Reflections on crisis burials related to past plague epidemics

Pandemic Events Caused by Bacteria Throughout Human History and the Risks of Antimicrobial Resistance Today

During human history, many pandemic events have threatened and taken many human lives over the years. The deadliest outbreaks were caused by bacteria such as Yersinia pestis. Nowadays, antimicrobial resistance (AMR) in bacteria is a huge problem for the public worldwide, threatening and taking many lives each year. The present work aimed to gather current evidence published in scientific literature that addresses AMR risks. A literature review was conducted using the following descriptors: antimicrobial resistance, AMR, bacteria, and Boolean operators. The results showed that antimicrobial-resistant genes and antibiotic-resistant bacteria in organisms cause critical infectious diseases and are responsible for the infections caused by antibiotic-resistant bacteria (ARB). This review emphasizes the importance of this topic. It sheds light on the risk of reemerging infections and their relationship with AMR. In addition, it discusses the mechanisms and actions of antibiotics and the mechanisms behind the development of resistance by bacteria, focusing on demonstrating the importance of the search for new drugs, for which research involving peptides is fundamental.

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.

Dangers of Noncritical Use of Historical Plague Data

Researchers have published several articles using historical data sets on plague epidemics using impressive digital databases that contain thousands of recorded outbreaks across Europe over the past several centuries. Through the digitization of preexisting data sets, scholars have unprecedented access to the historical record of plague occurrences. However, although these databases offer new research opportunities, noncritical use and reproduction of preexisting data sets can also limit our understanding of how infectious diseases evolved. Many scholars have performed investigations using Jean-Noël Biraben’s data, which contains information on mentions of plague from various kinds of sources, many of which were not cited. When scholars fail to apply source criticism or do not reflect on the content of the data they use, the reliability of their results becomes highly questionable. Researchers using these databases going forward need to verify and restrict content spatially and temporally, and historians should be encouraged to compile the work.

Paleogenetics and Past Infections: the Two Faces of the Coin of Human Immune Evolution

With the advent of next-generation sequencing, paleogenetics has considerably expanded over the past few years and notably encompassed the characterization of the genomes of archaic humans who lived more than 30,000 years ago. These paleogenetics investigations have revealed that admixture between modern and archaic humans occurred, with Neanderthals having contributed to 1.5% to 2.1% of modern Eurasian genomes, and Denisovans to 3% to 6% of modern Melanesian genomes and to approximately 0.2% of modern Asian genomes. Although these contributions are modest, they played a major role in shaping immune gene families, such as the HLA class I genes, for which the archaic alleles now represent more than 50% of the alleles in Europe and Asia. Such a high frequency is consistent with these archaic HLA class I variants having been positively selected because of their protective effect against contagious and devastating epidemics, such as those due to the plague agent Yersinia pestis or to Mycobacterium tuberculosis, which is responsible for deadly tuberculosis. While the exact nature of the infectious agents that contributed to the selection of the archaic variants is unknown, we are entering an exciting period in which paleogenetics and paleomicrobiology data can be integrated to generate a clearer picture of how the immune system of modern populations was shaped and the role admixture and epidemics have played in such evolutions.

Extraction of Aerosol-Deposited Yersinia pestis from Indoor Surfaces To Determine Bacterial Environmental Decay

Public health and decontamination decisions following an event that causes indoor contamination with a biological agent require knowledge of the environmental persistence of the agent. The goals of this study were to develop methods for experimentally depositing bacteria onto indoor surfaces via aerosol, evaluate methods for sampling and enumerating the agent on surfaces, and use these methods to determine bacterial surface decay. A specialized aerosol deposition chamber was constructed, and methods were established for reproducible and uniform aerosol deposition of bacteria onto four coupon types. The deposition chamber facilitated the control of relative humidity (RH; 10 to 70%) following particle deposition to mimic the conditions of indoor environments, as RH is not controlled by standard heating, ventilation, and air conditioning (HVAC) systems. Extraction and culture-based enumeration methods to quantify the viable bacteria on coupons were shown to be highly sensitive and reproducible. To demonstrate the usefulness of the system for decay studies,Yersinia pestis persistence as a function of surface type at 21 °C and 40% RH was determined to be >40%/min for all surfaces. Based upon these results, at typical indoor temperature and RH, a 6-log reduction in titer would expected to be achieved within 1 h as the result of environmental decay on surfaces without active decontamination. The developed approach will facilitate future persistence and decontamination studies with a broad range of biological agents and surfaces, providing agent decay data to inform both assessments of risk to personnel entering a contaminated site and decontamination decisions following biological contamination of an indoor environment.

IMPORTANCE

Public health and decontamination decisions following contamination of an indoor environment with a biological agent require knowledge of the environmental persistence of the agent. Previous studies on Y. pestis persistence have utilized large liquid droplet deposition to provide persistence data. As a result, methods were developed to deposit aerosols containing bacteria onto indoor surfaces, reproducibly enumerate bacteria harvested from coupons, and determine surface decay utilizing Y. pestis The results of this study provide foundational methods required to evaluate surface decay of bacteria and potentially other biological agents, such as viruses, in aerosol particles as a function of surface type and environment. Integrating the data from both aerosol and liquid deposition surface decay studies will provide medical and public health personnel with a more complete understanding of agent persistence on surfaces in contaminated areas for assessment of health risks and to inform decontamination decisions.

Historical Epidemics Cartography Generated by Spatial Analysis: Mapping the Heterogeneity of Three Medieval "Plagues" in Dijon

OBJECTIVES

This work was designed to adapt Geographical Information System-based spatial analysis to the study of historical epidemics. We mapped "plague" deaths during three epidemics of the early 15th century, analyzed spatial distributions by applying the Kulldorff's method, and determined their relationships with the distribution of socio-professional categories in the city of Dijon.

MATERIALS AND METHODS

Our study was based on a database including 50 annual tax registers (established from 1376 to 1447) indicating deaths and survivors among the heads of households, their home location, tax level and profession. The households of the deceased and survivors during 6 years with excess mortality were individually located on a georeferenced medieval map, established by taking advantage of the preserved geography of the historical center of Dijon. We searched for clusters of heads of households characterized by shared tax levels (high-tax payers, the upper decile; low-tax payers, the half charged at the minimum level) or professional activities and for clusters of differential mortality.

RESULTS

High-tax payers were preferentially in the northern intramural part, as well as most wealthy or specialized professionals, whereas low-tax payers were preferentially in the southern part. During two epidemics, in 1400-1401 and 1428, areas of higher mortality were found in the northern part whereas areas of lower mortality were in the southern one. A high concentration of housing and the proximity to food stocks were common features of the most affected areas, creating suitable conditions for rats to pullulate. A third epidemic, lasting from 1438 to 1440 had a different and evolving geography: cases were initially concentrated around the southern gate, at the confluence of three rivers, they were then diffuse, and ended with residual foci of deaths in the northern suburb.

CONCLUSION

Using a selected historical source, we designed an approach allowing spatial analysis of urban medieval epidemics. Our results fit with the view that the 1400-1401 epidemic was a Black Death recurrence. They suggest that this was also the case in 1428, whereas in 1438-1440 a different, possibly waterborne, disease was involved.

Plague in the genomic area

With plague being not only a subject of interest for historians, but still a disease of public health concern in several countries, mainly in Africa, there were hopes that analyses of the Yersinia pestis genomes would put an end to this deadly epidemic pathogen. Genomics revealed that Y. pestis isolates evolved from Yersinia pseudotuberculosis in Central Asia some millennia ago, after the acquisition of two Y. pestis-specific plasmids balanced genomic reduction parallel with the expansion of insertion sequences, illustrating the modern concept that, except for the acquisition of plasmid-borne toxin-encoding genes, the increased virulence of Y. pestis resulted from gene loss rather than gene acquisition. The telluric persistence of Y. pestis reminds us of this close relationship, and matters in terms of plague epidemiology. Whereas biotype Orientalis isolates spread worldwide, the Antiqua and Medievalis isolates showed more limited expansion. In addition to animal ectoparasites, human ectoparasites such as the body louse may have participated in this expansion and in devastating historical epidemics. The recent analysis of a Black Death genome indicated that it was more closely related to the Orientalis branch than to the Medievalis branch. Modern Y. pestis isolates grossly exhibit the same gene content, but still undergo micro-evolution in geographically limited areas by differing in the genome architecture, owing to inversions near insertion sequences and the stabilization of the YpfPhi prophage in Orientalis biotype isolates. Genomics have provided several new molecular tools for the genotyping and phylogeographical tracing of isolates and description of plague foci. However, genomics and post-genomics approaches have not yet provided new tools for the prevention, diagnosis and management of plague patients and the plague epidemics still raging in some sub-Saharan countries.