Jessica Hider , Ana T. Duggan , Jennifer Klunk , Katherine Eaton , George S. Long , Emil Karpinski , Valentina Giuffra , Luca Ventura , Antonio Fornaciari , Gino Fornaciari , G. Brian Golding , Tracy L. Prowse , Hendrik N. Poinar
{"title":"在一名14世纪意大利修士(圣福)感染布鲁氏菌的遗骸上检测病原体DNA恢复","authors":"Jessica Hider , Ana T. Duggan , Jennifer Klunk , Katherine Eaton , George S. Long , Emil Karpinski , Valentina Giuffra , Luca Ventura , Antonio Fornaciari , Gino Fornaciari , G. Brian Golding , Tracy L. Prowse , Hendrik N. Poinar","doi":"10.1016/j.ijpp.2022.08.002","DOIUrl":null,"url":null,"abstract":"<div><h3>Objective</h3><p>To investigate variation in ancient DNA recovery of <em>Brucella melitensis,</em> the causative agent of brucellosis, from multiple tissues belonging to one individual</p></div><div><h3>Materials</h3><p>14 samples were analyzed from the mummified remains of the Blessed Sante, a 14 <sup>th</sup> century Franciscan friar from central Italy, with macroscopic diagnosis of probable brucellosis.</p></div><div><h3>Methods</h3><p>Shotgun sequencing data from was examined to determine the presence of <em>Brucella</em> DNA.</p></div><div><h3>Results</h3><p>Three of the 14 samples contained authentic ancient DNA, identified as belonging to <em>B. melitensis</em>. A genome (23.81X depth coverage, 0.98 breadth coverage) was recovered from a kidney stone. Nine of the samples contained reads classified as <em>B. melitensis</em> (7−169), but for many the data quality was insufficient to withstand our identification and authentication criteria.</p></div><div><h3>Conclusions</h3><p>We identified significant variation in the preservation and abundance of <em>B. melitensis</em> DNA present across multiple tissues, with calcified nodules yielding the highest number of authenticated reads. This shows how greatly sample selection can impact pathogen identification.</p></div><div><h3>Significance</h3><p>Our results demonstrate variation in the preservation and recovery of pathogen DNA across tissues. This study highlights the importance of sample selection in the reconstruction of infectious disease burden and highlights the importance of a holistic approach to identifying disease.</p></div><div><h3>Limitations</h3><p>Study focuses on pathogen recovery in a single individual.</p></div><div><h3>Suggestions for further research</h3><p>Further analysis of how sampling impacts aDNA recovery will improve pathogen aDNA recovery and advance our understanding of disease in past peoples</p></div>","PeriodicalId":48817,"journal":{"name":"International Journal of Paleopathology","volume":"39 ","pages":"Pages 20-34"},"PeriodicalIF":1.3000,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"1","resultStr":"{\"title\":\"Examining pathogen DNA recovery across the remains of a 14th century Italian friar (Blessed Sante) infected with Brucella melitensis\",\"authors\":\"Jessica Hider , Ana T. Duggan , Jennifer Klunk , Katherine Eaton , George S. Long , Emil Karpinski , Valentina Giuffra , Luca Ventura , Antonio Fornaciari , Gino Fornaciari , G. Brian Golding , Tracy L. Prowse , Hendrik N. Poinar\",\"doi\":\"10.1016/j.ijpp.2022.08.002\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Objective</h3><p>To investigate variation in ancient DNA recovery of <em>Brucella melitensis,</em> the causative agent of brucellosis, from multiple tissues belonging to one individual</p></div><div><h3>Materials</h3><p>14 samples were analyzed from the mummified remains of the Blessed Sante, a 14 <sup>th</sup> century Franciscan friar from central Italy, with macroscopic diagnosis of probable brucellosis.</p></div><div><h3>Methods</h3><p>Shotgun sequencing data from was examined to determine the presence of <em>Brucella</em> DNA.</p></div><div><h3>Results</h3><p>Three of the 14 samples contained authentic ancient DNA, identified as belonging to <em>B. melitensis</em>. A genome (23.81X depth coverage, 0.98 breadth coverage) was recovered from a kidney stone. Nine of the samples contained reads classified as <em>B. melitensis</em> (7−169), but for many the data quality was insufficient to withstand our identification and authentication criteria.</p></div><div><h3>Conclusions</h3><p>We identified significant variation in the preservation and abundance of <em>B. melitensis</em> DNA present across multiple tissues, with calcified nodules yielding the highest number of authenticated reads. This shows how greatly sample selection can impact pathogen identification.</p></div><div><h3>Significance</h3><p>Our results demonstrate variation in the preservation and recovery of pathogen DNA across tissues. This study highlights the importance of sample selection in the reconstruction of infectious disease burden and highlights the importance of a holistic approach to identifying disease.</p></div><div><h3>Limitations</h3><p>Study focuses on pathogen recovery in a single individual.</p></div><div><h3>Suggestions for further research</h3><p>Further analysis of how sampling impacts aDNA recovery will improve pathogen aDNA recovery and advance our understanding of disease in past peoples</p></div>\",\"PeriodicalId\":48817,\"journal\":{\"name\":\"International Journal of Paleopathology\",\"volume\":\"39 \",\"pages\":\"Pages 20-34\"},\"PeriodicalIF\":1.3000,\"publicationDate\":\"2022-12-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"1\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"International Journal of Paleopathology\",\"FirstCategoryId\":\"89\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1879981722000420\",\"RegionNum\":3,\"RegionCategory\":\"地球科学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"PALEONTOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"International Journal of Paleopathology","FirstCategoryId":"89","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1879981722000420","RegionNum":3,"RegionCategory":"地球科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"PALEONTOLOGY","Score":null,"Total":0}
Examining pathogen DNA recovery across the remains of a 14th century Italian friar (Blessed Sante) infected with Brucella melitensis
Objective
To investigate variation in ancient DNA recovery of Brucella melitensis, the causative agent of brucellosis, from multiple tissues belonging to one individual
Materials
14 samples were analyzed from the mummified remains of the Blessed Sante, a 14 th century Franciscan friar from central Italy, with macroscopic diagnosis of probable brucellosis.
Methods
Shotgun sequencing data from was examined to determine the presence of Brucella DNA.
Results
Three of the 14 samples contained authentic ancient DNA, identified as belonging to B. melitensis. A genome (23.81X depth coverage, 0.98 breadth coverage) was recovered from a kidney stone. Nine of the samples contained reads classified as B. melitensis (7−169), but for many the data quality was insufficient to withstand our identification and authentication criteria.
Conclusions
We identified significant variation in the preservation and abundance of B. melitensis DNA present across multiple tissues, with calcified nodules yielding the highest number of authenticated reads. This shows how greatly sample selection can impact pathogen identification.
Significance
Our results demonstrate variation in the preservation and recovery of pathogen DNA across tissues. This study highlights the importance of sample selection in the reconstruction of infectious disease burden and highlights the importance of a holistic approach to identifying disease.
Limitations
Study focuses on pathogen recovery in a single individual.
Suggestions for further research
Further analysis of how sampling impacts aDNA recovery will improve pathogen aDNA recovery and advance our understanding of disease in past peoples
期刊介绍：
Paleopathology is the study and application of methods and techniques for investigating diseases and related conditions from skeletal and soft tissue remains. The International Journal of Paleopathology (IJPP) will publish original and significant articles on human and animal (including hominids) disease, based upon the study of physical remains, including osseous, dental, and preserved soft tissues at a range of methodological levels, from direct observation to molecular, chemical, histological and radiographic analysis. Discussion of ways in which these methods can be applied to the reconstruction of health, disease and life histories in the past is central to the discipline, so the journal would also encourage papers covering interpretive and theoretical issues, and those that place the study of disease at the centre of a bioarchaeological or biocultural approach. Papers dealing with historical evidence relating to disease in the past (rather than history of medicine) will also be published. The journal will also accept significant studies that applied previously developed techniques to new materials, setting the research in the context of current debates on past human and animal health.
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