1
|
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.
Collapse
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
| |
Collapse
|
2
|
Soumya P, Kochupurackal J. Pineapple Peel Extract as an Effective Substrate for Esterase Production from Bacillus subtilis E9. Curr Microbiol 2020; 77:3024-3034. [PMID: 32683467 DOI: 10.1007/s00284-020-02073-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 06/03/2020] [Indexed: 12/24/2022]
Abstract
Esterase, belonging to hydrolase class of enzymes catalyzes the cleavage and formation of ester bonds. Esterase producing isolates E9 and E46, isolated from pineapple waste enriched soil were identified as Bacillus subtilis E9 and Bacillus sp. E46 respectively. Bacillus subtilis E9 with 10 U/mg esterase activity in basal media was further chosen for media optimization studies. Several factors including the effect of organic solvents and fruit peel extracts were studied by one factor at a time optimization method and statistical models. An enhanced enzyme production of 250.50 U/mg could be obtained under the optimal conditions of pH 6.5, incubation time 25 h and 1.8%v/v of acetone extract of pineapple peel. The four-stage purification improved the purity of the enzyme by 1.5-fold with 5.3% recovery and specific activity of 384 U/mg. The monomeric nature and the molecular weight (45 KDa) of the enzyme were determined by performing SDS PAGE and its activity was confirmed by zymogram analysis. The substrate specificity of the purified fraction exhibited a higher activity towards lower chain length esters, indicating the enzyme as esterase. The partially purified esterase showed an optimal temperature of 40 °C at an optimum pH of 7. Km and Vmax of the enzyme were 1.12 mM and 1.18 mM of released pNP · min-1 respectively.
Collapse
|
3
|
Nystrom KC, Tilley L. Mummy studies and the bioarchaeology of care. INTERNATIONAL JOURNAL OF PALEOPATHOLOGY 2019; 25:64-71. [PMID: 30017496 DOI: 10.1016/j.ijpp.2018.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 06/18/2018] [Accepted: 06/18/2018] [Indexed: 06/08/2023]
Abstract
The bioarchaeology of care is a framework through which researchers can begin to infer the level of care an individual may have required based on the presence of paleopathological evidence. To date, all of the research that has employed the framework has been based on evidence derived from skeletal material. This special issue was organized in order to highlight how the analysis of mummified soft tissue, as well as other sources of data commonly associated with mummified remains, such as coprolites and intestinal contents, has the potential to provide valuable insight into the reconstruction of care in the past.
Collapse
Affiliation(s)
- Kenneth C Nystrom
- Department of Anthropology, State University of New York at New Paltz, USA.
| | | |
Collapse
|
4
|
Abstract
Smallpox is considered among the most devastating of human diseases. Its spread in populations, initiated for thousands of years following a probable transmission from an animal host, was concomitant with movements of people across regions and continents, trade and wars. Literature permitted to retrace the occurrence of epidemics from ancient times to recent human history, smallpox having affected all levels of past society including famous monarchs. The disease was officially declared eradicated in 1979 following intensive vaccination campaigns.Paleomicrobiology dedicated to variola virus is restricted to few studies, most unsuccessful, involving ancient material. Only one recent approach allowed the identification of viral DNA fragments from lung tissue of a 300-year-old body excavated from permafrost in Eastern Siberia; phylogenetic analysis revealed that this ancient strain was distinct from those described during the 20th century.
Collapse
|
5
|
Drancourt M, Aboudharam G, Croce O, Armougom F, Robert C, Raoult D. Dental pulp as a source of low-contaminated DNA. Microb Pathog 2017; 105:63-67. [PMID: 28188902 DOI: 10.1016/j.micpath.2017.02.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 01/10/2017] [Accepted: 02/01/2017] [Indexed: 11/19/2022]
Abstract
The in-laboratory contamination of the ancient samples hinders the result interpretation of the investigations in the field of paleomicrobiology. We had promoted the dental pulp as a sample that limits the risks of in-laboratory contamination of the ancient material. In this work, we measured the contamination of the dental pulp manipulated according to paleomicrobiology protocol, used as a source of a total DNA for metagenomics. First, total DNA extracted from two dog canines was sequenced using next generation sequencing. This yielded a total of 487,828 trimmed reads with a length of 227 ± 35 bp. Sequence analysis of the final dataset using Blast algorithm search and stringent thresholds for sequence identity and coverage against a database including both Canis lupus familiaris and Homo sapiens complete genomes showed that 95% of reads were assigned to C. familiaris whereas 0.03% was assigned to H. sapiens. In a second step, two teeth collected from two 12th century mammals were manipulated following the same protocol. A total of 13,890 trimmed reads with a 157 ± 67 bp length yielded 0-0.35% reads assigned to H. sapiens. This study indicates that the dental pulp is a useful for detecting the significant nucleic sequences in both modern and ancient samples.
Collapse
Affiliation(s)
- Michel Drancourt
- Aix Marseille Université, IHU Méditerranée Infection, URMITE, UM 63, UMR_S 1095, UMR 7278, France
| | - Gérard Aboudharam
- Aix Marseille Université, IHU Méditerranée Infection, URMITE, UM 63, UMR_S 1095, UMR 7278, France
| | - Olivier Croce
- Aix Marseille Université, IHU Méditerranée Infection, URMITE, UM 63, UMR_S 1095, UMR 7278, France
| | - Fabrice Armougom
- Aix Marseille Université, IHU Méditerranée Infection, URMITE, UM 63, UMR_S 1095, UMR 7278, France
| | - Catherine Robert
- Aix Marseille Université, IHU Méditerranée Infection, URMITE, UM 63, UMR_S 1095, UMR 7278, France
| | - Didier Raoult
- Aix Marseille Université, IHU Méditerranée Infection, URMITE, UM 63, UMR_S 1095, UMR 7278, France.
| |
Collapse
|
6
|
Paleomicrobiology Data: Authentification and Interpretation. Microbiol Spectr 2016; 4. [PMID: 27337456 DOI: 10.1128/microbiolspec.poh-0017-2015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The authenticity of some of the very first works in the field of paleopathology has been questioned, and standards have been progressively established for the experiments and the interpretation of data. Whereas most problems initially arose from the contamination of ancient specimens with modern human DNA, the situation is different in the field of paleomicrobiology, in which the risk for contamination is well-known and adequately managed by any laboratory team with expertise in the routine diagnosis of modern-day infections. Indeed, the exploration of ancient microbiota and pathogens is best done by such laboratory teams, with research directed toward the discovery and implementation of new techniques and the interpretation of data.
Collapse
|
7
|
Abstract
Biothreats are a high priority concern for public safety and national security. The field of microbial forensics was developed to analyze evidence associated with biological crimes in which microbes or their toxins are used as weapons. Microbial forensics is the scientific discipline dedicated to analyzing evidence from a bioterrorism act, biocrime, hoax, or inadvertent microorganism/toxin release for attribution purposes. Microbial forensics combines the practices of epidemiology with the characterization of microbial and microbial-related evidence to assist in determining the specific source of the sample, as individualizing as possible, and/or the methods, means, processes and locations involved to determine the identity of the perpetrator(s) of an attack.
Collapse
|
8
|
Der Sarkissian C, Ermini L, Jónsson H, Alekseev AN, Crubezy E, Shapiro B, Orlando L. Shotgun microbial profiling of fossil remains. Mol Ecol 2014; 23:1780-98. [PMID: 24612293 DOI: 10.1111/mec.12690] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/23/2014] [Accepted: 02/02/2014] [Indexed: 01/20/2023]
Abstract
Millions to billions of DNA sequences can now be generated from ancient skeletal remains thanks to the massive throughput of next-generation sequencing platforms. Except in cases of exceptional endogenous DNA preservation, most of the sequences isolated from fossil material do not originate from the specimen of interest, but instead reflect environmental organisms that colonized the specimen after death. Here, we characterize the microbial diversity recovered from seven c. 200- to 13 000-year-old horse bones collected from northern Siberia. We use a robust, taxonomy-based assignment approach to identify the microorganisms present in ancient DNA extracts and quantify their relative abundance. Our results suggest that molecular preservation niches exist within ancient samples that can potentially be used to characterize the environments from which the remains are recovered. In addition, microbial community profiling of the seven specimens revealed site-specific environmental signatures. These microbial communities appear to comprise mainly organisms that colonized the fossils recently. Our approach significantly extends the amount of useful data that can be recovered from ancient specimens using a shotgun sequencing approach. In future, it may be possible to correlate, for example, the accumulation of postmortem DNA damage with the presence and/or abundance of particular microbes.
Collapse
Affiliation(s)
- C Der Sarkissian
- Centre for Geogenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, Copenhagen K, 1350, Denmark
| | | | | | | | | | | | | |
Collapse
|
9
|
|
10
|
Dabernat H, Thèves C, Bouakaze C, Nikolaeva D, Keyser C, Mokrousov I, Géraut A, Duchesne S, Gérard P, Alexeev AN, Crubézy E, Ludes B. Tuberculosis epidemiology and selection in an autochthonous Siberian population from the 16th-19th century. PLoS One 2014; 9:e89877. [PMID: 24587092 PMCID: PMC3935942 DOI: 10.1371/journal.pone.0089877] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2013] [Accepted: 01/27/2014] [Indexed: 11/18/2022] Open
Abstract
Tuberculosis is one of most ancient diseases affecting human populations. Although numerous studies have tried to detect pathogenic DNA in ancient skeletons, the successful identification of ancient tuberculosis strains remains rare. Here, we describe a study of 140 ancient subjects inhumed in Yakutia (Eastern Siberia) during a tuberculosis outbreak, dating from the 16(th)-19(th) century. For a long time, Yakut populations had remained isolated from European populations, and it was not until the beginning of the 17(th) century that first contacts were made with European settlers. Subsequently, tuberculosis spread throughout Yakutia, and the evolution of tuberculosis frequencies can be tracked until the 19(th) century. This study took a multidisciplinary approach, examining historical and paleo-epidemiological data to understand the impact of tuberculosis on ancient Yakut population. In addition, molecular identification of the ancient tuberculosis strain was realized to elucidate the natural history and host-pathogen co-evolution of human tuberculosis that was present in this population. This was achieved by the molecular detection of the IS6110 sequence and SNP genotyping by the SNaPshot technique. Results demonstrated that the strain belongs to cluster PGG2-SCG-5, evocating a European origin. Our study suggests that the Yakut population may have been shaped by selection pressures, exerted by several illnesses, including tuberculosis, over several centuries. This confirms the validity and necessity of using a multidisciplinary approach to understand the natural history of Mycobacterium tuberculosis infection and disease.
Collapse
MESH Headings
- Cluster Analysis
- Ethnicity/genetics
- Ethnicity/history
- Genotype
- History, 16th Century
- History, 17th Century
- History, 18th Century
- History, 19th Century
- Humans
- Mycobacterium tuberculosis/genetics
- Polymorphism, Single Nucleotide/genetics
- Selection, Genetic
- Sequence Analysis, DNA/methods
- Siberia/epidemiology
- Tuberculosis, Osteoarticular/diagnosis
- Tuberculosis, Osteoarticular/epidemiology
- Tuberculosis, Osteoarticular/history
- Tuberculosis, Osteoarticular/pathology
Collapse
Affiliation(s)
- Henri Dabernat
- Molecular Anthropology and Image Synthesis (AMIS) Laboratory, UMR 5288, CNRS, University of Toulouse (Paul Sabatier 3); University of Strasbourg, Toulouse, France
| | - Catherine Thèves
- Molecular Anthropology and Image Synthesis (AMIS) Laboratory, UMR 5288, CNRS, University of Toulouse (Paul Sabatier 3); University of Strasbourg, Toulouse, France
| | - Caroline Bouakaze
- Molecular Anthropology and Image Synthesis (AMIS) Laboratory, UMR 5288, CNRS, University of Toulouse (Paul Sabatier 3); University of Strasbourg, Toulouse, France
| | - Dariya Nikolaeva
- Cultural History Centre of Contemporary Societies (CHCSC), University of Versailles Saint-Quentin-en-Yvelines, Versailles, France
| | - Christine Keyser
- Molecular Anthropology and Image Synthesis (AMIS) Laboratory, UMR 5288, CNRS, University of Toulouse (Paul Sabatier 3); University of Strasbourg, Toulouse, France
| | - Igor Mokrousov
- Laboratory of Molecular Microbiology, St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Annie Géraut
- Molecular Anthropology and Image Synthesis (AMIS) Laboratory, UMR 5288, CNRS, University of Toulouse (Paul Sabatier 3); University of Strasbourg, Toulouse, France
| | - Sylvie Duchesne
- Molecular Anthropology and Image Synthesis (AMIS) Laboratory, UMR 5288, CNRS, University of Toulouse (Paul Sabatier 3); University of Strasbourg, Toulouse, France
| | - Patrice Gérard
- Molecular Anthropology and Image Synthesis (AMIS) Laboratory, UMR 5288, CNRS, University of Toulouse (Paul Sabatier 3); University of Strasbourg, Toulouse, France
| | - Anatoly N. Alexeev
- Institute of the Humanities and the Indigenous Peoples of the North, Siberian Branch of the Russian Academy of Sciences, Yakutsk, Russia
| | - Eric Crubézy
- Molecular Anthropology and Image Synthesis (AMIS) Laboratory, UMR 5288, CNRS, University of Toulouse (Paul Sabatier 3); University of Strasbourg, Toulouse, France
| | - Bertrand Ludes
- Molecular Anthropology and Image Synthesis (AMIS) Laboratory, UMR 5288, CNRS, University of Toulouse (Paul Sabatier 3); University of Strasbourg, Toulouse, France
- Institute of Legal Medicine, University Paris Descartes, Paris, France
| |
Collapse
|
11
|
Campana MG, Robles García N, Rühli FJ, Tuross N. False positives complicate ancient pathogen identifications using high-throughput shotgun sequencing. BMC Res Notes 2014; 7:111. [PMID: 24568097 PMCID: PMC3938818 DOI: 10.1186/1756-0500-7-111] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Accepted: 02/20/2014] [Indexed: 12/23/2022] Open
Abstract
Background Identification of historic pathogens is challenging since false positives and negatives are a serious risk. Environmental non-pathogenic contaminants are ubiquitous. Furthermore, public genetic databases contain limited information regarding these species. High-throughput sequencing may help reliably detect and identify historic pathogens. Results We shotgun-sequenced 8 16th-century Mixtec individuals from the site of Teposcolula Yucundaa (Oaxaca, Mexico) who are reported to have died from the huey cocoliztli (‘Great Pestilence’ in Nahautl), an unknown disease that decimated native Mexican populations during the Spanish colonial period, in order to identify the pathogen. Comparison of these sequences with those deriving from the surrounding soil and from 4 precontact individuals from the site found a wide variety of contaminant organisms that confounded analyses. Without the comparative sequence data from the precontact individuals and soil, false positives for Yersinia pestis and rickettsiosis could have been reported. Conclusions False positives and negatives remain problematic in ancient DNA analyses despite the application of high-throughput sequencing. Our results suggest that several studies claiming the discovery of ancient pathogens may need further verification. Additionally, true single molecule sequencing’s short read lengths, inability to sequence through DNA lesions, and limited ancient-DNA-specific technical development hinder its application to palaeopathology.
Collapse
Affiliation(s)
- Michael G Campana
- Department of Human Evolutionary Biology, Harvard University, Peabody Museum, 11 Divinity Avenue, Cambridge, MA 02138, USA.
| | | | | | | |
Collapse
|
12
|
Fontenete S, Guimarães N, Leite M, Figueiredo C, Wengel J, Filipe Azevedo N. Hybridization-based detection of Helicobacter pylori at human body temperature using advanced locked nucleic acid (LNA) probes. PLoS One 2013; 8:e81230. [PMID: 24278398 PMCID: PMC3838382 DOI: 10.1371/journal.pone.0081230] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 10/10/2013] [Indexed: 12/16/2022] Open
Abstract
The understanding of the human microbiome and its influence upon human life has long been a subject of study. Hence, methods that allow the direct detection and visualization of microorganisms and microbial consortia (e.g. biofilms) within the human body would be invaluable. In here, we assessed the possibility of developing a variant of fluorescence in situ hybridization (FISH), named fluorescence in vivo hybridization (FIVH), for the detection of Helicobacter pylori. Using oligonucleotide variations comprising locked nucleic acids (LNA) and 2’-O-methyl RNAs (2’OMe) with two types of backbone linkages (phosphate or phosphorothioate), we were able to successfully identify two probes that hybridize at 37 °C with high specificity and sensitivity for H. pylori, both in pure cultures and in gastric biopsies. Furthermore, the use of this type of probes implied that toxic compounds typically used in FISH were either found to be unnecessary or could be replaced by a non-toxic substitute. We show here for the first time that the use of advanced LNA probes in FIVH conditions provides an accurate, simple and fast method for H. pylori detection and location, which could be used in the future for potential in vivo applications either for this microorganism or for others.
Collapse
Affiliation(s)
- Sílvia Fontenete
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
- ICBAS, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Nuno Guimarães
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Marina Leite
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Céu Figueiredo
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- FMUP, Faculty of Medicine of the University of Porto, Porto, Portugal
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Nuno Filipe Azevedo
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- * E-mail:
| |
Collapse
|