without culture or target-specific amplification or capture, to detect and characterise strains from the Mycobacterium tuberculosis complex in smear-positive sputum samples obtained from The Gambia in West Africa. Eight smear- and culture-positive sputum samples were investigated using a differential-lysis protocol followed by a kit-based DNA extraction method, with sequencing performed on a benchtop sequencing instrument, the Illumina MiSeq. The number of sequence reads in each sputum-derived metagenome ranged from 989,442 to 2,818,238. The proportion of reads in each metagenome mapping against the human genome ranged from 20% to 99%. We were able to detect sequences from the M. tuberculosis complex in all eight samples, with coverage of the H37Rv reference genome ranging from 0.002X to 0.7X. By analysing the distribution of large sequence polymorphisms (deletions and the locations of the insertion element IS6110) and single nucleotide polymorphisms (SNPs), we were able to assign seven of eight metagenome-derived genomes to a species and lineage within the M. tuberculosis complex. Two metagenome-derived mycobacterial genomes were assigned to M. africanum, a species largely confined to West Africa; the others that could be assigned belonged to lineages T, H or LAM within the clade of "modern" M. tuberculosis strains. We have provided proof of principle that shotgun metagenomics can be used to detect and characterise M. tuberculosis sequences from sputum samples without culture or target-specific amplification or capture, using an accessible benchtop-sequencing platform, the Illumina MiSeq, and relatively simple DNA extraction, sequencing and bioinformatics protocols. In our hands, sputum metagenomics does not yet deliver sufficient depth of coverage to allow sequence-based sensitivity testing; it remains to be determined whether improvements in DNA extraction protocols alone can deliver this or whether culture, capture or amplification steps will be required. Nonetheless, we can foresee a tipping point when a unified automated metagenomics-based workflow might start to compete with the plethora of methods currently in use in the diagnostic microbiology laboratory.
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Affiliation(s)
- Emma L. Doughty
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Martin J. Sergeant
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | | | - Martin Antonio
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
- Medical Research Council Unit, Fajara, The Gambia
| | - Mark J. Pallen
- Microbiology and Infection Unit, Warwick Medical School, University of Warwick, Coventry, United Kingdom
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Abstract
The potentially debilitating zoonotic disease brucellosis is thought to have been a scourge of mankind throughout history. New work by Kay et al. [mBio 5(4):e01337-14, 2014] adds to evidence for this by exploiting the huge advances in next-generation sequencing technology and applying shotgun metagenomics to a calcified nodule obtained from a 14th-century skeleton from Sardinia. While not the first DNA-based confirmation of Brucella in medieval DNA samples, Kay et al.'s study goes much further than previous reports based on single gene fragments in that it allows a full-genome reconstruction and thus facilitates meaningful comparative analysis of relationships with extant Brucella strains. These analyses confirm the close relationship of the genome to contemporary isolates from the western Mediterranean, illustrating the continuity of this lineage in the region over centuries. The study, along with recent studies characterizing other ancient-pathogen genomes, confirms that shotgun metagenomics offers us a powerful tool to fully characterize pathogens from ancient samples. Such studies promise to revolutionize our understanding of the nature of infectious disease in these materials and of the wider picture of the emergence, evolution, and spread of bacterial pathogens over history.
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