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Wang W, Li X, Wu J, Fu X, Li B. Imaging analysis of pneumonic plague infection in Xizang, China: a case report and literature review. BMC Pulm Med 2024; 24:378. [PMID: 39090583 PMCID: PMC11295852 DOI: 10.1186/s12890-024-03187-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Plague is an acute infectious disease caused by the Yersinia pestis. Historically, it has been a major pandemic with high mortality rates, known as the "Black Death" in the 14th century, which resulted in millions of deaths in Europe. With increasing economic prosperity, more and more people are traveling to Xizang. However, this trend also hides significant safety hazards. Currently, there are few recent reports on plague, especially those with imaging manifestations available. In this study, we report the detailed clinical and radiological data of the patient with pneumonic plague in Xizang, China, in 2023. CASE PRESENTATION We report a case of pneumonic plague in Xizang, which occurred in a herdsman living in an area where dead marmots were found. The patient presented with symptoms such as fever, hemoptysis, dyspnea and coma. Chest computed tomography (CT) scans showed multiple nodules distributed in the central regions of lung lobes, consolidation distributed in secondary pulmonary lobules, and had a gravity-dependent distribution pattern. These imaging findings were consistent with pulmonary hemorrhage and diffuse alveolar damage. Despite emergency treatment, the patient died within 48 h of admission. Through retrospective medical history investigation, laboratory examination and autopsy, the final diagnosis was confirmed as pneumonic plague. CONCLUSION Pneumonic plague is the most deadly infectious disease, and its pathological features mainly include damage to the alveoli, pulmonary hemorrhage, and pulmonary edema. Corresponding to CT, it manifests as acute and rapidly progressing pneumonia, alveolar damage, and pulmonary hemorrhage. The value of this article lies in the completeness and typicality of the imaging data, vivid hand-drawn illustrations of transmission pathways, and comprehensive literature review, all of which serve to enhance public understanding of plague and play an important warning role.
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Affiliation(s)
- Wei Wang
- Department of Radiology, Dongsheng People's Hospital, Erdos, Inner Mongolia, China
| | - Xiaoran Li
- Department of Radiology, Nanjing Gaochun People's Hospital, No.53, Maoshan Road, Nanjing, Jiangsu, 211300, China
| | - Jing Wu
- Department of Radiology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaoming Fu
- Department of Radiology, Nanjing Gaochun People's Hospital, No.53, Maoshan Road, Nanjing, Jiangsu, 211300, China.
| | - Binjie Li
- Department of Radiology, Shannan People's Hospital, No.16, Zedang Road, Naidong District, Shannan, Xizang, 856000, China.
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Lyu D, Duan Q, Duan R, Qin S, Zheng X, Lu X, Bukai A, Zhang P, Han H, He Z, Sha H, Wu D, Xiao M, Jing H, Wang X. Symbiosis of a lytic bacteriophage and Yersinia pestis and characteristics of plague in Marmota himalayana. Appl Environ Microbiol 2024:e0099524. [PMID: 39023266 DOI: 10.1128/aem.00995-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/27/2024] [Indexed: 07/20/2024] Open
Abstract
Surveillance for animal plague was conducted in the Marmota himalayana plague focus of the Qinghai-Tibet Plateau from 2020 to 2023. A 22.89% positive rate of serum F1 antibody was detected in live-caught marmots, alongside a 43.40% incidence of Yersinia pestis isolation from marmot carcasses. Marmot carcasses infected with plague exhibited a significantly higher spleen-somatic index (P < 0.05). Twenty-one Y. pestis-specific phages were isolated, among which one Y. pestis lytic phage (AKS2022HT87GU_phi) was isolated from the bone marrow of a marmot carcass (no. AKS2022HT87) and was found to be symbiotic with Y. pestis. Microscopy revealed the coexistence of lysed and non-lysed colonies of Y. pestis AKS2022HT87. Genome-wide analysis showed that certain strains of the Y. pestis AKS2022HT87 carried phage DNA fragments consistent with phage AKS2022HT87GU_phi. The rare symbiotic relationship between a lytic phage and Y. pestis observed in vitro was highlighted in this study, laying the basis for further exploring the relationship between Y. pestis and its bacteriophages.IMPORTANCEBacteriophages and host bacteria commonly coexist in vivo or in soil environments through complex and interdependent microbial interactions. However, recapitulating this symbiotic state remains challenging in vitro due to limited medium nutrients. In this work, the natural symbiosis between Yersinia pestis and specific phages has been discovered in a Marmota himalayana specimen. Epidemiological analysis presented the characteristics of the Y. pestis and specific phages in the area with a strong plague epidemic. Crucially, comparative genomics has been conducted to analyze the genetic changes in both the Y. pestis and phages over different periods, revealing the dynamic and evolving nature of their symbiosis. These are the critical steps to study the mechanism of the symbiosis.
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Affiliation(s)
- Dongyue Lyu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Qun Duan
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ran Duan
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Shuai Qin
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiaojin Zheng
- Akesai Kazakh Autonomous County Center for Disease Control and Prevention, Jiuquan, Gansu, China
| | - Xinmin Lu
- Akesai Kazakh Autonomous County Center for Disease Control and Prevention, Jiuquan, Gansu, China
| | - Asaiti Bukai
- Akesai Kazakh Autonomous County Center for Disease Control and Prevention, Jiuquan, Gansu, China
| | - Peng Zhang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Haonan Han
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhaokai He
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hanyu Sha
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Di Wu
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Meng Xiao
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Huaiqi Jing
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xin Wang
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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3
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Guo J, Shi W, Li X, Yang B, Qin C, Su L. Comparative Analysis of Gut Microbiomes in Laboratory Chinchillas, Ferrets, and Marmots: Implications for Pathogen Infection Research. Microorganisms 2024; 12:646. [PMID: 38674591 PMCID: PMC11051751 DOI: 10.3390/microorganisms12040646] [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: 02/20/2024] [Revised: 03/17/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
Gut microbes play a vital role in the health and disease of animals, especially in relation to pathogen infections. Chinchillas, ferrets, and marmots are commonly used as important laboratory animals for infectious disease research. Here, we studied the bacterial and fungal microbiota and discovered that chinchillas had higher alpha diversity and a higher abundance of bacteria compared to marmots and ferrets by using the metabarcoding of 16S rRNA genes and ITS2, coupled with co-occurrence network analysis. The dominant microbes varied significantly among the three animal species, particularly in the gut mycobiota. In the ferrets, the feces were dominated by yeast such as Rhodotorula and Kurtzmaniella, while in the chinchillas, we found Teunomyces and Penicillium dominating, and Acaulium, Piromyces, and Kernia in the marmots. Nevertheless, the dominant bacterial genera shared some similarities, such as Clostridium and Pseudomonas across the three animal species. However, there were significant differences observed, such as Vagococcus and Ignatzschineria in the ferrets, Acinetobacter and Bacteroides in the chinchillas, and Bacteroides and Cellvibrio in the marmots. Additionally, our differential analysis revealed significant differences in classification levels among the three different animal species, as well as variations in feeding habitats that resulted in distinct contributions from the host microbiome. Therefore, our data are valuable for monitoring and evaluating the impacts of the microbiome, as well as considering potential applications.
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Affiliation(s)
| | | | | | | | | | - Lei Su
- NHC Key Laboratory of Human Disease Comparative Medicine, Beijing Engineering Research Center for Experimental Animal Models of Human Critical Diseases, International Center for Technology and Innovation of Animal Model, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences (CAMS) & Comparative Medicine Center, Peking Union Medical College (PUMC), Beijing 100021, China; (J.G.); (W.S.); (X.L.); (B.Y.); (C.Q.)
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4
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Bourner J, Andriamarohasina L, Salam A, Kayem ND, Randremanana R, Olliaro P. A systematic review of the clinical profile of patients with bubonic plague and the outcome measures used in research settings. PLoS Negl Trop Dis 2023; 17:e0011509. [PMID: 37943880 PMCID: PMC10662759 DOI: 10.1371/journal.pntd.0011509] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 11/21/2023] [Accepted: 10/14/2023] [Indexed: 11/12/2023] Open
Abstract
BACKGROUND Plague is a zoonotic disease that, despite affecting humans for more than 5000 years, has historically been the subject of limited drug development activity. Drugs that are currently recommended in treatment guidelines have been approved based on animal studies alone-no pivotal clinical trials in humans have yet been completed. As a result of the sparse clinical research attention received, there are a number of methodological challenges that need to be addressed in order to facilitate the collection of clinical trial data that can meaningfully inform clinicians and policy-makers. One such challenge is the identification of clinically-relevant endpoints, which are informed by understanding the clinical characterisation of the disease-how it presents and evolves over time, and important patient outcomes, and how these can be modified by treatment. METHODOLOGY/PRINCIPAL FINDINGS This systematic review aims to summarise the clinical profile of 1343 patients with bubonic plague described in 87 publications, identified by searching bibliographic databases for studies that meet pre-defined eligibility criteria. The majority of studies were individual case reports. A diverse group of signs and symptoms were reported at baseline and post-baseline timepoints-the most common of which was presence of a bubo, for which limited descriptive and longitudinal information was available. Death occurred in 15% of patients; although this varied from an average 10% in high-income countries to an average 17% in low- and middle-income countries. The median time to death was 1 day, ranging from 0 to 16 days. CONCLUSIONS/SIGNIFICANCE This systematic review elucidates the restrictions that limited disease characterisation places on clinical trials for infectious diseases such as plague, which not only impacts the definition of trial endpoints but has the knock-on effect of challenging the interpretation of a trial's results. For this reason and despite interventional trials for plague having taken place, questions around optimal treatment for plague persist.
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Affiliation(s)
- Josephine Bourner
- ISARIC, Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
| | | | - Alex Salam
- ISARIC, Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
| | | | | | - Piero Olliaro
- ISARIC, Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
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5
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Xu L, Wang Q, Yang R, Ganbold D, Tsogbadrakh N, Dong K, Liu M, Altantogtokh D, Liu Q, Undrakhbold S, Boldgiv B, Liang W, Stenseth NC. Climate-driven marmot-plague dynamics in Mongolia and China. Sci Rep 2023; 13:11906. [PMID: 37488160 PMCID: PMC10366125 DOI: 10.1038/s41598-023-38966-1] [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: 03/31/2023] [Accepted: 07/18/2023] [Indexed: 07/26/2023] Open
Abstract
The incidence of plague has rebounded in the Americas, Asia, and Africa alongside rapid globalization and climate change. Previous studies have shown local climate to have significant nonlinear effects on plague dynamics among rodent communities. We analyzed an 18-year database of plague, spanning 1998 to 2015, in the foci of Mongolia and China to trace the associations between marmot plague and climate factors. Our results suggested a density-dependent effect of precipitation and a geographic location-dependent effect of temperature on marmot plague. That is, a significantly positive relationship was evident between risk of plague and precipitation only when the marmot density exceeded a certain threshold. The geographical heterogeneity of the temperature effect and the contrasting slopes of influence for the Qinghai-Tibet Plateau (QTP) and other regions in the study (nQTP) were primarily related to diversity of climate and landscape types.
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Affiliation(s)
- Lei Xu
- Vanke School of Public Health, Tsinghua University, Beijing, 100084, China
| | - Qian Wang
- Vanke School of Public Health, Tsinghua University, Beijing, 100084, China
| | - Ruifu Yang
- Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Dalantai Ganbold
- National Center for Zoonotic Diseases, Ulaanbaatar, 211137, Mongolia
| | | | - Kaixing Dong
- Vanke School of Public Health, Tsinghua University, Beijing, 100084, China
| | - Min Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing, 100191, China
| | | | - Qiyong Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Changping, Beijing, 102206, China
| | - Sainbileg Undrakhbold
- Professional Biological Society of Mongolia, Ulaanbaatar, 14201, Mongolia
- Department of Biology, National University of Mongolia, Ulaanbaatar, 14201, Mongolia
| | - Bazartseren Boldgiv
- Department of Biology, National University of Mongolia, Ulaanbaatar, 14201, Mongolia.
| | - Wannian Liang
- Vanke School of Public Health, Tsinghua University, Beijing, 100084, China.
| | - Nils Chr Stenseth
- Vanke School of Public Health, Tsinghua University, Beijing, 100084, China.
- The Centre for Pandemics and One-Health Research, Faculty of Medicine, University of Oslo, Oslo, Norway.
- Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway.
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6
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Chen C, Chen S, Wang B. A glance at the gut microbiota and the functional roles of the microbes based on marmot fecal samples. Front Microbiol 2023; 14:1035944. [PMID: 37125200 PMCID: PMC10140447 DOI: 10.3389/fmicb.2023.1035944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/13/2023] [Indexed: 05/02/2023] Open
Abstract
Research on the gut microbiota, which involves a large and complex microbial community, is an important part of infectious disease control. In China, few studies have been reported on the diversity of the gut microbiota of wild marmots. To obtain full details of the gut microbiota, including bacteria, fungi, viruses and archaea, in wild marmots, we have sequenced metagenomes from five sample-sites feces on the Hulun Buir Grassland in Inner Mongolia, China. We have created a comprehensive database of bacterial, fungal, viral, and archaeal genomes and aligned metagenomic sequences (determined based on marmot fecal samples) against the database. We delineated the detailed and distinct gut microbiota structures of marmots. A total of 5,891 bacteria, 233 viruses, 236 fungi, and 217 archaea were found. The dominant bacterial phyla were Firmicutes, Proteobacteria, Bacteroidetes, and Actinomycetes. The viral families were Myoviridae, Siphoviridae, Phycodnaviridae, Herpesviridae and Podoviridae. The dominant fungi phyla were Ascomycota, Basidiomycota, and Blastocladiomycota. The dominant archaea were Biobacteria, Omoarchaea, Nanoarchaea, and Microbacteria. Furthermore, the gut microbiota was affected by host species and environment, and environment was the most important factor. There were 36,989 glycoside hydrolase genes in the microbiota, with 365 genes homologous to genes encoding β-glucosidase, cellulase, and cellulose β-1,4-cellobiosidase. Additionally, antibiotic resistance genes such as macB, bcrA, and msbA were abundant. To sum up, the gut microbiota of marmot had population diversity and functional diversity, which provides a basis for further research on the regulatory effects of the gut microbiota on the host. In addition, metagenomics revealed that the gut microbiota of marmots can degrade cellulose and hemicellulose.
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Affiliation(s)
- Chuizhe Chen
- Department of Pathology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, NHC Key Laboratory of Tropical Disease Control, School of Tropical Medicine and the Second Affiliated Hospital, Hainan Medical University, Haikou, China
| | - Shu Chen
- Medical Laboratory Center, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Bo Wang
- Department of Pathology, Hainan General Hospital, Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
- *Correspondence: Bo Wang,
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Neumann GU, Skourtanioti E, Burri M, Nelson EA, Michel M, Hiss AN, McGeorge PJP, Betancourt PP, Spyrou MA, Krause J, Stockhammer PW. Ancient Yersinia pestis and Salmonella enterica genomes from Bronze Age Crete. Curr Biol 2022; 32:3641-3649.e8. [PMID: 35882233 DOI: 10.1016/j.cub.2022.06.094] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/25/2022] [Accepted: 06/30/2022] [Indexed: 12/13/2022]
Abstract
During the late 3rd millennium BCE, the Eastern Mediterranean and Near East witnessed societal changes in many regions, which are usually explained with a combination of social and climatic factors.1-4 However, recent archaeogenetic research forces us to rethink models regarding the role of infectious diseases in past societal trajectories.5 The plague bacterium Yersinia pestis, which was involved in some of the most destructive historical pandemics,5-8 circulated across Eurasia at least from the onset of the 3rd millennium BCE,9-13 but the challenging preservation of ancient DNA in warmer climates has restricted the identification of Y.pestis from this period to temperate climatic regions. As such, evidence from culturally prominent regions such as the Eastern Mediterranean is currently lacking. Here, we present genetic evidence for the presence of Y. pestis and Salmonella enterica, the causative agent of typhoid/enteric fever, from this period of transformation in Crete, detected at the cave site Hagios Charalambos. We reconstructed one Y. pestis genome that forms part of a now-extinct lineage of Y. pestis strains from the Late Neolithic and Bronze Age that were likely not yet adapted for transmission via fleas. Furthermore, we reconstructed two ancient S. enterica genomes from the Para C lineage, which cluster with contemporary strains that were likely not yet fully host adapted to humans. The occurrence of these two virulent pathogens at the end of the Early Minoan period in Crete emphasizes the necessity to re-introduce infectious diseases as an additional factor possibly contributing to the transformation of early complex societies in the Aegean and beyond.
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Affiliation(s)
- Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Eirini Skourtanioti
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Marta Burri
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Swiss Ornithological Institute, Seerose 1, 6204 Sempach, Switzerland
| | - Elizabeth A Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Department of Anthropology, University of Connecticut, 354 Mansfield Road, Storrs, CT 06269, USA
| | - Megan Michel
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Human Evolutionary Biology, Harvard University, 10 Divinity Avenue, Cambridge, MA 02138, USA
| | - Alina N Hiss
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany
| | | | - Philip P Betancourt
- Department of Art History and Archaeology, Temple University, 2001 N. 13(th) St., Philadelphia, PA 19122, USA
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Institute for Archaeological Sciences, Eberhard Karls University of Tübingen, Hölderlinstr. 12, 72074 Tübingen, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.
| | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean (MHAAM), Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University, Geschwister-Scholl-Platz 1, 80799 München, Germany.
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Stone Age Yersinia pestis genomes shed light on the early evolution, diversity, and ecology of plague. Proc Natl Acad Sci U S A 2022; 119:e2116722119. [PMID: 35412864 PMCID: PMC9169917 DOI: 10.1073/pnas.2116722119] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
The bacterium Yersinia pestis has caused numerous historically documented outbreaks of plague and research using ancient DNA could demonstrate that it already affected human populations during the Neolithic. However, the pathogen’s genetic diversity, geographic spread, and transmission dynamics during this early period of Y. pestis evolution are largely unexplored. Here, we describe a set of ancient plague genomes up to 5,000 y old from across Eurasia. Our data demonstrate that two genetically distinct forms of Y. pestis evolved in parallel and were both distributed across vast geographic distances, potentially occupying different ecological niches. Interpreted within the archeological context, our results suggest that the spread of plague during this period was linked to increased human mobility and intensification of animal husbandry. The bacterial pathogen Yersinia pestis gave rise to devastating outbreaks throughout human history, and ancient DNA evidence has shown it afflicted human populations as far back as the Neolithic. Y. pestis genomes recovered from the Eurasian Late Neolithic/Early Bronze Age (LNBA) period have uncovered key evolutionary steps that led to its emergence from a Yersinia pseudotuberculosis-like progenitor; however, the number of reconstructed LNBA genomes are too few to explore its diversity during this critical period of development. Here, we present 17 Y. pestis genomes dating to 5,000 to 2,500 y BP from a wide geographic expanse across Eurasia. This increased dataset enabled us to explore correlations between temporal, geographical, and genetic distance. Our results suggest a nonflea-adapted and potentially extinct single lineage that persisted over millennia without significant parallel diversification, accompanied by rapid dispersal across continents throughout this period, a trend not observed in other pathogens for which ancient genomes are available. A stepwise pattern of gene loss provides further clues on its early evolution and potential adaptation. We also discover the presence of the flea-adapted form of Y. pestis in Bronze Age Iberia, previously only identified in in the Caucasus and the Volga regions, suggesting a much wider geographic spread of this form of Y. pestis. Together, these data reveal the dynamic nature of plague’s formative years in terms of its early evolution and ecology.
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Fijn N, Terbish B. The Multiple Faces of the Marmot: Associations with the Plague, Hunting, and Cosmology in Mongolia. HUMAN ECOLOGY: AN INTERDISCIPLINARY JOURNAL 2021; 49:539-549. [PMID: 34658483 PMCID: PMC8513552 DOI: 10.1007/s10745-021-00264-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
Mongolians have long known of the association between marmots and the plague. We examine their understanding of the marmot not only as a biological species that can harbour the plague, but also from a cosmological perspective as a chimerical being with potential punishment on hunters who have transgressed ancient taboos. To do so we deconstruct the multiple image of the chimerical marmot in legends, stories, and beliefs. Many Mongolians believe that if the marmot is over-exploited and the population decimated through excessive hunting, hunting households may be punished with infections of the plague.
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Affiliation(s)
- Natasha Fijn
- The Mongolia Institute, College of Asia and the Pacific, The Australian National University, Canberra, Australia
| | - Baasanjav Terbish
- Mongolia Inner Asia Studies Unit, University of Cambridge, Cambridge, England
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10
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Molecular diagnostic of toxigenic Corynebacterium diphtheriae strain by DNA sensor potentially suitable for electrochemical point-of-care diagnostic. Talanta 2021; 227:122161. [PMID: 33714465 DOI: 10.1016/j.talanta.2021.122161] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/21/2021] [Accepted: 01/26/2021] [Indexed: 12/12/2022]
Abstract
The presented study is focused on the development of electrochemical genosensor for detection of tox gene fragment of toxigenic Corynebacterium diphtheriae strain. Together with our previous studies it fulfils the whole procedure for fast and accurate diagnostic of diphtheria at its early stage of infection with the use of electrochemical methods. The developed DNA sensor potentially can be used in more sophisticated portable device. After the electrochemical stem-loop probe structure optimization the conditions for real asymmetric PCR (aPCR) product detection were selected. As was shown it was crucial to optimize the magnesium and organic solvent concentrations in detection buffer. Under optimal conditions it was possible to selectively detect as low as 20.8 nM of complementary stand in 5 min or 0.5 nM in 30 min with sensitivity of 12.81 and 0.24 1⋅μM-1 respectively. The unspecific biosensor response was elucidated with the use of new electrode blocking agent, diethyldithiocarbamate. Its application in electrochemical genosensors lead to significant higher current values and the biosensor response even in conditions with magnesium ion depletion. The developed biosensor selectivity was examined using samples containing genetic material originated from a number of non-target bacterial species which potentially can be present in the human upper respiratory tract.
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