DNA examination of ancient dental pulp incriminates typhoid fever as a probable cause of the Plague of Athens

The Importance of the One Health Concept in Combating Zoonoses

One Health fundamentally acknowledges that human health is linked to animal health and the environment. One of the pillars One Health is built on is zoonoses. Through the years, zoonotic infections have caused numerous outbreaks and pandemics, as well as millions of fatalities, with the COVID-19 pandemic being the latest one. Apart from the consequences to public health, zoonoses also affect society and the economy. Since its establishment, One Health has contributed significantly to the protection of humans, animals, and the environment, through preparedness, surveillance, and mitigation of such public dangers.

Historical microbiology: researching past bioevents by integrating scholarship (re)sources with paleomicrobiology assets

The analysis of past epidemics and pandemics, either spontaneous or of human origin, may revise the physical history of microbiota and create a temporal context in our understanding regarding pathogen attributes like virulence, evolution, transmission and disease dynamics. The data of high-tech scientific methods seem reliable, but their interpretation may still be biased when tackling events of the distant past. Such endeavors should be adjusted to other cognitive resources including historical accounts reporting the events of interest and references in alien medical cultures and terminologies; the latter may contextualize them differently from current practices. Thus 'historical microbiology' emerges. Validating such resources requires utmost care, as these may be susceptible to different biases regarding the interpretation of facts and phenomena; biases partly due to methodological limitations.

Historic and Prehistoric Epidemics: An Overview of Sources Available for the Study of Ancient Pathogens

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.

A Historical Review of Military Medical Strategies for Fighting Infectious Diseases: From Battlefields to Global Health

The environmental conditions generated by war and characterized by poverty, undernutrition, stress, difficult access to safe water and food as well as lack of environmental and personal hygiene favor the spread of many infectious diseases. Epidemic typhus, plague, malaria, cholera, typhoid fever, hepatitis, tetanus, and smallpox have nearly constantly accompanied wars, frequently deeply conditioning the outcome of battles/wars more than weapons and military strategy. At the end of the nineteenth century, with the birth of bacteriology, military medical researchers in Germany, the United Kingdom, and France were active in discovering the etiological agents of some diseases and in developing preventive vaccines. Emil von Behring, Ronald Ross and Charles Laveran, who were or served as military physicians, won the first, the second, and the seventh Nobel Prize for Physiology or Medicine for discovering passive anti-diphtheria/tetanus immunotherapy and for identifying mosquito Anopheline as a malaria vector and plasmodium as its etiological agent, respectively. Meanwhile, Major Walter Reed in the United States of America discovered the mosquito vector of yellow fever, thus paving the way for its prevention by vector control. In this work, the military relevance of some vaccine-preventable and non-vaccine-preventable infectious diseases, as well as of biological weapons, and the military contributions to their control will be described. Currently, the civil-military medical collaboration is getting closer and becoming interdependent, from research and development for the prevention of infectious diseases to disasters and emergencies management, as recently demonstrated in Ebola and Zika outbreaks and the COVID-19 pandemic, even with the high biocontainment aeromedical evacuation, in a sort of global health diplomacy.

Insights in paediatric virology during the COVID-19 era (Review)

The present article provides an overview of the key messages of the topics discussed at the '7th Workshop on Paediatric Virology', which was organised virtually on December 20, 2021 by the Institute of Paediatric Virology, located on the Island of Euboea in Greece. The workshop's plenary lectures were on: i) viral pandemics and epidemics in the ancient Mediterranean; ii) the impact of obesity on the outcome of viral infections in children and adolescents; and iii) COVID-19 and artificial intelligence. Despite the scarcity of evidence from fossils and remnants, viruses have been recognised as significant causes of several epidemics in the ancient Mediterranean. Paediatric obesity, a modifiable critical health risk factor, has been shown to impact on the development, progression and severity of viral infections. Thus, the prevention of paediatric obesity should be included in formulating public health policies and decision-making strategies against emerging global viral threats. During the current COVID-19 pandemic, artificial intelligence has been used to facilitate the identification, monitoring and prevention of SARS-CoV-2. In the future, it will play a fundamental role in the surveillance of epidemic-prone infectious diseases, in the repurposing of older therapies and in the design of novel therapeutic agents against viral infections. The collaboration between different medical specialties and other diverse scientific fields, including archaeology, history, epidemiology, nutritional technologies, mathematics, computer technology, engineering, medical law and ethics is essential for the successful management of paediatric viral infections. The current COVID-19 pandemic has underscored this need, which should be further encouraged in modern medical education.

Preventive Measures against Pandemics from the Beginning of Civilization to Nowadays—How Everything Has Remained the Same over the Millennia

As of 27 March 2022, the β-coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has infected more than 487 million individuals worldwide, causing more than 6.14 million deaths. SARS-CoV-2 spreads through close contact, causing the coronavirus disease 2019 (COVID-19); thus, emergency lockdowns have been implemented worldwide to avoid its spread. COVID-19 is not the first infectious disease that humankind has had to face during its history. Indeed, humans have recurrently been threatened by several emerging pathogens that killed a substantial fraction of the population. Historical sources document that as early as between the 10th and the 6th centuries BCE, the authorities prescribed physical–social isolation, physical distancing, and quarantine of the infected subjects until the end of the disease, measures that strongly resemble containment measures taken nowadays. In this review, we show a historical and literary overview of different epidemic diseases and how the recommendations in the pre-vaccine era were, and still are, effective in containing the contagion.

Epidemic Spreading in Trajectory Networks

Epidemics of infectious diseases, such as the one caused by the rapid spread of the coronavirus disease 2019 (COVID-19), have tested the world's more advanced health systems and have caused an enormous societal and economic damage. The mechanism of contagion is well understood. As people move around, over time, they regularly engage in social interactions. The spatiotemporal network representing these interactions constitutes the backbone on which an epidemic spreads, causing outbreaks. At the same time, advanced technological responses have claimed some success in controlling the epidemic based on digital contact tracing technologies. Motivated by these observations, we design, develop and evaluate a stochastic agent-basedSEIRmodel of epidemic spreading in spatiotemporal networks informed by mobility data of individuals (trajectories). The model focuses on individual variation in mobility patterns that affects the degree of exposure to the disease. Understanding the role that individual nodes play in the process of disease spreading through network effects is fundamental as it allows to (i) assess the risk of infection of individuals, (ii) assess the size of a disease outbreak due to specific individuals, and (iii) assess targeted intervention strategies that aim to control the epidemic spreading. We perform a comprehensive analysis of the model employing COVID-19 as a use case. The results indicate that simple individual-based intervention strategies that exhibit significant network effects can effectively control the spread of an epidemic. We have also demonstrated that targeted interventions can outperform generic intervention strategies. Overall, our work provides an evidence-based data-driven model to support decision making and inform public policy regarding intervention strategies for containing or mitigating the epidemic spread.

The COVID-19 pandemic and the "Plague of Athens": comparable features 25 centuries apart

Motivated by the up to now disastrous outcomes of the COVID-19 pandemic, we attempted a flashback to the so-called "Plague of Athens," which indicated a serious contagious disease, having taken place between 430 and 426 BC. The ancient pandemic was meticulously described by the Athenian historian and general Thucydides. We compared, as much as possible, the following parameters: background conditions, spreading of the pandemics, preceded and concurrent adverse events, duration and waves of the pandemics, symptoms, implicated infectious agents/diseases and mental/psychosocial consequences. The current pandemic was preceded by a global economic crisis, which particularly affected deprived population groups, while the ancient one started on the second year of a catastrophic civil war. Rivalry and different political systems between now (US/China) and then (Athens/Sparta) superpowers were the basis for conspiracy scenarios, concerning origins of the pandemics, which resulted to huge numbers of deaths, particularly in overcrowded and poor areas/cities. Both pandemics not sparing any age, sex, nationality, social group, may have had a zoonotic component, besides being air-born. However, their spreading is/was remarkably rapid, presenting 3-4 waves and lasting for several years. Some somatic signs and symptoms of the diseases coincide. Although for COVID-19, SARS-CoV-2 has been identified as causing agent, the antique pandemic has most probably been attributed to typhoid fever, although this is still a matter of debate. Additionally, both pandemics affected mental health and psychosocial behavior in close similarity. It is noteworthy, that in both eras physicians and healthcare workers, despite physical and psychological exhaustion, in the majority, presented admirable resilience and willingness to help suffering fellow people, often at the expense of their own lives. The considerable number of comparable features between COVID-19 and the "Plague of Athens" confirms that pandemics may present over time important similarities in their origin, evolution and outcomes.

Travel vaccines throughout history

Vaccinations are an important component of travel medicine. Beyond protection of travelers, vaccines are administered to prevent the importation of vaccine-preventable diseases at home and at destination. Proof of immunization to travel dates back to the first smallpox vaccine, developed by Edward Jenner in 1796. However, it took one century to generate the next vaccines against cholera, rabies, and typhoid fever. During the 20th century the armamentarium of vaccines used in travelers largely expanded with yellow fever, poliomyelitis, tetravalent meningococcal, and hepatitis A vaccines. The International Certificate of Inoculation and Vaccination was implemented in 1933. Currently there are vaccines administered to travelers following risk assessment, but also vaccines required according to the 2005 International Health Regulations and vaccines required at certain countries. Finally, within less than one year after the declaration of the coronavirus disease 2019 (COVID-19) pandemic, the first COVID-19 vaccines were launched and approved for emergency use to control the pandemic. Despite practical and ethical challenges, COVID-19 vaccine verifications have been widely used since spring 2021 in many activities, including international travel. In this article, we review the course of development of travel vaccines focusing on those for which a proof of vaccination has been or is required.

A Needle-Free Jet Injection System for Controlled Release and Repeated Biopharmaceutical Delivery

Swift vaccination is necessary as a response to disease outbreaks and pandemics; otherwise, the species under attack is at risk of a high fatality rate or even mass extinction. Statistics suggest that at least 16 billion injections are administered worldwide every year. Such a high rate of needle/syringe injection administration worldwide is alarming due to the risk of needle-stick injuries, disease spread due to cross-contamination and the reuse of needles, and the misuse of needles. In addition, there are production, handling, and disposal costs. Needle phobia is an additional issue faced by many recipients of injections with needles. In addition to a detailed literature review highlighting the need for needle-free injection systems, a compressed air-driven needle-free jet injection system with a hydro-pneumatic mechanism was designed and developed by employing an axiomatic design approach. The proposed injection system has higher flexibility, uninterrupted force generation, and provides the possibility of delivering repeated injections at different tissue depths from the dermis to the muscle (depending on the drug delivery requirements) by controlling the inlet compressed air pressure. The designed needle-free jet injector consists of two primary circuits: the pneumatic and the hydraulic circuit. The pneumatic circuit is responsible for driving, pressurizing, and repeatability. The hydraulic circuit precisely injects and contains the liquid jet, allowing us to control the volume of the liquid jet at elevated pressure by offering flexibility in the dose volume per injection. Finally, in this paper we report on the successful design and working model of an air-driven needle-free jet injector for 0.2–0.5 mL drug delivery by ex vivo experimental validation.

Emotional Analysis of Twitter Posts During the First Phase of the COVID-19 Pandemic in Greece: Infoveillance Study

BACKGROUND

The effectiveness of public health measures depends upon a community's compliance as well as on its positive or negative emotions.

OBJECTIVE

The purpose of this study was to perform an analysis of the expressed emotions in English tweets by Greek Twitter users during the first phase of the COVID-19 pandemic in Greece.

METHODS

The period of this study was from January 25, 2020 to June 30, 2020. Data collection was performed by using appropriate search words with the filter-streaming application programming interface of Twitter. The emotional analysis of the tweets that satisfied the inclusion criteria was achieved using a deep learning approach that performs better by utilizing recurrent neural networks on sequences of characters. Emotional epidemiology tools such as the 6 basic emotions, that is, joy, sadness, disgust, fear, surprise, and anger based on the Paul Ekman classification were adopted.

RESULTS

The most frequent emotion that was detected in the tweets was "surprise" at the emerging contagion, while the imposed isolation resulted mostly in "anger" (odds ratio 2.108, 95% CI 0.986-4.506). Although the Greeks felt rather safe during the first phase of the COVID-19 pandemic, their positive and negative emotions reflected a masked "flight or fight" or "fear versus anger" response to the contagion.

CONCLUSIONS

The findings of our study show that emotional analysis emerges as a valid tool for epidemiology evaluations, design, and public health strategy and surveillance.

Salmonella enterica from a soldier from the 1652 siege of Barcelona (Spain) supports historical transatlantic epidemic contacts

Ancient pathogen genomics is an emerging field allowing reconstruction of past epidemics. The demise of post-contact American populations may, at least in part, have been caused by paratyphoid fever brought by Europeans. We retrieved genome-wide data from two Spanish soldiers who were besieging the city of Barcelona in 1652, during the Reapers' War. Their ancestry derived from the Basque region and Sardinia, respectively, (at that time, this island belonged to the Spanish kingdom). Despite the proposed plague epidemic, we could not find solid evidence for the presence of the causative plague agent in these individuals. However, we retrieved from one individual a substantial fraction of the Salmonella enterica serovar Paratyphi C lineage linked to paratyphoid fever in colonial period Mexico. Our results support a growing body of evidence that Paratyphi C enteric fever was more prevalent in Europe and the Americas in the past than it is today.

Pandemics: Historically Slow "Learning Curve" Leading to Biomedical Informatics and Vaccine Breakthroughs

BACKGROUND

The worldwide tragedy of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic vividly demonstrates just how inadequate mitigation and control of the spread of infectious diseases can be when faced with a new microorganism with unknown pathogenic effects. Responses by governments in charge of public health, and all other involved organizations, have proved largely wanting. Data infrastructure and the information and communication systems needed to deal with the pandemic have likewise not been up to the task. Nevertheless, after a year of the worldwide outbreak, hope arises from this being the first major pandemic event in history where genomic and related biosciences - relying on biomedical informatics - have been essential in decoding the viral sequence data and producing the mRNA and other biotechnologies that unexpectedly rapidly have led to investigation, design, development, and testing of useful vaccines. Medical informatics may also help support public health actions and clinical interventions - but scalability and impact will depend on overcoming ingrained human shortcomings to deal with complex socio-economic, political, and technological disruptions together with the many ethical challenges presented by pandemics.

OBJECTIVES

The principal goal is to review the history of biomedical information and healthcare practices related to past pandemics in order to illustrate just how exceptional and dependent on biomedical informatics are the recent scientific insights into human immune responses to viral infection, which are enabling rapid antiviral vaccine development and clinical management of severe cases - despite the many societal challenges ahead.

METHODS

This paper briefly reviews some of the key historical antecedents leading up to modern insights into epidemic and pandemic processes with their biomedical and healthcare information intended to guide practitioners, agencies, and the lay public in today's ongoing pandemic events.

CONCLUSIONS

Poor scientific understanding and excessively slow learning about infectious disease processes and mitigating behaviors have stymied effective treatment until the present time. Advances in insights about immune systems, genomes, proteomes, and all the other -omes, became a reality thanks to the key sequencing technologies and biomedical informatics that enabled the Human Genome Project, and only now, 20 years later, are having an impact in ameliorating devastating zoonotic infectious pandemics, including the present SARS-CoV-2 event through unprecedently rapid vaccine development. In the future these advances will hopefully also enable more targeted prevention and treatment of disease. However, past and present shortcomings of most of the COVID-19 pandemic responses illustrate just how difficult it is to persuade enough people - and especially political leaders - to adopt societally beneficial risk-avoidance behaviors and policies, even as these become better understood.

Emerging complexities and rising omission: Contrasts among socio-ecological contexts of infectious diseases, research and policy in Brazil

In this article, we explore elements that highlight the interdependent nature of demands for knowledge production and decision-making related to the appearance of emerging diseases. To this end, we refer to scientific production and current contextual evidence to verify situations mainly related to the Brazilian Amazon, which suffers systematic disturbances and is characterized as a possible source of pathogenic microorganisms. With the acceleration of the Anthropocene's environmental changes, socio-ecological instabilities and the possibility of the emergence of infectious diseases merge into a background of a ´twin insurgency´. Furthermore, there is a tendency to impose economic hegemony in the current Brazilian context, corroborating discourses and pressures to a scientific simplification and denial. With this, we assert that developmental sectoral actions and monoculture of knowledge characterize an agenda of omission, that is, a process of decision making that indirectly reinforces ecological degradation and carelessness in the face of the possibility of the emergence and spreading of new diseases, such as COVID-19. Tackling the socio-ecological complexity inherent in the risk of the emergence of infectious diseases requires robust co-construction of scientific knowledge, eco-social approaches, and corresponding governance and sophisticated decision-making arrangements.

Water Quality and Life Expectancy: Parallel Courses in Time

Since ancient times, the need for healthy water has resulted in the development of various kinds of water supply systems. From early history, civilizations have developed water purification devices and treatment methods. The necessity for fresh water has influenced individual lives as well as communities and societies. During the last two hundred years, intensive and effective efforts have been made internationally for sufficient water quantity and quality. At the same time, human life expectancy has increased all over the globe at unprecedented rates. The present work represents an effort to sketch out how water purity and life expectancy have entangled, thus influencing one another. Water properties and characteristics have directly affected life quality and longevity. The dramatic increase in life expectancy has been, indisputably, affected by the improvement in water quality, but also in other concomitant factors, varying temporally and spatially in different parts of the world throughout the centuries. Water technologies and engineering have an unequivocal role on life expectancy. In some cases, they appear to have taken place earlier than the progress of modern medicine. Among these, improved sanitation, personal hygiene, progress in medicine, and better standards of economic living have played the greatest roles.

Yersinia pestis: the Natural History of Plague

The Gram-negative bacterium Yersinia pestis is responsible for deadly plague, a zoonotic disease established in stable foci in the Americas, Africa, and Eurasia. Its persistence in the environment relies on the subtle balance between Y. pestis-contaminated soils, burrowing and nonburrowing mammals exhibiting variable degrees of plague susceptibility, and their associated fleas. Transmission from one host to another relies mainly on infected flea bites, inducing typical painful, enlarged lymph nodes referred to as buboes, followed by septicemic dissemination of the pathogen. In contrast, droplet inhalation after close contact with infected mammals induces primary pneumonic plague. Finally, the rarely reported consumption of contaminated raw meat causes pharyngeal and gastrointestinal plague. Point-of-care diagnosis, early antibiotic treatment, and confinement measures contribute to outbreak control despite residual mortality. Mandatory primary prevention relies on the active surveillance of established plague foci and ectoparasite control. Plague is acknowledged to have infected human populations for at least 5,000 years in Eurasia. Y. pestis genomes recovered from affected archaeological sites have suggested clonal evolution from a common ancestor shared with the closely related enteric pathogen Yersinia pseudotuberculosis and have indicated that ymt gene acquisition during the Bronze Age conferred Y. pestis with ectoparasite transmissibility while maintaining its enteric transmissibility. Three historic pandemics, starting in 541 AD and continuing until today, have been described. At present, the third pandemic has become largely quiescent, with hundreds of human cases being reported mainly in a few impoverished African countries, where zoonotic plague is mostly transmitted to people by rodent-associated flea bites.

Modeling epidemics by the lattice Boltzmann method

In this paper, we demonstrate that the lattice Boltzmann method can be successfully adopted to investigate the dynamics of epidemics. Numerical simulations prove the excellent accuracy properties of the approach, which recovers the solution of the popular SIR model. Because spatial effects are naturally accounted for in the lattice Boltzmann formulation, the present scheme appears to be more competitive than traditional solution procedures. Interestingly, it allows us to simulate scenarios characterized by selective lockdown configurations.

The past, present and future of ancient bacterial DNA

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.

Psychosocial Reactions to Plagues in the Cultural History of Medicine: A Medical Humanities Approach

The aim of this work is to elucidate psychosocial reactions to plagues by analyzing three landmark descriptions from different eras: Thucydides' description of the plague of Athens (430 BC) in The History of the Peloponnesian War, Giovanni Boccaccio's description of the plague in Florence (1348) in The Decameron, and Albert Camus' description in The Plague (1947). Using a narrative inquiry, we found psychosocial reactions to be complex and ambivalent and could discern several coping strategies. We propose that this knowledge can help psychiatrists and other healthcare professionals during the ongoing COVID-19 pandemic.

Ancient dental pulp: Masterpiece tissue for paleomicrobiology

Introduction

Dental pulp with special structure has become a good reference sample in paleomicrobiology‐related blood‐borne diseases, many pathogens were detected by different methods based on the diagnosis of nucleic acids and proteins.

Objectives

This review aims to propose the preparation process from ancient teeth collection to organic molecule extraction of dental pulp and summary, analyze the methods that have been applied to detect septicemic pathogens through ancient dental pulps during the past 20 years following the first detection of an ancient microbe.

Methods

The papers used in this review with two main objectives were obtained from PubMed and Google scholar with combining keywords: “ancient,” “dental pulp,” “teeth,” “anatomy,” “structure,” “collection,” “preservation,” “selection,” “photography,” “radiography,” “contamination,” “decontamination,” “DNA,” “protein,” “extraction,” “bone,” “paleomicrobiology,” “bacteria,” “virus,” “pathogen,” “molecular biology,” “proteomics,” “PCR,” “MALDI‐TOF,” “LC/MS,” “ELISA,” “immunology,” “immunochromatography,” “genome,” “microbiome,” “metagenomics.”

Results

The analysis of ancient dental pulp should have a careful preparation process with many different steps to give highly accurate results, each step complies with the rules in archaeology and paleomicrobiology. After the collection of organic molecules from dental pulp, they were investigated for pathogen identification based on the analysis of DNA and protein. Actually, DNA approach takes a principal role in diagnosis while the protein approach is more and more used. A total of seven techniques was used and ten bacteria (Yersinia pestis, Bartonella quintana, Salmonella enterica serovar Typhi, Salmonella enterica serovar Paratyphi C, Mycobacterium leprae, Mycobacterium tuberculosis, Rickettsia prowazeki, Staphylococcus aureus, Borrelia recurrentis, Bartonella henselae) and one virus (Anelloviridae) were identified. Y. pestis had the most published in quantity and all methods were investigated for this pathogen, S. aureus and B. recurrentis were identified by three different methods and others only by one. The combining methods interestingly increase the positive rate with ELISA, PCR and iPCR in Yersinia pestis diagnosis. Twenty‐seven ancient genomes of Y. pestis and one ancient genome of B. recurrentis were reconstructed. Comparing to the ancient bone, ancient teeth showed more advantage in septicemic diagnosis. Beside pathogen identification, ancient pulp help to distinguish species.

Conclusions

Dental pulp with specific tissue is a suitable sample for detection of the blood infection in the past through DNA and protein identification with the correct preparation process, furthermore, it helps to more understand the pathogens of historic diseases and epidemics.

Paleomicrobiology: Diagnosis and Evolution of Ancient Pathogens

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.

Two thousand years of epidemics in Marseille and the Mediterranean Basin

Marseille has been exposed to epidemics for two millennia, including plague, cholera and yellow fever. This long-standing exposure to epidemics has given the people of Marseilles a particular expertise in fighting epidemics. Lazarets and other quarantine measures were implemented as a response to preventing the further spread of the disease in the community. The Institut Hospitalier Universitaire Méditerranée Infection is paving the way today, with its responses built on the region's long history and knowledge of epidemics, infectious diseases and medical microbiology.

Paleoproteomics of the Dental Pulp: The plague paradigm

Chemical decomposition and fragmentation may limit the detection of ancient host and microbial DNA while some proteins can be detected for extended periods of time. We applied paleoproteomics on 300-year-old dental pulp specimens recovered from 16 individuals in two archeological funeral sites in France, comprising one documented plague site and one documented plague-negative site. The dental pulp paleoproteome of the 16 teeth comprised 439 peptides representative of 30 proteins of human origin and 211 peptides representative of 27 proteins of non-human origin. Human proteins consisted of conjunctive tissue and blood proteins including IgA immunoglobulins. Four peptides were indicative of three presumable Yersinia pestis proteins detected in 3/8 dental pulp specimens from the plague-positive site but not in the eight dental pulp specimens collected in the plague-negative site. Paleoproteomics applied to the dental pulp is a new and innovative approach to screen ancient individuals for the detection of blood-borne pathogens and host inflammatory response.

Paleopathology of Human Infections: Old Bones, Antique Books, Ancient and Modern Molecules

Paleopathology studies the traces of disease on human and animal remains from ancient times. Infectious diseases have been, for over a century, one of its main fields of interest. The applications of paleogenetics methods to microbial aDNA, that started in the 90s combined to the recent development of new sequencing techniques allowing 'paleogenomics' approaches, have completely renewed the issue of the infections in the past. These advances open up new challenges in the understanding of the evolution of human-pathogen relationships, integrated in "One Health" concept.In this perspective, an integrative multidisciplinary approach combining data from ancient texts and old bones to those of old molecules is of great interest for reconstructing the past of human infections. Despite some too optimistic prediction of their eradication in the late 20th century, some of these ancient human diseases, such as plague, leprosy or tuberculosis, are still present and continue their evolution at the beginning of this 21rst century. Better know the past to predict a part of the future of human diseases remains, more than ever, the motto of the paleopathological science.

Dental pulp as a source of low-contaminated DNA

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.

Challenges and Opportunities for Typhoid Fever Control: A Call for Coordinated Action

The burden of enteric fever caused by Salmonella enterica serovars Typhi and Paratyphi is substantial and has high impact in toddlers and young children. This burden is relatively well documented in Asia, and this supplement provides new data on the substantial burden in several sub-Saharan African countries. Challenges in standardized surveillance and imperfect diagnostic tools have resulted in patchy local disease data, which are not well acknowledged or integrated into local country evidence and health awareness for decision making. There is a need to strengthen diagnostics for the generation of burden data in country. Furthermore, the guidelines and training for treatment of enteric fever cases in Africa are sorely needed to help mitigate the inappropriate use of antimicrobial treatment. Classic water safety and access to sanitation development remain powerful tools for the control of typhoid fever, yet the huge economic costs and long timelines are unlikely to provide a short- to middle-term solution. Emerging threats, including multidrug resistance and increasing urbanization in regions such as sub-Saharan Africa, warrant focused attention to shorter-term interventions including immunization, and must include vaccine strategies with the new typhoid conjugate vaccines.

Comparative Microbial Genomics and Forensics

Forensic science concerns the application of scientific techniques to questions of a legal nature and may also be used to address questions of historical importance. Forensic techniques are often used in legal cases that involve crimes against persons or property, and they increasingly may involve cases of bioterrorism, crimes against nature, medical negligence, or tracing the origin of food- and crop-borne disease. Given the rapid advance of genome sequencing and comparative genomics techniques, we ask how these might be used to address cases of a forensic nature, focusing on the use of microbial genome sequence analysis. Such analyses rely on the increasingly large numbers of microbial genomes present in public databases, the ability of individual investigators to rapidly sequence whole microbial genomes, and an increasing depth of understanding of their evolution and function. Suggestions are made as to how comparative microbial genomics might be applied forensically and may represent possibilities for the future development of forensic techniques. A particular emphasis is on the nascent field of genomic epidemiology, which utilizes rapid whole-genome sequencing to identify the source and spread of infectious outbreaks. Also discussed is the application of comparative microbial genomics to the study of historical epidemics and deaths and how the approaches developed may also be applicable to more recent and actionable cases.

Ebola Emergency Preparedness: Simulation Training for Frontline Health Care Professionals

INTRODUCTION

At Brigham and Women's Hospital, we identified the need for a comprehensive training program designed to prepare frontline staff to safely manage a patient with Ebola viral disease (EVD). The primary goal of this program was to ensure the safety of staff, patients, and the general public by training staff in the correct use of personal protective equipment (PPE) before, during, and after care of patients with EVD.

METHODS

We delivered a 4-hour experiential training program to frontline health care professionals who would be expected to care for a patient with EVD. The program occurred in a simulation center with multiple flexible spaces and consisted of demonstration, multiple skills practice sessions, and a patient simulation case. We analyzed completed pre- and posttraining questionnaires. The questionnaire assessed their subjective level of confidence in three key areas: donning and doffing PPE, performing clinical skills while wearing PPE, and management of a contamination breach.

RESULTS

This program was effectively deployed in the STRATUS Center for Medical Simulation over a 4-month period, with 220 health care professionals participating in the training and 195 participants completing the pre-/posttraining questionnaires. Our intervention significantly increased the confidence of participants on each primary objective (p = .001 for all three stations).

DISCUSSION

This interprofessional simulation-based program has been shown to be a well-received method of training clinicians to manage patients collaboratively during an EVD outbreak. Our intent is that the skills taught in this training program would also be transferable to management of other infectious diseases in the clinical setting.

Paleomicrobiology: a Snapshot of Ancient Microbes and Approaches to Forensic Microbiology

Paleomicrobiology, or the study of ancient microorganisms, has raised both fascination and skepticism for many years. While paleomicrobiology is not a recent field, the application of emerging techniques, such as DNA sequencing, is proving essential and has provided novel information regarding the evolution of viruses, antibiotic resistance, saprophytes, and pathogens, as well as ancient health and disease status, cultural customs, ethnic diets, and historical events. In this review, we highlight the importance of studying ancient microbial DNA, its contributions to current knowledge, and the role that forensic paleomicrobiology has played in deciphering historical enigmas. We also discuss the emerging techniques used to study the microbial composition of ancient samples as well as major concerns that accompany ancient DNA analyses.

Typhoid toxin provides a window into typhoid fever and the biology of Salmonella Typhi

Salmonella Typhi is the cause of typhoid fever, a disease that has challenged humans throughout history and continues to be a major public health concern. Unlike infections with most other Salmonellae, which result in self-limiting gastroenteritis, typhoid fever is a life-threatening systemic disease. Furthermore, in contrast to most Salmonellae, which can infect a broad range of hosts, S. Typhi is a strict human pathogen. The unique features of S. Typhi pathogenesis and its stringent host specificity have been a long-standing puzzle. The discovery of typhoid toxin not only has provided major insight into these questions but also has offered unique opportunities to develop novel therapeutic and prevention strategies to combat typhoid fever.

Mechanisms of Salmonella Typhi Host Restriction

Salmonella enterica serovar Typhi (S. Typhi) is the cause of typhoid fever, a life-threatening bacterial infection that is very common in the developing world. Recent spread of antimicrobial resistant isolates of S. Typhi makes typhoid fever, a global public health risk. Despite being a common disease, still very little is known about the molecular mechanisms underlying typhoid fever and S. Typhi pathogenesis. In contrast to other Salmonellae, S. Typhi can only infect humans. The molecular bases of this human restriction are mostly unknown. Recent studies identified a novel pathway that contributes to S. Typhi human restriction and is required for killing S. Typhi in macrophages of nonsusceptible species. The small Rab GTPase Rab32 and its guanine nucleotide exchange factor BLOC-3 are the critical components of this pathway. These proteins were already well known as important regulators of intracellular membrane transport. In particular, they are central for the transport of enzymes that synthetize melanin in pigment cells. The recent findings that Rab32 and BLOC-3 are required for S. Typhi host restriction point out to a novel mechanism restricting the growth of bacterial pathogen, dependent on the transport of still unknown molecule(s) to the S. Typhi vacuole. The identification of this novel antimicrobial pathway constitutes a critical starting point to study molecular mechanisms killing bacterial pathogens and possibly identify novel antimicrobial molecules.

The History of Biological Weapons Use: What We Know and What We Don't

This article critically reviews the literature on the history of biological warfare, bioterrorism, and biocrimes. The first serious effort to review this entire history, made in 1969, had numerous limitations. In recent decades, several authors have filled many of the gaps in our understanding of the past use of biological agents (including both pathogens and toxins), making it possible to reconstruct that history with greater fidelity than previously possible. Nevertheless, there are numerous remaining gaps, and closer inspection indicates that some supposed uses of biological weapons never took place or are poorly substantiated. Topics requiring additional research are identified.

How to optimise the yield of forensic and clinical post-mortem microbiology with an adequate sampling: a proposal for standardisation

Post-mortem microbiology (PMM) is an important tool in forensic pathology, helping to determine the cause and manner of death, especially in difficult scenarios such as sudden unexpected death (SD). Currently, there is a lack of standardization of PMM sampling throughout Europe. We present recommendations elaborated by a panel of European experts aimed to standardize microbiological sampling in the most frequent forensic and clinical post-mortem situations. A network of forensic microbiologists, pathologists and physicians from Spain, England, Belgium, Italy and Turkey shaped a flexible protocol providing minimal requirements for PMM sampling at four practical scenarios: SD, bioterrorism, tissue and cell transplantation (TCT) and paleomicrobiology. Biosafety recommendations were also included. SD was categorized into four subgroups according to the age of the deceased and circumstances at autopsy: (1) included SD in infancy and childhood (0-16 years); (2) corresponded to SD in the young (17-35 years); (3) comprised SD at any age with clinical symptoms; and (4) included traumatic/iatrogenic SD. For each subgroup, a minimum set of samples and general recommendations for microbiological analyses were established. Sampling recommendations for main bioterrorism scenarios were provided. In the TCT setting, the Belgian sampling protocol was presented as an example. Finally, regarding paleomicrobiology, the sampling selection for different types of human remains was reviewed. This proposal for standardization in the sampling constitutes the first step towards a consensus in PMM procedures. In addition, the protocol flexibility to adapt the sampling to the clinical scenario and specific forensic findings adds a cost-benefit value.

A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome

The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes.

False positives complicate ancient pathogen identifications using high-throughput shotgun sequencing

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.

Palaeopathology and genes: investigating the genetics of infectious diseases in excavated human skeletal remains and mummies from past populations

The aim of this paper is to review the use of genetics in palaeomicrobiology, and to highlight the importance of understanding past diseases. Palaeomicrobiology is the study of disease pathogens in skeletal and mummified remains from archaeological contexts. It has revolutionarised our understanding of health in the past by enabling a deeper knowledge of the origins and evolution of many diseases that have shaped us as a species. Bacterial diseases explored include tuberculosis, leprosy, bubonic plague, typhoid, syphilis, endemic and epidemic typhus, trench fever, and Helicobacter pylori. Viral diseases discussed include influenza, hepatitis B, human papilloma virus (HPV), human T-cell lymphotrophic virus (HTLV-1) and human immunodeficiency virus (HIV). Parasitic diseases investigated include malaria, leishmaniasis, Chagas' disease, roundworm, whipworm, pinworm, Chinese liver fluke, fleas and lice. Through a better understanding of disease origins and their evolution, we can place into context how many infectious diseases are changing over time, and so help us estimate how they may change in the future.

Responses to Natural Disasters in the Greek and Roman World

Ancient Greek and Roman records contain many references to natural disasters. Analyzing the immediate reactions to the events, as well as the ensuing responses, is only possible where there is dependable evidence. Two case studies offer eyewitness accounts of disaster, as well as archaeological and scientific studies. These are the plague that struck Athens in 430 BCE during the Peloponnesian War, described by Thucydides who witnessed and suffered from it, and the eruption of Vesuvius in 79 CE, recorded in letters by Pliny the Younger, who saw it and fled from it during its height. The victims of these disasters were plunged into confusion and uncertainty about what to do to survive. In many cases, social cohesion dissolved, and individuals broke norms and traditions. Some sought help from the gods, and others felt there were no gods. In the aftermath, leaders responded with measures intended to help people, restore the body politic, and rebuild. Although frustrated by physical and social barriers, they achieved a degree of success.

Small oversights that led to the Great Plague of Marseille (1720-1723): lessons from the past

In recent decades, the issue of emerging and re-emerging infectious diseases has become an increasingly important area of concern in public health. Today, like centuries ago, infectious diseases confront us with the fear of death and have heavily influenced social behaviors and policy decisions at local, national and international levels. Remarkably, an infectious disease such as plague, which is disseminated from one country to another mainly by commercial transportation, remains today, as it was in the distant past, a threat for human societies. Throughout history, plague outbreaks prevailed on numerous occasions in Mediterranean harbors, including Marseille in the south of France. A few months ago, the municipal authorities of the city of Marseille, announced the archaeological discovery of the last remnants of a "lazaretto" or "lazaret" (http://20.minutes.fr, March 3th, 2012), a place equipped with an infirmary and destined to isolate ship passengers quarantined for health reasons. More recently, on September 16th, 2012, the anchor of the ship "Grand Saint Antoine" responsible for bringing the plague to Marseille in 1720, was recovered and it will be restored before being presented to the public in 2013 (http://www.libemarseille.fr/henry/2012/09/lancre-du-bateau-qui-amena-la-grande-peste-%C3%A0-marseille.html). In the light of these recent archaeological discoveries, it is quite instructive to revisit the sequence of events and decisions that led to the outbreak of the Great Plague of Marseille between 1720 and 1723. It comes to the evidence that although the threat was known and health surveillance existed with quite effective preventive measures such as quarantine, the accumulation of small negligence led to one of the worst epidemics in the city (about 30% of casualties among the inhabitants). This is an excellent model to illustrate the issues we are facing with emerging and re-emerging infectious diseases today and to define how to improve biosurveillance and response tomorrow. Importantly, the risk of plague dissemination by transport trade is negligible between developed countries, however, this risk still persists in developing countries. In addition, the emergence of antibiotic resistant strains of Yersinia pestis, the infectious agent of plague, is raising serious concerns for public health.

Heat degradation of eukaryotic and bacterial DNA: an experimental model for paleomicrobiology

Background

Theoretical models suggest that DNA degradation would sharply limit the PCR-based detection of both eukaryotic and prokaryotic DNA within ancient specimens. However, the relative extent of decay of eukaryote and prokaryote DNA over time is a matter of debate. In this study, the murine macrophage cell line J774, alone or infected with Mycobacterium smegmatis bacteria, were killed after exposure to 90°C dry heat for intervals ranging from 1 to 48 h in order to compare eukaryotic cells, extracellular bacteria and intracellular bacteria. The sizes of the resulting mycobacterial rpoB and murine rpb2 homologous gene fragments were then determined by real-time PCR and fluorescent probing.

Findings

The cycle threshold (Ct) values of PCR-amplified DNA fragments from J774 cells and the M. smegmatis negative controls (without heat exposure) varied from 26–33 for the J774 rpb2 gene fragments and from 24–29 for M. smegmatis rpoB fragments. After 90°C dry heat incubation for up to 48 h, the Ct values of test samples increased relative to those of the controls for each amplicon size. For each dry heat exposure time, the Ct values of the 146-149-bp fragments were lower than those of 746-747-bp fragments. During the 4- to 24-h dry heat incubation, the non-infected J774 cell DNA was degraded into 597-bp rpb2 fragments. After 48 h, however, only 450-bp rpb2 fragments of both non-infected and infected J774 cells could be amplified. In contrast, the 746-bp rpoB fragments of M. smegmatis DNA could be amplified after the 48-h dry heat exposure in all experiments. Infected and non-infected J774 cell DNA was degraded more rapidly than M. smegmatis DNA after dry heat exposure (ANOVA test, p < 0.05).

Conclusion

In this study, mycobacterial DNA was more resistant to dry-heat stress than eukaryotic DNA. Therefore, the detection of large, experimental, ancient mycobacterial DNA fragments is a suitable approach for paleomicrobiological studies.

The plague of Thebes, a historical epidemic in Sophocles' Oedipus Rex

Sophocles, one of the most noted playwrights of the ancient world, wrote the tragedy Oedipus Rex in the first half of the decade 430-420 bc. A lethal plague is described in this drama. We adopted a critical approach to Oedipus Rex in analyzing the literary description of the disease, unraveling its clinical features, and defining a possible underlying cause. Our goals were to clarify whether the plague described in Oedipus Rex reflects an actual historical event; to compare it with the plague of Athens, which was described by Thucydides as occurring around the same time Sophocles wrote; and to propose a likely causative pathogen. A critical reading of Oedipus Rex and a comparison with Thucydides' history, as well as a systematic review of historical data, strongly suggests that this epidemic was an actual event, possibly caused by Brucella abortus.